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Conserved domains on  [gi|2181405656|ref|NP_001387026|]
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transcription elongation regulator 1 isoform 13 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRP40 super family cl34905
Splicing factor [RNA processing and modification];
400-907 1.26e-29

Splicing factor [RNA processing and modification];


The actual alignment was detected with superfamily member COG5104:

Pssm-ID: 227435 [Multi-domain]  Cd Length: 590  Bit Score: 125.58  E-value: 1.26e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  400 ASPATLAGATAVSEWTEYKTADGKTYYYNNRTLESTWEKPQElkekekleekikepIKEPSEEPLPMEteeedpkeepik 479
Cdd:COG5104      3 AALLGMASGEARSEWEELKAPDGRIYYYNKRTGKSSWEKPKE--------------LLKGSEEDLDVD------------ 56

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  480 eikeepkeeemteeekaaqkakpvatapipgtPWCVVWTGDERVFFYNPTTRLSMWDRpddligradvdkiiqePPHKKG 559
Cdd:COG5104     57 --------------------------------PWKECRTADGKVYYYNSITRESRWKI----------------PPERKK 88

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  560 MEELKKLRHPTPTMLSIQKWQFSMSAIkEEQELMEEINEDEPVKAKKRKRDdnkdidsekeaameaeikAARERAivpLE 639
Cdd:COG5104     89 VEPIAEQKHDERSMIGGNGNDMAITDH-ETSEPKYLLGRLMSQYGITSTKD------------------AVYRLT---KE 146

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  640 ARMKQFKDMLLERGVSAFSTWEKELHKIVfDPRYLLL--NPKERKQVFDQYVKTRAEEERREKKNKIMQAKEDFKKMME- 716
Cdd:COG5104    147 EAEKEFITMLKENQVDSTWPIFRAIEELR-DPRYWMVdtDPLWRKDLFKKYFENQEKDQREEEENKQRKYINEFCKMLAg 225

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  717 EAKFNPRATFSEFAAKHAKDSRFKAIEKMKDREALFNEFVAAARKKEKEDSKTRGEKIKSDFFELLSNHHLDSQSRWSKV 796
Cdd:COG5104    226 NSHIKYYTDWFTFKSIFSKHPYYSSVVNEKTKRQTFQKYKDKLGCYEKYVGKHMGGTALGRLEEVLRSLGSETFIIWLLN 305

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  797 KDKVESDPRYkavdsssMREDLFKqYIEKIAKVrssdVSWSDTRRTLRKDhrwesgsLLEREEKEKLFNEHIEaltKKKR 876
Cdd:COG5104    306 HYVFDSVVRY-------LKNKEMK-PLDRKDIL----FSFIRYVRRLEKE-------LLSAIEERKAAAAQNA---RHHR 363

                          490       500       510
                   ....*....|....*....|....*....|....
gi 2181405656  877 EHFRQLLDETSA---ITLTSTWKEVKKIIKEDPR 907
Cdd:COG5104    364 DEFRTLLRKLYSegkIYYRMKWKNAYPLIKDDPR 397
WW pfam00397
WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds ...
 137-162 9.43e-08

WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.


:

Pssm-ID: 459800 [Multi-domain]  Cd Length: 30  Bit Score: 48.66  E-value: 9.43e-08
                           10        20
                   ....*....|....*....|....*.
gi 2181405656  137 WVENKTPDGKVYYYNARTRESAWTKP 162
Cdd:pfam00397    5 WEERWDPDGRVYYYNHETGETQWEKP 30
Herpes_BLLF1 super family cl37540
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 260-365 7.06e-06

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


The actual alignment was detected with superfamily member pfam05109:

Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 50.30  E-value: 7.06e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  260 TPTTSSPAPAVSTSTSsstpssttsttttatsvaqTVSTPTTQDQTPSSAVSVATP-----TVSVSTPAPTAT------- 327
Cdd:pfam05109  517 TPNATSPTPAVTTPTP-------------------NATSPTLGKTSPTSAVTTPTPnatspTPAVTTPTPNATiptlgkt 577

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 2181405656  328 -PVQTVPQPHPQTLPPAVPHSVPQPTT------AIPAFPPVMVPP 365
Cdd:pfam05109  578 sPTSAVTTPTPNATSPTVGETSPQANTtnhtlgGTSSTPVVTSPP 622
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 931-995 4.32e-05

Contains two conserved F residues; A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.


:

Pssm-ID: 128718 [Multi-domain]  Cd Length: 55  Bit Score: 41.79  E-value: 4.32e-05
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2181405656   931 ITAKADFRTLLKETKFITYrskkliqesDQHLKDVEKILQNDKRYLVLDcVPEERRKLIVAYVDD 995
Cdd:smart00441    1 EEAKEAFKELLKEHEVITP---------DTTWSEARKKLKNDPRYKALL-SESEREQLFEDHIEE 55
 
Name Accession Description Interval E-value
PRP40 COG5104
Splicing factor [RNA processing and modification];
400-907 1.26e-29

Splicing factor [RNA processing and modification];


Pssm-ID: 227435 [Multi-domain]  Cd Length: 590  Bit Score: 125.58  E-value: 1.26e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  400 ASPATLAGATAVSEWTEYKTADGKTYYYNNRTLESTWEKPQElkekekleekikepIKEPSEEPLPMEteeedpkeepik 479
Cdd:COG5104      3 AALLGMASGEARSEWEELKAPDGRIYYYNKRTGKSSWEKPKE--------------LLKGSEEDLDVD------------ 56

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  480 eikeepkeeemteeekaaqkakpvatapipgtPWCVVWTGDERVFFYNPTTRLSMWDRpddligradvdkiiqePPHKKG 559
Cdd:COG5104     57 --------------------------------PWKECRTADGKVYYYNSITRESRWKI----------------PPERKK 88

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  560 MEELKKLRHPTPTMLSIQKWQFSMSAIkEEQELMEEINEDEPVKAKKRKRDdnkdidsekeaameaeikAARERAivpLE 639
Cdd:COG5104     89 VEPIAEQKHDERSMIGGNGNDMAITDH-ETSEPKYLLGRLMSQYGITSTKD------------------AVYRLT---KE 146

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  640 ARMKQFKDMLLERGVSAFSTWEKELHKIVfDPRYLLL--NPKERKQVFDQYVKTRAEEERREKKNKIMQAKEDFKKMME- 716
Cdd:COG5104    147 EAEKEFITMLKENQVDSTWPIFRAIEELR-DPRYWMVdtDPLWRKDLFKKYFENQEKDQREEEENKQRKYINEFCKMLAg 225

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  717 EAKFNPRATFSEFAAKHAKDSRFKAIEKMKDREALFNEFVAAARKKEKEDSKTRGEKIKSDFFELLSNHHLDSQSRWSKV 796
Cdd:COG5104    226 NSHIKYYTDWFTFKSIFSKHPYYSSVVNEKTKRQTFQKYKDKLGCYEKYVGKHMGGTALGRLEEVLRSLGSETFIIWLLN 305

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  797 KDKVESDPRYkavdsssMREDLFKqYIEKIAKVrssdVSWSDTRRTLRKDhrwesgsLLEREEKEKLFNEHIEaltKKKR 876
Cdd:COG5104    306 HYVFDSVVRY-------LKNKEMK-PLDRKDIL----FSFIRYVRRLEKE-------LLSAIEERKAAAAQNA---RHHR 363

                          490       500       510
                   ....*....|....*....|....*....|....
gi 2181405656  877 EHFRQLLDETSA---ITLTSTWKEVKKIIKEDPR 907
Cdd:COG5104    364 DEFRTLLRKLYSegkIYYRMKWKNAYPLIKDDPR 397
FF pfam01846
FF domain; This domain has been predicted to be involved in protein-protein interaction. This ...
 773-822 2.72e-14

FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions.


