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Conserved domains on  [gi|261206062|ref|XP_002627768|]
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transcription initiation protein spt5 [Blastomyces gilchristii SLH14081]

Protein Classification

transcription elongation factor SPT5( domain architecture ID 13776982)

transcription elongation factor SPT5 is a component of the SPT4-SPT5 complex that mediates both activation and inhibition of transcription elongation, and plays a role in pre-mRNA processing

Gene Ontology:  GO:0032784|GO:0006357|GO:0003723
PubMed:  22982195|8987397

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
 233-321 1.53e-31

Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1); The N-Utilization Substance G (NusG) protein and its eukaryotic homolog, Spt5, are involved in transcription elongation and termination. NusG contains an NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus. Spt5 forms an Spt4-Spt5 complex that is an essential RNA polymerase II elongation factor. NusG was originally discovered as an N-dependent antitermination enhancing activity in Escherichia coli, and has a variety of functions such as its involvement in RNA polymerase elongation and Rho-termination in bacteria. Orthologs of the NusG gene exist in all bacteria, but their functions and requirements are different. Spt5-like is homologous to the Spt5 proteins present in all eukaryotes, which is unique as it encodes a protein with an additional long carboxy-terminal extension that contains WG/GW motifs. Spt5-like, or KTF1 (KOW domain-containing Transcription Factor 1), is a RNA-directed DNA methylation (RdDM) pathway effector in plants.


:

Pssm-ID: 193577 [Multi-domain]  Cd Length: 86  Bit Score: 118.40  E-value: 1.53e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  233 SIWAVKCRPGKEREIVFNIMKRIEDRPPdSRRPIRIMSAFERGGtMSGYIYVEARKQADVLDALNDMSNVYTkSKMILIS 312
Cdd:cd09888     1 KLWAVKCKPGKEREIVISLMRKFLDLQR-TGNPLGIKSVFARDG-LKGYIYIEARKEAHVKDAIEGLRGVYL-NTIKLVP 77


                  ....*....
gi 261206062  313 VKEMPDLLR 321
Cdd:cd09888    78 IKEMPDVLS 86
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 754-805 3.60e-25

KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


:

Pssm-ID: 240509  Cd Length: 52  Bit Score: 99.10  E-value: 3.60e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 261206062  754 GRDRTIGKTVTIRKGPFKGLLGIVKDTTDAQARVELHSKNKVITVDKDMLAI 805
Cdd:cd06085     1 GRDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLAV 52
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 541-592 1.90e-19

KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


:

Pssm-ID: 240507  Cd Length: 51  Bit Score: 82.57  E-value: 1.90e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 261206062  541 RFQEGDHVKVIGGsRFRDELGMVVRIKDDRVTLLSDMSMQEITVFSKDIREA 592
Cdd:cd06083     1 HFKVGDHVKVISG-RHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 157-227 1.13e-17

Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal region of the early transcription elongation factor Spt5. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4.


:

Pssm-ID: 463406  Cd Length: 97  Bit Score: 79.23  E-value: 1.13e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 261206062   157 DGFVA--EHPDDLDAlpvgAETDDRRHRELDRKRDLEATMDAEKQAQALKERYGRNRAVAADL---VVVPKRLLLP 227
Cdd:pfam11942   26 DDFIEddEEDEDEED----GRRDDRRHRELDRRRELEEDEDAEEIAEYLKERYGRSSSDAYRGdaeEGVPQRLLLP 97
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 865-959 1.83e-16

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteriztic TPA motif.


:

Pssm-ID: 372327 [Multi-domain]  Cd Length: 71  Bit Score: 74.79  E-value: 1.83e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062   865 SSRTPAWGSAtaSGSRTPAWKADGSRTSNPYD-GSRTayggttfgggrtPAWTSGTKTPYDSssgfggsstsgfdafAAG 943
Cdd:pfam12815    1 GSRTPAYNSA--GGSRTPAWGADGSRTPAYGGaGGRT------------PAYNQGGKTPAWG---------------GAG 51

                           90
                   ....*....|....*...
gi 261206062   944 SRTPAYPG--GGSRTPAW 959
Cdd:pfam12815   52 SRTPAYYGawGGSRTPAY 69
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 489-540 2.31e-15

KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


:

Pssm-ID: 240506  Cd Length: 51  Bit Score: 70.99  E-value: 2.31e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 261206062  489 YLPGDTVEVFQGEQQGVVGRTVSTRGDIVSIKVTQGELeGQQIDVPIKGLRK 540
Cdd:cd06082     1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDL-KEPLEFPAKELRK 51
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 331-368 6.89e-15

KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


:

Pssm-ID: 240505  Cd Length: 38  Bit Score: 69.42  E-value: 6.89e-15
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 261206062  331 GGWVRIKRGKYQGDLAQLEDVETNGLDVTVRLVPRLDY 368
Cdd:cd06081     1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 668-708 8.60e-12

KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


:

Pssm-ID: 240508  Cd Length: 43  Bit Score: 60.61  E-value: 8.60e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 261206062  668 GDTVREVTGE--QRTGAIIHIHRSFLFLNNKDASDNAGIIVTR 708
Cdd:cd06084     1 GDTVKVVDGPykGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 943-1070 1.70e-09

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


:

Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 56.76  E-value: 1.70e-09
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062    943 GSRTPAYPGGGSRTPAWaPGSAAPPPIGHSSGSKSSYDAPTPSTDYS-APTPGPYGGAPTPGATAAtphgWADNAPTPGA 1021
Cdd:smart01104    1 GGRTPAWGASGSKTPAW-GSRTPGTAAGGAPTARGGSGSRTPAWGGAgSRTPAWGGAGPTGSRTPA----WGGASAWGNK 75

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*....
gi 261206062   1022 ihAPTPDASGYSAkRTGELYDAPTPAAIGGGRPYDAPTPAMGAGIPATP 1070
Cdd:smart01104   76 --SSEGSASSWAA-GPGGAYGAPTPGYGGTPSAYGPATPGGGAMAGSAS 121
CTD super family cl37848
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 834-873 2.91e-03

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteriztic TPA motif.


The actual alignment was detected with superfamily member pfam12815:

Pssm-ID: 372327 [Multi-domain]  Cd Length: 71  Bit Score: 37.42  E-value: 2.91e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 261206062   834 YGSSAAPPDW-SGSRTPLAANDASRTPAWRSSS--SRTPAWGS 873
Cdd:pfam12815   29 GGAGGRTPAYnQGGKTPAWGGAGSRTPAYYGAWggSRTPAYGG 71
 
Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
 233-321 1.53e-31

Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1); The N-Utilization Substance G (NusG) protein and its eukaryotic homolog, Spt5, are involved in transcription elongation and termination. NusG contains an NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus. Spt5 forms an Spt4-Spt5 complex that is an essential RNA polymerase II elongation factor. NusG was originally discovered as an N-dependent antitermination enhancing activity in Escherichia coli, and has a variety of functions such as its involvement in RNA polymerase elongation and Rho-termination in bacteria. Orthologs of the NusG gene exist in all bacteria, but their functions and requirements are different. Spt5-like is homologous to the Spt5 proteins present in all eukaryotes, which is unique as it encodes a protein with an additional long carboxy-terminal extension that contains WG/GW motifs. Spt5-like, or KTF1 (KOW domain-containing Transcription Factor 1), is a RNA-directed DNA methylation (RdDM) pathway effector in plants.


Pssm-ID: 193577 [Multi-domain]  Cd Length: 86  Bit Score: 118.40  E-value: 1.53e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  233 SIWAVKCRPGKEREIVFNIMKRIEDRPPdSRRPIRIMSAFERGGtMSGYIYVEARKQADVLDALNDMSNVYTkSKMILIS 312
Cdd:cd09888     1 KLWAVKCKPGKEREIVISLMRKFLDLQR-TGNPLGIKSVFARDG-LKGYIYIEARKEAHVKDAIEGLRGVYL-NTIKLVP 77


                  ....*....
gi 261206062  313 VKEMPDLLR 321
Cdd:cd09888    78 IKEMPDVLS 86
Spt5-NGN pfam03439
Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG ...
 233-320 3.51e-28

Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit.


