NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2118028303|ref|XP_044307575|]
View 

protein polybromo-1 isoform X6 [Varanus komodoensis]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 65-175 8.49e-68

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


:

Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 223.36  E-value: 8.49e-68
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   65 VDPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNA 144
Cdd:cd05524      1 LDPIAVCQELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNA 80

                           90       100       110
                   ....*....|....*....|....*....|.
gi 2118028303  145 KSYYKPDSPEYKAACKLWDLYIRTKNEFVQK 175
Cdd:cd05524     81 KAYYKPDSPEHKDACKLWELFLSARNEVLSG 111
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 511-612 8.48e-62

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


:

Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 206.14  E-value: 8.48e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  511 QRMKILYNVVLEAREpGTGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHY 590
Cdd:cd05518      3 KRMLALFLYVLEYRE-GSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHY 81

                           90       100
                   ....*....|....*....|..
gi 2118028303  591 NEEGSQVYNDAHILEKILKEKR 612
Cdd:cd05518     82 NEEGSQVYEDANILEKVLKEKR 103
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 372-474 1.14e-60

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


:

Pssm-ID: 99951  Cd Length: 103  Bit Score: 202.95  E-value: 1.14e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  372 ASNPLYQLYDIVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKR 451
Cdd:cd05520      1 SSNPLWQLYDTIRNARNNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKR 80

                           90       100
                   ....*....|....*....|...
gi 2118028303  452 YNVPNSAIYKRVLKMQQVMQAKK 474
Cdd:cd05520     81 YNVPNSRIYKDAEKLQKLMQAKK 103
BAH_polybromo cd04717
BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human ...
 1203-1321 5.87e-60

BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


:

Pssm-ID: 240068  Cd Length: 121  Bit Score: 201.27  E-value: 5.87e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1203 DMWLKVGDCVFIKSHG-LVRPRVGRIEKMWVR-DGAAYFFGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1280
Cdd:cd04717      1 GLQYRVGDCVYVANPEdPSKPIIFRIERLWKDeDGEKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGK 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2118028303 1281 CAVLSFKDFLSCRPTEISENDVLLCESRYNESDKQMKKFKG 1321
Cdd:cd04717     81 CAVMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKIKT 121
Bromo_polybromo_VI cd05526
Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which ...
 765-872 2.69e-59

Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


:

Pssm-ID: 99956  Cd Length: 110  Bit Score: 199.13  E-value: 2.69e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  765 TLLIQELIHNLFVSVMSHQDDEGRCYSDSLAEIP--AVDPNFPNKPPLTFDIIRKNVETNRYRRLDLFQEHMFEVLERAR 842
Cdd:cd05526      1 QLLVQELLATLFVSVMNHQDEEGRCYSDSLAELPelAVDGVGPKKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERAR 80

                           90       100       110
                   ....*....|....*....|....*....|
gi 2118028303  843 RMNRTDSEIYEDAVELQQFFIKIRDELCKN 872
Cdd:cd05526     81 RLSRTDSEIYEDAVELQQFFIKIRDELCKN 110
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 648-752 6.87e-59

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


:

Pssm-ID: 99946  Cd Length: 105  Bit Score: 197.91  E-value: 6.87e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  648 MQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACT 727
Cdd:cd05515      1 MQQKLWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACK 80

                           90       100
                   ....*....|....*....|....*
gi 2118028303  728 YNEPESLIYKDALVLHKVLLETRRD 752
Cdd:cd05515     81 YNEPDSQIYKDALTLQKVLLETKRE 105
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 203-305 1.56e-56

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


:

Pssm-ID: 99948  Cd Length: 103  Bit Score: 191.11  E-value: 1.56e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  203 LKEILEQLLEAVAVATNPTGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKT 282
Cdd:cd05517      1 LKQILEQLLEAVMTATDPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKT 80

                           90       100
                   ....*....|....*....|...
gi 2118028303  283 YNEPGSQVFKDANAIKKIFNMKK 305
Cdd:cd05517     81 FNEPGSQVYKDANAIKKIFTAKK 103
BAH_polybromo cd04717
BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human ...
 947-1121 6.51e-54

BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


:

Pssm-ID: 240068  Cd Length: 121  Bit Score: 184.32  E-value: 6.51e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  947 MYHVGDYVYVEPAEANLQPHIVCIERLWEDSADsctgnaplpsrrcrgrprtvcrppseggagarcrtgsvavhkahnvm 1026
Cdd:cd04717      3 QYRVGDCVYVANPEDPSKPIIFRIERLWKDEDG----------------------------------------------- 35

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1027 qrrtsssgtrEKWLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKIPVSKILGKCVVMFVKEYFKLCPENFRDEDVYVC 1106
Cdd:cd04717     36 ----------EKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGKCAVMDVKDYIKGRPTEISEEDVYVC 105

                          170
                   ....*....|....*
gi 2118028303 1107 ESRYSAKTKSFKKIK 1121
Cdd:cd04717    106 ESRYNESAKSFKKIK 120
HMG-box_PB1 cd21984
high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, ...
 1428-1483 1.93e-32

high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, also called BRG1-associated factor 180 (BAF180), or polybromo-1D, is a subunit of the PBAF (polybromo/Brg1-associated factor) chromatin-remodeling complex required for kinetochore localization during mitosis and the transcription of estrogen-responsive genes. It is involved in transcriptional activation and repression of select genes by chromatin remodeling. It acts as a negative regulator of cell proliferation.


:

Pssm-ID: 438800 [Multi-domain]  Cd Length: 60  Bit Score: 120.42  E-value: 1.93e-32
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2118028303 1428 KINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAKV 1483
Cdd:cd21984      1 KRNPSGYILFSSEVRKSIKAENPDYSFGEISRLVGTEWRNLPAEKKAEYEERAQKQ 56
Atrophin-1 super family cl38111
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1502-1645 2.26e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


The actual alignment was detected with superfamily member pfam03154:

Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 46.30  E-value: 2.26e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1502 PRAGTPVGALMGVVPPPTPmGMLNPQLTPVAGMLGGYPPVLPPLQ-GPvdgivsmgsmpplhpgVPPPHQLPPgmPGIPL 1580
Cdd:pfam03154  240 QRLPSPHPPLQPMTQPPPP-SQVSPQPLPQPSLHGQMPPMPHSLQtGP----------------SHMQHPVPP--QPFPL 300

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2118028303 1581 PGVMGQNVssmvGAPAPGSPFGQQMSILGPPGQQAPPPYPGQNPAAQQVMQQPTTPMFVSPPPKT 1645
Cdd:pfam03154  301 TPQSSQSQ----VPPGPSPAAPGQSQQRIHTPPSQSQLQSQQPPREQPLPPAPLSMPHIKPPPTT 361
 
Name Accession Description Interval E-value
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 65-175 8.49e-68

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 223.36  E-value: 8.49e-68
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   65 VDPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNA 144
Cdd:cd05524      1 LDPIAVCQELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNA 80

                           90       100       110
                   ....*....|....*....|....*....|.
gi 2118028303  145 KSYYKPDSPEYKAACKLWDLYIRTKNEFVQK 175
Cdd:cd05524     81 KAYYKPDSPEHKDACKLWELFLSARNEVLSG 111
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 511-612 8.48e-62

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 206.14  E-value: 8.48e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  511 QRMKILYNVVLEAREpGTGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHY 590
Cdd:cd05518      3 KRMLALFLYVLEYRE-GSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHY 81

                           90       100
                   ....*....|....*....|..
gi 2118028303  591 NEEGSQVYNDAHILEKILKEKR 612
Cdd:cd05518     82 NEEGSQVYEDANILEKVLKEKR 103
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 372-474 1.14e-60

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 202.95  E-value: 1.14e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  372 ASNPLYQLYDIVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKR 451
Cdd:cd05520      1 SSNPLWQLYDTIRNARNNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKR 80

                           90       100
                   ....*....|....*....|...
gi 2118028303  452 YNVPNSAIYKRVLKMQQVMQAKK 474
Cdd:cd05520     81 YNVPNSRIYKDAEKLQKLMQAKK 103
BAH_polybromo cd04717
BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human ...
 1203-1321 5.87e-60

BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240068  Cd Length: 121  Bit Score: 201.27  E-value: 5.87e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1203 DMWLKVGDCVFIKSHG-LVRPRVGRIEKMWVR-DGAAYFFGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1280
Cdd:cd04717      1 GLQYRVGDCVYVANPEdPSKPIIFRIERLWKDeDGEKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGK 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2118028303 1281 CAVLSFKDFLSCRPTEISENDVLLCESRYNESDKQMKKFKG 1321
Cdd:cd04717     81 CAVMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKIKT 121
Bromo_polybromo_VI cd05526
Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which ...
 765-872 2.69e-59

Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99956  Cd Length: 110  Bit Score: 199.13  E-value: 2.69e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  765 TLLIQELIHNLFVSVMSHQDDEGRCYSDSLAEIP--AVDPNFPNKPPLTFDIIRKNVETNRYRRLDLFQEHMFEVLERAR 842
Cdd:cd05526      1 QLLVQELLATLFVSVMNHQDEEGRCYSDSLAELPelAVDGVGPKKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERAR 80

                           90       100       110
                   ....*....|....*....|....*....|
gi 2118028303  843 RMNRTDSEIYEDAVELQQFFIKIRDELCKN 872
Cdd:cd05526     81 RLSRTDSEIYEDAVELQQFFIKIRDELCKN 110
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 648-752 6.87e-59

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 197.91  E-value: 6.87e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  648 MQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACT 727
Cdd:cd05515      1 MQQKLWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACK 80

                           90       100
                   ....*....|....*....|....*
gi 2118028303  728 YNEPESLIYKDALVLHKVLLETRRD 752
Cdd:cd05515     81 YNEPDSQIYKDALTLQKVLLETKRE 105
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 203-305 1.56e-56

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 191.11  E-value: 1.56e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  203 LKEILEQLLEAVAVATNPTGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKT 282
Cdd:cd05517      1 LKQILEQLLEAVMTATDPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKT 80

                           90       100
                   ....*....|....*....|...
gi 2118028303  283 YNEPGSQVFKDANAIKKIFNMKK 305
Cdd:cd05517     81 FNEPGSQVYKDANAIKKIFTAKK 103
BAH_polybromo cd04717
BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human ...
 947-1121 6.51e-54

BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240068  Cd Length: 121  Bit Score: 184.32  E-value: 6.51e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  947 MYHVGDYVYVEPAEANLQPHIVCIERLWEDSADsctgnaplpsrrcrgrprtvcrppseggagarcrtgsvavhkahnvm 1026
Cdd:cd04717      3 QYRVGDCVYVANPEDPSKPIIFRIERLWKDEDG----------------------------------------------- 35

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1027 qrrtsssgtrEKWLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKIPVSKILGKCVVMFVKEYFKLCPENFRDEDVYVC 1106
Cdd:cd04717     36 ----------EKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGKCAVMDVKDYIKGRPTEISEEDVYVC 105

                          170
                   ....*....|....*
gi 2118028303 1107 ESRYSAKTKSFKKIK 1121
Cdd:cd04717    106 ESRYNESAKSFKKIK 120
BAH pfam01426
BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been ...
 946-1121 2.97e-34

BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction.


Pssm-ID: 460207  Cd Length: 120  Bit Score: 127.81  E-value: 2.97e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  946 SMYHVGDYVYVEPAEANLQPHIVCIERLWEDSADSctgnaplpsrrcrgrprtvcrppseggagarcrtgsvavhkahnv 1025
Cdd:pfam01426    1 ETYSVGDFVLVEPDDADEPYYVARIEELFEDTKNG--------------------------------------------- 35

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1026 mqrrtsssgtrEKWLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKIPVSKILGKCVVMFVKEYFKLCPENFRDEDVYV 1105
Cdd:pfam01426   36 -----------KKMVRVQWFYRPEETVHRAGKAFNKDELFLSDEEDDVPLSAIIGKCSVLHKSDLESLDPYKIKEPDDFF 104

                          170
                   ....*....|....*.
gi 2118028303 1106 CESRYSAKTKSFKKIK 1121
Cdd:pfam01426  105 CELLYDPKTKSFKKLP 120
BAH pfam01426
BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been ...
 1204-1320 3.21e-34

BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction.


Pssm-ID: 460207  Cd Length: 120  Bit Score: 127.81  E-value: 3.21e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1204 MWLKVGDCVFIKSHG-LVRPRVGRIEKMWVRDGA--AYFFGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1280
Cdd:pfam01426    1 ETYSVGDFVLVEPDDaDEPYYVARIEELFEDTKNgkKMVRVQWFYRPEETVHRAGKAFNKDELFLSDEEDDVPLSAIIGK 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2118028303 1281 CAVLSFKDFLSCRPTEISENDVLLCESRYNESDKQMKKFK 1320
Cdd:pfam01426   81 CSVLHKSDLESLDPYKIKEPDDFFCELLYDPKTKSFKKLP 120
HMG-box_PB1 cd21984
high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, ...
 1428-1483 1.93e-32

high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, also called BRG1-associated factor 180 (BAF180), or polybromo-1D, is a subunit of the PBAF (polybromo/Brg1-associated factor) chromatin-remodeling complex required for kinetochore localization during mitosis and the transcription of estrogen-responsive genes. It is involved in transcriptional activation and repression of select genes by chromatin remodeling. It acts as a negative regulator of cell proliferation.


Pssm-ID: 438800 [Multi-domain]  Cd Length: 60  Bit Score: 120.42  E-value: 1.93e-32
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2118028303 1428 KINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAKV 1483
Cdd:cd21984      1 KRNPSGYILFSSEVRKSIKAENPDYSFGEISRLVGTEWRNLPAEKKAEYEERAQKQ 56
BAH smart00439
Bromo adjacent homology domain;
1205-1320 4.38e-31

Bromo adjacent homology domain;


Pssm-ID: 214664 [Multi-domain]  Cd Length: 121  Bit Score: 118.93  E-value: 4.38e-31
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  1205 WLKVGDCVFIKSH-GLVRPRVGRIEKMWVRDG---AAYFFGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1280
Cdd:smart00439    1 TISVGDFVLVEPDdADEPYYIGRIEEIFETKKnseSKMVRVRWFYRPEETVLEKAALFDKNEVFLSDEYDTVPLSDIIGK 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|.
gi 2118028303  1281 CAVLSFKDFLSCRPTEIS-ENDVLLCESRYNESDKQMKKFK 1320
Cdd:smart00439   81 CNVLYKSDYPGLRPEGSIgEPDVFFCESAYDPEKGSFKKLP 121
BAH smart00439
Bromo adjacent homology domain;
947-1121 9.99e-31

Bromo adjacent homology domain;


Pssm-ID: 214664 [Multi-domain]  Cd Length: 121  Bit Score: 117.78  E-value: 9.99e-31
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   947 MYHVGDYVYVEPAEANLQPHIVCIERLWEDSADSctgnaplpsrrcrgrprtvcrppseggagarcrtgsvavhkahnvm 1026
Cdd:smart00439    1 TISVGDFVLVEPDDADEPYYIGRIEEIFETKKNS---------------------------------------------- 34

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  1027 qrrtsssgtREKWLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKIPVSKILGKCVVMFVKEYFKLCPENFRD-EDVYV 1105
Cdd:smart00439   35 ---------ESKMVRVRWFYRPEETVLEKAALFDKNEVFLSDEYDTVPLSDIIGKCNVLYKSDYPGLRPEGSIGePDVFF 105

                           170
                    ....*....|....*.
gi 2118028303  1106 CESRYSAKTKSFKKIK 1121
Cdd:smart00439  106 CESAYDPEKGSFKKLP 121
BROMO smart00297
bromo domain;
641-753 2.10e-30

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 116.61  E-value: 2.10e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   641 KSKYMTPMQQKLNEVYEAVKNYtdkrgrRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVM 720
Cdd:smart00297    1 DPKLQKKLQELLKAVLDKLDSH------PLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNL 74

                            90       100       110
                    ....*....|....*....|....*....|...
gi 2118028303   721 MFNNACTYNEPESLIYKDALVLHKVLLETRRDI 753
Cdd:smart00297   75 MFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 107
BROMO smart00297
bromo domain;
202-308 7.65e-30

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 114.68  E-value: 7.65e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   202 YLKEILEQLLEAVAVatnptgHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAK 281
Cdd:smart00297    7 KLQELLKAVLDKLDS------HPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80

                            90       100
                    ....*....|....*....|....*..
gi 2118028303   282 TYNEPGSQVFKDANAIKKIFNMKKAEI 308
Cdd:smart00297   81 TYNGPDSEVYKDAKKLEKFFEKKLREL 107
BROMO smart00297
bromo domain;
511-615 1.63e-28

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 111.22  E-value: 1.63e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   511 QRMKILYNVVLEAREpgtGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHY 590
Cdd:smart00297    6 KKLQELLKAVLDKLD---SHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTY 82

                            90       100
                    ....*....|....*....|....*
gi 2118028303   591 NEEGSQVYNDAHILEKILKEKRKEL 615
Cdd:smart00297   83 NGPDSEVYKDAKKLEKFFEKKLREL 107
BROMO smart00297
bromo domain;
374-477 8.82e-27

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 106.21  E-value: 8.82e-27
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   374 NPLYQLYDIVRNCRNNQgqLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYN 453
Cdd:smart00297    6 KKLQELLKAVLDKLDSH--PLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYN 83

                            90       100
                    ....*....|....*....|....
gi 2118028303   454 VPNSAIYKRVLKMQQVMQAKKKEL 477
Cdd:smart00297   84 GPDSEVYKDAKKLEKFFEKKLREL 107
BROMO smart00297
bromo domain;
70-172 7.84e-26

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 103.51  E-value: 7.84e-26
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303    70 VCHELYNTIRDYKDEqgRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYK 149
Cdd:smart00297    7 KLQELLKAVLDKLDS--HPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNG 84