Pssm-ID: 426471 [Multi-domain]  Cd Length: 50  Bit Score: 67.87  E-value: 2.72e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 2181405656  773 KIKSDFFELLSNHHLDSQSRWSKVKDKVESDPRYKAVDSSSMREDLFKQY 822
Cdd:pfam01846    1 KAREAFKELLKEHKITPYSTWSEIKKKIENDPRYKALLDGSEREELFEDY 50
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 873-928 1.60e-10

Contains two conserved F residues; A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.


Pssm-ID: 128718 [Multi-domain]  Cd Length: 55  Bit Score: 57.20  E-value: 1.60e-10
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*.
gi 2181405656   873 KKKREHFRQLLDETSAITLTSTWKEVKKIIKEDPRCiKFSSSDRKKQREFEEYIRD 928
Cdd:smart00441    1 EEAKEAFKELLKEHEVITPDTTWSEARKKLKNDPRY-KALLSESEREQLFEDHIEE 55
WW cd00201
Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; ...
 412-439 3.48e-08

Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.


Pssm-ID: 238122 [Multi-domain]  Cd Length: 31  Bit Score: 50.22  E-value: 3.48e-08
                           10        20
                   ....*....|....*....|....*...
gi 2181405656  412 SEWTEYKTADGKTYYYNNRTLESTWEKP 439
Cdd:cd00201      2 PGWEERWDPDGRVYYYNHNTKETQWEDP 29
WW pfam00397
WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds ...
 137-162 9.43e-08

WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.


Pssm-ID: 459800 [Multi-domain]  Cd Length: 30  Bit Score: 48.66  E-value: 9.43e-08
                           10        20
                   ....*....|....*....|....*.
gi 2181405656  137 WVENKTPDGKVYYYNARTRESAWTKP 162
Cdd:pfam00397    5 WEERWDPDGRVYYYNHETGETQWEKP 30
WW smart00456
Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds ...
 132-164 1.06e-07

Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.


Pssm-ID: 197736 [Multi-domain]  Cd Length: 33  Bit Score: 48.75  E-value: 1.06e-07
                            10        20        30
                    ....*....|....*....|....*....|...
gi 2181405656   132 PTEEIWVENKTPDGKVYYYNARTRESAWTKPDG 164
Cdd:smart00456    1 PLPPGWEERKDPDGRPYYYNHETKETQWEKPRE 33
WW cd00201
Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; ...
 137-164 2.54e-07

Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.


Pssm-ID: 238122 [Multi-domain]  Cd Length: 31  Bit Score: 47.52  E-value: 2.54e-07
                           10        20
                   ....*....|....*....|....*...
gi 2181405656  137 WVENKTPDGKVYYYNARTRESAWTKPDG 164
Cdd:cd00201      4 WEERWDPDGRVYYYNHNTKETQWEDPRE 31
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 260-365 7.06e-06

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 50.30  E-value: 7.06e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  260 TPTTSSPAPAVSTSTSsstpssttsttttatsvaqTVSTPTTQDQTPSSAVSVATP-----TVSVSTPAPTAT------- 327
Cdd:pfam05109  517 TPNATSPTPAVTTPTP-------------------NATSPTLGKTSPTSAVTTPTPnatspTPAVTTPTPNATiptlgkt 577

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 2181405656  328 -PVQTVPQPHPQTLPPAVPHSVPQPTT------AIPAFPPVMVPP 365
Cdd:pfam05109  578 sPTSAVTTPTPNATSPTVGETSPQANTtnhtlgGTSSTPVVTSPP 622
PRP40 COG5104
Splicing factor [RNA processing and modification];
136-173 8.61e-06

Splicing factor [RNA processing and modification];


Pssm-ID: 227435 [Multi-domain]  Cd Length: 590  Bit Score: 49.69  E-value: 8.61e-06
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 2181405656  136 IWVENKTPDGKVYYYNARTRESAWTKPDgvKVIQQSEL 173
Cdd:COG5104     16 EWEELKAPDGRIYYYNKRTGKSSWEKPK--ELLKGSEE 51
PHA02682 PHA02682
ORF080 virion core protein; Provisional
 292-421 1.17e-05

ORF080 virion core protein; Provisional


Pssm-ID: 177464 [Multi-domain]  Cd Length: 280  Bit Score: 48.32  E-value: 1.17e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  292 VAQTVSTPTTQDQTPSSAVSVATPTVSVSTPAPtATPVQTVPqphpqTLPPavPHSVPQPTTAIPAFPP--VMVPPfRVP 369
Cdd:PHA02682    82 LAPSPACAAPAPACPACAPAAPAPAVTCPAPAP-ACPPATAP-----TCPP--PAVCPAPARPAPACPPstRQCPP-APP 152

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2181405656  370 LPgMPIPLPGVLPGMAPPIVPmihPQVAIAASPATLAGATAVSEWTEYKTAD 421
Cdd:PHA02682   153 LP-TPKPAPAAKPIFLHNQLP---PPDYPAASCPTIETAPAASPVLEPRIPD 200
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 931-995 4.32e-05

Contains two conserved F residues; A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.


Pssm-ID: 128718 [Multi-domain]  Cd Length: 55  Bit Score: 41.79  E-value: 4.32e-05
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2181405656   931 ITAKADFRTLLKETKFITYrskkliqesDQHLKDVEKILQNDKRYLVLDcVPEERRKLIVAYVDD 995
Cdd:smart00441    1 EEAKEAFKELLKEHEVITP---------DTTWSEARKKLKNDPRYKALL-SESEREQLFEDHIEE 55
FF pfam01846
FF domain; This domain has been predicted to be involved in protein-protein interaction. This ...
 933-992 5.03e-05

FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions.


Pssm-ID: 426471 [Multi-domain]  Cd Length: 50  Bit Score: 41.67  E-value: 5.03e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  933 AKADFRTLLKETKfITYRSkkliqesdqHLKDVEKILQNDKRYLVLDcVPEERRKLIVAY 992
Cdd:pfam01846    2 AREAFKELLKEHK-ITPYS---------TWSEIKKKIENDPRYKALL-DGSEREELFEDY 50
KLF3_N cd21577
N-terminal domain of Kruppel-like factor 3; Kruppel-like factor 3 (KLF3; also called ...
 306-394 6.06e-05

N-terminal domain of Kruppel-like factor 3; Kruppel-like factor 3 (KLF3; also called Krueppel-like factor 3 and originally called Basic Kruppel-like Factor/BKLF), was the third member of the KLF family of zinc finger transcription factors to be discovered. KLF3 possesses a wide range of biological impacts on regulating apoptosis, differentiation, and proliferation in various tissues during the entire progression process. It has been proposed as a tumor suppressor in colorectal cancer. It appears to function predominantly as a repressor of transcription, turning genes off by recruiting the C-terminal Binding Protein co-repressors CtBP1 and CtBP2. CtBP docks onto a short motif (residues 61-65) in the N-terminus of KLF3, through the Proline-X-Aspartate-Leucine-Serine (PXDLS) motif. CtBP in turn recruits histone modifying enzymes to alter chromatin and repress gene expression. KLF3 belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF3.


Pssm-ID: 410554 [Multi-domain]  Cd Length: 214  Bit Score: 45.41  E-value: 6.06e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  306 PSSAVSVATPTVSVSTPAPTATPvqtvPQPH--------PQTLPPAVPHSVPQPTTAIPAFPPVMVPPFRVPLPGMPIPL 377
Cdd:cd21577     33 PSSSSSSSSSSSSSSSPSSRASP----PSPYskssppspPQQRPLSPPLSLPPPVAPPPLSPGSVPGGLPVISPVMVQPV 108

                           90
                   ....*....|....*....
gi 2181405656  378 PGVLPG--MAPPIVPMIHP 394
Cdd:cd21577    109 PVLYPPhlHQPIMVSSSPP 127
half-pint TIGR01645
poly-U binding splicing factor, half-pint family; The proteins represented by this model ...
 297-413 7.81e-05

poly-U binding splicing factor, half-pint family; The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.