Pssm-ID: 397481  Cd Length: 84  Bit Score: 108.44  E-value: 3.51e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062   233 SIWAVKCRPGKEREIVFNIMKRIEDRPPdsRRPIRIMSAFERGGtMSGYIYVEARKQADVLDALNDMSNVYTkSKMILIS 312
Cdd:pfam03439    1 KIWAVKCTPGQEREVALSLMRKILALAK--TNNLGIYSVFAPDG-LKGYIYVEADRQAAVKRALEGIPNVRG-LVPGLVP 76


                   ....*...
gi 261206062   313 VKEMPDLL 320
Cdd:pfam03439   77 IKEMEHLL 84
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 754-805 3.60e-25

KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240509  Cd Length: 52  Bit Score: 99.10  E-value: 3.60e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 261206062  754 GRDRTIGKTVTIRKGPFKGLLGIVKDTTDAQARVELHSKNKVITVDKDMLAI 805
Cdd:cd06085     1 GRDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLAV 52
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 541-592 1.90e-19

KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240507  Cd Length: 51  Bit Score: 82.57  E-value: 1.90e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 261206062  541 RFQEGDHVKVIGGsRFRDELGMVVRIKDDRVTLLSDMSMQEITVFSKDIREA 592
Cdd:cd06083     1 HFKVGDHVKVISG-RHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 157-227 1.13e-17

Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal region of the early transcription elongation factor Spt5. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4.


Pssm-ID: 463406  Cd Length: 97  Bit Score: 79.23  E-value: 1.13e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 261206062   157 DGFVA--EHPDDLDAlpvgAETDDRRHRELDRKRDLEATMDAEKQAQALKERYGRNRAVAADL---VVVPKRLLLP 227
Cdd:pfam11942   26 DDFIEddEEDEDEED----GRRDDRRHRELDRRRELEEDEDAEEIAEYLKERYGRSSSDAYRGdaeEGVPQRLLLP 97
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 865-959 1.83e-16

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteriztic TPA motif.


Pssm-ID: 372327 [Multi-domain]  Cd Length: 71  Bit Score: 74.79  E-value: 1.83e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062   865 SSRTPAWGSAtaSGSRTPAWKADGSRTSNPYD-GSRTayggttfgggrtPAWTSGTKTPYDSssgfggsstsgfdafAAG 943
Cdd:pfam12815    1 GSRTPAYNSA--GGSRTPAWGADGSRTPAYGGaGGRT------------PAYNQGGKTPAWG---------------GAG 51

                           90
                   ....*....|....*...
gi 261206062   944 SRTPAYPG--GGSRTPAW 959
Cdd:pfam12815   52 SRTPAYYGawGGSRTPAY 69
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 489-540 2.31e-15

KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240506  Cd Length: 51  Bit Score: 70.99  E-value: 2.31e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 261206062  489 YLPGDTVEVFQGEQQGVVGRTVSTRGDIVSIKVTQGELeGQQIDVPIKGLRK 540
Cdd:cd06082     1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDL-KEPLEFPAKELRK 51
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 331-368 6.89e-15

KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240505  Cd Length: 38  Bit Score: 69.42  E-value: 6.89e-15
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 261206062  331 GGWVRIKRGKYQGDLAQLEDVETNGLDVTVRLVPRLDY 368
Cdd:cd06081     1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 855-1009 1.03e-14

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 71.40  E-value: 1.03e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062    855 ASRTPAWRSSSSRTPAWgsatasGSRTPAWKADGSRTSNPYDGSRTayggttfgggrtPAW-TSGTKTPYDsssgfggss 933
Cdd:smart01104    1 GGRTPAWGASGSKTPAW------GSRTPGTAAGGAPTARGGSGSRT------------PAWgGAGSRTPAW--------- 53

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 261206062    934 tsgFDAFAAGSRTPAYPGGGSRTPAWAPGSAAPPpighSSGSKSSYDAPTPstdYSAPTPGPYGGAPTPGATAATP 1009
Cdd:smart01104   54 ---GGAGPTGSRTPAWGGASAWGNKSSEGSASSW----AAGPGGAYGAPTP---GYGGTPSAYGPATPGGGAMAGS 119
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 668-708 8.60e-12

KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240508  Cd Length: 43  Bit Score: 60.61  E-value: 8.60e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 261206062  668 GDTVREVTGE--QRTGAIIHIHRSFLFLNNKDASDNAGIIVTR 708
Cdd:cd06084     1 GDTVKVVDGPykGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 233-322 5.66e-10

In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, this domain may confer affinity for Spt4p.Spt4p


Pssm-ID: 197850 [Multi-domain]  Cd Length: 106  Bit Score: 57.38  E-value: 5.66e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062    233 SIWAVKCRPGKEREIVFNIMKRIEDR-----------PPDSRRPIRIMSAFERGGTMS-GYIYVEARKQADVLDALNDMS 300
Cdd:smart00738    1 NWYAVRTTSGQEKRVAENLERKAEALgledkivsilvPTEEVKEIRRGKKKVVERKLFpGYIFVEADLEDEVWTAIRGTP 80

                            90       100
                    ....*....|....*....|....*.
gi 261206062    301 NVY----TKSKMILISVKEMPDLLRV 322
Cdd:smart00738   81 GVRgfvgGGGKPTPVPDDEIEKILKP 106
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 943-1070 1.70e-09

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 56.76  E-value: 1.70e-09
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062    943 GSRTPAYPGGGSRTPAWaPGSAAPPPIGHSSGSKSSYDAPTPSTDYS-APTPGPYGGAPTPGATAAtphgWADNAPTPGA 1021
Cdd:smart01104    1 GGRTPAWGASGSKTPAW-GSRTPGTAAGGAPTARGGSGSRTPAWGGAgSRTPAWGGAGPTGSRTPA----WGGASAWGNK 75

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*....
gi 261206062   1022 ihAPTPDASGYSAkRTGELYDAPTPAAIGGGRPYDAPTPAMGAGIPATP 1070
Cdd:smart01104   76 --SSEGSASSWAA-GPGGAYGAPTPGYGGTPSAYGPATPGGGAMAGSAS 121
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 835-1087 2.39e-08

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 58.64  E-value: 2.39e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  835 GSSAAPPDWSGSRTPLAANDASRTPAWRSSSSR-TPAWGSATASGSRTPAWKADGSRTSNPYDGSRTAYGGTTFGGGRTP 913
Cdd:PHA03307  187 SSPPAEPPPSTPPAAASPRPPRRSSPISASASSpAPAPGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLP 266

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  914 AWTSGTKTPYDSSSGFGGSSTSGFDAFAAGSRTPAYPGGGSRTPAwapgsaaPPPIGHSSGSKSS-YDAPTPSTDYSAPT 992
Cdd:PHA03307  267 TRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSS-------PRASSSSSSSRESsSSSTSSSSESSRGA 339

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  993 PGPYGGAPTPGATAATPHGWADNAPTPGAIHAPTPDASGYSAKRTGELYDApTPAAIGGGRPYDAPtPAMGAGIPAtPSA 1072
Cdd:PHA03307  340 AVSPGPSPSRSPSPSRPPPPADPSSPRKRPRPSRAPSSPAASAGRPTRRRA-RAAVAGRARRRDAT-GRFPAGRPR-PSP 416

                         250
                  ....*....|....*
gi 261206062 1073 GDDGGPRYEECTPSP 1087
Cdd:PHA03307  417 LDAGAASGAFYARYP 431
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 939-1087 1.50e-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: 52.61  E-value: 1.50e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062   939 AFAAGSRTPAYPGGGS-RTPAWAPGSA----------APPPIGHSSGSKSSYDAPTPStDYSAPTPGPYGGAPTPGATAA 1007
Cdd:pfam05109  438 GFAAPNTTTGLPSSTHvPTNLTAPASTgptvstadvtSPTPAGTTSGASPVTPSPSPR-DNGTESKAPDMTSPTSAVTTP 516