                            90       100
                    ....*....|....*....|...
gi 2118028303   150 PDSPEYKAACKLWDLYIRTKNEF 172
Cdd:smart00297   85 PDSEVYKDAKKLEKFFEKKLREL 107
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 205-611 1.69e-25

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 110.67  E-value: 1.69e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  205 EILEQLLEAVAVATNPTGHLISELfqklPSKVQYPDYYAIIKEPIDLKTIAQRiQNGYYKSIHAMAKDIDLLVKNAKTYN 284
Cdd:COG5076     20 EFGNELLRLVDNDSSPFPNAPEEE----GSKNLFQKQLKRMPKEYITSIVDDR-EPGSMANVNDDLENVGGITYSPFEKN 94

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  285 EPGSqvfkdanaikkifnMKKAEIERSELTKSSLRVSNKRAvqgdrlsaitmalqYGSESDEDavlaaaaRYEEGESEAE 364
Cdd:COG5076     95 RPES--------------LRFDEIVFLAIESVTPESGLGSL--------------LMAHLKTS-------VKKRKTPKIE 139

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  365 SITSFMDASNPLYQLYDIVrncrNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNL 444
Cdd:COG5076    140 DELLYADNKAIAKFKKQLF----LRDGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNL 215

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  445 MFENAKRYNVPNSAIYKRVLKMQQVMQAKKKELAGRDDiedgDSMIssatsdagsskrkskknikkQRMKILYNVVLEAR 524
Cdd:COG5076    216 MFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPEEML----ELSI--------------------KPGREEREERESVL 271

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  525 EPGTGRRLCEL-FMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSQVYNDAHI 603
Cdd:COG5076    272 ITNSQAHVGAWpFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVTDYYKNANV 351


                   ....*...
gi 2118028303  604 LEKILKEK 611
Cdd:COG5076    352 LEDFVIKK 359
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 203-294 4.80e-22

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 91.61  E-value: 4.80e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  203 LKEILEQLLEavavatnptgHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKT 282
Cdd:pfam00439    1 CLEILDKLME----------HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNART 70

                           90
                   ....*....|..
gi 2118028303  283 YNEPGSQVFKDA 294
Cdd:pfam00439   71 YNGPGSVIYKAA 82
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 75-160 6.41e-20

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 85.83  E-value: 6.41e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   75 YNTIRDYKDEQGRllCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPE 154
Cdd:pfam00439    1 CLEILDKLMEHPI--AAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVI 78


                   ....*.
gi 2118028303  155 YKAACK 160
Cdd:pfam00439   79 YKAAEK 84
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 392-461 3.47e-18

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 80.82  E-value: 3.47e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  392 QLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYK 461
Cdd:pfam00439   11 HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 530-603 1.56e-16

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 76.20  E-value: 1.56e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2118028303  530 RRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSQVYNDAHI 603
Cdd:pfam00439   11 HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAEK 84
BROMO smart00297
bromo domain;
769-869 3.16e-16

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 76.16  E-value: 3.16e-16
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   769 QELIHNLFVSVMSHQDDegRCYSDSLAEIPAVD--PNFPN--KPPLTFDIIRKNVETNRYRRLDLFQEHMFEVLERARRM 844
Cdd:smart00297    5 QKKLQELLKAVLDKLDS--HPLSWPFLKPVSRKeaPDYYDiiKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTY 82

                            90       100
                    ....*....|....*....|....*
gi 2118028303   845 NRTDSEIYEDAVELQQFFIKIRDEL 869
Cdd:smart00297   83 NGPDSEVYKDAKKLEKFFEKKLREL 107
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 668-739 3.08e-14

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 69.65  E-value: 3.08e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2118028303  668 RRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTYNEPESLIYKDA 739
Cdd:pfam00439   11 HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAA 82
HMG smart00398
high mobility group;
1426-1482 6.42e-14

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 68.11  E-value: 6.42e-14
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 2118028303  1426 KRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:smart00398    1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKK 57
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 779-857 5.73e-13

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 65.80  E-value: 5.73e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  779 VMSHQDDEGRCYSDSLAEIPAVDPNFPN--KPPLTFDIIRKNVETNRYRRLDLFQEHMFEVLERARRMNRTDSEIYEDAV 856
Cdd:pfam00439    4 ILDKLMEHPIAAPFLEPVDPDEYPDYYSviKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAE 83


                   .
gi 2118028303  857 E 857
Cdd:pfam00439   84 K 84
HMG_box pfam00505
HMG (high mobility group) box;
1428-1482 3.47e-12

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 63.01  E-value: 3.47e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2118028303 1428 KINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:pfam00505    2 KRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEK 56
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
1389-1480 2.20e-08

Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 56.41  E-value: 2.20e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1389 TIPQLQTPLSNELdimpyTPPQSTPKSAKGSVKK---EGSKRkiNMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEW 1465
Cdd:COG5648     37 TLVELEKPLQQLL-----TKPRKKTKSKRLVRKKkdpNGPKR--PLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKW 109

                           90
                   ....*....|....*
gi 2118028303 1466 RNLEATKKAEYEERA 1480
Cdd:COG5648    110 KELTDEEKEPYYKEA 124
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1502-1645 2.26e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 46.30  E-value: 2.26e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1502 PRAGTPVGALMGVVPPPTPmGMLNPQLTPVAGMLGGYPPVLPPLQ-GPvdgivsmgsmpplhpgVPPPHQLPPgmPGIPL 1580
Cdd:pfam03154  240 QRLPSPHPPLQPMTQPPPP-SQVSPQPLPQPSLHGQMPPMPHSLQtGP----------------SHMQHPVPP--QPFPL 300

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2118028303 1581 PGVMGQNVssmvGAPAPGSPFGQQMSILGPPGQQAPPPYPGQNPAAQQVMQQPTTPMFVSPPPKT 1645
Cdd:pfam03154  301 TPQSSQSQ----VPPGPSPAAPGQSQQRIHTPPSQSQLQSQQPPREQPLPPAPLSMPHIKPPPTT 361
PTZ00199 PTZ00199
high mobility group protein; Provisional
 1414-1481 2.79e-03

high mobility group protein; Provisional


Pssm-ID: 185511 [Multi-domain]  Cd Length: 94  Bit Score: 38.68  E-value: 2.79e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2118028303 1414 KSAKGSVKKEGSKRKIN-------MSGYILFSSEMRAVIKAQHPDYS--FGELSRLVGTEWRNLEATKKAEYEERAA 1481
Cdd:PTZ00199     3 KKQGKVLVRKNKRKKKDpnapkraLSAYMFFAKEKRAEIIAENPELAkdVAAVGKMVGEAWNKLSEEEKAPYEKKAQ 79
 
Name Accession Description Interval E-value
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 65-175 8.49e-68

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 223.36  E-value: 8.49e-68
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   65 VDPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNA 144
Cdd:cd05524      1 LDPIAVCQELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNA 80

                           90       100       110
                   ....*....|....*....|....*....|.
gi 2118028303  145 KSYYKPDSPEYKAACKLWDLYIRTKNEFVQK 175
Cdd:cd05524     81 KAYYKPDSPEHKDACKLWELFLSARNEVLSG 111
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 511-612 8.48e-62

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 206.14  E-value: 8.48e-62
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  511 QRMKILYNVVLEAREpGTGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHY 590
Cdd:cd05518      3 KRMLALFLYVLEYRE-GSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHY 81

                           90       100
                   ....*....|....*....|..
gi 2118028303  591 NEEGSQVYNDAHILEKILKEKR 612
Cdd:cd05518     82 NEEGSQVYEDANILEKVLKEKR 103
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 372-474 1.14e-60

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 202.95  E-value: 1.14e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  372 ASNPLYQLYDIVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKR 451
Cdd:cd05520      1 SSNPLWQLYDTIRNARNNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKR 80

                           90       100
                   ....*....|....*....|...
gi 2118028303  452 YNVPNSAIYKRVLKMQQVMQAKK 474
Cdd:cd05520     81 YNVPNSRIYKDAEKLQKLMQAKK 103
BAH_polybromo cd04717
BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human ...
 1203-1321 5.87e-60

BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240068  Cd Length: 121  Bit Score: 201.27  E-value: 5.87e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1203 DMWLKVGDCVFIKSHG-LVRPRVGRIEKMWVR-DGAAYFFGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1280
Cdd:cd04717      1 GLQYRVGDCVYVANPEdPSKPIIFRIERLWKDeDGEKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGK 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2118028303 1281 CAVLSFKDFLSCRPTEISENDVLLCESRYNESDKQMKKFKG 1321
Cdd:cd04717     81 CAVMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKIKT 121
Bromo_polybromo_VI cd05526
Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which ...
 765-872 2.69e-59

Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99956  Cd Length: 110  Bit Score: 199.13  E-value: 2.69e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  765 TLLIQELIHNLFVSVMSHQDDEGRCYSDSLAEIP--AVDPNFPNKPPLTFDIIRKNVETNRYRRLDLFQEHMFEVLERAR 842
Cdd:cd05526      1 QLLVQELLATLFVSVMNHQDEEGRCYSDSLAELPelAVDGVGPKKIPLTLDIIKRNVDKGRYRRLDKFQEDMFEVLERAR 80

                           90       100       110
                   ....*....|....*....|....*....|
gi 2118028303  843 RMNRTDSEIYEDAVELQQFFIKIRDELCKN 872
Cdd:cd05526     81 RLSRTDSEIYEDAVELQQFFIKIRDELCKN 110
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 648-752 6.87e-59

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 197.91  E-value: 6.87e-59
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  648 MQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACT 727
Cdd:cd05515      1 MQQKLWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACK 80

                           90       100
                   ....*....|....*....|....*
gi 2118028303  728 YNEPESLIYKDALVLHKVLLETRRD 752
Cdd:cd05515     81 YNEPDSQIYKDALTLQKVLLETKRE 105
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 203-305 1.56e-56

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 191.11  E-value: 1.56e-56
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  203 LKEILEQLLEAVAVATNPTGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKT 282
Cdd:cd05517      1 LKQILEQLLEAVMTATDPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKT 80

                           90       100
                   ....*....|....*....|...
gi 2118028303  283 YNEPGSQVFKDANAIKKIFNMKK 305
Cdd:cd05517     81 FNEPGSQVYKDANAIKKIFTAKK 103
BAH_polybromo cd04717
BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human ...
 947-1121 6.51e-54

BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240068  Cd Length: 121  Bit Score: 184.32  E-value: 6.51e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  947 MYHVGDYVYVEPAEANLQPHIVCIERLWEDSADsctgnaplpsrrcrgrprtvcrppseggagarcrtgsvavhkahnvm 1026
Cdd:cd04717      3 QYRVGDCVYVANPEDPSKPIIFRIERLWKDEDG----------------------------------------------- 35

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1027 qrrtsssgtrEKWLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKIPVSKILGKCVVMFVKEYFKLCPENFRDEDVYVC 1106
Cdd:cd04717     36 ----------EKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGKCAVMDVKDYIKGRPTEISEEDVYVC 105

                          170
                   ....*....|....*
gi 2118028303 1107 ESRYSAKTKSFKKIK 1121
Cdd:cd04717    106 ESRYNESAKSFKKIK 120
BAH pfam01426
BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been ...
 946-1121 2.97e-34

BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction.


Pssm-ID: 460207  Cd Length: 120  Bit Score: 127.81  E-value: 2.97e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  946 SMYHVGDYVYVEPAEANLQPHIVCIERLWEDSADSctgnaplpsrrcrgrprtvcrppseggagarcrtgsvavhkahnv 1025
Cdd:pfam01426    1 ETYSVGDFVLVEPDDADEPYYVARIEELFEDTKNG--------------------------------------------- 35

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1026 mqrrtsssgtrEKWLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKIPVSKILGKCVVMFVKEYFKLCPENFRDEDVYV 1105
Cdd:pfam01426   36 -----------KKMVRVQWFYRPEETVHRAGKAFNKDELFLSDEEDDVPLSAIIGKCSVLHKSDLESLDPYKIKEPDDFF 104

                          170
                   ....*....|....*.
gi 2118028303 1106 CESRYSAKTKSFKKIK 1121
Cdd:pfam01426  105 CELLYDPKTKSFKKLP 120
BAH pfam01426
BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been ...
 1204-1320 3.21e-34

BAH domain; This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction.


Pssm-ID: 460207  Cd Length: 120  Bit Score: 127.81  E-value: 3.21e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1204 MWLKVGDCVFIKSHG-LVRPRVGRIEKMWVRDGA--AYFFGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1280
Cdd:pfam01426    1 ETYSVGDFVLVEPDDaDEPYYVARIEELFEDTKNgkKMVRVQWFYRPEETVHRAGKAFNKDELFLSDEEDDVPLSAIIGK 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 2118028303 1281 CAVLSFKDFLSCRPTEISENDVLLCESRYNESDKQMKKFK 1320
Cdd:pfam01426   81 CSVLHKSDLESLDPYKIKEPDDFFCELLYDPKTKSFKKLP 120
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
 513-611 1.76e-33

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99950  Cd Length: 103  Bit Score: 125.14  E-value: 1.76e-33
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  513 MKILYNVVLEArEPGTGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNE 592
Cdd:cd05519      5 MLEIYDAVLNC-EDETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQ 83

                           90
                   ....*....|....*....
gi 2118028303  593 EGSQVYNDAHILEKILKEK 611
Cdd:cd05519     84 EGSIVYEDAVEMEKAFKKK 102
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 511-614 1.01e-32

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 122.80  E-value: 1.01e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  511 QRMKILYNVVLEAREPGtGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHY 590
Cdd:cd05515      3 QKLWELYNAVKNYTDGR-GRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKY 81

                           90       100
                   ....*....|....*....|....
gi 2118028303  591 NEEGSQVYNDAHILEKILKEKRKE 614
Cdd:cd05515     82 NEPDSQIYKDALTLQKVLLETKRE 105
HMG-box_PB1 cd21984
high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, ...
 1428-1483 1.93e-32

high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins; PB1, also called BRG1-associated factor 180 (BAF180), or polybromo-1D, is a subunit of the PBAF (polybromo/Brg1-associated factor) chromatin-remodeling complex required for kinetochore localization during mitosis and the transcription of estrogen-responsive genes. It is involved in transcriptional activation and repression of select genes by chromatin remodeling. It acts as a negative regulator of cell proliferation.


Pssm-ID: 438800 [Multi-domain]  Cd Length: 60  Bit Score: 120.42  E-value: 1.93e-32
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2118028303 1428 KINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAKV 1483
Cdd:cd21984      1 KRNPSGYILFSSEVRKSIKAENPDYSFGEISRLVGTEWRNLPAEKKAEYEERAQKQ 56
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
 648-749 5.90e-32

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99950  Cd Length: 103  Bit Score: 120.91  E-value: 5.90e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  648 MQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACT 727
Cdd:cd05519      1 LKAAMLEIYDAVLNCEDETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANART 80

                           90       100
                   ....*....|....*....|..
gi 2118028303  728 YNEPESLIYKDALVLHKVLLET 749
Cdd:cd05519     81 YNQEGSIVYEDAVEMEKAFKKK 102
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 203-307 1.73e-31

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 119.33  E-value: 1.73e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  203 LKEILEQLLEAVAVATNPTGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKT 282
Cdd:cd05515      1 MQQKLWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACK 80

                           90       100
                   ....*....|....*....|....*
gi 2118028303  283 YNEPGSQVFKDANAIKKIFNMKKAE 307
Cdd:cd05515     81 YNEPDSQIYKDALTLQKVLLETKRE 105
BAH smart00439
Bromo adjacent homology domain;
1205-1320 4.38e-31

Bromo adjacent homology domain;


Pssm-ID: 214664 [Multi-domain]  Cd Length: 121  Bit Score: 118.93  E-value: 4.38e-31
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  1205 WLKVGDCVFIKSH-GLVRPRVGRIEKMWVRDG---AAYFFGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGK 1280
Cdd:smart00439    1 TISVGDFVLVEPDdADEPYYIGRIEEIFETKKnseSKMVRVRWFYRPEETVLEKAALFDKNEVFLSDEYDTVPLSDIIGK 80

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|.
gi 2118028303  1281 CAVLSFKDFLSCRPTEIS-ENDVLLCESRYNESDKQMKKFK 1320
Cdd:smart00439   81 CNVLYKSDYPGLRPEGSIgEPDVFFCESAYDPEKGSFKKLP 121
BAH smart00439
Bromo adjacent homology domain;
947-1121 9.99e-31

Bromo adjacent homology domain;


Pssm-ID: 214664 [Multi-domain]  Cd Length: 121  Bit Score: 117.78  E-value: 9.99e-31
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   947 MYHVGDYVYVEPAEANLQPHIVCIERLWEDSADSctgnaplpsrrcrgrprtvcrppseggagarcrtgsvavhkahnvm 1026
Cdd:smart00439    1 TISVGDFVLVEPDDADEPYYIGRIEEIFETKKNS---------------------------------------------- 34

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  1027 qrrtsssgtREKWLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKIPVSKILGKCVVMFVKEYFKLCPENFRD-EDVYV 1105
Cdd:smart00439   35 ---------ESKMVRVRWFYRPEETVLEKAALFDKNEVFLSDEYDTVPLSDIIGKCNVLYKSDYPGLRPEGSIGePDVFF 105

                           170
                    ....*....|....*.
gi 2118028303  1106 CESRYSAKTKSFKKIK 1121
Cdd:smart00439  106 CESAYDPEKGSFKKLP 121
BROMO smart00297
bromo domain;
641-753 2.10e-30

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 116.61  E-value: 2.10e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   641 KSKYMTPMQQKLNEVYEAVKNYtdkrgrRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVM 720
Cdd:smart00297    1 DPKLQKKLQELLKAVLDKLDSH------PLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNL 74