Pssm-ID: 130706 [Multi-domain]  Cd Length: 612  Bit Score: 46.60  E-value: 7.81e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  297 STPTTQDQTPSSAVSvATPTvSVSTPaPTATPVQTVPQPHPqTLPPAVPHSV-PQPTTAI-PAFPPVMVPPFRVPLPGMP 374
Cdd:TIGR01645  322 AVLGPRAQSPATPSS-SLPT-DIGNK-AVVSSAKKEAEEVP-PLPQAAPAVVkPGPMEIPtPVPPPGLAIPSLVAPPGLV 397

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2181405656  375 IPLPGVLPGMAPPIVPMIHPQVAIAASP--ATLAGATAVSE 413
Cdd:TIGR01645  398 APTEINPSFLASPRKKMKREKLPVTFGAldDTLAWKEPSKE 438
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 313-423 6.03e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 43.55  E-value: 6.03e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  313 ATPTVSVSTPAPTATPVQTVPQPHPQTLPPAVPHSVPQPTTAIPafPPVMVPPFRVPLPGMPiplpgvlPGMAPPIVPMI 392
Cdd:PRK14951   369 AAEAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAAS--APAAPPAAAPPAPVAA-------PAAAAPAAAPA 439

                           90       100       110
                   ....*....|....*....|....*....|.
gi 2181405656  393 HPQVAIAASPATLAGATAVSEWTEYKTADGK 423
Cdd:PRK14951   440 AAPAAVALAPAPPAQAAPETVAIPVRVAPEP 470
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
 299-404 8.60e-04

Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide.


Pssm-ID: 197891 [Multi-domain]  Cd Length: 165  Bit Score: 41.31  E-value: 8.60e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656   299 PTTQDQTPSSAVSV--ATPTVSVSTPAPTATPVQTVPQPHPQT--------LPPAVPHSVpQPTTAIPAFPPVMVPPFRV 368
Cdd:smart00818   41 PVSQQHPPTHTLQPhhHIPVLPAQQPVVPQQPLMPVPGQHSMTptqhhqpnLPQPAQQPF-QPQPLQPPQPQQPMQPQPP 119

                            90       100       110
                    ....*....|....*....|....*....|....*...
gi 2181405656   369 PLPGMPIPLPGVLPGMAP--PIVPMIhPQVAIAASPAT 404
Cdd:smart00818  120 VHPIPPLPPQPPLPPMFPmqPLPPLL-PDLPLEAWPAT 156
 
Name Accession Description Interval E-value
PRP40 COG5104
Splicing factor [RNA processing and modification];
400-907 1.26e-29

Splicing factor [RNA processing and modification];


Pssm-ID: 227435 [Multi-domain]  Cd Length: 590  Bit Score: 125.58  E-value: 1.26e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  400 ASPATLAGATAVSEWTEYKTADGKTYYYNNRTLESTWEKPQElkekekleekikepIKEPSEEPLPMEteeedpkeepik 479
Cdd:COG5104      3 AALLGMASGEARSEWEELKAPDGRIYYYNKRTGKSSWEKPKE--------------LLKGSEEDLDVD------------ 56

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  480 eikeepkeeemteeekaaqkakpvatapipgtPWCVVWTGDERVFFYNPTTRLSMWDRpddligradvdkiiqePPHKKG 559
Cdd:COG5104     57 --------------------------------PWKECRTADGKVYYYNSITRESRWKI----------------PPERKK 88

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  560 MEELKKLRHPTPTMLSIQKWQFSMSAIkEEQELMEEINEDEPVKAKKRKRDdnkdidsekeaameaeikAARERAivpLE 639
Cdd:COG5104     89 VEPIAEQKHDERSMIGGNGNDMAITDH-ETSEPKYLLGRLMSQYGITSTKD------------------AVYRLT---KE 146

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  640 ARMKQFKDMLLERGVSAFSTWEKELHKIVfDPRYLLL--NPKERKQVFDQYVKTRAEEERREKKNKIMQAKEDFKKMME- 716
Cdd:COG5104    147 EAEKEFITMLKENQVDSTWPIFRAIEELR-DPRYWMVdtDPLWRKDLFKKYFENQEKDQREEEENKQRKYINEFCKMLAg 225

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  717 EAKFNPRATFSEFAAKHAKDSRFKAIEKMKDREALFNEFVAAARKKEKEDSKTRGEKIKSDFFELLSNHHLDSQSRWSKV 796
Cdd:COG5104    226 NSHIKYYTDWFTFKSIFSKHPYYSSVVNEKTKRQTFQKYKDKLGCYEKYVGKHMGGTALGRLEEVLRSLGSETFIIWLLN 305

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  797 KDKVESDPRYkavdsssMREDLFKqYIEKIAKVrssdVSWSDTRRTLRKDhrwesgsLLEREEKEKLFNEHIEaltKKKR 876
Cdd:COG5104    306 HYVFDSVVRY-------LKNKEMK-PLDRKDIL----FSFIRYVRRLEKE-------LLSAIEERKAAAAQNA---RHHR 363

                          490       500       510
                   ....*....|....*....|....*....|....
gi 2181405656  877 EHFRQLLDETSA---ITLTSTWKEVKKIIKEDPR 907
Cdd:COG5104    364 DEFRTLLRKLYSegkIYYRMKWKNAYPLIKDDPR 397
FF pfam01846
FF domain; This domain has been predicted to be involved in protein-protein interaction. This ...
 773-822 2.72e-14

FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions.


Pssm-ID: 426471 [Multi-domain]  Cd Length: 50  Bit Score: 67.87  E-value: 2.72e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 2181405656  773 KIKSDFFELLSNHHLDSQSRWSKVKDKVESDPRYKAVDSSSMREDLFKQY 822
Cdd:pfam01846    1 KAREAFKELLKEHKITPYSTWSEIKKKIENDPRYKALLDGSEREELFEDY 50
FF pfam01846
FF domain; This domain has been predicted to be involved in protein-protein interaction. This ...
 706-755 3.22e-12

FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions.


Pssm-ID: 426471 [Multi-domain]  Cd Length: 50  Bit Score: 62.09  E-value: 3.22e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 2181405656  706 QAKEDFKKMMEEAKFNPRATFSEFAAKHAKDSRFKAIEKMKDREALFNEF 755
Cdd:pfam01846    1 KAREAFKELLKEHKITPYSTWSEIKKKIENDPRYKALLDGSEREELFEDY 50
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 873-928 1.60e-10

Contains two conserved F residues; A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.


Pssm-ID: 128718 [Multi-domain]  Cd Length: 55  Bit Score: 57.20  E-value: 1.60e-10
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*.
gi 2181405656   873 KKKREHFRQLLDETSAITLTSTWKEVKKIIKEDPRCiKFSSSDRKKQREFEEYIRD 928
Cdd:smart00441    1 EEAKEAFKELLKEHEVITPDTTWSEARKKLKNDPRY-KALLSESEREQLFEDHIEE 55
FF pfam01846
FF domain; This domain has been predicted to be involved in protein-protein interaction. This ...
 641-688 2.20e-10

FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions.


Pssm-ID: 426471 [Multi-domain]  Cd Length: 50  Bit Score: 56.70  E-value: 2.20e-10
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 2181405656  641 RMKQFKDMLLERGVSAFSTWEKELHKIVFDPRYL-LLNPKERKQVFDQY 688
Cdd:pfam01846    2 AREAFKELLKEHKITPYSTWSEIKKKIENDPRYKaLLDGSEREELFEDY 50
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 772-825 3.53e-10

Contains two conserved F residues; A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.


Pssm-ID: 128718 [Multi-domain]  Cd Length: 55  Bit Score: 56.43  E-value: 3.53e-10
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*
gi 2181405656   772 EKIKSDFFELLSNHHLD-SQSRWSKVKDKVESDPRYKAVDSSSMREDLFKQYIEK 825
Cdd:smart00441    1 EEAKEAFKELLKEHEVItPDTTWSEARKKLKNDPRYKALLSESEREQLFEDHIEE 55
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 705-758 3.19e-08

Contains two conserved F residues; A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.


Pssm-ID: 128718 [Multi-domain]  Cd Length: 55  Bit Score: 50.65  E-value: 3.19e-08
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*
gi 2181405656   705 MQAKEDFKKMMEEAKFN-PRATFSEFAAKHAKDSRFKAIEKMKDREALFNEFVAA 758
Cdd:smart00441    1 EEAKEAFKELLKEHEVItPDTTWSEARKKLKNDPRYKALLSESEREQLFEDHIEE 55
WW cd00201
Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; ...
 412-439 3.48e-08

Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.


Pssm-ID: 238122 [Multi-domain]  Cd Length: 31  Bit Score: 50.22  E-value: 3.48e-08
                           10        20
                   ....*....|....*....|....*...
gi 2181405656  412 SEWTEYKTADGKTYYYNNRTLESTWEKP 439
Cdd:cd00201      2 PGWEERWDPDGRVYYYNHNTKETQWEDP 29
WW pfam00397
WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds ...
 412-439 5.62e-08

WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.


Pssm-ID: 459800 [Multi-domain]  Cd Length: 30  Bit Score: 49.43  E-value: 5.62e-08
                           10        20
                   ....*....|....*....|....*...
gi 2181405656  412 SEWTEYKTADGKTYYYNNRTLESTWEKP 439
Cdd:pfam00397    3 PGWEERWDPDGRVYYYNHETGETQWEKP 30
FF pfam01846
FF domain; This domain has been predicted to be involved in protein-protein interaction. This ...
 874-925 7.97e-08

FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions.


Pssm-ID: 426471 [Multi-domain]  Cd Length: 50  Bit Score: 49.38  E-value: 7.97e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2181405656  874 KKREHFRQLLDETSaITLTSTWKEVKKIIKEDPRCIKFSSSDRKKQrEFEEY 925
Cdd:pfam01846    1 KAREAFKELLKEHK-ITPYSTWSEIKKKIENDPRYKALLDGSEREE-LFEDY 50
WW pfam00397
WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds ...
 137-162 9.43e-08

WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.


Pssm-ID: 459800 [Multi-domain]  Cd Length: 30  Bit Score: 48.66  E-value: 9.43e-08
                           10        20
                   ....*....|....*....|....*.
gi 2181405656  137 WVENKTPDGKVYYYNARTRESAWTKP 162
Cdd:pfam00397    5 WEERWDPDGRVYYYNHETGETQWEKP 30
WW smart00456
Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds ...
 132-164 1.06e-07

Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.


Pssm-ID: 197736 [Multi-domain]  Cd Length: 33  Bit Score: 48.75  E-value: 1.06e-07
                            10        20        30
                    ....*....|....*....|....*....|...
gi 2181405656   132 PTEEIWVENKTPDGKVYYYNARTRESAWTKPDG 164
Cdd:smart00456    1 PLPPGWEERKDPDGRPYYYNHETKETQWEKPRE 33
WW smart00456
Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds ...
 414-440 2.24e-07

Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.


Pssm-ID: 197736 [Multi-domain]  Cd Length: 33  Bit Score: 47.98  E-value: 2.24e-07
                            10        20
                    ....*....|....*....|....*..
gi 2181405656   414 WTEYKTADGKTYYYNNRTLESTWEKPQ 440
Cdd:smart00456    6 WEERKDPDGRPYYYNHETKETQWEKPR 32
WW cd00201
Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; ...
 137-164 2.54e-07

Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.


Pssm-ID: 238122 [Multi-domain]  Cd Length: 31  Bit Score: 47.52  E-value: 2.54e-07
                           10        20
                   ....*....|....*....|....*...
gi 2181405656  137 WVENKTPDGKVYYYNARTRESAWTKPDG 164
Cdd:cd00201      4 WEERWDPDGRVYYYNHNTKETQWEDPRE 31
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 639-690 1.59e-06

Contains two conserved F residues; A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.


Pssm-ID: 128718 [Multi-domain]  Cd Length: 55  Bit Score: 46.03  E-value: 1.59e-06
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....
gi 2181405656   639 EARMKQFKDMLLERGVS-AFSTWEKELHKIVFDPRY-LLLNPKERKQVFDQYVK 690
Cdd:smart00441    1 EEAKEAFKELLKEHEVItPDTTWSEARKKLKNDPRYkALLSESEREQLFEDHIE 54
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 260-365 7.06e-06

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 50.30  E-value: 7.06e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  260 TPTTSSPAPAVSTSTSsstpssttsttttatsvaqTVSTPTTQDQTPSSAVSVATP-----TVSVSTPAPTAT------- 327
Cdd:pfam05109  517 TPNATSPTPAVTTPTP-------------------NATSPTLGKTSPTSAVTTPTPnatspTPAVTTPTPNATiptlgkt 577

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 2181405656  328 -PVQTVPQPHPQTLPPAVPHSVPQPTT------AIPAFPPVMVPP 365
Cdd:pfam05109  578 sPTSAVTTPTPNATSPTVGETSPQANTtnhtlgGTSSTPVVTSPP 622
PRP40 COG5104
Splicing factor [RNA processing and modification];
136-173 8.61e-06

Splicing factor [RNA processing and modification];


Pssm-ID: 227435 [Multi-domain]  Cd Length: 590  Bit Score: 49.69  E-value: 8.61e-06
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 2181405656  136 IWVENKTPDGKVYYYNARTRESAWTKPDgvKVIQQSEL 173
Cdd:COG5104     16 EWEELKAPDGRIYYYNKRTGKSSWEKPK--ELLKGSEE 51
PHA02682 PHA02682
ORF080 virion core protein; Provisional
 292-421 1.17e-05

ORF080 virion core protein; Provisional


Pssm-ID: 177464 [Multi-domain]  Cd Length: 280  Bit Score: 48.32  E-value: 1.17e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  292 VAQTVSTPTTQDQTPSSAVSVATPTVSVSTPAPtATPVQTVPqphpqTLPPavPHSVPQPTTAIPAFPP--VMVPPfRVP 369
Cdd:PHA02682    82 LAPSPACAAPAPACPACAPAAPAPAVTCPAPAP-ACPPATAP-----TCPP--PAVCPAPARPAPACPPstRQCPP-APP 152

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2181405656  370 LPgMPIPLPGVLPGMAPPIVPmihPQVAIAASPATLAGATAVSEWTEYKTAD 421
Cdd:PHA02682   153 LP-TPKPAPAAKPIFLHNQLP---PPDYPAASCPTIETAPAASPVLEPRIPD 200
WW smart00456
Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds ...
 512-540 1.79e-05

Domain with 2 conserved Trp (W) residues; Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides.


Pssm-ID: 197736 [Multi-domain]  Cd Length: 33  Bit Score: 42.59  E-value: 1.79e-05
                            10        20
                    ....*....|....*....|....*....
gi 2181405656   512 PWCVVWTGDERVFFYNPTTRLSMWDRPDD 540
Cdd:smart00456    5 GWEERKDPDGRPYYYNHETKETQWEKPRE 33
WW cd00201
Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; ...
 511-540 2.80e-05

Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs.


Pssm-ID: 238122 [Multi-domain]  Cd Length: 31  Bit Score: 41.74  E-value: 2.80e-05
                           10        20        30
                   ....*....|....*....|....*....|
gi 2181405656  511 TPWCVVWTGDERVFFYNPTTRLSMWDRPDD 540
Cdd:cd00201      2 PGWEERWDPDGRVYYYNHNTKETQWEDPRE 31
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 259-410 2.99e-05

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 47.99  E-value: 2.99e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  259 STPTTSSPAPAVSTSTSSSTPSSTTSTTTTATSVAQTVSTPTTQDQTPSSavSVATPTVSVSTPAPTAT--------PVQ 330
Cdd:pfam05109  469 STADVTSPTPAGTTSGASPVTPSPSPRDNGTESKAPDMTSPTSAVTTPTP--NATSPTPAVTTPTPNATsptlgktsPTS 546

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  331 TVPQPHPQTLPPAVPHSVPQPTTAIPAFPPVMvppfrvPLPGMPIPLPGVlpgmAPPIVPMIHPQVaiAASPATLAGATA 410
Cdd:pfam05109  547 AVTTPTPNATSPTPAVTTPTPNATIPTLGKTS------PTSAVTTPTPNA----TSPTVGETSPQA--NTTNHTLGGTSS 614
PRP40 COG5104
Splicing factor [RNA processing and modification];
137-172 3.92e-05

Splicing factor [RNA processing and modification];


Pssm-ID: 227435 [Multi-domain]  Cd Length: 590  Bit Score: 47.38  E-value: 3.92e-05
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 2181405656  137 WVENKTPDGKVYYYNARTRESAWTKPDGVKVIQQSE 172
Cdd:COG5104     58 WKECRTADGKVYYYNSITRESRWKIPPERKKVEPIA 93
FF smart00441
Contains two conserved F residues; A novel motif that often accompanies WW domains. Often ...
 931-995 4.32e-05

Contains two conserved F residues; A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.


Pssm-ID: 128718 [Multi-domain]  Cd Length: 55  Bit Score: 41.79  E-value: 4.32e-05
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2181405656   931 ITAKADFRTLLKETKFITYrskkliqesDQHLKDVEKILQNDKRYLVLDcVPEERRKLIVAYVDD 995
Cdd:smart00441    1 EEAKEAFKELLKEHEVITP---------DTTWSEARKKLKNDPRYKALL-SESEREQLFEDHIEE 55
FF pfam01846
FF domain; This domain has been predicted to be involved in protein-protein interaction. This ...
 933-992 5.03e-05

FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions.


Pssm-ID: 426471 [Multi-domain]  Cd Length: 50  Bit Score: 41.67  E-value: 5.03e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  933 AKADFRTLLKETKfITYRSkkliqesdqHLKDVEKILQNDKRYLVLDcVPEERRKLIVAY 992
Cdd:pfam01846    2 AREAFKELLKEHK-ITPYS---------TWSEIKKKIENDPRYKALL-DGSEREELFEDY 50
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 258-395 5.17e-05

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: 47.45  E-value: 5.17e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  258 ASTPTTSSPAPAVSTSTSSSTPSSTTSTTTTATSVAQTVSTPTTQDQTPSSAVSVATPTVSVSTP------------APT 325
Cdd:pfam03154  176 AQSGAASPPSPPPPGTTQAATAGPTPSAPSVPPQGSPATSQPPNQTQSTAAPHTLIQQTPTLHPQrlpsphpplqpmTQP 255

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  326 ATPVQTVPQPHP---------------QTLPPAVPHSVPQ-----------------PTTAIP-------------AFPP 360
Cdd:pfam03154  256 PPPSQVSPQPLPqpslhgqmppmphslQTGPSHMQHPVPPqpfpltpqssqsqvppgPSPAAPgqsqqrihtppsqSQLQ 335

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 2181405656  361 VMVPPFRVPLPGMPIPLPGVLPGMAPPIVPMIHPQ 395
Cdd:pfam03154  336 SQQPPREQPLPPAPLSMPHIKPPPTTPIPQLPNPQ 370
KLF3_N cd21577
N-terminal domain of Kruppel-like factor 3; Kruppel-like factor 3 (KLF3; also called ...
 306-394 6.06e-05

N-terminal domain of Kruppel-like factor 3; Kruppel-like factor 3 (KLF3; also called Krueppel-like factor 3 and originally called Basic Kruppel-like Factor/BKLF), was the third member of the KLF family of zinc finger transcription factors to be discovered. KLF3 possesses a wide range of biological impacts on regulating apoptosis, differentiation, and proliferation in various tissues during the entire progression process. It has been proposed as a tumor suppressor in colorectal cancer. It appears to function predominantly as a repressor of transcription, turning genes off by recruiting the C-terminal Binding Protein co-repressors CtBP1 and CtBP2. CtBP docks onto a short motif (residues 61-65) in the N-terminus of KLF3, through the Proline-X-Aspartate-Leucine-Serine (PXDLS) motif. CtBP in turn recruits histone modifying enzymes to alter chromatin and repress gene expression. KLF3 belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF3.


Pssm-ID: 410554 [Multi-domain]  Cd Length: 214  Bit Score: 45.41  E-value: 6.06e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  306 PSSAVSVATPTVSVSTPAPTATPvqtvPQPH--------PQTLPPAVPHSVPQPTTAIPAFPPVMVPPFRVPLPGMPIPL 377
Cdd:cd21577     33 PSSSSSSSSSSSSSSSPSSRASP----PSPYskssppspPQQRPLSPPLSLPPPVAPPPLSPGSVPGGLPVISPVMVQPV 108

                           90
                   ....*....|....*....
gi 2181405656  378 PGVLPG--MAPPIVPMIHP 394
Cdd:cd21577    109 PVLYPPhlHQPIMVSSSPP 127
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 293-402 6.89e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 46.63  E-value: 6.89e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  293 AQTVSTPTTQDQTPSSAVSVATPTVSVSTPAPTATPVQTVP-QPHPQTLPPAVPHSVPQPtTAIPAFPPVMVPPFRVPLP 371
Cdd:PRK14951   385 EAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPvAAPAAAAPAAAPAAAPAA-VALAPAPPAQAAPETVAIP 463

                           90       100       110
                   ....*....|....*....|....*....|.
gi 2181405656  372 GMPIPLPGVLPgmAPPIVPMIHPQVAIAASP 402
Cdd:PRK14951   464 VRVAPEPAVAS--AAPAPAAAPAAARLTPTE 492
FF pfam01846
FF domain; This domain has been predicted to be involved in protein-protein interaction. This ...
 815-867 7.75e-05

FF domain; This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions.


Pssm-ID: 426471 [Multi-domain]  Cd Length: 50  Bit Score: 40.90  E-value: 7.75e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2181405656  815 REDLFKQYIEKiaKVRSSDVSWSDTRRTLRKDHRWEsgSLLEREEKEKLFNEH 867
Cdd:pfam01846    2 AREAFKELLKE--HKITPYSTWSEIKKKIENDPRYK--ALLDGSEREELFEDY 50
half-pint TIGR01645
poly-U binding splicing factor, half-pint family; The proteins represented by this model ...
 297-413 7.81e-05

poly-U binding splicing factor, half-pint family; The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA.


Pssm-ID: 130706 [Multi-domain]  Cd Length: 612  Bit Score: 46.60  E-value: 7.81e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  297 STPTTQDQTPSSAVSvATPTvSVSTPaPTATPVQTVPQPHPqTLPPAVPHSV-PQPTTAI-PAFPPVMVPPFRVPLPGMP 374
Cdd:TIGR01645  322 AVLGPRAQSPATPSS-SLPT-DIGNK-AVVSSAKKEAEEVP-PLPQAAPAVVkPGPMEIPtPVPPPGLAIPSLVAPPGLV 397

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2181405656  375 IPLPGVLPGMAPPIVPMIHPQVAIAASP--ATLAGATAVSE 413
Cdd:TIGR01645  398 APTEINPSFLASPRKKMKREKLPVTFGAldDTLAWKEPSKE 438
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 293-407 1.03e-04

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 46.18  E-value: 1.03e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  293 AQTVSTPTTQDQTPSSAVSVATPTVSVSTPAPtATPVQTVPQPHPQTLPPAVPHSVPQPTTAIPAFPPVMV--------- 363
Cdd:pfam09770  228 QQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQ-GHPVTILQRPQSPQPDPAQPSIQPQAQQFHQQPPPVPVqptqilqnp 306

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 2181405656  364 ---PPFRVPLPGMPIPLPGVLPG-MAPPIVPMIHPQVAIAASPATLAG 407
Cdd:pfam09770  307 nrlSAARVGYPQNPQPGVQPAPAhQAHRQQGSFGRQAPIITHPQQLAQ 354
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 295-411 1.07e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 46.25  E-value: 1.07e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  295 TVSTPTTQDQTPSSAVSVATPTVSVSTPAPTATPVQTVP---QPHPQTLPPAVPHSVPQPTTAIPAFP------PVMVPP 365
Cdd:PRK14951   385 EAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPapvAAPAAAAPAAAPAAAPAAVALAPAPPaqaapeTVAIPV 464

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 2181405656  366 FRVPLPGMPIPLPGVLPGMAPPIVPMIHPQVAIAASPATLAGATAV 411
Cdd:PRK14951   465 RVAPEPAVASAAPAPAAAPAAARLTPTEEGDVWHATVQQLAAAEAI 510
PRK14950 PRK14950
DNA polymerase III subunits gamma and tau; Provisional
 292-400 1.76e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237864 [Multi-domain]  Cd Length: 585  Bit Score: 45.57  E-value: 1.76e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  292 VAQTVSTPTTQDQTPSSAVsvATPTVSVSTPAPTATPVQTVPQPHPQTlpPAVPHSVPQPTTAIP--AFPPVMVPPFRVP 369
Cdd:PRK14950   355 VIEALLVPVPAPQPAKPTA--AAPSPVRPTPAPSTRPKAAAAANIPPK--EPVRETATPPPVPPRpvAPPVPHTPESAPK 430

                           90       100       110
                   ....*....|....*....|....*....|.
gi 2181405656  370 LPGMPIPLPgVLPGMAPPIVPMIHPQVAIAA 400
Cdd:PRK14950   431 LTRAAIPVD-EKPKYTPPAPPKEEEKALIAD 460
DUF5585 pfam17823
Family of unknown function (DUF5585); This is a family of unknown function found in chordata.
 258-466 2.00e-04

Family of unknown function (DUF5585); This is a family of unknown function found in chordata.


Pssm-ID: 465521 [Multi-domain]  Cd Length: 506  Bit Score: 45.34  E-value: 2.00e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  258 ASTPTTSSPAPAVSTSTSSSTPSSTTSTTTTATSVAQTVSTPTTQDQTPSSAVSVATPTVSVSTPA-PTATPVQTVPQPH 336
Cdd:pfam17823  165 ASAPHAASPAPRTAASSTTAASSTTAASSAPTTAASSAPATLTPARGISTAATATGHPAAGTALAAvGNSSPAAGTVTAA 244

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  337 PQTLPPAVPHSVPQP--TTAIPAFPPVMVPPF-RVPLPGMPIPlpgvLPGMAPPIVPMIHPQVAIAASPATlagatavSE 413
Cdd:pfam17823  245 VGTVTPAALATLAAAagTVASAAGTINMGDPHaRRLSPAKHMP----SDTMARNPAAPMGAQAQGPIIQVS-------TD 313

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2181405656  414 WTEYKTADGKTYYYNNRTLESTWEKPQELKEKEKLEEKIKEPiKEPSEEPLPM 466
Cdd:pfam17823  314 QPVHNTAGEPTPSPSNTTLEPNTPKSVASTNLAVVTTTKAQA-KEPSASPVPV 365
PRK14971 PRK14971
DNA polymerase III subunit gamma/tau;
296-397 2.09e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237874 [Multi-domain]  Cd Length: 614  Bit Score: 45.15  E-value: 2.09e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  296 VSTPTTQDQTPSSAVSVATPTVSVSTPAPTATPVQTVPQPHPQT--LPPAVPHSVPQPTTAIPAFPPVMVPPFRvplpgm 373
Cdd:PRK14971   383 FTQPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTvsVDPPAAVPVNPPSTAPQAVRPAQFKEEK------ 456

                           90       100
                   ....*....|....*....|....
gi 2181405656  374 PIPLPGVlPGMAPPIVPMIHPQVA 397
Cdd:PRK14971   457 KIPVSKV-SSLGPSTLRPIQEKAE 479
WW pfam00397
WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds ...
 511-538 2.89e-04

WW domain; The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro.


Pssm-ID: 459800 [Multi-domain]  Cd Length: 30  Bit Score: 39.03  E-value: 2.89e-04
                           10        20
                   ....*....|....*....|....*...
gi 2181405656  511 TPWCVVWTGDERVFFYNPTTRLSMWDRP 538
Cdd:pfam00397    3 PGWEERWDPDGRVYYYNHETGETQWEKP 30
motB PRK12799
flagellar motor protein MotB; Reviewed
 258-365 3.66e-04

flagellar motor protein MotB; Reviewed


Pssm-ID: 183756 [Multi-domain]  Cd Length: 421  Bit Score: 44.32  E-value: 3.66e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  258 ASTPTTSSPAPAVSTSTSSSTPSSTTSTTTTATSVAQTVSTPTTQdqTPSSAVSVATPTVSVSTPAPTATPVQTVPQPH- 336
Cdd:PRK12799   303 AVTPSSAVTQSSAITPSSAAIPSPAVIPSSVTTQSATTTQASAVA--LSSAGVLPSDVTLPGTVALPAAEPVNMQPQPMs 380

                           90       100       110
                   ....*....|....*....|....*....|...
gi 2181405656  337 -PQTLPPAVPHSVP---QPTTAIPAFPPVMVPP 365
Cdd:PRK12799   381 tTETQQSSTGNITStanGPTTSLPAAPASNIPV 413
PRK12727 PRK12727
flagellar biosynthesis protein FlhF;
262-408 5.89e-04

flagellar biosynthesis protein FlhF;


Pssm-ID: 237182 [Multi-domain]  Cd Length: 559  Bit Score: 43.83  E-value: 5.89e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  262 TTSSPAPAVSTSTSSSTPSSTTSTTTTATSVAQTVSTPTTQDQTpSSAVSVATPtVSVSTPAPTATPVQTVPQPHP---Q 338
Cdd:PRK12727    65 TAAAPAPAPQAPTKPAAPVHAPLKLSANANMSQRQRVASAAEDM-IAAMALRQP-VSVPRQAPAAAPVRAASIPSPaaqA 142

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  339 TLPPAVPHSVPQPTTAIPAFPPVMvppFRVPLPGMPIPLPGVLPGMAPPIVPMihpQVAIAASPATLAGA 408
Cdd:PRK12727   143 LAHAAAVRTAPRQEHALSAVPEQL---FADFLTTAPVPRAPVQAPVVAAPAPV---PAIAAALAAHAAYA 206
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 313-423 6.03e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 43.55  E-value: 6.03e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  313 ATPTVSVSTPAPTATPVQTVPQPHPQTLPPAVPHSVPQPTTAIPafPPVMVPPFRVPLPGMPiplpgvlPGMAPPIVPMI 392
Cdd:PRK14951   369 AAEAAAPAEKKTPARPEAAAPAAAPVAQAAAAPAPAAAPAAAAS--APAAPPAAAPPAPVAA-------PAAAAPAAAPA 439