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  1008 TPHGwadNAPTPgAIHAPTPDASGYSAKRTG--ELYDAPTPAAIgggrpydAPTPAMGAGIP--ATPSAGDDgGPRYEEC 1083
Cdd:pfam05109  517 TPNA---TSPTP-AVTTPTPNATSPTLGKTSptSAVTTPTPNAT-------SPTPAVTTPTPnaTIPTLGKT-SPTSAVT 584


                   ....
gi 261206062  1084 TPSP 1087
Cdd:pfam05109  585 TPTP 588
Chi1 COG3469
Chitinase [Carbohydrate transport and metabolism];
842-1078 3.02e-06

Chitinase [Carbohydrate transport and metabolism];


Pssm-ID: 442692 [Multi-domain]  Cd Length: 534  Bit Score: 51.29  E-value: 3.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  842 DWSGSRTPLAANDASRTPAWRSSSSRTPAWGSATASGSRTPAWKADGSRTSNPYDGSRTAYGGTTFGGGRTPAWTSGTKT 921
Cdd:COG3469     1 SSSVSTAASPTAGGASATAVTLLGAAATAASVTLTAATATTVVSTTGSVVVAASGSAGSGTGTTAASSTAATSSTTSTTA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  922 PYdsssgfggsstsgfdafaaGSRTPAYPGGGSRTPAWAPGSAAPPPIGHSSGSKSSYDAPTPSTDYSAPTPGpyggapT 1001
Cdd:COG3469    81 TA-------------------TAAAAAATSTSATLVATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTT------T 135

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 261206062 1002 PGATAATPHGWADNAPTPGAIHAPTPDASGYSAKRTGELYDAPTPAAIGGGRPYDAPTPAMGAGIPATPSAGDDGGP 1078
Cdd:COG3469   136 SGASATSSAGSTTTTTTVSGTETATGGTTTTSTTTTTTSASTTPSATTTATATTASGATTPSATTTATTTGPPTPGL 212
Chi1 COG3469
Chitinase [Carbohydrate transport and metabolism];
832-1028 1.33e-04

Chitinase [Carbohydrate transport and metabolism];


Pssm-ID: 442692 [Multi-domain]  Cd Length: 534  Bit Score: 45.90  E-value: 1.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  832 IPYGSSAAPPDWSGSRTPLAaNDASRTPAWRSSSSRTPAWGSATASGSRTPAWKADGSRTSNPYDGSRTAYGGTTFGGGR 911
Cdd:COG3469    20 VTLLGAAATAASVTLTAATA-TTVVSTTGSVVVAASGSAGSGTGTTAASSTAATSSTTSTTATATAAAAAATSTSATLVA 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  912 TPAWTSGTKTPYDSSSGFGGSSTSGFD--AFAAGSRTPAYPGGGSRTPAWAPGSAAPPPIGHSSGSKSSYDAPTPSTDYS 989
Cdd:COG3469    99 TSTASGANTGTSTVTTTSTGAGSVTSTtsSTAGSTTTSGASATSSAGSTTTTTTVSGTETATGGTTTTSTTTTTTSASTT 178

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 261206062  990 APTPGPYGGAPTPGATAATPhgwADNAPTPGAIHAPTPD 1028
Cdd:COG3469   179 PSATTTATATTASGATTPSA---TTTATTTGPPTPGLPK 214
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 759-790 9.02e-04

KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and NusG.


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 37.75  E-value: 9.02e-04
                           10        20        30
                   ....*....|....*....|....*....|..
gi 261206062   759 IGKTVTIRKGPFKGLLGIVKDTTDAQARVELH 790
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
PHA03378 PHA03378
EBNA-3B; Provisional
 836-1027 1.86e-03

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 42.36  E-value: 1.86e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  836 SSAAPPDWSGSRTPLAANDASRTPA-WRSSSSRTPAWGSATASGSRTPAWKADGSRTSNPYDGSRTAyggttfggGRTPA 914
Cdd:PHA03378  617 ETSAPRQWPMPLRPIPMRPLRMQPItFNVLVFPTPHQPPQVEITPYKPTWTQIGHIPYQPSPTGANT--------MLPIQ 688

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  915 WTSGTKTPydsssgfggsstsgFDAFAAGSRTPAYPGGGSRTPAWAPGSAaPPPIGHSSGSKSSYDAPTPSTDYSApTPG 994
Cdd:PHA03378  689 WAPGTMQP--------------PPRAPTPMRPPAAPPGRAQRPAAATGRA-RPPAAAPGRARPPAAAPGRARPPAA-APG 752

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 261206062  995 ---PYGGAP--------TPGATAATPHGWADNAPTPGAIHAPTP 1027
Cdd:PHA03378  753 rarPPAAAPgrarppaaAPGAPTPQPPPQAPPAPQQRPRGAPTP 796
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 544-576 2.41e-03

KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and NusG.


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 36.60  E-value: 2.41e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 261206062   544 EGDHVKVIGGsRFRDELGMVVRIKDDRVTLLSD 576
Cdd:pfam00467    1 KGDVVRVIAG-PFKGKVGKVVEVDDKKNRVLVE 32
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 834-873 2.91e-03

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteriztic TPA motif.


Pssm-ID: 372327 [Multi-domain]  Cd Length: 71  Bit Score: 37.42  E-value: 2.91e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 261206062   834 YGSSAAPPDW-SGSRTPLAANDASRTPAWRSSS--SRTPAWGS 873
Cdd:pfam12815   29 GGAGGRTPAYnQGGKTPAWGGAGSRTPAYYGAWggSRTPAYGG 71
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 541-569 6.84e-03

KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.


Pssm-ID: 128978  Cd Length: 28  Bit Score: 35.00  E-value: 6.84e-03
                            10        20
                    ....*....|....*....|....*....
gi 261206062    541 RFQEGDHVKVIGGsRFRDELGMVVRIKDD 569
Cdd:smart00739    1 KFEVGDTVRVIAG-PFKGKVGKVLEVDGE 28
 
Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
 233-321 1.53e-31

Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1); The N-Utilization Substance G (NusG) protein and its eukaryotic homolog, Spt5, are involved in transcription elongation and termination. NusG contains an NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus. Spt5 forms an Spt4-Spt5 complex that is an essential RNA polymerase II elongation factor. NusG was originally discovered as an N-dependent antitermination enhancing activity in Escherichia coli, and has a variety of functions such as its involvement in RNA polymerase elongation and Rho-termination in bacteria. Orthologs of the NusG gene exist in all bacteria, but their functions and requirements are different. Spt5-like is homologous to the Spt5 proteins present in all eukaryotes, which is unique as it encodes a protein with an additional long carboxy-terminal extension that contains WG/GW motifs. Spt5-like, or KTF1 (KOW domain-containing Transcription Factor 1), is a RNA-directed DNA methylation (RdDM) pathway effector in plants.


Pssm-ID: 193577 [Multi-domain]  Cd Length: 86  Bit Score: 118.40  E-value: 1.53e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  233 SIWAVKCRPGKEREIVFNIMKRIEDRPPdSRRPIRIMSAFERGGtMSGYIYVEARKQADVLDALNDMSNVYTkSKMILIS 312
Cdd:cd09888     1 KLWAVKCKPGKEREIVISLMRKFLDLQR-TGNPLGIKSVFARDG-LKGYIYIEARKEAHVKDAIEGLRGVYL-NTIKLVP 77


                  ....*....
gi 261206062  313 VKEMPDLLR 321
Cdd:cd09888    78 IKEMPDVLS 86
Spt5-NGN pfam03439
Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG ...
 233-320 3.51e-28

Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit.


Pssm-ID: 397481  Cd Length: 84  Bit Score: 108.44  E-value: 3.51e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062   233 SIWAVKCRPGKEREIVFNIMKRIEDRPPdsRRPIRIMSAFERGGtMSGYIYVEARKQADVLDALNDMSNVYTkSKMILIS 312
Cdd:pfam03439    1 KIWAVKCTPGQEREVALSLMRKILALAK--TNNLGIYSVFAPDG-LKGYIYVEADRQAAVKRALEGIPNVRG-LVPGLVP 76


                   ....*...
gi 261206062   313 VKEMPDLL 320
Cdd:pfam03439   77 IKEMEHLL 84
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 754-805 3.60e-25

KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240509  Cd Length: 52  Bit Score: 99.10  E-value: 3.60e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 261206062  754 GRDRTIGKTVTIRKGPFKGLLGIVKDTTDAQARVELHSKNKVITVDKDMLAI 805
Cdd:cd06085     1 GRDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLAV 52
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 541-592 1.90e-19

KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240507  Cd Length: 51  Bit Score: 82.57  E-value: 1.90e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 261206062  541 RFQEGDHVKVIGGsRFRDELGMVVRIKDDRVTLLSDMSMQEITVFSKDIREA 592
Cdd:cd06083     1 HFKVGDHVKVISG-RHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 157-227 1.13e-17

Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal region of the early transcription elongation factor Spt5. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4.