                            90       100       110
                    ....*....|....*....|....*....|...
gi 2118028303   721 MFNNACTYNEPESLIYKDALVLHKVLLETRRDI 753
Cdd:smart00297   75 MFSNARTYNGPDSEVYKDAKKLEKFFEKKLREL 107
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 376-476 5.13e-30

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 115.09  E-value: 5.13e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  376 LYQLYDIVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVP 455
Cdd:cd05515      5 LWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEP 84

                           90       100
                   ....*....|....*....|.
gi 2118028303  456 NSAIYKRVLKMQQVMQAKKKE 476
Cdd:cd05515     85 DSQIYKDALTLQKVLLETKRE 105
BROMO smart00297
bromo domain;
202-308 7.65e-30

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 114.68  E-value: 7.65e-30
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   202 YLKEILEQLLEAVAVatnptgHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAK 281
Cdd:smart00297    7 KLQELLKAVLDKLDS------HPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNAR 80

                            90       100
                    ....*....|....*....|....*..
gi 2118028303   282 TYNEPGSQVFKDANAIKKIFNMKKAEI 308
Cdd:smart00297   81 TYNGPDSEVYKDAKKLEKFFEKKLREL 107
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 202-304 1.59e-29

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 113.62  E-value: 1.59e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  202 YLKEILEQLLEAVavatnptgHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAK 281
Cdd:cd04369      4 KLRSLLDALKKLK--------RDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAK 75

                           90       100
                   ....*....|....*....|...
gi 2118028303  282 TYNEPGSQVFKDANAIKKIFNMK 304
Cdd:cd04369     76 TYNGPGSPIYKDAKKLEKLFEKL 98
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 650-753 7.23e-29

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 112.14  E-value: 7.23e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  650 QKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTYN 729
Cdd:cd05516      4 KKMNKIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFN 83

                           90       100
                   ....*....|....*....|....
gi 2118028303  730 EPESLIYKDALVLHKVLLETRRDI 753
Cdd:cd05516     84 LEGSLIYEDSIVLQSVFKSARQKI 107
BROMO smart00297
bromo domain;
511-615 1.63e-28

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 111.22  E-value: 1.63e-28
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   511 QRMKILYNVVLEAREpgtGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHY 590
Cdd:smart00297    6 KKLQELLKAVLDKLD---SHPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTY 82

                            90       100
                    ....*....|....*....|....*
gi 2118028303   591 NEEGSQVYNDAHILEKILKEKRKEL 615
Cdd:smart00297   83 NGPDSEVYKDAKKLEKFFEKKLREL 107
Bromo_polybromo_V cd05515
Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which ...
 71-171 2.37e-27

Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99946  Cd Length: 105  Bit Score: 107.78  E-value: 2.37e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   71 CHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKP 150
Cdd:cd05515      5 LWELYNAVKNYTDGRGRRLSLIFMRLPSKSEYPDYYDVIKKPIDMEKIRSKIEGNQYQSLDDMVSDFVLMFDNACKYNEP 84

                           90       100
                   ....*....|....*....|.
gi 2118028303  151 DSPEYKAACKLWDLYIRTKNE 171
Cdd:cd05515     85 DSQIYKDALTLQKVLLETKRE 105
BROMO smart00297
bromo domain;
374-477 8.82e-27

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 106.21  E-value: 8.82e-27
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   374 NPLYQLYDIVRNCRNNQgqLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYN 453
Cdd:smart00297    6 KKLQELLKAVLDKLDSH--PLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYN 83

                            90       100
                    ....*....|....*....|....
gi 2118028303   454 VPNSAIYKRVLKMQQVMQAKKKEL 477
Cdd:smart00297   84 GPDSEVYKDAKKLEKFFEKKLREL 107
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 530-611 1.01e-26

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 105.53  E-value: 1.01e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  530 RRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILK 609
Cdd:cd04369     17 RDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGSPIYKDAKKLEKLFE 96


                   ..
gi 2118028303  610 EK 611
Cdd:cd04369     97 KL 98
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 649-750 3.42e-26

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 104.45  E-value: 3.42e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  649 QQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTY 728
Cdd:cd05518      2 KKRMLALFLYVLEYREGSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHY 81

                           90       100
                   ....*....|....*....|..
gi 2118028303  729 NEPESLIYKDALVLHKVLLETR 750
Cdd:cd05518     82 NEEGSQVYEDANILEKVLKEKR 103
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
 203-304 4.10e-26

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99950  Cd Length: 103  Bit Score: 103.96  E-value: 4.10e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  203 LKEILEQLLEAVAVATNPTGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKT 282
Cdd:cd05519      1 LKAAMLEIYDAVLNCEDETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANART 80

                           90       100
                   ....*....|....*....|..
gi 2118028303  283 YNEPGSQVFKDANAIKKIFNMK 304
Cdd:cd05519     81 YNQEGSIVYEDAVEMEKAFKKK 102
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 511-615 7.21e-26

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 103.66  E-value: 7.21e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  511 QRMKILYNVVLEAREpGTGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHY 590
Cdd:cd05516      4 KKMNKIVDVVIKYKD-SDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTF 82

                           90       100
                   ....*....|....*....|....*
gi 2118028303  591 NEEGSQVYNDAHILEKILKEKRKEL 615
Cdd:cd05516     83 NLEGSLIYEDSIVLQSVFKSARQKI 107
BROMO smart00297
bromo domain;
70-172 7.84e-26

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 103.51  E-value: 7.84e-26
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303    70 VCHELYNTIRDYKDEqgRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYK 149
Cdd:smart00297    7 KLQELLKAVLDKLDS--HPLSWPFLKPVSRKEAPDYYDIIKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTYNG 84

                            90       100
                    ....*....|....*....|...
gi 2118028303   150 PDSPEYKAACKLWDLYIRTKNEF 172
Cdd:smart00297   85 PDSEVYKDAKKLEKFFEKKLREL 107
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 647-750 7.94e-26

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 103.19  E-value: 7.94e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  647 PMQQklneVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNAC 726
Cdd:cd05520      4 PLWQ----LYDTIRNARNNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAK 79

                           90       100
                   ....*....|....*....|....
gi 2118028303  727 TYNEPESLIYKDALVLHKVLLETR 750
Cdd:cd05520     80 RYNVPNSRIYKDAEKLQKLMQAKK 103
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 203-301 8.67e-26

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 103.28  E-value: 8.67e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  203 LKEILEQLLEAVAVATNPTGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKT 282
Cdd:cd05516      2 LTKKMNKIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQT 81

                           90
                   ....*....|....*....
gi 2118028303  283 YNEPGSQVFKDANAIKKIF 301
Cdd:cd05516     82 FNLEGSLIYEDSIVLQSVF 100
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 511-612 9.26e-26

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 102.90  E-value: 9.26e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  511 QRMKILYNVVLEAREPGtGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHY 590
Cdd:cd05517      3 QILEQLLEAVMTATDPS-GRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTF 81

                           90       100
                   ....*....|....*....|..
gi 2118028303  591 NEEGSQVYNDAHILEKILKEKR 612
Cdd:cd05517     82 NEPGSQVYKDANAIKKIFTAKK 103
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 209-305 1.05e-25

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 102.80  E-value: 1.05e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  209 QLLEAVAVATNPTGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYNEPGS 288
Cdd:cd05520      7 QLYDTIRNARNNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPNS 86

                           90
                   ....*....|....*..
gi 2118028303  289 QVFKDANAIKKIFNMKK 305
Cdd:cd05520     87 RIYKDAEKLQKLMQAKK 103
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 205-611 1.69e-25

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 110.67  E-value: 1.69e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  205 EILEQLLEAVAVATNPTGHLISELfqklPSKVQYPDYYAIIKEPIDLKTIAQRiQNGYYKSIHAMAKDIDLLVKNAKTYN 284
Cdd:COG5076     20 EFGNELLRLVDNDSSPFPNAPEEE----GSKNLFQKQLKRMPKEYITSIVDDR-EPGSMANVNDDLENVGGITYSPFEKN 94

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  285 EPGSqvfkdanaikkifnMKKAEIERSELTKSSLRVSNKRAvqgdrlsaitmalqYGSESDEDavlaaaaRYEEGESEAE 364
Cdd:COG5076     95 RPES--------------LRFDEIVFLAIESVTPESGLGSL--------------LMAHLKTS-------VKKRKTPKIE 139

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  365 SITSFMDASNPLYQLYDIVrncrNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNL 444
Cdd:COG5076    140 DELLYADNKAIAKFKKQLF----LRDGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNL 215

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  445 MFENAKRYNVPNSAIYKRVLKMQQVMQAKKKELAGRDDiedgDSMIssatsdagsskrkskknikkQRMKILYNVVLEAR 524
Cdd:COG5076    216 MFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPEEML----ELSI--------------------KPGREEREERESVL 271

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  525 EPGTGRRLCEL-FMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSQVYNDAHI 603
Cdd:COG5076    272 ITNSQAHVGAWpFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVTDYYKNANV 351


                   ....*...
gi 2118028303  604 LEKILKEK 611
Cdd:COG5076    352 LEDFVIKK 359
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 398-756 1.82e-25

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 110.28  E-value: 1.82e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  398 FFHLPSKKKYPDYYQQiKMPISlqqIRTKLKNHEYET-----LDHLEcDLNLMFENAKRYNVPNSAIYKRV--LKMQQVM 470
Cdd:COG5076     39 APEEEGSKNLFQKQLK-RMPKE---YITSIVDDREPGsmanvNDDLE-NVGGITYSPFEKNRPESLRFDEIvfLAIESVT 113

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  471 QAKKKELAGRDDIEDGDSMISSATsdagsskrKSKKNIKKQRMKILYNVVLEAREPGTGRRLceLFMVKPSKKDYPDYYK 550
Cdd:COG5076    114 PESGLGSLLMAHLKTSVKKRKTPK--------IEDELLYADNKAIAKFKKQLFLRDGRFLSS--IFLGLPSKREYPDYYE 183

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  551 IILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILKekrKELGPLLEDDEVASPKLK 630
Cdd:COG5076    184 IIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFL---KLIEEIPEEMLELSIKPG 260

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  631 lsrktgispKKSKYMTPmqqklnevyeaVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQD 710
Cdd:COG5076    261 ---------REEREERE-----------SVLITNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRP 320

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*.
gi 2118028303  711 IDAMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDIEGD 756
Cdd:COG5076    321 EETFVRDAKLFFDNCVMYNGEVTDYYKNANVLEDFVIKKTRLIREY 366
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 72-169 2.22e-25

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 102.03  E-value: 2.22e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   72 HELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPD 151
Cdd:cd05520      6 WQLYDTIRNARNNQGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNVPN 85

                           90
                   ....*....|....*...
gi 2118028303  152 SPEYKAACKLWDLYIRTK 169
Cdd:cd05520     86 SRIYKDAEKLQKLMQAKK 103
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 203-305 3.39e-25

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 101.37  E-value: 3.39e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  203 LKEILEQLLEAVAVATNPTGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKT 282
Cdd:cd05518      1 RKKRMLALFLYVLEYREGSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARH 80

                           90       100
                   ....*....|....*....|...
gi 2118028303  283 YNEPGSQVFKDANAIKKIFNMKK 305
Cdd:cd05518     81 YNEEGSQVYEDANILEKVLKEKR 103
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 648-748 1.17e-24

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 99.75  E-value: 1.17e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  648 MQQKLNEVYEAVKnytdKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACT 727
Cdd:cd04369      1 LKKKLRSLLDALK----KLKRDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKT 76

                           90       100
                   ....*....|....*....|.
gi 2118028303  728 YNEPESLIYKDALVLHKVLLE 748
Cdd:cd04369     77 YNGPGSPIYKDAKKLEKLFEK 97
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 378-482 1.72e-24

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 99.72  E-value: 1.72e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  378 QLYDIVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNS 457
Cdd:cd05524      9 ELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDS 88

                           90       100
                   ....*....|....*....|....*
gi 2118028303  458 AIYKRVLKMQQVMQAKKKELAGRDD 482
Cdd:cd05524     89 PEHKDACKLWELFLSARNEVLSGGE 113
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 378-473 1.78e-24

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 99.37  E-value: 1.78e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  378 QLYDIVRNCRNNQGQlISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNS 457
Cdd:cd04369      4 KLRSLLDALKKLKRD-LSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTYNGPGS 82

                           90
                   ....*....|....*.
gi 2118028303  458 AIYKRVLKMQQVMQAK 473
Cdd:cd04369     83 PIYKDAKKLEKLFEKL 98
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 383-468 1.87e-24

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 99.24  E-value: 1.87e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  383 VRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKR 462
Cdd:cd05522     13 LRKERDENGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKD 92


                   ....*.
gi 2118028303  463 VLKMQQ 468
Cdd:cd05522     93 AVLLEK 98
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
 378-473 2.14e-24

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99950  Cd Length: 103  Bit Score: 99.34  E-value: 2.14e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  378 QLYDIVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNS 457
Cdd:cd05519      7 EIYDAVLNCEDETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTYNQEGS 86

                           90
                   ....*....|....*.
gi 2118028303  458 AIYKRVLKMQQVMQAK 473
Cdd:cd05519     87 IVYEDAVEMEKAFKKK 102
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 651-758 4.62e-24

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 98.56  E-value: 4.62e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  651 KLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTYNE 730
Cdd:cd05524      6 VCQELYDTIRNYKSEDGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYK 85

                           90       100
                   ....*....|....*....|....*...
gi 2118028303  731 PESLIYKDALVLHKVLLETRRDIEGDED 758
Cdd:cd05524     86 PDSPEHKDACKLWELFLSARNEVLSGGE 113
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 41-304 2.96e-23

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 103.73  E-value: 2.96e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   41 DDGHHATNTPGPSRKRRRLSNLPTVDPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQ 120
Cdd:COG5076    117 GLGSLLMAHLKTSVKKRKTPKIEDELLYADNKAIAKFKKQLFLRDGRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQK 196

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  121 KLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAAcklwdlyirtknEFVQKGDAEDDddddeghdnqGTISEISSP 200
Cdd:COG5076    197 KLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDA------------KELEKYFLKLI----------EEIPEEMLE 254

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  201 GYLKEILEQLLEAVAVA-TNPTGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKN 279
Cdd:COG5076    255 LSIKPGREEREERESVLiTNSQAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDN 334

                          250       260
                   ....*....|....*....|....*
gi 2118028303  280 AKTYNEPGSQVFKDANAIKKIFNMK 304
Cdd:COG5076    335 CVMYNGEVTDYYKNANVLEDFVIKK 359
BAH cd04370
BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). ...
 945-1121 4.76e-23

BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.


Pssm-ID: 239835 [Multi-domain]  Cd Length: 123  Bit Score: 95.92  E-value: 4.76e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  945 NSMYHVGDYVYVEPAE--ANLQPHIVCIERLWEDSADSctgnaplpsrrcrgrprtvcrppseggagarcrtgsvavhka 1022
Cdd:cd04370      1 GITYEVGDSVYVEPDDsiKSDPPYIARIEELWEDTNGS------------------------------------------ 38

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1023 hnvmqrrtsssgtreKWLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKIPVSKILGKCVVMFVKEYFKLC-PENFRDE 1101
Cdd:cd04370     39 ---------------KQVKVRWFYRPEETPKGLSPFALRRELFLSDHLDEIPVESIIGKCKVLFVSEFEGLKqRPNKIDT 103

                          170       180
                   ....*....|....*....|
gi 2118028303 1102 DVYVCESRYSAKTKSFKKIK 1121
Cdd:cd04370    104 DDFFCRLAYDPTTKEFKALE 123
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 203-294 4.80e-22

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 91.61  E-value: 4.80e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  203 LKEILEQLLEavavatnptgHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKT 282
Cdd:pfam00439    1 CLEILDKLME----------HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNART 70

                           90
                   ....*....|..
gi 2118028303  283 YNEPGSQVFKDA 294
Cdd:pfam00439   71 YNGPGSVIYKAA 82
Bromodomain cd04369
Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear ...
 68-165 1.43e-21

Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine.