                           90       100       110
                   ....*....|....*....|....*....|.
gi 2181405656  393 HPQVAIAASPATLAGATAVSEWTEYKTADGK 423
Cdd:PRK14951   440 AAPAAVALAPAPPAQAAPETVAIPVRVAPEP 470
PRK10856 PRK10856
cytoskeleton protein RodZ;
293-371 6.66e-04

cytoskeleton protein RodZ;


Pssm-ID: 236776 [Multi-domain]  Cd Length: 331  Bit Score: 43.09  E-value: 6.66e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2181405656  293 AQTVSTPTTQDQTPSSAVSVATPTVSVSTPAPTATPVQTvPQPHPQTLPPAVPHSVPQPTTAIPAFPPVMVPPFRVPLP 371
Cdd:PRK10856   161 SVPLDTSTTTDPATTPAPAAPVDTTPTNSQTPAVATAPA-PAVDPQQNAVVAPSQANVDTAATPAPAAPATPDGAAPLP 238
Amelogenin smart00818
Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem ...
 299-404 8.60e-04

Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth; They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a "beta-spiral" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide.


Pssm-ID: 197891 [Multi-domain]  Cd Length: 165  Bit Score: 41.31  E-value: 8.60e-04
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656   299 PTTQDQTPSSAVSV--ATPTVSVSTPAPTATPVQTVPQPHPQT--------LPPAVPHSVpQPTTAIPAFPPVMVPPFRV 368
Cdd:smart00818   41 PVSQQHPPTHTLQPhhHIPVLPAQQPVVPQQPLMPVPGQHSMTptqhhqpnLPQPAQQPF-QPQPLQPPQPQQPMQPQPP 119

                            90       100       110
                    ....*....|....*....|....*....|....*...
gi 2181405656   369 PLPGMPIPLPGVLPGMAP--PIVPMIhPQVAIAASPAT 404
Cdd:smart00818  120 VHPIPPLPPQPPLPPMFPmqPLPPLL-PDLPLEAWPAT 156
rne PRK10811
ribonuclease E; Reviewed
 292-418 9.21e-04

ribonuclease E; Reviewed


Pssm-ID: 236766 [Multi-domain]  Cd Length: 1068  Bit Score: 43.49  E-value: 9.21e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  292 VAQTVSTPTTQDQTPSSAVSVATPTVSVSTPAPTATPVQTVPQPHPQTLPPAVPHSVPQPTTAIPAFPPVMVPPFRVPLP 371
Cdd:PRK10811   887 VVEAVAEVVEEPVVVAEPQPEEVVVVETTHPEVIAAPVTEQPQVITESDVAVAQEVAEHAEPVVEPQDETADIEEAAETA 966

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
gi 2181405656  372 GMPIPLPGVLPGMAPPIVPMIHPQVAIAASPATLAGATAVSEWTEYK 418
Cdd:PRK10811   967 EVVVAEPEVVAQPAAPVVAEVAAEVETVTAVEPEVAPAQVPEATVEH 1013
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
258-403 1.21e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 42.94  E-value: 1.21e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  258 ASTPTTSSPAPAVSTSTSSSTPSSTTSTTTTATSVAQTVSTPTTQDQTPSSAVSVATPTVSVSTPAPTATP--VQTVPQP 335
Cdd:PRK12323   394 AAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPAPAAAPAAAARPaaAGPRPVA 473

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2181405656  336 HPQTLPPAVPHSVPQPTTAIPAFPP--VMVPPFRVPLPGMPIPLP-------GVLPGMAPPIVPMIHPQVAIAASPA 403
Cdd:PRK12323   474 AAAAAAPARAAPAAAPAPADDDPPPweELPPEFASPAPAQPDAAPagwvaesIPDPATADPDDAFETLAPAPAAAPA 550
PTZ00121 PTZ00121
MAEBL; Provisional
 588-921 1.26e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 42.82  E-value: 1.26e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  588 EEQELMEEINEDEPVKAKK--RKRDDNKDIDSEKEAAMEAEIKAAR----ERAIVPL----EARMKQFKDMLLERGVSAF 657
Cdd:PTZ00121  1173 EDAKKAEAARKAEEVRKAEelRKAEDARKAEAARKAEEERKAEEARkaedAKKAEAVkkaeEAKKDAEEAKKAEEERNNE 1252

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  658 STWEKELHKIVFDPRYLLLNPKERKQVFDQYVKT----RAEEERR-EKKNKIMQAK---------EDFKKMMEEAKFNpr 723
Cdd:PTZ00121  1253 EIRKFEEARMAHFARRQAAIKAEEARKADELKKAeekkKADEAKKaEEKKKADEAKkkaeeakkaDEAKKKAEEAKKK-- 1330

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  724 atfSEFAAKHAKDSRFKAIEKMKDREALFNEFVAAARKKEKEDSKTRGEKIKSDffelLSNHHLDSQSRWSKVKDKVESD 803
Cdd:PTZ00121  1331 ---ADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKAD----AAKKKAEEKKKADEAKKKAEED 1403

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  804 PryKAVDSSSMREDLFKQYIEkiAKVRSSDVSWSDTRRTLRKDHRWESGSLLEREEKEKLFNEHIEALTKKKREHFRQLL 883
Cdd:PTZ00121  1404 K--KKADELKKAAAAKKKADE--AKKKAEEKKKADEAKKKAEEAKKADEAKKKAEEAKKAEEAKKKAEEAKKADEAKKKA 1479

                          330       340       350
                   ....*....|....*....|....*....|....*....
gi 2181405656  884 DET-SAITLTSTWKEVKKIIKEdprcIKFSSSDRKKQRE 921
Cdd:PTZ00121  1480 EEAkKADEAKKKAEEAKKKADE----AKKAAEAKKKADE 1514
PRK10263 PRK10263
DNA translocase FtsK; Provisional
 266-410 1.53e-03

DNA translocase FtsK; Provisional


Pssm-ID: 236669 [Multi-domain]  Cd Length: 1355  Bit Score: 42.76  E-value: 1.53e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  266 PAPAVSTSTSSSTPSSTTSTTTTATSVAQTVSTPTTQdQTPSSAVSVATPTVSVSTPAPTATPVQTVPQPHPQTLPPAVP 345
Cdd:PRK10263   403 PQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYYAPAPE-QPVAGNAWQAEEQQSTFAPQSTYQTEQTYQQPAAQEPLYQQP 481

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  346 HSVPQPTTAIPAFPPVMVPPFRVPLPGM-------------------PIPLPGVLPgmaPPIVPMIHPQVAIAASPATLA 406
Cdd:PRK10263   482 QPVEQQPVVEPEPVVEETKPARPPLYYFeeveekrarereqlaawyqPIPEPVKEP---EPIKSSLKAPSVAAVPPVEAA 558


                   ....
gi 2181405656  407 GATA 410
Cdd:PRK10263   559 AAVS 562
PRK13729 PRK13729
conjugal transfer pilus assembly protein TraB; Provisional
 323-392 1.72e-03

conjugal transfer pilus assembly protein TraB; Provisional


Pssm-ID: 184281 [Multi-domain]  Cd Length: 475  Bit Score: 42.12  E-value: 1.72e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2181405656  323 APTATPVQTVPQPHPQT-LPPAVPHSVPQPTTAIPAFPP---VMVPPFRVPLPGMPIPLPgvlPGMAPPIVPMI 392
Cdd:PRK13729   122 ALGANPVTATGEPVPQMpASPPGPEGEPQPGNTPVSFPPqgsVAVPPPTAFYPGNGVTPP---PQVTYQSVPVP 192
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
257-424 2.09e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 42.17  E-value: 2.09e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  257 GASTPTTSSPAPAVSTSTSSSTPSSTTSTTTTATSVAQTVSTPTTQDQTPSSAVSVATPTVSVSTPAPTATPVQTVPQPH 336
Cdd:PRK12323   370 GGAGPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAPA 449

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  337 PQTLPPAVPHSVPQPTTAIPAFPPV---MVPPFRVPlPGMPIPLPGVLPGM--APPIVPMIHPqVAIAASPATLAGATAV 411
Cdd:PRK12323   450 PAPAPAAAPAAAARPAAAGPRPVAAaaaAAPARAAP-AAAPAPADDDPPPWeeLPPEFASPAP-AQPDAAPAGWVAESIP 527

                          170
                   ....*....|...
gi 2181405656  412 SEWTEYKTADGKT 424
Cdd:PRK12323   528 DPATADPDDAFET 540
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 306-410 3.14e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 41.24  E-value: 3.14e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  306 PSSAVSVATPTVSVSTPAPTATPvqtVPQPHPQTLPPAVPHSVPQPTTAIPAFPPVMVPPFRVPLPGM--PIPLPGVLPG 383
Cdd:PRK14951   367 AAAAEAAAPAEKKTPARPEAAAP---AAAPVAQAAAAPAPAAAPAAAASAPAAPPAAAPPAPVAAPAAaaPAAAPAAAPA 443

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2181405656  384 MAPP--------------IVPMIHPQVAIAASPATLAGATA 410
Cdd:PRK14951   444 AVALapappaqaapetvaIPVRVAPEPAVASAAPAPAAAPA 484
DUF3729 pfam12526
Protein of unknown function (DUF3729); This family of proteins is found in viruses. Proteins ...
 306-379 3.20e-03

Protein of unknown function (DUF3729); This family of proteins is found in viruses. Proteins in this family are typically between 145 and 1707 amino acids in length. The family is found in association with pfam01443, pfam01661, pfam05417, pfam01660, pfam00978. There is a single completely conserved residue L that may be functionally important.


Pssm-ID: 372164 [Multi-domain]  Cd Length: 115  Bit Score: 38.52  E-value: 3.20e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2181405656  306 PSSAVSVATPTVSVSTPAPTATPVQTVPQPHPqtlpPAVPHSVPQPTTAIPAFPPVMVPPfRVPLPGMPIPLPG 379
Cdd:pfam12526   37 PDPPPPVGDPRPPVVDTPPPVSAVWVLPPPSE----PAAPEPDLVPPVTGPAGPPSPLAP-PAPAQKPPLPPPR 105
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 295-413 3.60e-03

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 41.44  E-value: 3.60e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  295 TVSTPTTQDQTPSSAVSVATPTVSVSTP--------APTAT-PVQTVPQPHPQTLPPAVPHSVPQPTTAIPAFPPVM-VP 364
Cdd:pfam05109  467 TVSTADVTSPTPAGTTSGASPVTPSPSPrdngteskAPDMTsPTSAVTTPTPNATSPTPAVTTPTPNATSPTLGKTSpTS 546

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2181405656  365 PFRVPLPGMPIPLPGV---LPGMAPPIVPMIHPQVAIaASPATLAGATAVSE 413
Cdd:pfam05109  547 AVTTPTPNATSPTPAVttpTPNATIPTLGKTSPTSAV-TTPTPNATSPTVGE 597
Atrophin-1 pfam03154
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ...
 304-403 4.15e-03

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: 41.29  E-value: 4.15e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  304 QTPSSAVSVATPTVSVSTPAPTATPvqtvpqphpqtlPPAVPHSVPQPTtaipafPPVMVPPFRVPLPGMPIPLPGVLPG 383
Cdd:pfam03154  175 QAQSGAASPPSPPPPGTTQAATAGP------------TPSAPSVPPQGS------PATSQPPNQTQSTAAPHTLIQQTPT 236

                           90       100
                   ....*....|....*....|
gi 2181405656  384 MAPPIVPMIHPQVAIAASPA 403
Cdd:pfam03154  237 LHPQRLPSPHPPLQPMTQPP 256
PHA03378 PHA03378
EBNA-3B; Provisional
 299-411 4.96e-03

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 40.82  E-value: 4.96e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  299 PTTQdQTPSSAVSVATPTVSVSTPA--PTATPVQTVP---QPHPQTLPPAVPHSVPQPTTAIPAFPPVMVPPFRVP---- 369
Cdd:PHA03378   691 PGTM-QPPPRAPTPMRPPAAPPGRAqrPAAATGRARPpaaAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARppaa 769

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 2181405656  370 LPGMPIPLPgvlPGMAPPiVPMIHPQVAIAASPATLAGATAV 411
Cdd:PHA03378   770 APGAPTPQP---PPQAPP-APQQRPRGAPTPQPPPQAGPTSM 807
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 292-410 5.03e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 40.74  E-value: 5.03e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  292 VAQTVSTPTTQDQTPSSAVSVATPTvsvstPAPTATPVQTVPQPHPQTLPPAVPHSVPQPTTAIPAFPPVMVPPFRVPLP 371
Cdd:PRK07764   387 VAGGAGAPAAAAPSAAAAAPAAAPA-----PAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAA 461

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 2181405656  372 GMPIPLPGVLPGMAPPIVPMIHPQVAIAASPATLAGATA 410
Cdd:PRK07764   462 PSAQPAPAPAAAPEPTAAPAPAPPAAPAPAAAPAAPAAP 500
PRK14971 PRK14971
DNA polymerase III subunit gamma/tau;
293-375 6.98e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237874 [Multi-domain]  Cd Length: 614  Bit Score: 40.14  E-value: 6.98e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  293 AQTVSTPTTQDQTPSSAVSVATPTVSVSTPAPTATPVQ-TVPQPHPQTLPPavPHSVPQPTTAIPAFPPVMVPPFRVPLP 371
Cdd:PRK14971   389 APQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTvSVDPPAAVPVNP--PSTAPQAVRPAQFKEEKKIPVSKVSSL 466


                   ....
gi 2181405656  372 GMPI 375
Cdd:PRK14971   467 GPST 470
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 293-416 7.57e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 40.35  E-value: 7.57e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  293 AQTVSTPTTQDQTPSSAvSVATPTVSVSTPAPTATPvQTVPQPHPQTLPPAVPHS----VPQPTTAIPAFPPVMVPPFRV 368
Cdd:PRK07764   395 AAAAPSAAAAAPAAAPA-PAAAAPAAAAAPAPAAAP-QPAPAPAPAPAPPSPAGNapagGAPSPPPAAAPSAQPAPAPAA 472

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 2181405656  369 PLPGMPIPLPGVLPGMAPPIVPMIhPQVAiAASPATLAGATAVSEWTE 416
Cdd:PRK07764   473 APEPTAAPAPAPPAAPAPAAAPAA-PAAP-AAPAGADDAATLRERWPE 518
PRK14959 PRK14959
DNA polymerase III subunits gamma and tau; Provisional
 293-374 8.01e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184923 [Multi-domain]  Cd Length: 624  Bit Score: 40.05  E-value: 8.01e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2181405656  293 AQTVSTPTTQ-DQTPSSAVSVATPTVSVSTPAPTATPVQTVPQphpQTLPPAVPHSvpqpttAIPAFPPVMVPPfRVPLP 371
Cdd:PRK14959   394 AATIPTPGTQgPQGTAPAAGMTPSSAAPATPAPSAAPSPRVPW---DDAPPAPPRS------GIPPRPAPRMPE-ASPVP 463


                   ...
gi 2181405656  372 GMP 374
Cdd:PRK14959   464 GAP 466
 
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.
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