Pssm-ID: 463406  Cd Length: 97  Bit Score: 79.23  E-value: 1.13e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 261206062   157 DGFVA--EHPDDLDAlpvgAETDDRRHRELDRKRDLEATMDAEKQAQALKERYGRNRAVAADL---VVVPKRLLLP 227
Cdd:pfam11942   26 DDFIEddEEDEDEED----GRRDDRRHRELDRRRELEEDEDAEEIAEYLKERYGRSSSDAYRGdaeEGVPQRLLLP 97
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 865-959 1.83e-16

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteriztic TPA motif.


Pssm-ID: 372327 [Multi-domain]  Cd Length: 71  Bit Score: 74.79  E-value: 1.83e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062   865 SSRTPAWGSAtaSGSRTPAWKADGSRTSNPYD-GSRTayggttfgggrtPAWTSGTKTPYDSssgfggsstsgfdafAAG 943
Cdd:pfam12815    1 GSRTPAYNSA--GGSRTPAWGADGSRTPAYGGaGGRT------------PAYNQGGKTPAWG---------------GAG 51

                           90
                   ....*....|....*...
gi 261206062   944 SRTPAYPG--GGSRTPAW 959
Cdd:pfam12815   52 SRTPAYYGawGGSRTPAY 69
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 489-540 2.31e-15

KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240506  Cd Length: 51  Bit Score: 70.99  E-value: 2.31e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 261206062  489 YLPGDTVEVFQGEQQGVVGRTVSTRGDIVSIKVTQGELeGQQIDVPIKGLRK 540
Cdd:cd06082     1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDL-KEPLEFPAKELRK 51
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 331-368 6.89e-15

KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240505  Cd Length: 38  Bit Score: 69.42  E-value: 6.89e-15
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 261206062  331 GGWVRIKRGKYQGDLAQLEDVETNGLDVTVRLVPRLDY 368
Cdd:cd06081     1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 855-1009 1.03e-14

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 71.40  E-value: 1.03e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062    855 ASRTPAWRSSSSRTPAWgsatasGSRTPAWKADGSRTSNPYDGSRTayggttfgggrtPAW-TSGTKTPYDsssgfggss 933
Cdd:smart01104    1 GGRTPAWGASGSKTPAW------GSRTPGTAAGGAPTARGGSGSRT------------PAWgGAGSRTPAW--------- 53

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 261206062    934 tsgFDAFAAGSRTPAYPGGGSRTPAWAPGSAAPPpighSSGSKSSYDAPTPstdYSAPTPGPYGGAPTPGATAATP 1009
Cdd:smart01104   54 ---GGAGPTGSRTPAWGGASAWGNKSSEGSASSW----AAGPGGAYGAPTP---GYGGTPSAYGPATPGGGAMAGS 119
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 668-708 8.60e-12

KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases.


Pssm-ID: 240508  Cd Length: 43  Bit Score: 60.61  E-value: 8.60e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 261206062  668 GDTVREVTGE--QRTGAIIHIHRSFLFLNNKDASDNAGIIVTR 708
Cdd:cd06084     1 GDTVKVVDGPykGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 233-322 5.66e-10

In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, this domain may confer affinity for Spt4p.Spt4p


Pssm-ID: 197850 [Multi-domain]  Cd Length: 106  Bit Score: 57.38  E-value: 5.66e-10
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062    233 SIWAVKCRPGKEREIVFNIMKRIEDR-----------PPDSRRPIRIMSAFERGGTMS-GYIYVEARKQADVLDALNDMS 300
Cdd:smart00738    1 NWYAVRTTSGQEKRVAENLERKAEALgledkivsilvPTEEVKEIRRGKKKVVERKLFpGYIFVEADLEDEVWTAIRGTP 80

                            90       100
                    ....*....|....*....|....*.
gi 261206062    301 NVY----TKSKMILISVKEMPDLLRV 322
Cdd:smart00738   81 GVRgfvgGGGKPTPVPDDEIEKILKP 106
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 943-1070 1.70e-09

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 56.76  E-value: 1.70e-09
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062    943 GSRTPAYPGGGSRTPAWaPGSAAPPPIGHSSGSKSSYDAPTPSTDYS-APTPGPYGGAPTPGATAAtphgWADNAPTPGA 1021
Cdd:smart01104    1 GGRTPAWGASGSKTPAW-GSRTPGTAAGGAPTARGGSGSRTPAWGGAgSRTPAWGGAGPTGSRTPA----WGGASAWGNK 75

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|....*....
gi 261206062   1022 ihAPTPDASGYSAkRTGELYDAPTPAAIGGGRPYDAPTPAMGAGIPATP 1070
Cdd:smart01104   76 --SSEGSASSWAA-GPGGAYGAPTPGYGGTPSAYGPATPGGGAMAGSAS 121
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 835-1087 2.39e-08

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 58.64  E-value: 2.39e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  835 GSSAAPPDWSGSRTPLAANDASRTPAWRSSSSR-TPAWGSATASGSRTPAWKADGSRTSNPYDGSRTAYGGTTFGGGRTP 913
Cdd:PHA03307  187 SSPPAEPPPSTPPAAASPRPPRRSSPISASASSpAPAPGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLP 266

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  914 AWTSGTKTPYDSSSGFGGSSTSGFDAFAAGSRTPAYPGGGSRTPAwapgsaaPPPIGHSSGSKSS-YDAPTPSTDYSAPT 992
Cdd:PHA03307  267 TRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSS-------PRASSSSSSSRESsSSSTSSSSESSRGA 339

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  993 PGPYGGAPTPGATAATPHGWADNAPTPGAIHAPTPDASGYSAKRTGELYDApTPAAIGGGRPYDAPtPAMGAGIPAtPSA 1072
Cdd:PHA03307  340 AVSPGPSPSRSPSPSRPPPPADPSSPRKRPRPSRAPSSPAASAGRPTRRRA-RAAVAGRARRRDAT-GRFPAGRPR-PSP 416

                         250
                  ....*....|....*
gi 261206062 1073 GDDGGPRYEECTPSP 1087
Cdd:PHA03307  417 LDAGAASGAFYARYP 431
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 941-1087 9.82e-08

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 56.15  E-value: 9.82e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  941 AAGSRTPAYPGGGSRTPAWAPGSAAPPPIGhSSGSKSSYDAPTPSTDYSAPTPGPYGGAPTPGATAATPHGWADNAPTPG 1020
Cdd:PRK07764  620 APAAPAAPAPAGAAAAPAEASAAPAPGVAA-PEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAP 698

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 261206062 1021 AIHAPTPDASGYSAKRtgelyDAPTPAAIGGGRPYDAPTPAMGAGIPATPSAGDDGGPRYEECTPSP 1087
Cdd:PRK07764  699 AQPAPAPAATPPAGQA-----DDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPP 760
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 845-923 1.47e-07

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 50.98  E-value: 1.47e-07
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062    845 GSRTPLAANDASRTPAWRSSSSRTPAWGSATASGSRTPAWKADGSRTSNPYDGSRTAYGGTTFGGGRTPA-WTSGTKTPY 923
Cdd:smart01104   27 GGAPTARGGSGSRTPAWGGAGSRTPAWGGAGPTGSRTPAWGGASAWGNKSSEGSASSWAAGPGGAYGAPTpGYGGTPSAY 106
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 939-1087 1.50e-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: 52.61  E-value: 1.50e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062   939 AFAAGSRTPAYPGGGS-RTPAWAPGSA----------APPPIGHSSGSKSSYDAPTPStDYSAPTPGPYGGAPTPGATAA 1007
Cdd:pfam05109  438 GFAAPNTTTGLPSSTHvPTNLTAPASTgptvstadvtSPTPAGTTSGASPVTPSPSPR-DNGTESKAPDMTSPTSAVTTP 516

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  1008 TPHGwadNAPTPgAIHAPTPDASGYSAKRTG--ELYDAPTPAAIgggrpydAPTPAMGAGIP--ATPSAGDDgGPRYEEC 1083
Cdd:pfam05109  517 TPNA---TSPTP-AVTTPTPNATSPTLGKTSptSAVTTPTPNAT-------SPTPAVTTPTPnaTIPTLGKT-SPTSAVT 584


                   ....
gi 261206062  1084 TPSP 1087
Cdd:pfam05109  585 TPTP 588
Chi1 COG3469
Chitinase [Carbohydrate transport and metabolism];
842-1078 3.02e-06

Chitinase [Carbohydrate transport and metabolism];


Pssm-ID: 442692 [Multi-domain]  Cd Length: 534  Bit Score: 51.29  E-value: 3.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  842 DWSGSRTPLAANDASRTPAWRSSSSRTPAWGSATASGSRTPAWKADGSRTSNPYDGSRTAYGGTTFGGGRTPAWTSGTKT 921
Cdd:COG3469     1 SSSVSTAASPTAGGASATAVTLLGAAATAASVTLTAATATTVVSTTGSVVVAASGSAGSGTGTTAASSTAATSSTTSTTA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  922 PYdsssgfggsstsgfdafaaGSRTPAYPGGGSRTPAWAPGSAAPPPIGHSSGSKSSYDAPTPSTDYSAPTPGpyggapT 1001
Cdd:COG3469    81 TA-------------------TAAAAAATSTSATLVATSTASGANTGTSTVTTTSTGAGSVTSTTSSTAGSTT------T 135

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 261206062 1002 PGATAATPHGWADNAPTPGAIHAPTPDASGYSAKRTGELYDAPTPAAIGGGRPYDAPTPAMGAGIPATPSAGDDGGP 1078
Cdd:COG3469   136 SGASATSSAGSTTTTTTVSGTETATGGTTTTSTTTTTTSASTTPSATTTATATTASGATTPSATTTATTTGPPTPGL 212
PHA03247 PHA03247
large tegument protein UL36; Provisional
 833-1071 3.02e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 51.86  E-value: 3.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  833 PYGSSAAPPDWSGSRTPLAANDASRTPawRSSSSRTPAWGSATASGSRTPAWKAD-GSRTS--NPYDGSRTAyggttfgG 909
Cdd:PHA03247 2639 DPHPPPTVPPPERPRDDPAPGRVSRPR--RARRLGRAAQASSPPQRPRRRAARPTvGSLTSlaDPPPPPPTP-------E 2709

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  910 GRTPAWTSGTKTPYDSSSGFGGSSTSGFD----AFAAGSRTPAYP----------GGGSRTPAWAPGSAAP-----PPIG 970
Cdd:PHA03247 2710 PAPHALVSATPLPPGPAAARQASPALPAApappAVPAGPATPGGParparppttaGPPAPAPPAAPAAGPPrrltrPAVA 2789

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  971 HSSGSKSSYDAPTPSTDYSAPTPGPYGGAPTPGATAATphgwadNAPTPGAIHAPTPDASGYSAKrtgelYDAPTPAAIG 1050
Cdd:PHA03247 2790 SLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGP------LPPPTSAQPTAPPPPPGPPPP-----SLPLGGSVAP 2858

                         250       260
                  ....*....|....*....|.
gi 261206062 1051 GGRPYDAPTPAMGAGIPATPS 1071
Cdd:PHA03247 2859 GGDVRRRPPSRSPAAKPAAPA 2879
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
950-1087 9.78e-06

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 49.87  E-value: 9.78e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  950 PGGGSRTPAWAPGSAAPPPIGHSSGSKSSYDAPTPSTDYSAPTPGPYGGAPTPG----------ATAATPHGWADNAPTP 1019
Cdd:PRK12323  365 PGQSGGGAGPATAAAAPVAQPAPAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAvaaaparrspAPEALAAARQASARGP 444

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 261206062 1020 GAIHAPTPDASGYSAKRtgelydAPTPAAIGGGRPYDAPTPAMGAGIPATPSAGDDGGPRYEECTPSP 1087
Cdd:PRK12323  445 GGAPAPAPAPAAAPAAA------ARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPPPWEELPPEF 506
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 964-1079 2.67e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 48.44  E-value: 2.67e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  964 AAPPPIGHSSGSKSSYDAPTPSTDYSAPTPGPYGGAPTPGATAATPHGWADNAPTPGAIHAPTPDASGYSAKRTGELYDA 1043
Cdd:PRK07764  588 VGPAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGD 667

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 261206062 1044 PTPAAIGGGRPY-DAPTPAMGAGIPATPSAGDDGGPR 1079
Cdd:PRK07764  668 GWPAKAGGAAPAaPPPAPAPAAPAAPAGAAPAQPAPA 704
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 940-1079 2.88e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 48.44  E-value: 2.88e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  940 FAAGSRTPAYPGGGSRTPAWAPGSAAPPPIGHSSGSKSSYDAPTPstdysaptpgpyggAPTPGATAATPHGWADNAPTP 1019
Cdd:PRK07764  387 VAGGAGAPAAAAPSAAAAAPAAAPAPAAAAPAAAAAPAPAAAPQP--------------APAPAPAPAPPSPAGNAPAGG 452

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 261206062 1020 GAIHAPTPDASGYSAKRTGelyDAPTPAAIGGGRPYDAPTPAMGAGIPATPSAG----DDGGPR 1079
Cdd:PRK07764  453 APSPPPAAAPSAQPAPAPA---AAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPagadDAATLR 513
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 869-1087 3.11e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 48.06  E-value: 3.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  869 PAWGSATASGSRTPAWKADGSRTSNPYDGSRTAYGGTTFGGG--RTPAWTSGTKTPYDSSSGFGGSSTSGFDAFAAGSRT 946
Cdd:PRK07764  590 PAPGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGaaAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGW 669

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  947 PAYPGGGSRT-PAWAPGSAAPPPIghSSGSKSSYDAPTPSTDYSAPTPGPYGGAPTPGATAATPHGWADNAPTPgaihAP 1025
Cdd:PRK07764  670 PAKAGGAAPAaPPPAPAPAAPAAP--AGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPL----PP 743

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 261206062 1026 TPDasgysakrtgelYDAPTPAAIGGGRPYDAPTPAMGAGIPATPSAGDDGGPRYEECTPSP 1087
Cdd:PRK07764  744 EPD------------DPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPSM 793
PRK04654 PRK04654
sec-independent translocase; Provisional
 954-1078 3.60e-05

sec-independent translocase; Provisional


Pssm-ID: 135173 [Multi-domain]  Cd Length: 214  Bit Score: 46.34  E-value: 3.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  954 SRTPAwapgsAAPPPIGHSSGSKSSY-DAPTPSTDYSAPTPGPyGGAPTPGATAATPHgwadnAPTPGAIHAPTPDASGY 1032
Cdd:PRK04654  104 SATPV-----ATPLELAHADLSASAQvDAAAGAEPGAGQAHTP-VPAPAPVIAQAQPI-----APAPHQTLVPAPHDTIV 172

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 261206062 1033 SAKRTGELYDAPTPAAIGGgrPYDAPTPAmgAGIPATPSAGDDGGP 1078
Cdd:PRK04654  173 PAPHAAHLPSAPATPVSVA--PVDAGTSA--SPTPSEPTKIQEKQP 214
DUF5585 pfam17823
Family of unknown function (DUF5585); This is a family of unknown function found in chordata.
 833-1087 8.14e-05

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: 46.49  E-value: 8.14e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062   833 PYGSSAAPPDWSGSRtplAANDASRTPAWRSSSSRTPAWGSATASGSRTPAWKADGSRTSNPYDGSRTAYGGTTFGGGRT 912
Cdd:pfam17823   92 PHGTDLSEPATREGA---ADGAASRALAAAASSSPSSAAQSLPAAIAALPSEAFSAPRAAACRANASAAPRAAIAAASAP 168

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062   913 PAWTSGTKTPYDSSSGFGGSSTSGFDAFAAGSRTPAypgggSRTPAwAPGSAAPPPIGHSSGSKSSYDAPTPSTdySAPT 992
Cdd:pfam17823  169 HAASPAPRTAASSTTAASSTTAASSAPTTAASSAPA-----TLTPA-RGISTAATATGHPAAGTALAAVGNSSP--AAGT 240

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062   993 PGPYGGAPTPGATAATPHGWADNAPTPGAIHAPTPDASGYS-AKRTGELYDAPTPAAIGGGRPyDAPTPAMGAGIPATPS 1071
Cdd:pfam17823  241 VTAAVGTVTPAALATLAAAAGTVASAAGTINMGDPHARRLSpAKHMPSDTMARNPAAPMGAQA-QGPIIQVSTDQPVHNT 319

                          250
                   ....*....|....*.
gi 261206062  1072 AGddggpryeECTPSP 1087
Cdd:pfam17823  320 AG--------EPTPSP 327
Chi1 COG3469
Chitinase [Carbohydrate transport and metabolism];
832-1028 1.33e-04

Chitinase [Carbohydrate transport and metabolism];


Pssm-ID: 442692 [Multi-domain]  Cd Length: 534  Bit Score: 45.90  E-value: 1.33e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  832 IPYGSSAAPPDWSGSRTPLAaNDASRTPAWRSSSSRTPAWGSATASGSRTPAWKADGSRTSNPYDGSRTAYGGTTFGGGR 911
Cdd:COG3469    20 VTLLGAAATAASVTLTAATA-TTVVSTTGSVVVAASGSAGSGTGTTAASSTAATSSTTSTTATATAAAAAATSTSATLVA 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  912 TPAWTSGTKTPYDSSSGFGGSSTSGFD--AFAAGSRTPAYPGGGSRTPAWAPGSAAPPPIGHSSGSKSSYDAPTPSTDYS 989
Cdd:COG3469    99 TSTASGANTGTSTVTTTSTGAGSVTSTtsSTAGSTTTSGASATSSAGSTTTTTTVSGTETATGGTTTTSTTTTTTSASTT 178

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 261206062  990 APTPGPYGGAPTPGATAATPhgwADNAPTPGAIHAPTPD 1028
Cdd:COG3469   179 PSATTTATATTASGATTPSA---TTTATTTGPPTPGLPK 214
PHA03378 PHA03378
EBNA-3B; Provisional
 954-1087 2.14e-04

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 45.44  E-value: 2.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  954 SRTPAWAPGSAAPPPighssgskssyDAPTPSTDYSAPtPGPY---GGAPTPG-ATAATPHGWADNAPTPGaiHAPTPDA 1029
Cdd:PHA03378  684 MLPIQWAPGTMQPPP-----------RAPTPMRPPAAP-PGRAqrpAAATGRArPPAAAPGRARPPAAAPG--RARPPAA 749

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 261206062 1030 SGYSAKRTGELYDAPTPAAIGGGRPYDAPTPAmgagIPATPSAGDDGGPryeecTPSP 1087
Cdd:PHA03378  750 APGRARPPAAAPGRARPPAAAPGAPTPQPPPQ----APPAPQQRPRGAP-----TPQP 798
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 939-1087 4.77e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 44.32  E-value: 4.77e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  939 AFAAGSRTPAYPGGGSRTPAwAPGSAAPPPIGHSSGSKSSYDAPTPSTDYSAPTPGPygGAPTPGATAATPHGWADNAPT 1018
Cdd:PRK14951  363 AFKPAAAAEAAAPAEKKTPA-RPEAAAPAAAPVAQAAAAPAPAAAPAAAASAPAAPP--AAAPPAPVAAPAAAAPAAAPA 439

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 261206062 1019 PGAIHAPTPDASgysakrtgELYDAPTPAAIgggrpydaptPAMGAGIPATPSAGDD--GGPRYEECTPSP 1087
Cdd:PRK14951  440 AAPAAVALAPAP--------PAQAAPETVAI----------PVRVAPEPAVASAAPApaAAPAAARLTPTE 492
PHA03247 PHA03247
large tegument protein UL36; Provisional
 839-1087 5.44e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 44.54  E-value: 5.44e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  839 APPDWSGSRTPLAANDASRTPAWRSSSS------RTPAWG---SATASGSRTPAWKADGSRTSNPYDGSRTAYGGTTFGG 909
Cdd:PHA03247 2591 APPQSARPRAPVDDRGDPRGPAPPSPLPpdthapDPPPPSpspAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRL 2670

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  910 GRTPAWTSGTKTPydsssgFGGSSTSGFDAFAAGSRTPAYPgggsRTPAWAP---GSAAPPPIGHSSGSKSSYDAPTPST 986
Cdd:PHA03247 2671 GRAAQASSPPQRP------RRRAARPTVGSLTSLADPPPPP----PTPEPAPhalVSATPLPPGPAAARQASPALPAAPA 2740

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  987 DYSAPTPGPYGGAPTPGATAATPHGWAdnAPTPGAIHAPTPDASgySAKRTGELYDAPTPAAIGGGRPYDAPTPAMGAGi 1066
Cdd:PHA03247 2741 PPAVPAGPATPGGPARPARPPTTAGPP--APAPPAAPAAGPPRR--LTRPAVASLSESRESLPSPWDPADPPAAVLAPA- 2815

                         250       260
                  ....*....|....*....|.
gi 261206062 1067 PATPSAGDDGGPRYEECTPSP 1087
Cdd:PHA03247 2816 AALPPAASPAGPLPPPTSAQP 2836
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 759-790 9.02e-04

KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and NusG.


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 37.75  E-value: 9.02e-04
                           10        20        30
                   ....*....|....*....|....*....|..
gi 261206062   759 IGKTVTIRKGPFKGLLGIVKDTTDAQARVELH 790
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
PHA03264 PHA03264
envelope glycoprotein D; Provisional
 957-1068 9.23e-04

envelope glycoprotein D; Provisional


Pssm-ID: 223029 [Multi-domain]  Cd Length: 416  Bit Score: 43.07  E-value: 9.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  957 PAWAPGSAAPPPighssgskssYDAPTPSTDYSAPTPGPYG---GAPTPGATAATPHGWADNAPTPGAiHAPTPDA---S 1030
Cdd:PHA03264  268 PAPSGGSPAPPG----------DDRPEAKPEPGPVEDGAPGretGGEGEGPEPAGRDGAAGGEPKPGP-PRPAPDAdrpE 336

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 261206062 1031 GYSAKRtGELYDAPTPAAIGggrPYDAPTPAMGAGIPA 1068
Cdd:PHA03264  337 GWPSLE-AITFPPPTPATPA---VPRARPVIVGTGIAA 370
PHA03291 PHA03291
envelope glycoprotein I; Provisional
 960-1081 1.13e-03

envelope glycoprotein I; Provisional


Pssm-ID: 223033 [Multi-domain]  Cd Length: 401  Bit Score: 42.63  E-value: 1.13e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  960 APGSAAPPPIGHSSGSKS-----SYDAP--TPSTDYSAPTPGPYGGAPTPGATAATPHGWADnaPTPGAIHAPTPDASGY 1032
Cdd:PHA03291  168 AEGTLAAPPLGEGSADGScdpalPLSAPrlGPADVFVPATPRPTPRTTASPETTPTPSTTTS--PPSTTIPAPSTTIAAP 245

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 261206062 1033 SAKRTGELYDAPTPAAIGGGRPYDAptpamgagiPATPSAGDDggpRYE 1081
Cdd:PHA03291  246 QAGTTPEAEGTPAPPTPGGGEAPPA---------NATPAPEAS---RYE 282
PRK14959 PRK14959
DNA polymerase III subunits gamma and tau; Provisional
 950-1079 1.17e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184923 [Multi-domain]  Cd Length: 624  Bit Score: 42.74  E-value: 1.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  950 PGGGSRTPAwaPGSAAPPPIGHSSGSkssydaptpstdysAPTPGPYGGAPTPGATAATPHGWADNAPTPGAIHA----- 1024
Cdd:PRK14959  373 PSGGGASAP--SGSAAEGPASGGAAT--------------IPTPGTQGPQGTAPAAGMTPSSAAPATPAPSAAPSprvpw 436

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 261206062 1025 ----PTPDASG---YSAKRTGELYDAP-TPAAIGGGRpyDAPtPAMGAgiPATPSAGDDGGPR 1079
Cdd:PRK14959  437 ddapPAPPRSGippRPAPRMPEASPVPgAPDSVASAS--DAP-PTLGD--PSDTAEHTPSGPR 494
PRK14959 PRK14959
DNA polymerase III subunits gamma and tau; Provisional
 941-1056 1.17e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184923 [Multi-domain]  Cd Length: 624  Bit Score: 42.74  E-value: 1.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  941 AAGSRTPAyPGGGSRTPAWAPGSAAPPPIGHSSGSKSSYDAPTPSTDYSAPTPG-PYGGA-PTPGATAATPHGWADNAPT 1018
Cdd:PRK14959  381 PSGSAAEG-PASGGAATIPTPGTQGPQGTAPAAGMTPSSAAPATPAPSAAPSPRvPWDDApPAPPRSGIPPRPAPRMPEA 459

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 261206062 1019 PGAIHAPTPDASGYSAKRTGELYDAPTPAAIGGGRPYD 1056
Cdd:PRK14959  460 SPVPGAPDSVASASDAPPTLGDPSDTAEHTPSGPRTWD 497
PHA03291 PHA03291
envelope glycoprotein I; Provisional
 939-1030 1.39e-03

envelope glycoprotein I; Provisional


Pssm-ID: 223033 [Multi-domain]  Cd Length: 401  Bit Score: 42.25  E-value: 1.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  939 AFAAGSRTPAYPGGGSRTPAWAPG--------SAAPPPIGHSSGSKSSYDAP-TPSTDYSAPTPGPYGGAPTPGATAATP 1009
Cdd:PHA03291  173 AAPPLGEGSADGSCDPALPLSAPRlgpadvfvPATPRPTPRTTASPETTPTPsTTTSPPSTTIPAPSTTIAAPQAGTTPE 252

                          90       100
                  ....*....|....*....|.
gi 261206062 1010 HGWADNAPTPGAIHAPTPDAS 1030
Cdd:PHA03291  253 AEGTPAPPTPGGGEAPPANAT 273
PHA03247 PHA03247
large tegument protein UL36; Provisional
 941-1063 1.52e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 43.00  E-value: 1.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  941 AAGSRTPAYPGGGSRTPAWAPGSAAPPPIGHSSGSKSSYDAPTPStdySAPTPGPYGGA----PTPGATAATPHGWADNA 1016
Cdd:PHA03247  369 SAGRHHPKRASLPTRKRRSARHAATPFARGPGGDDQTRPAAPVPA---SVPTPAPTPVPasapPPPATPLPSAEPGSDDG 445

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 261206062 1017 PTPGAIHAPTPDASGYSAKRTgelyDAPTPAAIGGGRPYDAPTPAMG 1063
Cdd:PHA03247  446 PAPPPERQPPAPATEPAPDDP----DDATRKALDALRERRPPEPPGA 488
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 938-1072 1.54e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 42.67  E-value: 1.54e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  938 DAFAAGSRTPAYPGGGSRTPAWAPGSAAPPPigHSSGSKSSYDAPTPSTDYSAPTPGPYGGAPTPGATAATPHGWADNAP 1017
Cdd:PRK07764  585 EAVVGPAPGAAGGEGPPAPASSGPPEEAARP--AAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDA 662

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 261206062 1018 TPGAIHAPTPDASGYSAKRTGELYDAPTPAAIGGGRPYDAPTPAMGAGIPATPSA 1072
Cdd:PRK07764  663 SDGGDGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDP 717
KOW_NusG cd06091
NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif ...
 542-584 1.58e-03

NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif is one of the two domains of N-Utilization Substance G (NusG) a transcription elongation and Rho-termination factor in bacteria and archaea. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The eukaryotic ortholog of NusG is Spt5 with multiple KOW motifs at its C-terminus.


Pssm-ID: 240515 [Multi-domain]  Cd Length: 56  Bit Score: 37.82  E-value: 1.58e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 261206062  542 FQEGDHVKVIGGSrFRDELGMVVRIKDD--RVTLLSDMSMQEITV 584
Cdd:cd06091     4 FEVGDTVRIISGP-FAGFEGKVEEIDEEkgKVKVLVEMFGRETPV 47
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 839-1059 1.75e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 42.28  E-value: 1.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  839 APPDWSGSRTPLAANDASRTPAWRSSSSRTPAWGSATASGSRTPAWKADGSRTSNPYDGSRTAYGGTTFGGGRTPAWTSG 918
Cdd:PRK07764  591 APGAAGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWP 670

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  919 TKTPydsssgfggSSTSGFDAFAAGSRTPAYPGGGSRTPAWAPGSAAPPPighSSGSKSSYDAPTPSTDYSAPTPGPYGG 998
Cdd:PRK07764  671 AKAG---------GAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPA---GQADDPAAQPPQAAQGASAPSPAADDP 738

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 261206062  999 AP---TPGATAATPHGWADNAPTPGAIHAPTPDASGYSAKRTGELYDAPTPAAIGGGRPYDAPT 1059
Cdd:PRK07764  739 VPlppEPDDPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSPPSEEEEMAEDDAPSMDDEDRRDAE 802
PHA03378 PHA03378
EBNA-3B; Provisional
 836-1027 1.86e-03

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 42.36  E-value: 1.86e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  836 SSAAPPDWSGSRTPLAANDASRTPA-WRSSSSRTPAWGSATASGSRTPAWKADGSRTSNPYDGSRTAyggttfggGRTPA 914
Cdd:PHA03378  617 ETSAPRQWPMPLRPIPMRPLRMQPItFNVLVFPTPHQPPQVEITPYKPTWTQIGHIPYQPSPTGANT--------MLPIQ 688

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  915 WTSGTKTPydsssgfggsstsgFDAFAAGSRTPAYPGGGSRTPAWAPGSAaPPPIGHSSGSKSSYDAPTPSTDYSApTPG 994
Cdd:PHA03378  689 WAPGTMQP--------------PPRAPTPMRPPAAPPGRAQRPAAATGRA-RPPAAAPGRARPPAAAPGRARPPAA-APG 752

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 261206062  995 ---PYGGAP--------TPGATAATPHGWADNAPTPGAIHAPTP 1027
Cdd:PHA03378  753 rarPPAAAPgrarppaaAPGAPTPQPPPQAPPAPQQRPRGAPTP 796
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
941-1087 2.04e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 42.17  E-value: 2.04e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  941 AAGSRTPAYPGGGSRTPAWAPGSAAPPPIGHSSGSKSSYDAPTP-STDYSAPTPGPYGGAPTPGATAATPHGWADNAPTP 1019
Cdd:PRK12323  403 PAAPAAAPAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGaPAPAPAPAAAPAAAARPAAAGPRPVAAAAAAAPAR 482

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062 1020 GAiHAPTPDASGYSAKRTGELydAPTPAAIGGGRPYDAPTPAMGAGI--PATPSAGDDGGPRYEECTPSP 1087
Cdd:PRK12323  483 AA-PAAAPAPADDDPPPWEEL--PPEFASPAPAQPDAAPAGWVAESIpdPATADPDDAFETLAPAPAAAP 549
PHA03247 PHA03247
large tegument protein UL36; Provisional
 949-1072 2.17e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 42.23  E-value: 2.17e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  949 YPGGGS--RTPAWAPGSAAPppiGHSSGSKSSYDAPTPSTDYSAptpGPYGGAPTpGATAATPHGWADNAPTPGAIHAPT 1026
Cdd:PHA03247  347 YPLGFPkrRRPTWTPPSSLE---DLSAGRHHPKRASLPTRKRRS---ARHAATPF-ARGPGGDDQTRPAAPVPASVPTPA 419

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 261206062 1027 PDASGYSAKRTGelyDAPTPAAIGGGRPYDAPTPAMGAGIPATPSA 1072
Cdd:PHA03247  420 PTPVPASAPPPP---ATPLPSAEPGSDDGPAPPPERQPPAPATEPA 462
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 944-1037 2.19e-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: 42.21  E-value: 2.19e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062   944 SRTPAYPGGGSRTPAW-APGSAAPPPIGHSSGSKSSYDAPTP----------STDYSAPTPGPYGGAPTPGATAATPHG- 1011
Cdd:pfam05109  491 SPSPRDNGTESKAPDMtSPTSAVTTPTPNATSPTPAVTTPTPnatsptlgktSPTSAVTTPTPNATSPTPAVTTPTPNAt 570

                           90       100
                   ....*....|....*....|....*....
gi 261206062  1012 ---WADNAPTpGAIHAPTPDASGYSAKRT 1037
Cdd:pfam05109  571 iptLGKTSPT-SAVTTPTPNATSPTVGET 598
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 544-576 2.41e-03

KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and NusG.


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 36.60  E-value: 2.41e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 261206062   544 EGDHVKVIGGsRFRDELGMVVRIKDDRVTLLSD 576
Cdd:pfam00467    1 KGDVVRVIAG-PFKGKVGKVVEVDDKKNRVLVE 32
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 834-873 2.91e-03

Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteriztic TPA motif.


Pssm-ID: 372327 [Multi-domain]  Cd Length: 71  Bit Score: 37.42  E-value: 2.91e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 261206062   834 YGSSAAPPDW-SGSRTPLAANDASRTPAWRSSS--SRTPAWGS 873
Cdd:pfam12815   29 GGAGGRTPAYnQGGKTPAWGGAGSRTPAYYGAWggSRTPAYGG 71
NGN_Arch cd09887
Archaeal N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance ...
 233-302 3.48e-03

Archaeal N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance G (NusG) protein and its eukaryotic homolog, Spt5, are involved in transcription elongation and termination. Transcription in archaea has a eukaryotic-type transcription apparatus, but contains bacterial-type transcription factors. NusG is one of the few archaeal transcription factors that has orthologs in both bacteria and eukaryotes. Archaeal NusG is similar to bacterial NusG, composed of an NGN domain and a Kyrpides Ouzounis and Woese (KOW) repeat. The eukaryotic ortholog, Spt5, is a large protein composed of an acidic N-terminus, an NGN domain, and multiple KOW motifs at its C-terminus. NusG was originally discovered as a N-dependent antitermination enhancing activity in Escherichia coli and has a variety of functions, such as being involved in RNA polymerase elongation and Rho-termination in bacteria. Archaeal NusG forms a complex with DNA-directed RNA polymerase subunit E (rpoE) that is similar to the Spt5-Spt4 complex in eukaryotes.


Pssm-ID: 193576  Cd Length: 82  Bit Score: 37.52  E-value: 3.48e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 261206062  233 SIWAVKCRPGKEREIVFNIMKRIEdrppDSRRPIR-IMSAFErggtMSGYIYVEARKQADVLDALNDMSNV 302
Cdd:cd09887     1 RIYAVKTTAGQERNVADLLAMRAE----KENLDVYsILVPEE----LKGYVFVEAEDPDRVEELIRGIPHV 63
PTZ00436 PTZ00436
60S ribosomal protein L19-like protein; Provisional
 942-1085 3.97e-03

60S ribosomal protein L19-like protein; Provisional


Pssm-ID: 185616 [Multi-domain]  Cd Length: 357  Bit Score: 40.70  E-value: 3.97e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  942 AGSRTPAYPGGGSRTPAWAPGSAAPPPIGHSSGSKSSYDAPTPSTDYSAPTPGPYGGAPTPGATAATPHGWADNAPTPGA 1021
Cdd:PTZ00436  203 AAAKKAAAPSGKKSAKAAAPAKAAAAPAKAAAPPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAA 282

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 261206062 1022 IhAPTPDASGYSAKRTGELYDAPTPAAIGGGRPYDAPTPAMGAGIP---ATPSAGDDGGPRYEECTP 1085
Cdd:PTZ00436  283 A-PPAKAAAPPAKAAAAPAKAAAAPAKAAAAPAKAAAPPAKAAAPPakaATPPAKAAAPPAKAAAAP 348
PTZ00436 PTZ00436
60S ribosomal protein L19-like protein; Provisional
 941-1076 4.04e-03

60S ribosomal protein L19-like protein; Provisional


Pssm-ID: 185616 [Multi-domain]  Cd Length: 357  Bit Score: 40.70  E-value: 4.04e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  941 AAGSRTPAYPGGGSRTPAWAPGSAAPPPIGHSSGSKSSYDAPTPSTDYSAPTPGPYGGAPTPGATAATPHGWADNAPTPG 1020
Cdd:PTZ00436  216 SAKAAAPAKAAAAPAKAAAPPAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKAAAPPAKA 295

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 261206062 1021 AIhAPTPDASGYSAKRTGELYDAPTPAAIGGGRPYDAPTPAMGAGIPATPSAGDDG 1076
Cdd:PTZ00436  296 AA-APAKAAAAPAKAAAAPAKAAAPPAKAAAPPAKAATPPAKAAAPPAKAAAAPVG 350
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 541-569 6.84e-03

KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.


Pssm-ID: 128978  Cd Length: 28  Bit Score: 35.00  E-value: 6.84e-03
                            10        20
                    ....*....|....*....|....*....
gi 261206062    541 RFQEGDHVKVIGGsRFRDELGMVVRIKDD 569
Cdd:smart00739    1 KFEVGDTVRVIAG-PFKGKVGKVLEVDGE 28
nusG PRK08559
transcription antitermination protein NusG; Validated
 230-363 7.54e-03

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 38.31  E-value: 7.54e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  230 DDPSIWAVKCRPGKEREIVFNIMKRIEDrppdSRRPIRIMSAFERggtMSGYIYVEARKQADVLDALNDMSNVytKSKMI 309
Cdd:PRK08559    4 EMSMIFAVKTTAGQERNVALMLAMRAKK----ENLPIYAILAPPE---LKGYVLVEAESKGAVEEAIRGIPHV--RGVVP 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 261206062  310 -LISVKEMPDLLRVTKS-EQLIPGGWVRIKRGKYQGDLAQLEDVETNGLDVTVRLV 363
Cdd:PRK08559   75 gEISFEEVEHFLKPKPIvEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELL 130
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
947-1072 7.64e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 40.22  E-value: 7.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  947 PAyPGGGSRTPAWAPGS---AAPPPIGHSSGSKSSYDAPTpstdySAPTPGPYGGAPTPGATAAtphgwADNAPTPGAIH 1023
Cdd:PRK07003  360 PA-VTGGGAPGGGVPARvagAVPAPGARAAAAVGASAVPA-----VTAVTGAAGAALAPKAAAA-----AAATRAEAPPA 428

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 261206062 1024 APTPDASGYSAKRTgelydAPTPAAIGGGRPYDAPTPAMGAGIPATPSA 1072
Cdd:PRK07003  429 APAPPATADRGDDA-----ADGDAPVPAKANARASADSRCDERDAQPPA 472
PHA03247 PHA03247
large tegument protein UL36; Provisional
 947-1070 8.49e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 40.31  E-value: 8.49e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 261206062  947 PAYPGGGSRT--PAWAPGSAAPPPIGHSSGSKSSYDAPTPST-DYSAPTPGPYGGAP------TPGATAATPHGWADNAP 1017
Cdd:PHA03247 2577 PSEPAVTSRArrPDAPPQSARPRAPVDDRGDPRGPAPPSPLPpDTHAPDPPPPSPSPaanepdPHPPPTVPPPERPRDDP 2656

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 261206062 1018 TPGAIHAPTPDASGYSAKRTGELYDAPTPAAI--------GGGRPYD---APTPAMGAGIPATP 1070
Cdd:PHA03247 2657 APGRVSRPRRARRLGRAAQASSPPQRPRRRAArptvgsltSLADPPPpppTPEPAPHALVSATP 2720
 
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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