Pssm-ID: 99922 [Multi-domain]  Cd Length: 99  Bit Score: 90.89  E-value: 1.43e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   68 IAVCHELYNTIRDYKdeqgRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSY 147
Cdd:cd04369      2 KKKLRSLLDALKKLK----RDLSEPFLEPVDPKEAPDYYEVIKNPMDLSTIKKKLKNGEYKSLEEFEADVRLIFSNAKTY 77

                           90
                   ....*....|....*...
gi 2118028303  148 YKPDSPEYKAACKLWDLY 165
Cdd:cd04369     78 NGPGSPIYKDAKKLEKLF 95
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 536-775 1.97e-21

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 98.34  E-value: 1.97e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  536 FMVKPSKKDYPDYYkiiLEPMDLKIIEHNIRSDKYsaEEAMIEDMRLMF-----RNARHYNEEGSQVYNDAHIL-EKILK 609
Cdd:COG5076     39 APEEEGSKNLFQKQ---LKRMPKEYITSIVDDREP--GSMANVNDDLENvggitYSPFEKNRPESLRFDEIVFLaIESVT 113

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  610 EKRKELGPLLEDDEVASPKLKlsrktgiSPKKSKYMTPMQQKLneVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLT 689
Cdd:COG5076    114 PESGLGSLLMAHLKTSVKKRK-------TPKIEDELLYADNKA--IAKFKKQLFLRDGRFLSSIFLGLPSKREYPDYYEI 184

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  690 IKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDIEGDEDSHVP-----NV 764
Cdd:COG5076    185 IKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLKLIEEIPEEMLELSIkpgreER 264

                          250
                   ....*....|.
gi 2118028303  765 TLLIQELIHNL 775
Cdd:COG5076    265 EERESVLITNS 275
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 378-469 2.16e-21

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 90.56  E-value: 2.16e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  378 QLYDIVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNS 457
Cdd:cd05516      8 KIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTFNLEGS 87

                           90
                   ....*....|..
gi 2118028303  458 AIYKRVLKMQQV 469
Cdd:cd05516     88 LIYEDSIVLQSV 99
Bromo_polybromo_III cd05520
Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which ...
 513-612 2.53e-21

Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99951  Cd Length: 103  Bit Score: 90.48  E-value: 2.53e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  513 MKILYNVVLEAREPgTGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNE 592
Cdd:cd05520      5 LWQLYDTIRNARNN-QGQLLAEPFLKLPSKRKYPDYYQEIKNPISLQQIRTKLKNGEYETLEELEADLNLMFENAKRYNV 83

                           90       100
                   ....*....|....*....|
gi 2118028303  593 EGSQVYNDAHILEKILKEKR 612
Cdd:cd05520     84 PNSRIYKDAEKLQKLMQAKK 103
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 374-474 3.07e-21

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 90.19  E-value: 3.07e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  374 NPLYQLYDIVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYN 453
Cdd:cd05517      3 QILEQLLEAVMTATDPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTFN 82

                           90       100
                   ....*....|....*....|.
gi 2118028303  454 VPNSAIYKRVLKMQQVMQAKK 474
Cdd:cd05517     83 EPGSQVYKDANAIKKIFTAKK 103
Bromo_polybromo_II cd05517
Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which ...
 649-745 9.66e-21

Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99948  Cd Length: 103  Bit Score: 88.65  E-value: 9.66e-21
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  649 QQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTY 728
Cdd:cd05517      2 KQILEQLLEAVMTATDPSGRLISELFQKLPSKVLYPDYYAVIKEPIDLKTIAQRIQSGYYKSIEDMEKDLDLMVKNAKTF 81

                           90
                   ....*....|....*..
gi 2118028303  729 NEPESLIYKDALVLHKV 745
Cdd:cd05517     82 NEPGSQVYKDANAIKKI 98
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 647-744 1.80e-20

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 88.07  E-value: 1.80e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  647 PMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNAC 726
Cdd:cd05522      1 PYEARIKNILKGLRKERDENGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAK 80

                           90
                   ....*....|....*...
gi 2118028303  727 TYNEPESLIYKDALVLHK 744
Cdd:cd05522     81 LYNENDSQEYKDAVLLEK 98
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 75-160 6.41e-20

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 85.83  E-value: 6.41e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   75 YNTIRDYKDEQGRllCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPE 154
Cdd:pfam00439    1 CLEILDKLMEHPI--AAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVI 78


                   ....*.
gi 2118028303  155 YKAACK 160
Cdd:pfam00439   79 YKAAEK 84
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 218-303 1.03e-19

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 85.76  E-value: 1.03e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  218 TNPTGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYNEPGSQVFKDANAI 297
Cdd:cd05522     17 RDENGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKDAVLL 96


                   ....*.
gi 2118028303  298 KKIFNM 303
Cdd:cd05522     97 EKEARL 102
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
 69-169 1.58e-19

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 85.52  E-value: 1.58e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   69 AVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYY 148
Cdd:cd05525      5 QVLKEICDAIITYKDSNGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYY 84

                           90       100
                   ....*....|....*....|.
gi 2118028303  149 KPDSPEYKAACKLWDLYIRTK 169
Cdd:cd05525     85 GRKSPIGRDVCRLRKAYYQAK 105
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 536-615 2.59e-19

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 84.53  E-value: 2.59e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  536 FMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILKEKRKEL 615
Cdd:cd05509     22 FLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKKLKEL 101
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 204-426 5.33e-19

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 91.02  E-value: 5.33e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  204 KEILEQLLEAVAVAtnptGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTY 283
Cdd:COG5076    148 KAIAKFKKQLFLRD----GRFLSSIFLGLPSKREYPDYYEIIKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLY 223

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  284 NEPGSQVFKDANAIKKIFNMkkaEIERSELTKSSLRVSNKRAVQGDRLSAITMALQYGSesdEDAVLAAAARYEEGESEA 363
Cdd:COG5076    224 NGPDSSVYVDAKELEKYFLK---LIEEIPEEMLELSIKPGREEREERESVLITNSQAHV---GAWPFLRPVSDEEVPDYY 297

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2118028303  364 ESITSFMDASNPLYQLydivrncRNNQGQliSEPFFHLPSKK--KYPDYYQQIKMPISLQQIRTK 426
Cdd:COG5076    298 KDIRDPMDLSTKELKL-------RNNYYR--PEETFVRDAKLffDNCVMYNGEVTDYYKNANVLE 353
Bromo_polybromo_IV cd05518
Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which ...
 74-161 5.54e-19

Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99949 [Multi-domain]  Cd Length: 103  Bit Score: 83.65  E-value: 5.54e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   74 LYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSP 153
Cdd:cd05518      8 LFLYVLEYREGSGRRLCDLFMEKPSKKDYPDYYKIILEPIDLKTIEHNIRNDKYATEEELMDDFKLMFRNARHYNEEGSQ 87


                   ....*...
gi 2118028303  154 EYKAACKL 161
Cdd:cd05518     88 VYEDANIL 95
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 78-161 6.26e-19

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 83.44  E-value: 6.26e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   78 IRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKA 157
Cdd:cd05522     13 LRKERDENGRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYNENDSQEYKD 92


                   ....
gi 2118028303  158 ACKL 161
Cdd:cd05522     93 AVLL 96
Bromo_SNF2 cd05519
Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in ...
 69-147 7.75e-19

Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99950  Cd Length: 103  Bit Score: 83.16  E-value: 7.75e-19
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2118028303   69 AVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSY 147
Cdd:cd05519      3 AAMLEIYDAVLNCEDETGRKLSELFLEKPSKKLYPDYYVIIKRPIALDQIKRRIEGRAYKSLEEFLEDFHLMFANARTY 81
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 511-606 2.80e-18

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 81.90  E-value: 2.80e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  511 QRMKILYNVVLEAREPGtGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHY 590
Cdd:cd05522      4 ARIKNILKGLRKERDEN-GRLLTLHFEKLPDKAREPEYYQEISNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLY 82

                           90
                   ....*....|....*.
gi 2118028303  591 NEEGSQVYNDAHILEK 606
Cdd:cd05522     83 NENDSQEYKDAVLLEK 98
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 392-461 3.47e-18

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 80.82  E-value: 3.47e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  392 QLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYK 461
Cdd:pfam00439   11 HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYK 80
Bromo_SNF2L2 cd05516
Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI ...
 72-147 6.25e-18

Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99947  Cd Length: 107  Bit Score: 80.93  E-value: 6.25e-18
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2118028303   72 HELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSY 147
Cdd:cd05516      7 NKIVDVVIKYKDSDGRQLAEVFIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLEDLEKDVMLLCQNAQTF 82
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 239-304 1.16e-17

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 79.91  E-value: 1.16e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2118028303  239 PDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYNEPGSQVFKDANAIKKIFNMK 304
Cdd:cd05509     32 PDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKK 97
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 203-302 1.61e-17

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99952  Cd Length: 106  Bit Score: 79.67  E-value: 1.61e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  203 LKEILEQLLEAVAVATNPTGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNgyYKSIHAMAKDIDLLVKNAKT 282
Cdd:cd05521      2 LSKKLKPLYDGIYTLKEENGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRLPH--YTNAQEFVNDLAQIPWNARL 79

                           90       100
                   ....*....|....*....|
gi 2118028303  283 YNEPGSQVFKDANAIKKIFN 302
Cdd:cd05521     80 YNTKGSVIYKYALILEKYIN 99
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 376-478 3.66e-17

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 78.98  E-value: 3.66e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  376 LYQLY-DIVRNcRNnqgqliSEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNV 454
Cdd:cd05504     17 LEQLLvEIVKH-KD------SWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNP 89

                           90       100
                   ....*....|....*....|....
gi 2118028303  455 PNSAIYKRVLKMQQVMQAKKKELA 478
Cdd:cd05504     90 EHTSVYKAGTRLQRFFIKRCRKLG 113
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 647-749 4.39e-17

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99952  Cd Length: 106  Bit Score: 78.52  E-value: 4.39e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  647 PMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMmaNKYQDIDAMVEDFVMMFNNAC 726
Cdd:cd05521      1 KLSKKLKPLYDGIYTLKEENGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRL--PHYTNAQEFVNDLAQIPWNAR 78

                           90       100
                   ....*....|....*....|...
gi 2118028303  727 TYNEPESLIYKDALVLHKVLLET 749
Cdd:cd05521     79 LYNTKGSVIYKYALILEKYINDV 101
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 530-603 1.56e-16

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 76.20  E-value: 1.56e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2118028303  530 RRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSQVYNDAHI 603
Cdd:pfam00439   11 HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAEK 84
BROMO smart00297
bromo domain;
769-869 3.16e-16

bromo domain;


Pssm-ID: 197636 [Multi-domain]  Cd Length: 107  Bit Score: 76.16  E-value: 3.16e-16
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   769 QELIHNLFVSVMSHQDDegRCYSDSLAEIPAVD--PNFPN--KPPLTFDIIRKNVETNRYRRLDLFQEHMFEVLERARRM 844
Cdd:smart00297    5 QKKLQELLKAVLDKLDS--HPLSWPFLKPVSRKeaPDYYDiiKKPMDLKTIKKKLENGKYSSVEEFVADFNLMFSNARTY 82

                            90       100
                    ....*....|....*....|....*
gi 2118028303   845 NRTDSEIYEDAVELQQFFIKIRDEL 869
Cdd:smart00297   83 NGPDSEVYKDAKKLEKFFEKKLREL 107
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 377-482 6.15e-16

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 75.38  E-value: 6.15e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  377 YQLYDIVRNCRNNQGqliSEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPN 456
Cdd:cd05511      3 FILDEIVNELKNLPD---SWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPD 79

                           90       100
                   ....*....|....*....|....*.
gi 2118028303  457 SAIYKrvlKMQQVMQAKKKELAGRDD 482
Cdd:cd05511     80 SVYTK---KAKEMLELAEELLAEREE 102
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 373-468 6.68e-16

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99952  Cd Length: 106  Bit Score: 75.05  E-value: 6.68e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  373 SNPLYQLYDIVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNheYETLDHLECDLNLMFENAKRY 452
Cdd:cd05521      3 SKKLKPLYDGIYTLKEENGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRLPH--YTNAQEFVNDLAQIPWNARLY 80

                           90
                   ....*....|....*.
gi 2118028303  453 NVPNSAIYKRVLKMQQ 468
Cdd:cd05521     81 NTKGSVIYKYALILEK 96
Bromo_polybromo_I cd05524
Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which ...
 516-616 7.84e-16

Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine.


Pssm-ID: 99954 [Multi-domain]  Cd Length: 113  Bit Score: 75.06  E-value: 7.84e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  516 LYNVVLEAREPgTGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGS 595
Cdd:cd05524     10 LYDTIRNYKSE-DGRILCESFIRVPKRRNEPEYYEVVSNPIDLLKIQQKLKTEEYDDVDDLTADFELLINNAKAYYKPDS 88

                           90       100
                   ....*....|....*....|.
gi 2118028303  596 QVYNDAHILEKILKEKRKELG 616
Cdd:cd05524     89 PEHKDACKLWELFLSARNEVL 109
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 540-617 2.90e-15

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 73.48  E-value: 2.90e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  540 PSKKDYPDYYKIILEPMDLKIIEHNIR---SDKYSAEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILKEKRKELG 616
Cdd:cd05502     28 PVSPSVPNYYKIIKTPMDLSLIRKKLQpksPQHYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELELFFEEQLKEIL 107


                   .
gi 2118028303  617 P 617
Cdd:cd05502    108 P 108
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 536-617 3.16e-15

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 73.58  E-value: 3.16e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  536 FMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILKEKRKEL 615
Cdd:cd05504     33 FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTRLQRFFIKRCRKL 112


                   ..
gi 2118028303  616 GP 617
Cdd:cd05504    113 GL 114
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 397-477 3.60e-15

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 72.59  E-value: 3.60e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  397 PFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKMQQVMQAKKKE 476
Cdd:cd05509     21 PFLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKFFWKKLKE 100


                   .
gi 2118028303  477 L 477
Cdd:cd05509    101 L 101
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 230-302 4.52e-15

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 73.53  E-value: 4.52e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2118028303  230 QKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYNEPGSQVfkdANAIKKIFN 302
Cdd:cd05529     50 YPVDLRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEI---AKKAKRLSD 119
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 220-304 6.13e-15

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 72.32  E-value: 6.13e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  220 PTGHLISELFQKLPSKV--QYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYNEPGSQVFKDANAI 297
Cdd:cd05499     15 PKHSAYNWPFLDPVDPValNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQL 94


                   ....*..
gi 2118028303  298 KKIFNMK 304
Cdd:cd05499     95 EEVFNDK 101
HMG-box_NHP6-like cd01390
high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone chromosomal ...
 1414-1482 1.01e-14

high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone chromosomal proteins NHP6A, NHP6B and similar proteins; This subfamily includes Saccharomyces cerevisiae high-mobility-group proteins NHP6A and its closely related paralog NHP6B. NHP6A and NHP6B seem to be functionally redundant. They are DNA-binding proteins that induce severe bending of DNA and are required for DNA-binding by the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. They augment the fidelity of transcription by RNA polymerase III independently of any role in the FACT complex. They may also play essential roles in transcriptional initiation fidelity of some but not all tRNA genes.


Pssm-ID: 438792 [Multi-domain]  Cd Length: 81  Bit Score: 70.86  E-value: 1.01e-14
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2118028303 1414 KSAKGSVKKEGSKRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:cd01390      1 KKKKGRKKKDPNAPKRGLSAYMFFSQDNREKVKEENPDATFGEVGKLLGEKWKELSEEEKAPYEEKAAK 69
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 233-304 1.01e-14

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 71.59  E-value: 1.01e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2118028303  233 PSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYNEPGSQVFKDANAIKKIFNMK 304
Cdd:cd05506     27 VVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMAKELLKIFETR 98
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 533-618 1.59e-14

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 71.14  E-value: 1.59e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  533 CELFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSQVYNDA-HIL---EKIL 608
Cdd:cd05511     18 SWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKAkEMLelaEELL 97

                           90
                   ....*....|
gi 2118028303  609 KEKRKELGPL 618
Cdd:cd05511     98 AEREEKLTQL 107
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 668-739 3.08e-14

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 69.65  E-value: 3.08e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2118028303  668 RRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTYNEPESLIYKDA 739
Cdd:pfam00439   11 HPIAAPFLEPVDPDEYPDYYSVIKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAA 82
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 538-611 4.02e-14

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 69.67  E-value: 4.02e-14
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2118028303  538 VKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILKEK 611
Cdd:cd05506     25 VDVVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMAKELLKIFETR 98
HMG smart00398
high mobility group;
1426-1482 6.42e-14

high mobility group;


Pssm-ID: 197700 [Multi-domain]  Cd Length: 70  Bit Score: 68.11  E-value: 6.42e-14
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 2118028303  1426 KRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:smart00398    1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKK 57
BAH cd04370
BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). ...
 1208-1320 7.11e-14

BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.


Pssm-ID: 239835 [Multi-domain]  Cd Length: 123  Bit Score: 69.73  E-value: 7.11e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1208 VGDCVFIK---SHGLVRPRVGRIEKMWVR-DGAAYFFGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGKCAV 1283
Cdd:cd04370      6 VGDSVYVEpddSIKSDPPYIARIEELWEDtNGSKQVKVRWFYRPEETPKGLSPFALRRELFLSDHLDEIPVESIIGKCKV 85

                           90       100       110
                   ....*....|....*....|....*....|....*...
gi 2118028303 1284 LSFKDFLS-CRPTEISENDVLLCESRYNESDKQMKKFK 1320
Cdd:cd04370     86 LFVSEFEGlKQRPNKIDTDDFFCRLAYDPTTKEFKALE 123
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
 376-469 9.72e-14

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 68.96  E-value: 9.72e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  376 LYQLYDIVRNCRNNQGQLISEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVP 455
Cdd:cd05525      7 LKEICDAIITYKDSNGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKYYGR 86

                           90
                   ....*....|....
gi 2118028303  456 NSAIYKRVLKMQQV 469
Cdd:cd05525     87 KSPIGRDVCRLRKA 100
HMG-box_SF cd00084
high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found ...
 1431-1482 9.79e-14

high mobility group (HMG)-box domain superfamily; The High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenetically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4, and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.


Pssm-ID: 438789 [Multi-domain]  Cd Length: 59  Bit Score: 67.16  E-value: 9.79e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2118028303 1431 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:cd00084      3 LSAYLLFSKEKRPKLKKENPDLSFTEISKLLGERWKELSEEEKQPYEEKAKE 54
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 223-307 1.07e-13

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 68.99  E-value: 1.07e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  223 HLISELFQKL--PSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYNEPGSQVFKDANAIKKI 300
Cdd:cd05497     20 HKFAWPFQQPvdAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLEKL 99


                   ....*..
gi 2118028303  301 FNMKKAE 307
Cdd:cd05497    100 FLQKLAQ 106
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 103-161 1.47e-13

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 68.35  E-value: 1.47e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2118028303  103 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKL 161
Cdd:cd05509     32 PDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKL 90
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 512-611 2.13e-13

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99952  Cd Length: 106  Bit Score: 67.73  E-value: 2.13e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  512 RMKILYNVVLEAREPgTGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRsdKYSAEEAMIEDMRLMFRNARHYN 591
Cdd:cd05521      5 KLKPLYDGIYTLKEE-NGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRLP--HYTNAQEFVNDLAQIPWNARLYN 81

                           90       100
                   ....*....|....*....|
gi 2118028303  592 EEGSQVYNDAHILEKILKEK 611
Cdd:cd05521     82 TKGSVIYKYALILEKYINDV 101
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
 203-301 2.40e-13

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 67.80  E-value: 2.40e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  203 LKEILEQLLEAVAVATNPTGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKT 282
Cdd:cd05525      3 LAQVLKEICDAIITYKDSNGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEK 82

                           90
                   ....*....|....*....
gi 2118028303  283 YNEPGSQVFKDANAIKKIF 301
Cdd:cd05525     83 YYGRKSPIGRDVCRLRKAY 101
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 536-612 2.63e-13

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 67.40  E-value: 2.63e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2118028303  536 FMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILkEKR 612
Cdd:cd05503     21 FLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRAGHNMRKFF-EKR 96
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 205-299 3.32e-13

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 67.47  E-value: 3.32e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  205 EILEQLLEAVAVATNPTGHliSELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYN 284
Cdd:cd05510      7 EFYESLDKVLNELKTYTEH--STPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYN 84

                           90
                   ....*....|....*.
gi 2118028303  285 EPGSQVFKD-ANAIKK 299
Cdd:cd05510     85 SDPSHPLRRhANFMKK 100
Bromodomain pfam00439
Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin ...
 779-857 5.73e-13

Bromodomain; Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 425683 [Multi-domain]  Cd Length: 84  Bit Score: 65.80  E-value: 5.73e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  779 VMSHQDDEGRCYSDSLAEIPAVDPNFPN--KPPLTFDIIRKNVETNRYRRLDLFQEHMFEVLERARRMNRTDSEIYEDAV 856
Cdd:pfam00439    4 ILDKLMEHPIAAPFLEPVDPDEYPDYYSviKKPMDLSTIKKKLENGEYKSLAEFLADVKLIFSNARTYNGPGSVIYKAAE 83


                   .
gi 2118028303  857 E 857
Cdd:pfam00439   84 K 84
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 538-615 6.20e-13

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 66.68  E-value: 6.20e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2118028303  538 VKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKY-SAEEAmIEDMRLMFRNARHYNEEGSQVYNDAHILEKILKEKRKEL 615
Cdd:cd05497     30 VDAVKLNLPDYHKIIKTPMDLGTIKKRLENNYYwSASEC-IQDFNTMFTNCYIYNKPGDDVVLMAQTLEKLFLQKLAQM 107
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 229-308 2.44e-12

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 65.00  E-value: 2.44e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  229 FQKlPSKVQYPDYYAIIKEPIDLKTIAQRIQNG---YYKSIHAMAKDIDLLVKNAKTYNEPGSQVFKDANAIKKIFNMKK 305
Cdd:cd05502     25 FHE-PVSPSVPNYYKIIKTPMDLSLIRKKLQPKspqHYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELELFFEEQL 103


                   ...
gi 2118028303  306 AEI 308
Cdd:cd05502    104 KEI 106
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 674-753 2.72e-12

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 65.11  E-value: 2.72e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  674 FLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRDI 753
Cdd:cd05504     33 FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTRLQRFFIKRCRKL 112
HMG_box pfam00505
HMG (high mobility group) box;
1428-1482 3.47e-12

HMG (high mobility group) box;


Pssm-ID: 459837 [Multi-domain]  Cd Length: 68  Bit Score: 63.01  E-value: 3.47e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2118028303 1428 KINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:pfam00505    2 KRPMSAFFLFSKEQRAKLKAENPGLKNAEISKILGEKWKALSEEEKKPYEEKAEK 56
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 226-312 4.06e-12

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 64.59  E-value: 4.06e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  226 SELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYNEPGSQVFKDAnaiKKIFNM-K 304
Cdd:cd05511     18 SWPFHTPVNKKKVPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKA---KEMLELaE 94


                   ....*...
gi 2118028303  305 KAEIERSE 312
Cdd:cd05511     95 ELLAEREE 102
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 207-292 4.42e-12

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 64.34  E-value: 4.42e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  207 LEQLLEAVavatnpTGHLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYNEP 286
Cdd:cd05504     17 LEQLLVEI------VKHKDSWPFLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPE 90


                   ....*.
gi 2118028303  287 GSQVFK 292
Cdd:cd05504     91 HTSVYK 96
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 546-611 5.00e-12

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 63.84  E-value: 5.00e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2118028303  546 PDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILKEK 611
Cdd:cd05499     36 PNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVFNDK 101
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 233-301 7.74e-12

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 63.49  E-value: 7.74e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2118028303  233 PSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYNEPGSQVFKDANAIKKIF 301
Cdd:cd05500     31 PVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQAAF 99
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 233-304 8.84e-12

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 63.07  E-value: 8.84e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2118028303  233 PSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYNEPGSQVFKDANAIKKIFNMK 304
Cdd:cd05498     30 PEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFEDR 101
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 538-611 1.41e-11

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 62.68  E-value: 1.41e-11
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2118028303  538 VKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILKEK 611
Cdd:cd05498     28 VDPEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVFEDR 101
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 678-745 1.78e-11

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 62.30  E-value: 1.78e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2118028303  678 PSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTYNEPESLIYKDALVLHKV 745
Cdd:cd05498     30 PEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDV 97
BAH_BAHCC1 cd04714
BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. ...
 1206-1310 1.93e-11

BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240065  Cd Length: 121  Bit Score: 62.80  E-value: 1.93e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1206 LKVGDCVFIKSHGLVR-PRVGRIEKMWVRDGAA------YFFgpifiHPEETEHEPTKMFYKKEVFLSNLEETCPMTCIL 1278
Cdd:cd04714      4 IRVGDCVLFKSPGRPSlPYVARIESLWEDPEGNmvvrvkWYY-----RPEETKGGRKPNHGEKELFASDHQDENSVQTIE 78

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 2118028303 1279 GKCAVLSFKDF---LSCRPTEISENDVLLCESRYN 1310
Cdd:cd04714     79 HKCYVLTFAEYerlARVKKKPQDGVDFYYCAGTYN 113
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 237-284 2.19e-11

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 62.37  E-value: 2.19e-11
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2118028303  237 QYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYN 284
Cdd:cd05528     32 EVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYN 79
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 538-606 2.28e-11

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 61.95  E-value: 2.28e-11
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2118028303  538 VKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEK 606
Cdd:cd05500     29 VDPVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQA 97
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 645-745 2.72e-11

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 61.95  E-value: 2.72e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  645 MTPMQQKLneVYEAVKNYtdKRGRrlSAIFLRLPS---RSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMM 721
Cdd:cd05500      1 MTKHQHKF--LLSSIRSL--KRLK--DARPFLVPVdpvKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLM 74

                           90       100
                   ....*....|....*....|....
gi 2118028303  722 FNNACTYNEPESLIYKDALVLHKV 745
Cdd:cd05500     75 VDNCLTFNGPEHPVSQMGKRLQAA 98
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 380-473 5.25e-11

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 60.75  E-value: 5.25e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  380 YDIVRNCRNNQGQLISEPFFHL--PSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNS 457
Cdd:cd05498      6 SGILKELFSKKHKAYAWPFYKPvdPEALGLHDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDH 85

                           90
                   ....*....|....*.
gi 2118028303  458 AIYKRVLKMQQVMQAK 473
Cdd:cd05498     86 PVHAMARKLQDVFEDR 101
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
 511-607 5.85e-11

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 60.87  E-value: 5.85e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  511 QRMKILYNVVLEAREPgTGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHY 590
Cdd:cd05525      5 QVLKEICDAIITYKDS-NGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEKY 83

                           90
                   ....*....|....*..
gi 2118028303  591 NEEGSQVYNDAHILEKI 607
Cdd:cd05525     84 YGRKSPIGRDVCRLRKA 100
Bromo_ASH1 cd05525
Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the ...
 648-750 8.80e-11

Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99955 [Multi-domain]  Cd Length: 106  Bit Score: 60.48  E-value: 8.80e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  648 MQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACT 727
Cdd:cd05525      3 LAQVLKEICDAIITYKDSNGQSLAIPFINLPSKKKNPDYYERITDPVDLSTIEKQILTGYYKTPEAFDSDMLKVFRNAEK 82

                           90       100
                   ....*....|....*....|...
gi 2118028303  728 YNEPESLIYKDALVLHKVLLETR 750
Cdd:cd05525     83 YYGRKSPIGRDVCRLRKAYYQAK 105
Bromo_gcn5_like cd05509
Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates ...
 674-745 1.35e-10

Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99941 [Multi-domain]  Cd Length: 101  Bit Score: 59.88  E-value: 1.35e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2118028303  674 FLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTYNEPESLIYKDALVLHKV 745
Cdd:cd05509     22 FLEPVDKEEAPDYYDVIKKPMDLSTMEEKLENGYYVTLEEFVADLKLIFDNCRLYNGPDTEYYKCANKLEKF 93
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 402-469 1.58e-10

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 59.63  E-value: 1.58e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2118028303  402 PSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKMQQV 469
Cdd:cd05500     31 PVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRLQAA 98
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 682-748 2.04e-10

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 59.36  E-value: 2.04e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2118028303  682 ELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLE 748
Cdd:cd05497     36 NLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKPGDDVVLMAQTLEKLFLQ 102
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 678-748 2.10e-10

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 59.38  E-value: 2.10e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2118028303  678 PSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLE 748
Cdd:cd05495     31 PKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVFEQ 101
HMG-box_HMG20 cd21980
high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; ...
 1431-1482 2.30e-10

high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily; The HMG20 subfamily includes HMG20A and HMG20B. HMG20A, also called HMG box-containing protein 20A, HMG domain-containing protein 1, HMG domain-containing protein HMGX1, HMGXB1, or iBRAF, is a chromatin-associated protein involved in neuronal differentiation and maturation. It is required for SNAI1-mediated epithelial to mesenchymal transition. HMG20A acts as an inhibitor of HMG20B. HMG20B, also called SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related, SMARCE1-related protein (SMARCE1R), BRCA2-associated factor 35 (BRAF35), HMG box-containing protein 20B, HMG domain-containing protein 2, HMG domain-containing protein HMGX2, Sox-like transcriptional factor, or structural DNA-binding protein BRAF35, is a DNA binding factor that acts as a repressor of erythroid differentiation. It is required for correct progression through the G2 phase of the cell cycle and entry into mitosis. It is also required for RCOR1/CoREST mediated repression of neuronal specific gene promoters. HMG20B is a core subunit of the Lys-specific demethylase 1/REST co-repressor 1 (LSD1-CoREST) histone demethylase complex. Both HMG20A and HMG20B contain one HMG-box.


Pssm-ID: 438796 [Multi-domain]  Cd Length: 81  Bit Score: 58.33  E-value: 2.30e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2118028303 1431 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:cd21980      6 LTGYVRFLNERREKLRAENPDLSFPEITKILGAEWSSLSAEEKQKYLDEAEK 57
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 395-477 2.32e-10

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 59.38  E-value: 2.32e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  395 SEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKRvlkMQQVMQAKK 474
Cdd:cd05510     26 STPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDPSHPLRR---HANFMKKKA 102


                   ...
gi 2118028303  475 KEL 477
Cdd:cd05510    103 EHL 105
Bromo_BDF1_2_I cd05500
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast ...
 97-161 3.12e-10

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99932  Cd Length: 103  Bit Score: 58.86  E-value: 3.12e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2118028303   97 PKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKL 161
Cdd:cd05500     31 PVKLNIPHYPTIIKKPMDLGTIERKLKSNVYTSVEEFTADFNLMVDNCLTFNGPEHPVSQMGKRL 95
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 516-621 3.29e-10

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 58.99  E-value: 3.29e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  516 LYNVVLEARepgTGRRLCELFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGS 595
Cdd:cd05510     12 LDKVLNELK---TYTEHSTPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLYNSDPS 88

                           90       100
                   ....*....|....*....|....*.
gi 2118028303  596 QVYNDAHILekiLKEKRKELGPLLED 621
Cdd:cd05510     89 HPLRRHANF---MKKKAEHLLKLIPD 111
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 389-467 3.35e-10

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99944  Cd Length: 98  Bit Score: 58.56  E-value: 3.35e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2118028303  389 NQGQLISEPFfhlpSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKMQ 467
Cdd:cd05512     17 DTAEIFSEPV----DLSEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYRAAVRLR 91
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 103-164 3.80e-10

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99944  Cd Length: 98  Bit Score: 58.56  E-value: 3.80e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2118028303  103 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKLWDL 164
Cdd:cd05512     32 PDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYRAAVRLRDQ 93
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 233-301 5.00e-10

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 58.22  E-value: 5.00e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2118028303  233 PSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYNEPGSQVFKDANAIKKIF 301
Cdd:cd05495     31 PKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVF 99
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 408-473 5.10e-10

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 58.07  E-value: 5.10e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2118028303  408 PDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKMQQVMQAK 473
Cdd:cd05499     36 PNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVFNDK 101
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 394-461 5.96e-10

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 58.89  E-value: 5.96e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2118028303  394 ISEPFFH-LPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYK 461
Cdd:cd05529     44 IAEYFEYpVDLRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAK 112
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 237-301 6.75e-10

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 57.77  E-value: 6.75e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2118028303  237 QYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYNEPGSQVFKDANAIKKIF 301
Cdd:cd05503     29 LVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRAGHNMRKFF 93
HMG-box_SSRP1-like cd21994
high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and ...
 1431-1482 7.14e-10

high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and similar proteins; SSRP1, also called FACT complex subunit SSRP1, chromatin-specific transcription elongation factor 80 kDa subunit, facilitates chromatin transcription complex 80 kDa subunit (FACT 80 kDa subunit or FACTp80), facilitates chromatin transcription complex subunit SSRP1, recombination signal sequence recognition protein 1, or T160, is a factor that facilitates transcript elongation through nucleosomes. It is a component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication, and DNA repair.


Pssm-ID: 438810 [Multi-domain]  Cd Length: 67  Bit Score: 56.54  E-value: 7.14e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2118028303 1431 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:cd21994      3 MSAYMLWLNENREKIKKENPGISVTEISKKAGEIWKELDEEDKEKWEQKAEK 54
HMG-box_AtSSRP1 cd22013
high mobility group (HMG)-box found in Arabidopsis thaliana FACT complex subunit SSRP1 and ...
 1421-1482 7.91e-10

high mobility group (HMG)-box found in Arabidopsis thaliana FACT complex subunit SSRP1 and similar proteins; SSRP1, also called facilitates chromatin transcription complex subunit SSRP1, high mobility group B protein 8, nucleosome/chromatin assembly factor group D 08 (or D 8), protein NUCLEAR FUSION DEFECTIVE 8, or recombination signal sequence recognition protein 1, is a component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication, and DNA repair. SSRP1 may bind specifically to double-stranded DNA. It is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. SSRP1 contains only one HMG-box domain.


Pssm-ID: 438829 [Multi-domain]  Cd Length: 80  Bit Score: 56.79  E-value: 7.91e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2118028303 1421 KKEGSKRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:cd22013      3 KKDPNAPKRALSGFMFFSLMERENLKKEKPGISFGEVGKVLGEKWKNMSADDKAPYEAKAQV 64
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 538-598 8.21e-10

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 57.84  E-value: 8.21e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2118028303  538 VKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSQVY 598
Cdd:cd05495     29 VDPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVY 89
Bromo_Acf1_like cd05504
Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was ...
 93-161 8.71e-10

Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99936  Cd Length: 115  Bit Score: 57.79  E-value: 8.71e-10
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2118028303   93 FIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKL 161
Cdd:cd05504     33 FLRPVSKIEVPDYYDIIKKPMDLGTIKEKLNMGEYKLAEEFLSDIQLVFSNCFLYNPEHTSVYKAGTRL 101
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 97-167 1.42e-09

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 57.07  E-value: 1.42e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2118028303   97 PKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYIR 167
Cdd:cd05495     31 PKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVFEQ 101
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 684-753 2.45e-09

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 56.26  E-value: 2.45e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  684 PDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTYNEPESLIYKDAlvlhKVLLETRRDI 753
Cdd:cd05513     32 PGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAA----KKLLHSGMKI 97
HMG-box_ROX1-like cd01389
high mobility group (HMG)-box found in Saccharomyces cerevisiae repressor ROX1 and similar ...
 1434-1483 2.57e-09

high mobility group (HMG)-box found in Saccharomyces cerevisiae repressor ROX1 and similar proteins; This family includes class I members of the HMG-box superfamily of DNA-binding proteins, including Saccharomyces cerevisiae repressor ROX1, Schizosaccharomyces pombe mating-type M-specific polypeptide Mc (mat-Mc), Schizosaccharomyces pombe transcription factor ste11, Podospora anserina MAT+ sexual cell fertilization-promoting factor (FPR1), Podospora anserina sporulation minus regulator 2 (SMR2) and Candida albicans repressor of filamentous growth 1 (RFG1). These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. ROX1, also called heme-dependent repression factor, or hypoxic function repressor, is a transcription factor that represses the expression of HEM13, COX5B, ANB1, CYC7 or AAC3. It binds to the DNA sequence 5'-RRRTAACAAGAG-3'. mat-Mc belongs to the mating type protein family, which contains sequence specific DNA-binding proteins that act as master switches in yeast differentiation by controlling gene expression in a cell type-specific fashion. mat-Mc is a positive regulator of MFM genes and is required for conjugation and efficient meiosis. Its HMG box recognizes the DNA sequence 5'-AACAAAG-3'. Ste11 is a key transcription factor for sexual development. It activates the transcription of the matp, matm, mei2, mfm, ste6 and rgs1 genes. It binds specifically to a DNA fragment carrying a 10-base motif 5'-TTCTTTGTTY-3'. FPR1 controls fertilization, probably by determining the mating type. SMR2 is a transcription factor that is required for post-fertilization events. It is required for the developmental events that occur in the female organ after fertilization. RFG1 is a transcription regulator that functions in both the positive and negative regulation of filamentous growth, depending upon environmental conditions.


Pssm-ID: 438791 [Multi-domain]  Cd Length: 72  Bit Score: 55.28  E-value: 2.57e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1434 YILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAKV 1483
Cdd:cd01389      8 FILFRKEKHKQLRAQNPGLTNSEISKIIGKMWKNLSEEEKEPYKELAEEE 57
HMG-box_HMGB_rpt2 cd21979
second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 1432-1482 2.60e-09

second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; HMGB proteins are chromatin-associated nuclear proteins that act as architectural factors in nucleoprotein structures, which regulate DNA-dependent processes including transcription. In mammals, four family members are present: HMGB1, HMGB2, HMGB3 and HMGB4. They regulate the expression of a wide range of genes through architectural remodeling of the chromatin structure. HMGB1, also called high mobility group protein 1 (HMG-1), is a prototypical alarmin or damage-associated molecular pattern (DAMP) molecule when released from cells. It plays important roles in the regulation of a wide range of processes, including transcription, replication, DNA repair, and nucleosome formation, in the nucleus. It also plays multiple roles in regulating inflammation and responses to cell and tissue stress. HMGB2, also called high mobility group protein 2 (HMG-2), has been implicated in numerous cellular processes, including proliferation, differentiation, apoptosis, and tumor growth. It acts as a chromatin-associated nonhistone protein involved in transcriptional regulation and nucleic-acid-mediated innate immune responses in mammalian. It binds DNA to stabilize nucleosomes and promote transcription. HMGB3, also called high mobility group protein 2a (HMG-2a), or high mobility group protein 4 (HMG-4), is an X-linked member of HMGB family and functions as a universal sentinel for nucleic acid-mediated innate immune responses. HMGB3 has been implicated in the regulation of cellular proliferation and differentiation, as well as inflammatory response. HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation. It is a factor that regulates chromatin and expression of neuronal differentiation markers. The family also includes high mobility group protein B1 pseudogene 1 (HMGB1P1) and nuclear auto-antigen Sp-100. HMGB1P1, also called putative high mobility group protein B1-like 1 (HMGB1L1), or putative high mobility group protein 1-like 1 (HMG-1L1), is an HMG-box containing protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. Sp-100, also called nuclear dot-associated Sp100 protein, or speckled 100 kDa. It is a tumor suppressor that is a major constituent of the promyelocytic leukemia (PML) bodies, a subnuclear organelle involved in many physiological processes including cell growth, differentiation and apoptosis. Through the regulation of ETS1, Sp-100 may play a role in angiogenesis, controlling endothelial cell motility and invasion. It may also play roles in the regulation of telomeres lengthening, TP53-mediated transcription, FAS-mediated apoptosis, etc. In addition, the family includes Drosophila melanogaster high mobility group protein DSP1 (dDSP1) and similar proteins. dDSP1, also called protein dorsal switch 1, is a Drosophila HMG1 protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. It converts Dorsal and nuclear factor (NF)-kappa B from transcriptional activators to repressors. Members of the HMGB family contain two HMG-box domains. This model corresponds to the second one.


Pssm-ID: 438795 [Multi-domain]  Cd Length: 71  Bit Score: 55.11  E-value: 2.60e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2118028303 1432 SGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:cd21979      8 SAFFLFCSEHRPKIKGEHPGLSIGDVAKKLGEMWNNTSAKDKQPYEKKAAK 58
Bromo_Rsc1_2_I cd05521
Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 74-169 3.44e-09

Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99952  Cd Length: 106  Bit Score: 55.79  E-value: 3.44e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   74 LYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKmeEYDDVNVLTADFQLLFNNAKSYYKPDSP 153
Cdd:cd05521      9 LYDGIYTLKEENGIEIHPIFNVLPLRKDYPDYYKIIKNPLSLNTVKKRLP--HYTNAQEFVNDLAQIPWNARLYNTKGSV 86

                           90
                   ....*....|....*.
gi 2118028303  154 EYKAACKLwDLYIRTK 169
Cdd:cd05521     87 IYKYALIL-EKYINDV 101
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 540-597 3.70e-09

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 55.62  E-value: 3.70e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2118028303  540 PSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSQV 597
Cdd:cd05505     25 VTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSYV 82
Bromo_Brdt_II_like cd05498
Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET ...
 103-165 4.85e-09

Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99930  Cd Length: 102  Bit Score: 55.36  E-value: 4.85e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2118028303  103 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLY 165
Cdd:cd05498     36 HDYHDIIKHPMDLSTIKKKLDNREYADAQEFAADVRLMFSNCYKYNPPDHPVHAMARKLQDVF 98
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 103-161 4.89e-09

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 55.11  E-value: 4.89e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2118028303  103 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKL 161
Cdd:cd05513     32 PGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAAKKL 90
Bromo_cbp_like cd05495
Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase ...
 395-472 5.80e-09

Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99927  Cd Length: 108  Bit Score: 55.53  E-value: 5.80e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  395 SEPFFHL--PSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKMQQVMQA 472
Cdd:cd05495     22 SLPFRQPvdPKLLGIPDYFDIVKNPMDLSTIRRKLDTGQYQDPWQYVDDVWLMFDNAWLYNRKTSRVYKYCTKLAEVFEQ 101
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 683-739 8.33e-09

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 54.96  E-value: 8.33e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2118028303  683 LPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTYNEPESLIYKDA 739
Cdd:cd05511     30 VPDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKA 86
BAH_Orc1p_like cd04715
BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of ...
 1195-1296 9.98e-09

BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins. Orc1 is part of the Yeast Sir1-origin recognition complex, the Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240066  Cd Length: 159  Bit Score: 55.97  E-value: 9.98e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1195 YYEQLCYNDMWLKVGDCVFIKsHGLVRPRVGRIEKMW---VRDGAAY-----FFGPIFIHPEeteHEPTKMFYKKEVFLS 1266
Cdd:cd04715     19 FYRSFTYDGVEYRLYDDVYVH-NGDSEPYIGKIIKIYetaIDSGKKKvkviwFFRPSEIRME---LKGEPKRHINEVFLA 94

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 2118028303 1267 -----NLEETCPMTCILGKCAVLSF-KDFLSCRPTE 1296
Cdd:cd04715     95 cgrgeGLANINLLESIIGKCNVVCIsEDFRNPQPSD 130
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 545-608 1.40e-08

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 55.04  E-value: 1.40e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2118028303  545 YPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKIL 608
Cdd:cd05529     58 YPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRLSDWL 121
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 399-453 1.54e-08

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 54.29  E-value: 1.54e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2118028303  399 FHLP-SKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYN 453
Cdd:cd05528     24 FTKPvDEEEVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYN 79
NHP6B COG5648
Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];
1389-1480 2.20e-08

Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics];


Pssm-ID: 227935 [Multi-domain]  Cd Length: 211  Bit Score: 56.41  E-value: 2.20e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1389 TIPQLQTPLSNELdimpyTPPQSTPKSAKGSVKK---EGSKRkiNMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEW 1465
Cdd:COG5648     37 TLVELEKPLQQLL-----TKPRKKTKSKRLVRKKkdpNGPKR--PLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKW 109

                           90
                   ....*....|....*
gi 2118028303 1466 RNLEATKKAEYEERA 1480
Cdd:COG5648    110 KELTDEEKEPYYKEA 124
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 87-161 3.07e-08

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 53.45  E-value: 3.07e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   87 RLLCELFIRAPKRRNQ-------PDYYEVVSQPIDLMKIQQKLKMEE---YDDVNVLTADFQLLFNNAKSYYKPDSPEYK 156
Cdd:cd05502     11 RLLLELYCHELSLPFHepvspsvPNYYKIIKTPMDLSLIRKKLQPKSpqhYSSPEEFVADVRLMFKNCYKFNEEDSEVAQ 90


                   ....*
gi 2118028303  157 AACKL 161
Cdd:cd05502     91 AGKEL 95
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 670-744 3.42e-08

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 53.06  E-value: 3.42e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2118028303  670 LSAIFLRlPSRSELPDYYLTIKKPVDMEKIRSHM---MANKYQDIDAMVEDFVMMFNNACTYNEPESLIYKDALVLHK 744
Cdd:cd05502     21 LSLPFHE-PVSPSVPNYYKIIKTPMDLSLIRKKLqpkSPQHYSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELEL 97
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 681-742 3.43e-08

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99944  Cd Length: 98  Bit Score: 52.79  E-value: 3.43e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2118028303  681 SELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTYNEPESLIYKDALVL 742
Cdd:cd05512     29 SEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYNAKDTIFYRAAVRL 90
Bromo_tif1_like cd05502
Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of ...
 399-479 3.73e-08

Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99934 [Multi-domain]  Cd Length: 109  Bit Score: 53.06  E-value: 3.73e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  399 FHLPSKKKYPDYYQQIKMPISLQQIRTKLK----NHeYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKMQQVMQAKK 474
Cdd:cd05502     25 FHEPVSPSVPNYYKIIKTPMDLSLIRKKLQpkspQH-YSSPEEFVADVRLMFKNCYKFNEEDSEVAQAGKELELFFEEQL 103


                   ....*
gi 2118028303  475 KELAG 479
Cdd:cd05502    104 KEILP 108
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 395-468 3.84e-08

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 52.54  E-value: 3.84e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2118028303  395 SEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKMQQ 468
Cdd:cd05505     18 SWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSYVLSCMRKTEQ 91
Bromo_Rsc1_2_II cd05522
Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are ...
 772-862 4.78e-08

Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99953 [Multi-domain]  Cd Length: 104  Bit Score: 52.63  E-value: 4.78e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  772 IHNLFVSVMSHQDDEGRCYSDSLAEIPavDPN-FPN-----KPPLTFDIIRKNVETNRYRRLDLFQEHMFEVLERARRMN 845
Cdd:cd05522      6 IKNILKGLRKERDENGRLLTLHFEKLP--DKArEPEyyqeiSNPISLDDIKKKVKRRKYKSFDQFLNDLNLMFENAKLYN 83

                           90
                   ....*....|....*..
gi 2118028303  846 RTDSEIYEDAVELQQFF 862
Cdd:cd05522     84 ENDSQEYKDAVLLEKEA 100
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 226-284 5.07e-08

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99928  Cd Length: 119  Bit Score: 52.85  E-value: 5.07e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2118028303  226 SELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYN 284
Cdd:cd05496     23 SEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYT 81
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 678-745 5.20e-08

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 52.29  E-value: 5.20e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2118028303  678 PSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTYNEPESLIYKDALVLHKV 745
Cdd:cd05499     30 PVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEV 97
HMG-box_HMG20A cd22017
high mobility group (HMG)-box found in high mobility group protein 20A (HMG20A) and similar ...
 1422-1482 5.51e-08

high mobility group (HMG)-box found in high mobility group protein 20A (HMG20A) and similar proteins; HMG20A, also called HMG box-containing protein 20A, HMG domain-containing protein 1 (HMGXB1), HMG domain-containing protein HMGX1, HMGXB1, or iBRAF, is a chromatin-associated protein involved in neuronal differentiation and maturation. It is required for SNAI1-mediated epithelial to mesenchymal transition. HMG20A acts as an inhibitor of HMG20B.


Pssm-ID: 438833 [Multi-domain]  Cd Length: 104  Bit Score: 52.64  E-value: 5.51e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2118028303 1422 KEGSKRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:cd22017     16 RDSNAPKAPLTGYVRFMNERREQLRAERPDVPFPEITRMLGNEWSKLPAEEKQRYLDEAEK 76
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 678-731 5.67e-08

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 52.33  E-value: 5.67e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2118028303  678 PSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTYNEP 731
Cdd:cd05506     27 VVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPP 80
HMG-box_HMG20B cd22018
high mobility group (HMG)-box found in high mobility group protein 20B (HMG20B) and similar ...
 1428-1482 5.68e-08

high mobility group (HMG)-box found in high mobility group protein 20B (HMG20B) and similar proteins; HMG20B, also called SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related, SMARCE1-related protein (SMARCE1R), BRCA2-associated factor 35 (BRAF35), HMG box-containing protein 20B, HMG domain-containing protein 2 (HMGXB2), HMG domain-containing protein HMGX2, Sox-like transcriptional factor, or structural DNA-binding protein BRAF35, is a DNA binding factor that acts as a repressor of erythroid differentiation. It is required for correct progression through the G2 phase of the cell cycle and entry into mitosis. It is also required for RCOR1/CoREST mediated repression of neuronal specific gene promoters. HMG20B is a core subunit of the Lys-specific demethylase 1/REST co-repressor 1 (LSD1-CoREST) histone demethylase complex.


Pssm-ID: 438834 [Multi-domain]  Cd Length: 85  Bit Score: 51.90  E-value: 5.68e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2118028303 1428 KINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:cd22018      3 KAPVTGYVRFLNERREQIRTQHPDLPFPEITKMLGAEWSKLQPHEKQRYLDEAER 57
HMG-box_TOX-like cd21995
high mobility group (HMG)-box found in the TOX high mobility group box family; The TOX family ...
 1432-1482 5.98e-08

high mobility group (HMG)-box found in the TOX high mobility group box family; The TOX family includes four members: TOX, TOX2, TOX3 and TOX4. TOX, also called thymus high mobility group box protein TOX, is a transcriptional regulator with a major role in neural stem cell commitment and corticogenesis as well as in lymphoid cell development and lymphoid tissue organogenesis. It binds to GC-rich DNA sequences in the proximity of transcription start sites and may alter chromatin structure, modifying access of transcription factors to DNA. TOX2, also called granulosa cell HMG box protein 1 (GCX-1), is a putative transcriptional activator involved in the hypothalamic-pituitary-gonadal system. TOX3, also called CAG trinucleotide repeat-containing gene F9 protein (CAGF9), or trinucleotide repeat-containing gene 9 protein (TNRC9), is a transcriptional coactivator of the p300/CBP-mediated transcription complex. It activates transactivation through cAMP response element (CRE) sites. It protects against cell death by inducing anti-apoptotic and repressing pro-apoptotic transcripts. TOX4, also called epidermal Langerhans cell protein LCP1, is a component of the PTW/PP1 phosphatase complex, which plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase. All family members contain one HMG-box domain.


Pssm-ID: 438811 [Multi-domain]  Cd Length: 70  Bit Score: 51.32  E-value: 5.98e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2118028303 1432 SGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEER--AAK 1482
Cdd:cd21995      5 SAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLDEEQKQVYKKKteAAK 57
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 682-750 7.55e-08

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 51.99  E-value: 7.55e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2118028303  682 ELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTYNEPESLIYKDALVLHKvLLETR 750
Cdd:cd05503     29 LVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRAGHNMRK-FFEKR 96
Bromo_BDF1_2_II cd05499
Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast ...
 97-165 1.17e-07

Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99931  Cd Length: 102  Bit Score: 51.52  E-value: 1.17e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2118028303   97 PKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLY 165
Cdd:cd05499     30 PVALNIPNYFSIIKKPMDLGTISKKLQNGQYQSAKEFERDVRLIFKNCYTFNPEGTDVYMMGHQLEEVF 98
BAH_plant_2 cd04718
BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH ...
 1226-1318 1.20e-07

BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240069  Cd Length: 148  Bit Score: 52.59  E-value: 1.20e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1226 RIEKMWVRDGAAYFFGPIFIHPEETEHEPTKMFYKKEVFLSNLEETCPMTCILGKCAVLSFKDFlscRPTEISENDVLLC 1305
Cdd:cd04718     57 RIEKLWEENGTYWYAARWYTLPEETHMGRQPHNLRRELYLTNDFADIEMECILRHCSVKCPKEF---RDASNDGDDVFLC 133

                           90
                   ....*....|...
gi 2118028303 1306 ESRYNESDKQMKK 1318
Cdd:cd04718    134 EYEYDVHWQSFKR 146
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 206-284 1.24e-07

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99944  Cd Length: 98  Bit Score: 51.25  E-value: 1.24e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2118028303  206 ILEQLLEAVAvaTNPTGHLISElfqKLPSKvQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYN 284
Cdd:cd05512      5 LLRKTLDQLQ--EKDTAEIFSE---PVDLS-EVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYN 77
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 399-477 1.57e-07

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 51.27  E-value: 1.57e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  399 FHLP---SKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDhlEC--DLNLMFENAKRYNVPNSAIYKRVLKMQQVMQAK 473
Cdd:cd05497     26 FQQPvdaVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSAS--ECiqDFNTMFTNCYIYNKPGDDVVLMAQTLEKLFLQK 103


                   ....
gi 2118028303  474 KKEL 477
Cdd:cd05497    104 LAQM 107
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 408-469 1.71e-07

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 50.87  E-value: 1.71e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2118028303  408 PDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKMQQV 469
Cdd:cd05513     32 PGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKAAKKLLHS 93
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 544-615 1.80e-07

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99928  Cd Length: 119  Bit Score: 51.30  E-value: 1.80e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2118028303  544 DYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYN-EEGSQVYNDAHILEKILKEKRKEL 615
Cdd:cd05496     34 KYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYTpNKRSRIYSMTLRLSALFEEHIKKI 106
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 397-459 2.46e-07

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 50.45  E-value: 2.46e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2118028303  397 PFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAI 459
Cdd:cd05503     20 PFLEPVNTKLVPGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEV 82
HMG-box_AtHMGB6-like_rpt2 cd22007
second high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 1431-1482 2.62e-07

second high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 6 (HMGB6) and similar proteins; HMGB6, also called nucleosome/chromatin assembly factor group D 06 (or D 6), WRKY transcription factor 53 (WRKY53), or WRKY DNA-binding protein 53, is a master regulator of age-induced leaf senescence. It acts in a complex transcription factor signaling network regulating senescence specific gene expression; hydrogen peroxide might be involved in signal transduction. The subfamily also includes Arabidopsis thaliana HMGB13 (also known as nucleosome/chromatin assembly factor group D 13). Both HMGB6 and HMGB13 contain three HMG-box domains. This model corresponds to the second one.


Pssm-ID: 438823 [Multi-domain]  Cd Length: 68  Bit Score: 49.18  E-value: 2.62e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2118028303 1431 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:cd22007      5 QSAYFLYANDRRAALKEENKNVKITEIAKMLGAEWKNLSDAKKKPYEEKAKK 56
BAH_BAHCC1 cd04714
BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. ...
 1043-1114 2.82e-07

BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240065  Cd Length: 121  Bit Score: 50.86  E-value: 2.82e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2118028303 1043 CWFYRPNETFHLATRKFLEKEVFKSDYYNKIPVSKILGKCVVMFVKEYFKL---CPENFRDEDVYVCESRYSAKT 1114
Cdd:cd04714     42 KWYYRPEETKGGRKPNHGEKELFASDHQDENSVQTIEHKCYVLTFAEYERLarvKKKPQDGVDFYYCAGTYNPDT 116
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 222-302 2.85e-07

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 50.10  E-value: 2.85e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  222 GHLISELFQKLPSKVQY--------PDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYNEPGSQVFKD 293
Cdd:cd05513      7 EQLIRQLQRKDPHGFFAfpvtdfiaPGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDTIYYKA 86


                   ....*....
gi 2118028303  294 AnaiKKIFN 302
Cdd:cd05513     87 A---KKLLH 92
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
 534-609 3.91e-07

Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99940  Cd Length: 99  Bit Score: 49.69  E-value: 3.91e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2118028303  534 ELFMVKPSKKDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSQVYNDAHILEKILK 609
Cdd:cd05508     21 EPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGGDHKLTQAAKAIVKICE 96
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 103-163 4.80e-07

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 50.05  E-value: 4.80e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2118028303  103 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKA----ACKLWD 163
Cdd:cd05528     34 PDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYNPDRDPADKLirsrACELRD 98
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 71-152 5.49e-07

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 49.46  E-value: 5.49e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303   71 CHELYNTIRDYKDEQGrllcelFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKP 150
Cdd:cd05505      5 CEEILSKILKYRFSWP------FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYEN 78


                   ..
gi 2118028303  151 DS 152
Cdd:cd05505     79 GS 80
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 229-290 6.35e-07

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 49.07  E-value: 6.35e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2118028303  229 FQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYNEPGSQV 290
Cdd:cd05505     21 FREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSYV 82
Bromo_RACK7 cd05508
Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) ...
 226-300 6.81e-07

Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99940  Cd Length: 99  Bit Score: 49.30  E-value: 6.81e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2118028303  226 SELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYNEPGSQVFKDANAIKKI 300
Cdd:cd05508     20 AEPFLKPVDLEQFPDYAQYVFKPMDLSTLEKNVRKKAYGSTDAFLADAKWILHNAIIYNGGDHKLTQAAKAIVKI 94
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 395-479 7.15e-07

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99928  Cd Length: 119  Bit Score: 49.76  E-value: 7.15e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  395 SEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNvPN--SAIYKRVLKMQQVMQA 472
Cdd:cd05496     23 SEPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSYT-PNkrSRIYSMTLRLSALFEE 101


                   ....*..
gi 2118028303  473 KKKELAG 479
Cdd:cd05496    102 HIKKIIS 108
HMG-box_HMGXB4 cd21982
high mobility group (HMG)-box found in HMG domain-containing protein 4 (HMGXB4) and similar ...
 1427-1480 1.01e-06

high mobility group (HMG)-box found in HMG domain-containing protein 4 (HMGXB4) and similar proteins; HMGXB4, also called HMG box-containing protein 4, high mobility group protein 2-like 1 (HMG2L1), or protein HMGBCG, is a non-histone chromosomal protein that negatively regulates Wnt/beta-catenin signaling during development. It plays a role in the hematopoietic system.


Pssm-ID: 438798 [Multi-domain]  Cd Length: 61  Bit Score: 47.66  E-value: 1.01e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2118028303 1427 RKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERA 1480
Cdd:cd21982      1 KKKNMSAYQVFCKEYRVSIVAEHPGIDFGELSKKLAEVWKQLPEKDKLVWKQKA 54
HMG_box_2 pfam09011
HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate ...
 1426-1480 1.01e-06

HMG-box domain; This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long highly acidic C-tail; and a diverse group of sequence-specific transcription factor-proteins with either a single HMG-box or up to six copies, and no acidic C-tail.


Pssm-ID: 430369 [Multi-domain]  Cd Length: 72  Bit Score: 47.79  E-value: 1.01e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2118028303 1426 KRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERA 1480
Cdd:pfam09011    3 KPKRARNAYAFFVQEMIPEHKRQNPVIGFAEVSKLCSERWKNLSEEEKEKYEEMA 57
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 647-733 1.65e-06

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 48.59  E-value: 1.65e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  647 PMQQKLNEVYEAVKNYTDKrgrrlSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNAC 726
Cdd:cd05510      7 EFYESLDKVLNELKTYTEH-----STPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCL 81


                   ....*..
gi 2118028303  727 TYNEPES 733
Cdd:cd05510     82 LYNSDPS 88
HMG-box_SOX cd22004
high mobility group (HMG)-box found in sex-determining region Y (SRY)-box (SOX) family ...
 1431-1480 1.83e-06

high mobility group (HMG)-box found in sex-determining region Y (SRY)-box (SOX) family transcription factors; The SOX gene family of transcription factors are characterized by the evolutionarily conserved SRY-type HMG box, which is a DNA binding domain that binds the minor groove of DNA on a common consensus site, (A/T)(A/T)CAA(A/T)G but with different levels of efficiency. Members include SRY and its homologs identified in mammals that can be subdivided into 8 groups (A, B1, B2, C, D, E, F, G, H). They are involved in embryonic development, regulating processes such as cell differentiation, maintenance of stemness, sex determination, and development of the central nervous, haematopoietic and other organ systems. The SOX gene family has a crucial role in carcinogenesis and cancer progression.


Pssm-ID: 438820 [Multi-domain]  Cd Length: 75  Bit Score: 47.15  E-value: 1.83e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1431 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERA 1480
Cdd:cd22004      6 MNAFMVWSQQERKKIAKQNPKLHNSEISKILGKEWKKLTEEEKRPYVEEA 55
HMG-box_ABF2_IXR1-like_rpt2 cd22012
second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 1431-1479 1.96e-06

second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ARS-binding factor 2 (ABF2), intrastrand cross-link recognition protein (Ixr1) and similar proteins; ABF2 is a close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria. It specifically binds to the autonomously replicating sequence 1 (ARS1). It might play a positive role in gene expression and replication. Ixr1, also called structure-specific recognition protein (SSRP), is a homolog of the yeast mitochondrial regulator ABF2. It binds to platinated DNA and confers sensitivity to the anticancer drug cisplatin. Both ABF2 and Ixr1 contain two HMG-box domains. This model corresponds to the second one.


Pssm-ID: 438828 [Multi-domain]  Cd Length: 64  Bit Score: 46.90  E-value: 1.96e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2118028303 1431 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEER 1479
Cdd:cd22012      6 ASAYFLFAKEVRPKLKEENPNEKYTDITKLISEKWRSLDESEKEPYQEE 54
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 97-161 2.06e-06

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 47.71  E-value: 2.06e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2118028303   97 PKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKL 161
Cdd:cd05506     27 VVALGLPDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVHTMAKEL 91
COG5076 COG5076
Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin ...
 652-864 2.31e-06

Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription];


Pssm-ID: 227408 [Multi-domain]  Cd Length: 371  Bit Score: 51.73  E-value: 2.31e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  652 LNEVYEAVKNYTDKRGRrlsaiFLRLPSRSELPDYYL------TIKKPVDMEKirSHMMANKYQDidamVEDFVMMFNNA 725
Cdd:COG5076     22 GNELLRLVDNDSSPFPN-----APEEEGSKNLFQKQLkrmpkeYITSIVDDRE--PGSMANVNDD----LENVGGITYSP 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  726 CTYNEPESLIYKDaLVLHKVLLETRRDIEG------DEDSHVPNVTLLIQELI---HNLFVSVMSHQ--DDEGRCYSDsL 794
Cdd:COG5076     91 FEKNRPESLRFDE-IVFLAIESVTPESGLGsllmahLKTSVKKRKTPKIEDELlyaDNKAIAKFKKQlfLRDGRFLSS-I 168

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2118028303  795 AEIPAVDPNFPN-----KPPLTFDIIRKNVETNRYRRLDLFQEHMFEVLERARRMNRTDSEIYEDAVELQQFFIK 864
Cdd:COG5076    169 FLGLPSKREYPDyyeiiKSPMDLLTIQKKLKNGRYKSFEEFVSDLNLMFDNCKLYNGPDSSVYVDAKELEKYFLK 243
Bromo_TFIID cd05511
Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, ...
 103-164 2.69e-06

Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99943 [Multi-domain]  Cd Length: 112  Bit Score: 47.64  E-value: 2.69e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2118028303  103 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKLWDL 164
Cdd:cd05511     31 PDYYKIIKRPMDLQTIRKKISKHKYQSREEFLEDIELIVDNSVLYNGPDSVYTKKAKEMLEL 92
Bromo_brd7_like cd05513
Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown ...
 546-601 6.01e-06

Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99945  Cd Length: 98  Bit Score: 46.25  E-value: 6.01e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2118028303  546 PDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSqVYNDA 601
Cdd:cd05513     32 PGYSSIIKHPMDFSTMKEKIKNNDYQSIEEFKDDFKLMCENAMKYNKPDT-IYYKA 86
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
 395-453 6.75e-06

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99933  Cd Length: 102  Bit Score: 46.27  E-value: 6.75e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2118028303  395 SEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYN 453
Cdd:cd05501     18 SKSGFFISKPYYIRDYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFY 76
HMG-box_AtHMGB9-like cd22009
high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 9 ...
 1428-1482 7.46e-06

high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 9 (HMGB9) and similar proteins; This subfamily contains a group of Arabidopsis thaliana HMGB family proteins, including HMGB9, 10, 11, and 15. They are DNA-binding proteins containing both HMG-box and AT-rich interaction domains. They bind preferentially to DNA with A/T-rich content. HMGB9 is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. Members of this subfamily have only one HMG-box domain.


Pssm-ID: 438825 [Multi-domain]  Cd Length: 67  Bit Score: 45.15  E-value: 7.46e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2118028303 1428 KINMSGYILFSSEMRAVIKAQHPDYSfGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:cd22009      2 KPNRSGYNFFFAEQHARLKALYPGKD-REISKMIGEMWSNLTEEEKEVYQDKGVE 55
Bromo_SPT7_like cd05510
Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the ...
 71-147 7.48e-06

Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99942 [Multi-domain]  Cd Length: 112  Bit Score: 46.67  E-value: 7.48e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2118028303   71 CHELYNTIRDYKDEQgrllcELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSY 147
Cdd:cd05510     12 LDKVLNELKTYTEHS-----TPFLTKVSKREAPDYYDIIKKPMDLGTMLKKLKNLQYKSKAEFVDDLNLIWKNCLLY 83
Bromo_WSTF_like cd05505
Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The ...
 669-735 9.55e-06

Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99937  Cd Length: 97  Bit Score: 45.99  E-value: 9.55e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2118028303  669 RLSAIFLRLPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTYNEPESLI 735
Cdd:cd05505     16 RFSWPFREPVTADEAEDYKKVITNPMDLQTMQTKCSCGSYSSVQEFLDDMKLVFSNAEKYYENGSYV 82
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
 223-297 9.92e-06

Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99939  Cd Length: 104  Bit Score: 45.82  E-value: 9.92e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2118028303  223 HLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGYYKSIHAMAKDIDLLVKNAKTYNEPGSQVFKDANAI 297
Cdd:cd05507     18 HRYASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDVYLMAVEM 92
HMG-box_UBF1_rpt4 cd22001
fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar ...
 1431-1482 1.22e-05

fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar proteins; UBF1, also called UBTF, nucleolar transcription factor 1, or auto-antigen NOR-90, is a nucleolar transcription factor that recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element. UBF1 contains six HMG-box domains. This model corresponds to the fourth one.


Pssm-ID: 438817 [Multi-domain]  Cd Length: 66  Bit Score: 44.60  E-value: 1.22e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2118028303 1431 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:cd22001      7 ISAMFIYSKEKRSKLKKKHPELSEQELTRLLAKKYNELPDKKKAKYKKKEAL 58
Bromo_Brdt_I_like cd05497
Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET ...
 97-150 1.33e-05

Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99929  Cd Length: 107  Bit Score: 45.88  E-value: 1.33e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2118028303   97 PKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKP 150
Cdd:cd05497     32 AVKLNLPDYHKIIKTPMDLGTIKKRLENNYYWSASECIQDFNTMFTNCYIYNKP 85
Bromo_WDR9_II cd05496
Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 71-147 1.60e-05

Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99928  Cd Length: 119  Bit Score: 45.91  E-value: 1.60e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2118028303   71 CHELYNTIRDYKDEqgrllcELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSY 147
Cdd:cd05496     10 CKELVNLMWDCEDS------EPFRQPVDLLKYPDYRDIIDTPMDLGTVKETLFGGNYDDPMEFAKDVRLIFSNSKSY 80
Bromo_plant1 cd05506
Bromodomain, uncharacterized subfamily specific to plants. Might function as a global ...
 408-460 1.88e-05

Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99938  Cd Length: 99  Bit Score: 45.01  E-value: 1.88e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2118028303  408 PDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAIY 460
Cdd:cd05506     33 PDYFDIIKKPMDLGTVKKKLEKGEYSSPEEFAADVRLTFANAMRYNPPGNDVH 85
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
 546-601 2.20e-05

Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99939  Cd Length: 104  Bit Score: 45.05  E-value: 2.20e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2118028303  546 PDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSQVYNDA 601
Cdd:cd05507     34 PGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDVYLMA 89
HMG-box_AtHMGB6-like_rpt3 cd22008
third high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 1422-1482 2.39e-05

third high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 6 (HMGB6) and similar proteins; HMGB6, also called nucleosome/chromatin assembly factor group D 06 (or D 6), WRKY transcription factor 53 (WRKY53), or WRKY DNA-binding protein 53, is a master regulator of age-induced leaf senescence. It acts in a complex transcription factor signaling network regulating senescence specific gene expression; hydrogen peroxide might be involved in signal transduction. The subfamily also includes Arabidopsis thaliana HMGB13 (also known as nucleosome/chromatin assembly factor group D 13). Both HMGB6 and HMGB13 contain three HMG-box domains. This model corresponds to the third one.


Pssm-ID: 438824 [Multi-domain]  Cd Length: 78  Bit Score: 44.17  E-value: 2.39e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2118028303 1422 KEGSKRKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:cd22008      5 VDPNKPKKPASSYLLFGKEYRKKLQEERPGANNATVTALISLKWKELGEEEKQVYNDKAAV 65
Bromo_brd8_like cd05507
Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with ...
 380-471 2.73e-05

Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99939  Cd Length: 104  Bit Score: 44.66  E-value: 2.73e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  380 YDIVRNCRNnqgqliSEPFFHLPSKKKYPDYYQQIKMPISLQQIRTKLKNHEYETLDHLECDLNLMFENAKRYNVPNSAI 459
Cdd:cd05507     12 YRTLASHRY------ASVFLKPVTEDIAPGYHSVVYRPMDLSTIKKNIENGTIRSTAEFQRDVLLMFQNAIMYNSSDHDV 85

                           90
                   ....*....|...
gi 2118028303  460 YKRVLKMQQ-VMQ 471
Cdd:cd05507     86 YLMAVEMQReVMS 98
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 544-591 5.52e-05

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 44.27  E-value: 5.52e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2118028303  544 DYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYN 591
Cdd:cd05528     32 EVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYN 79
HMG-box_AtHMGB1-like cd22005
high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 1 ...
 1432-1482 6.12e-05

high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 1 (HMGB1) and similar proteins; This subfamily contains a group of Arabidopsis thaliana HMGB family proteins, including HMGB1, 2, 3, 4, 5, 7, 12 and 14. They bind preferentially to double-stranded DNA. HMGB1 modulates general plant growth and stress tolerance and confers sensitivity to salt and genotoxic (methyl methanesulfonate, MMS) stresses. HMGB2 and HMGB5 confer sensitivity to salt and drought stresses. HMGB7 is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. Members of this subfamily contain only one HMG-box domain.


Pssm-ID: 438821 [Multi-domain]  Cd Length: 60  Bit Score: 42.30  E-value: 6.12e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2118028303 1432 SGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:cd22005      5 TAFFLFLADFRKTYKKKNPDKSVKAVGKAAGEKWKSMSDEEKAPYVEKAEK 55
HMG-box_WDHD1 cd21993
high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and ...
 1425-1482 7.02e-05

high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and similar proteins; WDHD1, also called acidic nucleoplasmic DNA-binding protein 1 (And-1), acts as a replication initiation factor that brings together the MCM2-7 helicase and the DNA polymerase alpha/primase complex in order to initiate DNA replication.


Pssm-ID: 438809 [Multi-domain]  Cd Length: 62  Bit Score: 42.24  E-value: 7.02e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2118028303 1425 SKRKInmSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:cd21993      2 NKKKK--SGFQLWLEENRSSIEEENPELSEAEIIKLAMQRFRALPKEEKQKWNEKAKG 57
HMG-box_AtHMGB6-like_rpt1 cd22006
first high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B ...
 1432-1479 7.46e-05

first high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 6 (HMGB6) and similar proteins; HMGB6, also called nucleosome/chromatin assembly factor group D 06 (or D 6), WRKY transcription factor 53 (WRKY53), or WRKY DNA-binding protein 53, is a master regulator of age-induced leaf senescence. It acts in a complex transcription factor signaling network regulating senescence specific gene expression; hydrogen peroxide might be involved in signal transduction. The subfamily also includes Arabidopsis thaliana HMGB13 (also known as nucleosome/chromatin assembly factor group D 13). Both HMGB6 and HMGB13 contain three HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438822 [Multi-domain]  Cd Length: 68  Bit Score: 42.44  E-value: 7.46e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2118028303 1432 SGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEER 1479
Cdd:cd22006      5 TAYFLWCKDQREEVKKENPNADFSEVSKILGAKWKNLSEEEKKPYEEK 52
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
 547-614 9.08e-05

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99933  Cd Length: 102  Bit Score: 43.19  E-value: 9.08e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2118028303  547 DYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYNEEGSQVyNDAHILEKILKEKRKE 614
Cdd:cd05501     32 DYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDDDFG-QVGITLEKKFEKNFKE 98
HMG-box_SMARCE1 cd21983
high mobility group (HMG)-box found in SWI/SNF-related matrix-associated actin-dependent ...
 1434-1478 9.57e-05

high mobility group (HMG)-box found in SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 (SMARCE1) and similar proteins; SMARCE1, also called BRG1-associated factor 57 (BAF57), is a ubiquitously expressed protein involved in transcriptional activation and repression of select genes by chromatin remodeling. It is a component of SWI/SNF chromatin remodeling complexes that carry out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner. SMARCE1 has a single HMG domain that displays non-specific DNA-binding characteristics. It also contains a kinesin-like coiled-coil (KLCC) domain.


Pssm-ID: 438799 [Multi-domain]  Cd Length: 73  Bit Score: 42.28  E-value: 9.57e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2118028303 1434 YILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEE 1478
Cdd:cd21983     12 YMRYSRKVWDQVKASNPDLKLWEIGKIIGQMWRELSDEEKQEYIE 56
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 677-752 1.27e-04

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 43.48  E-value: 1.27e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2118028303  677 LPSRSELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRD 752
Cdd:cd05529     52 VDLRAWYPDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRLSDWLLRILSS 127
HMG-box_BHMG1 cd21977
high mobility group (HMG)-box found in basic helix-loop-helix and HMG box domain-containing ...
 1427-1481 1.37e-04

high mobility group (HMG)-box found in basic helix-loop-helix and HMG box domain-containing protein 1 (BHMG1) and similar proteins; BHMG1 is an uncharacterized HMG-box containing protein that contains a degenerate basic motif not likely to bind DNA.


Pssm-ID: 438793 [Multi-domain]  Cd Length: 66  Bit Score: 41.53  E-value: 1.37e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2118028303 1427 RKINMSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAA 1481
Cdd:cd21977      1 KKKWVNGFIMFCRLNRKNYIDKHPGLASTELTKELGQLWRELSAEEKKPYCVRAR 55
BAH_plant_2 cd04718
BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH ...
 1039-1120 1.89e-04

BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.


Pssm-ID: 240069  Cd Length: 148  Bit Score: 43.34  E-value: 1.89e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1039 WLYGCWFYRPNETFHLATRKFLEKEVFKSDYYNKIPVSKILGKCVVMfvkeyfklCPENFRDE-----DVYVCESRYSAK 1113
Cdd:cd04718     69 WYAARWYTLPEETHMGRQPHNLRRELYLTNDFADIEMECILRHCSVK--------CPKEFRDAsndgdDVFLCEYEYDVH 140


                   ....*..
gi 2118028303 1114 TKSFKKI 1120
Cdd:cd04718    141 WQSFKRL 147
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 1502-1645 2.26e-04

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.


Pssm-ID: 460830 [Multi-domain]  Cd Length: 991  Bit Score: 46.30  E-value: 2.26e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1502 PRAGTPVGALMGVVPPPTPmGMLNPQLTPVAGMLGGYPPVLPPLQ-GPvdgivsmgsmpplhpgVPPPHQLPPgmPGIPL 1580
Cdd:pfam03154  240 QRLPSPHPPLQPMTQPPPP-SQVSPQPLPQPSLHGQMPPMPHSLQtGP----------------SHMQHPVPP--QPFPL 300

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2118028303 1581 PGVMGQNVssmvGAPAPGSPFGQQMSILGPPGQQAPPPYPGQNPAAQQVMQQPTTPMFVSPPPKT 1645
Cdd:pfam03154  301 TPQSSQSQ----VPPGPSPAAPGQSQQRIHTPPSQSQLQSQQPPREQPLPPAPLSMPHIKPPPTT 361
HMG-box_CIC-like cd21990
high mobility group (HMG)-box found in protein capicua (CIC) and similar proteins; CIC is a ...
 1431-1483 2.35e-04

high mobility group (HMG)-box found in protein capicua (CIC) and similar proteins; CIC is a transcriptional repressor which plays a role in the development of the central nervous system (CNS). In concert with ATXN1 and ATXN1L, CIC is involved in brain development.


Pssm-ID: 438806 [Multi-domain]  Cd Length: 78  Bit Score: 41.29  E-value: 2.35e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2118028303 1431 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAKV 1483
Cdd:cd21990      6 MNAFMIFSKRHRALVHQRHPNQDNRTVSKILGEWWYALGPEEKQKYHDLAFQV 58
HMG-box_ABF2-like_rpt1 cd22010
first high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ...
 1432-1482 2.45e-04

first high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ARS-binding factor 2 (ABF2) and similar proteins; ABF2 is a close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria. It specifically binds to the autonomously replicating sequence 1 (ARS1). It might play a positive role in gene expression and replication. ABF2 contains two HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438826 [Multi-domain]  Cd Length: 68  Bit Score: 40.98  E-value: 2.45e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2118028303 1432 SGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:cd22010      6 SAYFLYFQEHRSDFVKENPDAKMTEISKIGGDKWKNLSADDKKKYEDDFQR 56
HMG-box_PMS1 cd21985
high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; ...
 1431-1482 2.59e-04

high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins; PMS1, also called DNA mismatch repair protein PMS1, is probably involved in the repair of mismatches in DNA.


Pssm-ID: 438801 [Multi-domain]  Cd Length: 73  Bit Score: 40.99  E-value: 2.59e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2118028303 1431 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:cd21985      6 MSASALFEQETRPQFLAENPKASLQDITLKIEERWKNLSEEEKKKYEEKAAK 57
Bromo_brd1_like cd05512
Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein ...
 543-591 2.93e-04

Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99944  Cd Length: 98  Bit Score: 41.62  E-value: 2.93e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2118028303  543 KDYPDYYKIILEPMDLKIIEHNIRSDKYSAEEAMIEDMRLMFRNARHYN 591
Cdd:cd05512     29 SEVPDYLDHIKQPMDFSTMRKKLESQRYRTLEDFEADFNLIINNCLAYN 77
Bromo_SP100C_like cd05501
Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major ...
 93-151 3.41e-04

Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99933  Cd Length: 102  Bit Score: 41.64  E-value: 3.41e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2118028303   93 FIRAPKRRNqpDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPD 151
Cdd:cd05501     23 FISKPYYIR--DYCQGIKEPMWLNKVKERLNERVYHTVEGFVRDMRLIFHNHKLFYKDD 79
HMG-box_IXR1-like_rpt1 cd22011
first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link ...
 1432-1478 4.01e-04

first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link recognition protein (Ixr1) and similar proteins; Ixr1, also called structure-specific recognition protein (SSRP), is a homolog of the yeast mitochondrial regulator ABF2. It binds to platinated DNA and confers sensitivity to the anticancer drug cisplatin. Ixr1 contains two HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438827 [Multi-domain]  Cd Length: 75  Bit Score: 40.60  E-value: 4.01e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2118028303 1432 SGYILFSSEMRAVIKAQ-HPDYSFGELSRLVGTEWRNL-EATKKAEYEE 1478
Cdd:cd22011      6 SAYFLFSQEIRKNLKSQgSPEEKVPELSKRAAEQWRSLtLAEKQPYYDE 54
Bromo_AAA cd05528
Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long ...
 682-729 8.50e-04

Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver


Pssm-ID: 99957  Cd Length: 112  Bit Score: 40.80  E-value: 8.50e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 2118028303  682 ELPDYYLTIKKPVDMEKIRSHMMANKYQDIDAMVEDFVMMFNNACTYN 729
Cdd:cd05528     32 EVPDYYEIIKQPMDLQTILQKLDTHQYLTAKDFLKDIDLIVTNALEYN 79
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 103-172 9.05e-04

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 41.17  E-value: 9.05e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  103 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYIRTKNEF 172
Cdd:cd05529     59 PDYWNRVPVPMDLETIRSRLENRYYRSLEALRHDVRLILSNAETFNEPNSEIAKKAKRLSDWLLRILSSL 128
HMG-box_HMGB_rpt1 cd21978
first high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; ...
 1426-1482 1.03e-03

first high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family; HMGB proteins are chromatin-associated nuclear proteins that act as architectural factors in nucleoprotein structures, which regulate DNA-dependent processes including transcription. In mammals, four family members are present: HMGB1, HMGB2, HMGB3 and HMGB4. They regulate the expression of a wide range of genes through architectural remodeling of the chromatin structure. HMGB1, also called high mobility group protein 1 (HMG-1), is a prototypical alarmin or damage-associated molecular pattern (DAMP) molecule when released from cells. It plays important roles in the regulation of a wide range of processes, including transcription, replication, DNA repair, and nucleosome formation, in the nucleus. It also plays multiple roles in regulating inflammation and responses to cell and tissue stress. HMGB2, also called high mobility group protein 2 (HMG-2), has been implicated in numerous cellular processes, including proliferation, differentiation, apoptosis, and tumor growth. It acts as a chromatin-associated nonhistone protein involved in transcriptional regulation and nucleic-acid-mediated innate immune responses in mammalian cells. It binds DNA to stabilize nucleosomes and promote transcription. HMGB3, also called high mobility group protein 2a (HMG-2a), or high mobility group protein 4 (HMG-4), is an X-linked member of the HMGB family that functions as a universal sentinel for nucleic acid-mediated innate immune responses. HMGB3 has been implicated in the regulation of cellular proliferation and differentiation, as well as inflammatory responses. HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation. It is a factor that regulates chromatin and expression of neuronal differentiation markers. This family also includes high mobility group protein B1 pseudogene 1 (HMGB1P1) and nuclear auto-antigen Sp-100. HMGB1P1, also called putative high mobility group protein B1-like 1 (HMGB1L1), or putative high mobility group protein 1-like 1 (HMG-1L1), is an HMG-box containing protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. Sp-100, also called nuclear dot-associated Sp100 protein, or speckled 100 kDa, is a tumor suppressor that is a major constituent of promyelocytic leukemia (PML) bodies, a subnuclear organelle involved in many physiological processes including cell growth, differentiation and apoptosis. Through the regulation of ETS1, Sp-100 may play a role in angiogenesis, controlling endothelial cell motility and invasion. It may also play roles in the regulation of telomere lengthening, TP53-mediated transcription, FAS-mediated apoptosis, etc. In addition, the family includes Drosophila melanogaster high mobility group protein DSP1 (dDSP1) and similar proteins. dDSP1, also called protein dorsal switch 1, binds preferentially to single-stranded DNA and unwinds double-stranded DNA. It converts Dorsal and nuclear factor (NF)-kappa B from transcriptional activators to repressors. Members of the HMGB family contain two HMG-box domains. This model corresponds to the first one.


Pssm-ID: 438794 [Multi-domain]  Cd Length: 69  Bit Score: 39.21  E-value: 1.03e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2118028303 1426 KRKINMSGYILFSSEMRAVIKAQHPDYS--FGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:cd21978      1 KPRGKMSSYAFFVQTCREEHKKKHPNESvnFSEFSKKCSERWKTMSAKEKKKFEDMAKK 59
Bromo_BAZ2A_B_like cd05503
Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B ...
 103-157 2.39e-03

Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99935  Cd Length: 97  Bit Score: 38.89  E-value: 2.39e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2118028303  103 PDYYEVVSQPIDLMKIQQKLKMEEYDDVNVLTADFQLLFNNAKSYYKPDSPEYKA 157
Cdd:cd05503     31 PGYRKIIKKPMDFSTIREKLESGQYKTLEEFAEDVRLVFDNCETFNEDDSEVGRA 85
HMG-box_SoxF_SOX7 cd22046
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 7 (SOX7) and similar ...
 1419-1483 2.41e-03

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 7 (SOX7) and similar proteins; SOX-7 is an endothelial-associated transcription factor that acts as a tumor suppressor in a number of cancer types. It binds the DNA sequence 5'-AACAAT-3'. SOX-7 belongs to the group F of SRY-related high-mobility group (HMG) box (Sox) transcription factors.


Pssm-ID: 438849 [Multi-domain]  Cd Length: 88  Bit Score: 38.90  E-value: 2.41e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2118028303 1419 SVKKEGSKRKIN--MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAKV 1483
Cdd:cd22046      2 SPGEKGSEPRIRrpMNAFMVWAKDERKRLAVQNPDLHNAELSKMLGKSWKALTPSQKRPYVEEAERL 68
PTZ00199 PTZ00199
high mobility group protein; Provisional
 1414-1481 2.79e-03

high mobility group protein; Provisional


Pssm-ID: 185511 [Multi-domain]  Cd Length: 94  Bit Score: 38.68  E-value: 2.79e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2118028303 1414 KSAKGSVKKEGSKRKIN-------MSGYILFSSEMRAVIKAQHPDYS--FGELSRLVGTEWRNLEATKKAEYEERAA 1481
Cdd:PTZ00199     3 KKQGKVLVRKNKRKKKDpnapkraLSAYMFFAKEKRAEIIAENPELAkdVAAVGKMVGEAWNKLSEEEKAPYEKKAQ 79
Bromo_WDR9_I_like cd05529
Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome ...
 751-865 6.54e-03

Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.


Pssm-ID: 99958  Cd Length: 128  Bit Score: 38.47  E-value: 6.54e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2118028303  751 RDIEGDEDSHVPNVTLLIQELIHNLFVSVMSHQDDEGRCYSDSLAEIPAVDPNFPNkpPLTFDIIRKNVETNRYRRLDLF 830
Cdd:cd05529     12 FDPGWEQPHIRDEERERLISGLDKLLLSLQLEIAEYFEYPVDLRAWYPDYWNRVPV--PMDLETIRSRLENRYYRSLEAL 89

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 2118028303  831 QeHMFEVLER-ARRMNRTDSEIYEDAVELQQFFIKI 865
Cdd:cd05529     90 R-HDVRLILSnAETFNEPNSEIAKKAKRLSDWLLRI 124
HMG-box_HBP2 cd21989
high mobility group (HMG)-box found in HMG box-containing protein 2 (HBP2) and similar ...
 1431-1480 7.33e-03

high mobility group (HMG)-box found in HMG box-containing protein 2 (HBP2) and similar proteins; HBP2, also called HMG box transcription factor BBX, or Bobby sox homolog, is a transcription factor that is necessary for cell cycle progression from the G1 to S phase.


Pssm-ID: 438805 [Multi-domain]  Cd Length: 69  Bit Score: 36.62  E-value: 7.33e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 2118028303 1431 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERA 1480
Cdd:cd21989      4 MNAFLLFCKRHRSLVRERHPRLDNRGITKILGDWWAVLDPDEKQKYTDLA 53
HMG-box_SoxF_SOX17 cd22047
high mobility group (HMG)-box found in sex determining region Y (SRY)-box 17 (SOX17) and ...
 1431-1483 7.78e-03

high mobility group (HMG)-box found in sex determining region Y (SRY)-box 17 (SOX17) and similar proteins; SOX-17 is a developmental transcription regulator involved in endoderm formation, angiogenesis, and carcinogenesis. It acts as a tumor suppressor and modulates WNT signaling. SOX-17 binds target promoter DNA and bends the DNA. It binds to the sequences 5'-AACAAT-'3 or 5'-AACAAAG-3'. SOX-17 belongs to the group F of SRY-related high-mobility group (HMG) box (Sox) transcription factors.


Pssm-ID: 438850 [Multi-domain]  Cd Length: 81  Bit Score: 36.99  E-value: 7.78e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2118028303 1431 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAKV 1483
Cdd:cd22047     11 MNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERL 63
HMG-box_SoxA_SoxB_SoxG cd22028
high mobility group (HMG)-box found in group A, group B and group G of SRY-related ...
 1431-1482 8.39e-03

high mobility group (HMG)-box found in group A, group B and group G of SRY-related high-mobility group (HMG) box (Sox) transcription factors; This subfamily includes SoxA, SoxB, and SoxG proteins. SRY is the only member of group A SRY-related high-mobility group (HMG) box (Sox) transcription factors. SRY, also called testis-determining factor, is a transcriptional regulator that controls a genetic switch in male development. It promotes DNA bending and is also involved in pre-mRNA splicing. The SRY HMG box recognizes DNA by partial intercalation in the minor groove. It binds to the DNA consensus sequence 5'-[AT]AACAA[AT]-3'. SoxB transcription factors play critical roles in the regulation of neurogenesis. They can be divided into two main subgroups, SoxB1 (Sox-1/Sox-2/Sox-3) and SoxB2 (SOX-14/SOX-21). SoxB1 proteins suppress neurogenesis by maintaining neural cells in an undifferentiated state. SoxB2 proteins may have the opposite activity and promote neuronal differentiation. SOX-5 is the only member of group G Sox transcription factors. It is also called SOX-12, SOX-20, SOX-26, or SOX-27. SOX-5 is a crucial transcription factor involved in the regulation of embryonic development and in cell fate determination. It binds to the 5'-AACAAT-3' sequence. SOX-15 can be a tumor suppressor in multiple cancer types.


Pssm-ID: 438837 [Multi-domain]  Cd Length: 76  Bit Score: 36.95  E-value: 8.39e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2118028303 1431 MSGYILFSSEMRAVIKAQHPDYSFGELSRLVGTEWRNLEATKKAEYEERAAK 1482
Cdd:cd22028      6 MNAFMVWSREQRRKIAQENPKMHNSEISKRLGAEWKQLSEDEKRPFIDEAKR 57
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH