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Conserved domains on  [gi|1066729447|emb|CEK82252|]
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hypothetical protein [Arion vulgaris]

Protein Classification

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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 ...
 193-280 5.52e-40

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: 142.28  E-value: 5.52e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  193 NLWVVKCRMGEEKATVVHVMRKMITYQFTEEPLQIKSIVAKEGLKGYIYIEAFKQTHVKQAIEGIGNLRMGfyKQQMVPI 272
Cdd:cd09888      1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYLN--TIKLVPI 78


                   ....*...
gi 1066729447  273 REMTDVLK 280
Cdd:cd09888     79 KEMPDVLS 86
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 486-536 1.28e-26

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: 102.99  E-value: 1.28e-26
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1066729447  486 HFKMGDHVKVIAGRYEGDTGLIVRVEDNLIVLFSDLTMHELKVLPKDIQIC 536
Cdd:cd06083      1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 712-763 1.37e-26

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: 102.95  E-value: 1.37e-26
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1066729447  712 RDREIIGQTVRIVKGPFKGYIGIVKDATETTARIELHSSCKTISVDRSHLNN 763
Cdd:cd06085      1 GRDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLAV 52
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 436-485 4.72e-21

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: 87.17  E-value: 4.72e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1066729447  436 APGDVVVVAEGELQHLQGKVIRVDGNKITIMPKHEDLKDPLEFPYTELRK 485
Cdd:cd06082      2 QPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 1012-1074 2.42e-19

KOW domain of Spt5, repeat 6; 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: 240510  Cd Length: 58  Bit Score: 82.56  E-value: 2.42e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1066729447 1012 EHLEPVLPEKGDKAKVIIGDKRESTGTLISEDGDDGVFKLDtidieTKTDILMLPKHYLCKLV 1074
Cdd:cd06086      1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMD-----SDGDIKILPMNFLAKLV 58
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 612-654 6.93e-18

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: 77.95  E-value: 6.93e-18
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1066729447  612 RDIVNVIEGPHSGRTGEIKHLYRNFAFLNSRLMTDNGGYFVCR 654
Cdd:cd06084      1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 778-945 8.03e-18

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: 80.26  E-value: 8.03e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447   778 GARTPNY---GGQTPMYGSRTPMYlgsqTPLHDESRTPHYGGMTPSHE-SGGRTPSGGGssvWDPSNANTPSRNNDfefs 853
Cdd:smart01104    1 GGRTPAWgasGSKTPAWGSRTPGT----AAGGAPTARGGSGSRTPAWGgAGSRTPAWGG---AGPTGSRTPAWGGA---- 69

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447   854 YDDSPSPADFGTTPNPATPGyhadspapmGPYTPQTPGsvyspypaaspggfdaqspgYVGTpnpalmsspsPASFAGsP 933
Cdd:smart01104   70 SAWGNKSSEGSASSWAAGPG---------GAYGAPTPG--------------------YGGT----------PSAYGP-A 109

                           170
                    ....*....|..
gi 1066729447   934 SPMGYSPMTPAA 945
Cdd:smart01104  110 TPGGGAMAGSAS 121
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 291-328 6.68e-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: 6.68e-15
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1066729447  291 KAWVRLKRGVFKDDLAQVDIVYPSQNEVELKLIPRIDY 328
Cdd:cd06081      1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
 
Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
 193-280 5.52e-40

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: 142.28  E-value: 5.52e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  193 NLWVVKCRMGEEKATVVHVMRKMITYQFTEEPLQIKSIVAKEGLKGYIYIEAFKQTHVKQAIEGIGNLRMGfyKQQMVPI 272
Cdd:cd09888      1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYLN--TIKLVPI 78


                   ....*...
gi 1066729447  273 REMTDVLK 280
Cdd:cd09888     79 KEMPDVLS 86
Spt5-NGN pfam03439
Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG ...
 193-279 4.26e-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: 4.26e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  193 NLWVVKCRMGEEKATVVHVMRKMITYQFTEEpLQIKSIVAKEGLKGYIYIEAFKQTHVKQAIEGIGNLRMGfyKQQMVPI 272
Cdd:pfam03439    1 KIWAVKCTPGQEREVALSLMRKILALAKTNN-LGIYSVFAPDGLKGYIYVEADRQAAVKRALEGIPNVRGL--VPGLVPI 77


                   ....*..
gi 1066729447  273 REMTDVL 279
Cdd:pfam03439   78 KEMEHLL 84
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 486-536 1.28e-26

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: 102.99  E-value: 1.28e-26
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1066729447  486 HFKMGDHVKVIAGRYEGDTGLIVRVEDNLIVLFSDLTMHELKVLPKDIQIC 536
Cdd:cd06083      1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 712-763 1.37e-26

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: 102.95  E-value: 1.37e-26
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1066729447  712 RDREIIGQTVRIVKGPFKGYIGIVKDATETTARIELHSSCKTISVDRSHLNN 763
Cdd:cd06085      1 GRDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLAV 52
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 436-485 4.72e-21

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: 87.17  E-value: 4.72e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1066729447  436 APGDVVVVAEGELQHLQGKVIRVDGNKITIMPKHEDLKDPLEFPYTELRK 485
Cdd:cd06082      2 QPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 1012-1074 2.42e-19

KOW domain of Spt5, repeat 6; 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: 240510  Cd Length: 58  Bit Score: 82.56  E-value: 2.42e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1066729447 1012 EHLEPVLPEKGDKAKVIIGDKRESTGTLISEDGDDGVFKLDtidieTKTDILMLPKHYLCKLV 1074
Cdd:cd06086      1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMD-----SDGDIKILPMNFLAKLV 58
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 612-654 6.93e-18

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: 77.95  E-value: 6.93e-18
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1066729447  612 RDIVNVIEGPHSGRTGEIKHLYRNFAFLNSRLMTDNGGYFVCR 654
Cdd:cd06084      1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 778-945 8.03e-18

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: 80.26  E-value: 8.03e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447   778 GARTPNY---GGQTPMYGSRTPMYlgsqTPLHDESRTPHYGGMTPSHE-SGGRTPSGGGssvWDPSNANTPSRNNDfefs 853
Cdd:smart01104    1 GGRTPAWgasGSKTPAWGSRTPGT----AAGGAPTARGGSGSRTPAWGgAGSRTPAWGG---AGPTGSRTPAWGGA---- 69

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447   854 YDDSPSPADFGTTPNPATPGyhadspapmGPYTPQTPGsvyspypaaspggfdaqspgYVGTpnpalmsspsPASFAGsP 933
Cdd:smart01104   70 SAWGNKSSEGSASSWAAGPG---------GAYGAPTPG--------------------YGGT----------PSAYGP-A 109

                           170
                    ....*....|..
gi 1066729447   934 SPMGYSPMTPAA 945
Cdd:smart01104  110 TPGGGAMAGSAS 121
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 291-328 6.68e-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: 6.68e-15
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1066729447  291 KAWVRLKRGVFKDDLAQVDIVYPSQNEVELKLIPRIDY 328
Cdd:cd06081      1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 193-281 8.88e-12

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: 62.78  E-value: 8.88e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447   193 NLWVVKCRMGEEKATVVHVMRKMITYQFTEEPLQI--------------KSIVAKEGLKGYIYIEAFKQTHVKQAIEGIG 258
Cdd:smart00738    1 NWYAVRTTSGQEKRVAENLERKAEALGLEDKIVSIlvpteevkeirrgkKKVVERKLFPGYIFVEADLEDEVWTAIRGTP 80

                            90       100
                    ....*....|....*....|....*..
gi 1066729447   259 NLRmGF----YKQQMVPIREMTDVLKV 281
Cdd:smart00738   81 GVR-GFvgggGKPTPVPDDEIEKILKP 106
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 785-861 6.52e-11

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: 59.00  E-value: 6.52e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  785 GGQTPMY----GSRTPMY--LGSQTPLHDE--SRTPHYGgmtpsheSGGRTPSgggssvWDPSNANTPsRNNDfefSYDD 856
Cdd:pfam12815    1 GSRTPAYnsagGSRTPAWgaDGSRTPAYGGagGRTPAYN-------QGGKTPA------WGGAGSRTP-AYYG---AWGG 63


                   ....*
gi 1066729447  857 SPSPA 861
Cdd:pfam12815   64 SRTPA 68
nusG PRK08559
transcription antitermination protein NusG; Validated
 190-330 7.89e-11

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 61.42  E-value: 7.89e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  190 KDPNLWVVKCRMGEEKATVvhvmrKMITYQFTEEPLQIKSIVAKEGLKGYIYIEAFKQTHVKQAIEGIGNLRmGFYKQQm 269
Cdd:PRK08559     4 EMSMIFAVKTTAGQERNVA-----LMLAMRAKKENLPIYAILAPPELKGYVLVEAESKGAVEEAIRGIPHVR-GVVPGE- 76

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  270 VPIREMTDVLKVVKETASLKPKAWVRLKRGVFKDDLAQVDIVYPSQNEVELKL------IP---RIDYTR 330
Cdd:PRK08559    77 ISFEEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELleaavpIPvtvRGDQVR 146
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 770-959 4.12e-07

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 54.41  E-value: 4.12e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  770 AGAPASTYGARTPNYGGQTPMYGSrTPMYLGSQTPL----HDESRTP-HYGGMTPSHESGGRTPSGGGSSVWDPSNANTP 844
Cdd:PHA03307    16 EGGEFFPRPPATPGDAADDLLSGS-QGQLVSDSAELaavtVVAGAAAcDRFEPPTGPPPGPGTEAPANESRSTPTWSLST 94

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  845 --SRNNDFEFSY--DDSPSPADFGTTPNPATPGyhaDSPAPMGPYTPQTPGSVYSPYPAASPGGFDAQSPGYVGTPnpal 920
Cdd:PHA03307    95 laPASPAREGSPtpPGPSSPDPPPPTPPPASPP---PSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAA---- 167

                          170       180       190
                   ....*....|....*....|....*....|....*....
gi 1066729447  921 mSSPSPASFAGSPSPMGYSPMTPAAPFTPQTPGTVMEPT 959
Cdd:PHA03307   168 -SSRQAALPLSSPEETARAPSSPPAEPPPSTPPAAASPR 205
KLF1_N cd21581
N-terminal domain of Kruppel-like Factor 1; Kruppel-like Factor 1 (KLF1, also known as ...
 800-958 7.67e-06

N-terminal domain of Kruppel-like Factor 1; Kruppel-like Factor 1 (KLF1, also known as Krueppel-like factor 1 or Erythroid Kruppel-like Factor/EKLF) was the first Kruppel-like factor discovered. It was found to be vitally important for embryonic erythropoiesis in promoting the switch from fetal hemoglobin (Hemoglobin F) to adult hemoglobin (Hemoglobin A) gene expression by binding to highly conserved CACCC domains. EKLF ablation in mouse embryos produces a lethal anemic phenotype, causing death by embryonic day 14, and natural mutations lead to beta+ thalassemia in humans. However, expression of embryonic hemoglobin and fetal hemoglobin genes is normal in EKLF-deficient mice, suggesting other factors may be involved. KLF1 functions as a transcriptional activator. It belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specifity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF1, which is related to the N-terminal domains of KLF2 and KLF4.


Pssm-ID: 409227 [Multi-domain]  Cd Length: 278  Bit Score: 48.89  E-value: 7.67e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  800 GSQTPLHDESRTPHYGGMTPSHESGGRTPSGGGSSVWD---PSNANTPSRNNDFEFSYDDSPSPADFGTTPNPATPGY-- 874
Cdd:cd21581     86 NTQALPQEEQPGAYYEPPKKDQPGTEGLQVGGPGLMAEllsPEESTGWAPPEPHHGYPDAFVGPALFPAPANVDQFGFpq 165

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  875 ---------HADSPAP-MGPYTPQT-------PGSVYSP---YPAASPggfDAQSPGYVG--TPNPALMSSPSPASFAGS 932
Cdd:cd21581    166 ggsvdrrgnLSKSGSWdFGSYYPQQhpsvvafPDSRFGPlsgPQALTP---DPQHYGYFQlfRHNAALFPDYAHSPGPGH 242

                          170       180
                   ....*....|....*....|....*.
gi 1066729447  933 PSPmGYSPMTPAapftPQTPGTVMEP 958
Cdd:cd21581    243 LPL-GQQPLLPD----PPLPPGGAEG 263
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 486-513 9.34e-05

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


Pssm-ID: 128978  Cd Length: 28  Bit Score: 40.39  E-value: 9.34e-05
                            10        20
                    ....*....|....*....|....*...
gi 1066729447   486 HFKMGDHVKVIAGRYEGDTGLIVRVEDN 513
Cdd:smart00739    1 KFEVGDTVRVIAGPFKGKVGKVLEVDGE 28
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 717-748 2.49e-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: 39.29  E-value: 2.49e-04
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1066729447  717 IGQTVRIVKGPFKGYIGIVKDATETTARIELH 748
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 490-513 6.08e-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: 38.14  E-value: 6.08e-04
                           10        20
                   ....*....|....*....|....
gi 1066729447  490 GDHVKVIAGRYEGDTGLIVRVEDN 513
Cdd:pfam00467    2 GDVVRVIAGPFKGKVGKVVEVDDK 25
 
Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
 193-280 5.52e-40

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: 142.28  E-value: 5.52e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  193 NLWVVKCRMGEEKATVVHVMRKMITYQFTEEPLQIKSIVAKEGLKGYIYIEAFKQTHVKQAIEGIGNLRMGfyKQQMVPI 272
Cdd:cd09888      1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYLN--TIKLVPI 78


                   ....*...
gi 1066729447  273 REMTDVLK 280
Cdd:cd09888     79 KEMPDVLS 86
Spt5-NGN pfam03439
Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG ...
 193-279 4.26e-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: 4.26e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  193 NLWVVKCRMGEEKATVVHVMRKMITYQFTEEpLQIKSIVAKEGLKGYIYIEAFKQTHVKQAIEGIGNLRMGfyKQQMVPI 272
Cdd:pfam03439    1 KIWAVKCTPGQEREVALSLMRKILALAKTNN-LGIYSVFAPDGLKGYIYVEADRQAAVKRALEGIPNVRGL--VPGLVPI 77


                   ....*..
gi 1066729447  273 REMTDVL 279
Cdd:pfam03439   78 KEMEHLL 84
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 486-536 1.28e-26

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: 102.99  E-value: 1.28e-26
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1066729447  486 HFKMGDHVKVIAGRYEGDTGLIVRVEDNLIVLFSDLTMHELKVLPKDIQIC 536
Cdd:cd06083      1 HFKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 712-763 1.37e-26

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: 102.95  E-value: 1.37e-26
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 1066729447  712 RDREIIGQTVRIVKGPFKGYIGIVKDATETTARIELHSSCKTISVDRSHLNN 763
Cdd:cd06085      1 GRDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLAV 52
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 436-485 4.72e-21

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: 87.17  E-value: 4.72e-21
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1066729447  436 APGDVVVVAEGELQHLQGKVIRVDGNKITIMPKHEDLKDPLEFPYTELRK 485
Cdd:cd06082      2 QPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 1012-1074 2.42e-19

KOW domain of Spt5, repeat 6; 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: 240510  Cd Length: 58  Bit Score: 82.56  E-value: 2.42e-19
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1066729447 1012 EHLEPVLPEKGDKAKVIIGDKRESTGTLISEDGDDGVFKLDtidieTKTDILMLPKHYLCKLV 1074
Cdd:cd06086      1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMD-----SDGDIKILPMNFLAKLV 58
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 612-654 6.93e-18

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: 77.95  E-value: 6.93e-18
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1066729447  612 RDIVNVIEGPHSGRTGEIKHLYRNFAFLNSRLMTDNGGYFVCR 654
Cdd:cd06084      1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 778-945 8.03e-18

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: 80.26  E-value: 8.03e-18
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447   778 GARTPNY---GGQTPMYGSRTPMYlgsqTPLHDESRTPHYGGMTPSHE-SGGRTPSGGGssvWDPSNANTPSRNNDfefs 853
Cdd:smart01104    1 GGRTPAWgasGSKTPAWGSRTPGT----AAGGAPTARGGSGSRTPAWGgAGSRTPAWGG---AGPTGSRTPAWGGA---- 69

                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447   854 YDDSPSPADFGTTPNPATPGyhadspapmGPYTPQTPGsvyspypaaspggfdaqspgYVGTpnpalmsspsPASFAGsP 933
Cdd:smart01104   70 SAWGNKSSEGSASSWAAGPG---------GAYGAPTPG--------------------YGGT----------PSAYGP-A 109

                           170
                    ....*....|..
gi 1066729447   934 SPMGYSPMTPAA 945
Cdd:smart01104  110 TPGGGAMAGSAS 121
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 291-328 6.68e-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: 6.68e-15
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1066729447  291 KAWVRLKRGVFKDDLAQVDIVYPSQNEVELKLIPRIDY 328
Cdd:cd06081      1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 193-281 8.88e-12

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: 62.78  E-value: 8.88e-12
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447   193 NLWVVKCRMGEEKATVVHVMRKMITYQFTEEPLQI--------------KSIVAKEGLKGYIYIEAFKQTHVKQAIEGIG 258
Cdd:smart00738    1 NWYAVRTTSGQEKRVAENLERKAEALGLEDKIVSIlvpteevkeirrgkKKVVERKLFPGYIFVEADLEDEVWTAIRGTP 80

                            90       100
                    ....*....|....*....|....*..
gi 1066729447   259 NLRmGF----YKQQMVPIREMTDVLKV 281
Cdd:smart00738   81 GVR-GFvgggGKPTPVPDDEIEKILKP 106
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 785-861 6.52e-11

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: 59.00  E-value: 6.52e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  785 GGQTPMY----GSRTPMY--LGSQTPLHDE--SRTPHYGgmtpsheSGGRTPSgggssvWDPSNANTPsRNNDfefSYDD 856
Cdd:pfam12815    1 GSRTPAYnsagGSRTPAWgaDGSRTPAYGGagGRTPAYN-------QGGKTPA------WGGAGSRTP-AYYG---AWGG 63


                   ....*
gi 1066729447  857 SPSPA 861
Cdd:pfam12815   64 SRTPA 68
nusG PRK08559
transcription antitermination protein NusG; Validated
 190-330 7.89e-11

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 61.42  E-value: 7.89e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  190 KDPNLWVVKCRMGEEKATVvhvmrKMITYQFTEEPLQIKSIVAKEGLKGYIYIEAFKQTHVKQAIEGIGNLRmGFYKQQm 269
Cdd:PRK08559     4 EMSMIFAVKTTAGQERNVA-----LMLAMRAKKENLPIYAILAPPELKGYVLVEAESKGAVEEAIRGIPHVR-GVVPGE- 76

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  270 VPIREMTDVLKVVKETASLKPKAWVRLKRGVFKDDLAQVDIVYPSQNEVELKL------IP---RIDYTR 330
Cdd:PRK08559    77 ISFEEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELleaavpIPvtvRGDQVR 146
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 772-832 1.25e-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 characteriztic TPA motif.


Pssm-ID: 372327 [Multi-domain]  Cd Length: 71  Bit Score: 55.53  E-value: 1.25e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1066729447  772 APA-STYGARTPNYGGQtpmyGSRTPMY-LGSQTPLHDE--SRTPHYGGMtpshESGGRTPSGGG 832
Cdd:pfam12815   15 TPAwGADGSRTPAYGGA----GGRTPAYnQGGKTPAWGGagSRTPAYYGA----WGGSRTPAYGG 71
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 747-961 2.66e-07

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: 54.92  E-value: 2.66e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  747 LHSSCKTISVDRSHLNNLTGPKP---AGAPASTYGARTPNYGGqtpMYGSRTPMYLGSQTPLHDESRTPHYGGMTPSHES 823
Cdd:pfam05109  396 LGTAPKTLIITRTATNATTTTHKvifSKAPESTTTSPTLNTTG---FAAPNTTTGLPSSTHVPTNLTAPASTGPTVSTAD 472

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  824 GGRTPSGGGSSVWDPSNANTPSRNNDFEFSYDDSPSPADFGTTPNP---------ATPGYHADSPApMGPYTPQTpgSVY 894
Cdd:pfam05109  473 VTSPTPAGTTSGASPVTPSPSPRDNGTESKAPDMTSPTSAVTTPTPnatsptpavTTPTPNATSPT-LGKTSPTS--AVT 549

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1066729447  895 SPYPAASPGGFDAQSPgyvgTPNPAL--MSSPSPASFAGSPSPMGYSP----MTPAAPFTPQT-PGTVMEPTMT 961
Cdd:pfam05109  550 TPTPNATSPTPAVTTP----TPNATIptLGKTSPTSAVTTPTPNATSPtvgeTSPQANTTNHTlGGTSSTPVVT 619
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 770-959 4.12e-07

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 54.41  E-value: 4.12e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  770 AGAPASTYGARTPNYGGQTPMYGSrTPMYLGSQTPL----HDESRTP-HYGGMTPSHESGGRTPSGGGSSVWDPSNANTP 844
Cdd:PHA03307    16 EGGEFFPRPPATPGDAADDLLSGS-QGQLVSDSAELaavtVVAGAAAcDRFEPPTGPPPGPGTEAPANESRSTPTWSLST 94

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  845 --SRNNDFEFSY--DDSPSPADFGTTPNPATPGyhaDSPAPMGPYTPQTPGSVYSPYPAASPGGFDAQSPGYVGTPnpal 920
Cdd:PHA03307    95 laPASPAREGSPtpPGPSSPDPPPPTPPPASPP---PSPAPDLSEMLRPVGSPGPPPAASPPAAGASPAAVASDAA---- 167

                          170       180       190
                   ....*....|....*....|....*....|....*....
gi 1066729447  921 mSSPSPASFAGSPSPMGYSPMTPAAPFTPQTPGTVMEPT 959
Cdd:PHA03307   168 -SSRQAALPLSSPEETARAPSSPPAEPPPSTPPAAASPR 205
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 490-534 4.60e-07

KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); 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 KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues.


Pssm-ID: 240504  Cd Length: 49  Bit Score: 47.60  E-value: 4.60e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1066729447  490 GDHVKVIAGRYEGDTGLIVRVED----NLIVLFSDLTMHELKVLPKDIQ 534
Cdd:cd00380      1 GDVVRVLRGPYKGREGVVVDIDPrfgiVTVKGATGSKGAELKVRFDDVD 49
PHA03247 PHA03247
large tegument protein UL36; Provisional
 758-958 1.78e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 52.63  E-value: 1.78e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  758 RSHLNNLTGPKPAGAPASTYGARTPNYG----------------GQTPMYGSRTPMYLGSQTPLHDESRtPHYGGMTPS- 820
Cdd:PHA03247  2632 SPAANEPDPHPPPTVPPPERPRDDPAPGrvsrprrarrlgraaqASSPPQRPRRRAARPTVGSLTSLAD-PPPPPPTPEp 2710

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  821 --HESGGRTP------SGGGSSVWDPSNANTPSRNNDFEFSYDDSPsPADFGTTPNPATPGYHADSPAPMGPYTPQTPGS 892
Cdd:PHA03247  2711 apHALVSATPlppgpaAARQASPALPAAPAPPAVPAGPATPGGPAR-PARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVA 2789

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1066729447  893 VYSPYPAASPGGFD-AQSPGYVGTPNPALMSSPSPASFAGSP-SPMGYSPMTPAAPF-TPQTPGTVMEP 958
Cdd:PHA03247  2790 SLSESRESLPSPWDpADPPAAVLAPAAALPPAASPAGPLPPPtSAQPTAPPPPPGPPpPSLPLGGSVAP 2858
PHA03378 PHA03378
EBNA-3B; Provisional
 787-958 1.97e-06

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 51.99  E-value: 1.97e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  787 QTPMYGSRTPMYLGSQTPL---HDESRTPHY-----------GGMTPSHESGGRTPSGGGSSV---WDPSNANTPSRnnd 849
Cdd:PHA03378   623 QWPMPLRPIPMRPLRMQPItfnVLVFPTPHQppqveitpykpTWTQIGHIPYQPSPTGANTMLpiqWAPGTMQPPPR--- 699

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  850 fefsyddSPSPAdfgttPNPATPGYHADSP-APMGPYTP--QTPGSVYSPYPAASPGGFDAQSPGYVGTPNPALMSSPSP 926
Cdd:PHA03378   700 -------APTPM-----RPPAAPPGRAQRPaAATGRARPpaAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPP 767

                          170       180       190
                   ....*....|....*....|....*....|..
gi 1066729447  927 ASFAGSPSPMGYSPMTPAAPFTPQTPGTVMEP 958
Cdd:PHA03378   768 AAAPGAPTPQPPPQAPPAPQQRPRGAPTPQPP 799
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 837-958 2.10e-06

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 51.93  E-value: 2.10e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  837 DPSNANTPSRNNDFEFSyddSPSPADFGTTPNPATPGYHADSPAPMGPYtPQTPGSVYSPYPaasPGGFdaqspgyvgTP 916
Cdd:pfam09606  358 GGLGANPMQRGQPGMMS---SPSPVPGQQVRQVTPNQFMRQSPQPSVPS-PQGPGSQPPQSH---PGGM---------IP 421

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 1066729447  917 NPALMSSPSPASFAGSPSPMGYSPMTPAAPFtpQTPG--TVMEP 958
Cdd:pfam09606  422 SPALIPSPSPQMSQQPAQQRTIGQDSPGGSL--NTPGqsAVNSP 463
PHA03309 PHA03309
transcriptional regulator ICP4; Provisional
 804-960 5.56e-06

transcriptional regulator ICP4; Provisional


Pssm-ID: 165564 [Multi-domain]  Cd Length: 2033  Bit Score: 51.01  E-value: 5.56e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  804 PLHDESRTPHYGGMTPSHESGGRTPSGGGSSvwdPSNANTP-----------SRNNDFEFSYDDSPSPADfGTTP----- 867
Cdd:PHA03309  1029 PGRATASSPRTPASRPPHGSAAAPPSGRDSP---PGALNVPeaaeeelrlaaARDTTGDLLSDEAGTDDD-GDAPvvisy 1104

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  868 ----------NPATPGYHADSPAPMGpYTPQtPGSVYSPYPAASPGGFDAQSPGYVGTPNPAlMSSPSPASFAGSPspmg 937
Cdd:PHA03309  1105 vgpssppgveDPSPDGLAALRPLPEG-YVPR-PGDVLRGDPGADENDDDARAPCRVGDASPP-RQLPSSSSFASSS---- 1177

                          170       180
                   ....*....|....*....|...
gi 1066729447  938 yspMTPAAPFTPQTPGTVMEPTM 960
Cdd:PHA03309  1178 ---LASAVPGDPYLPRSVAEPTL 1197
KLF1_N cd21581
N-terminal domain of Kruppel-like Factor 1; Kruppel-like Factor 1 (KLF1, also known as ...
 800-958 7.67e-06

N-terminal domain of Kruppel-like Factor 1; Kruppel-like Factor 1 (KLF1, also known as Krueppel-like factor 1 or Erythroid Kruppel-like Factor/EKLF) was the first Kruppel-like factor discovered. It was found to be vitally important for embryonic erythropoiesis in promoting the switch from fetal hemoglobin (Hemoglobin F) to adult hemoglobin (Hemoglobin A) gene expression by binding to highly conserved CACCC domains. EKLF ablation in mouse embryos produces a lethal anemic phenotype, causing death by embryonic day 14, and natural mutations lead to beta+ thalassemia in humans. However, expression of embryonic hemoglobin and fetal hemoglobin genes is normal in EKLF-deficient mice, suggesting other factors may be involved. KLF1 functions as a transcriptional activator. It belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specifity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF1, which is related to the N-terminal domains of KLF2 and KLF4.


Pssm-ID: 409227 [Multi-domain]  Cd Length: 278  Bit Score: 48.89  E-value: 7.67e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  800 GSQTPLHDESRTPHYGGMTPSHESGGRTPSGGGSSVWD---PSNANTPSRNNDFEFSYDDSPSPADFGTTPNPATPGY-- 874
Cdd:cd21581     86 NTQALPQEEQPGAYYEPPKKDQPGTEGLQVGGPGLMAEllsPEESTGWAPPEPHHGYPDAFVGPALFPAPANVDQFGFpq 165

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  875 ---------HADSPAP-MGPYTPQT-------PGSVYSP---YPAASPggfDAQSPGYVG--TPNPALMSSPSPASFAGS 932
Cdd:cd21581    166 ggsvdrrgnLSKSGSWdFGSYYPQQhpsvvafPDSRFGPlsgPQALTP---DPQHYGYFQlfRHNAALFPDYAHSPGPGH 242

                          170       180
                   ....*....|....*....|....*.
gi 1066729447  933 PSPmGYSPMTPAapftPQTPGTVMEP 958
Cdd:cd21581    243 LPL-GQQPLLPD----PPLPPGGAEG 263
PHA03247 PHA03247
large tegument protein UL36; Provisional
 767-959 9.16e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 50.32  E-value: 9.16e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  767 PKPAGAPASTYGARTPNYGGQTPMYGSRTPMylGSQTPLHDESRTPHYGGMTPSHESGGRTPS-----GGGSSVWDP-SN 840
Cdd:PHA03247  2627 PPPSPSPAANEPDPHPPPTVPPPERPRDDPA--PGRVSRPRRARRLGRAAQASSPPQRPRRRAarptvGSLTSLADPpPP 2704

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  841 ANTPSRNNDFEFSYDDSPSPADFGTTPNPATPGYHADSPAPMGPYTPQTPGSVYSPypaASPGGFDAQSP--GYVGTPNP 918
Cdd:PHA03247  2705 PPTPEPAPHALVSATPLPPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARP---PTTAGPPAPAPpaAPAAGPPR 2781

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 1066729447  919 ALmssPSPASFAGSPS-PMGYSPMTPAAPFTPQTPGTVMEPT 959
Cdd:PHA03247  2782 RL---TRPAVASLSESrESLPSPWDPADPPAAVLAPAAALPP 2820
PHA03247 PHA03247
large tegument protein UL36; Provisional
 767-952 1.44e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 49.55  E-value: 1.44e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  767 PKPAGAPASTYGARTPNYGGQTPMYGSRTPMYLGSQTPLHDEsRTPHYGGMTPSHESGGRTPSGGGSSvwdPSNANTPSR 846
Cdd:PHA03247  2612 APPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPR-DDPAPGRVSRPRRARRLGRAAQASS---PPQRPRRRA 2687

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  847 NNDFEFSYDDSPSPADFGTTPNPATPGYHADSPAPMGPYTPQ--TPGSVYSPYPAASPGGfdaqsPGYVGTPNPAlmssP 924
Cdd:PHA03247  2688 ARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARqaSPALPAAPAPPAVPAG-----PATPGGPARP----A 2758

                          170       180
                   ....*....|....*....|....*...
gi 1066729447  925 SPASFAGSPSPMgySPMTPAAPFTPQTP 952
Cdd:PHA03247  2759 RPPTTAGPPAPA--PPAAPAAGPPRRLT 2784
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 766-816 2.88e-05

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: 43.20  E-value: 2.88e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1066729447  766 GPKPAGAPASTYGARTPNYGGQtpmyGSRTPMYLGSqtplHDESRTPHYGG 816
Cdd:pfam12815   29 GGAGGRTPAYNQGGKTPAWGGA----GSRTPAYYGA----WGGSRTPAYGG 71
PHA03247 PHA03247
large tegument protein UL36; Provisional
 767-958 4.14e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 48.01  E-value: 4.14e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  767 PKPAGAPASTYGARTPnyGGQTPMYGSRTPMYLGSQTPLHDESRTPHyGGMTPSHESGGRTPSGGGSSVWDPSNANTPSr 846
Cdd:PHA03247  2736 PAAPAPPAVPAGPATP--GGPARPARPPTTAGPPAPAPPAAPAAGPP-RRLTRPAVASLSESRESLPSPWDPADPPAAV- 2811

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  847 nndfefsyddSPSPADFGTTPNPATPGYHADSPAPMGPYTPQTPGSVYSPYPAA-SPGG-FDAQSPGYVGTPNPALMS-- 922
Cdd:PHA03247  2812 ----------LAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSvAPGGdVRRRPPSRSPAAKPAAPArp 2881

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*.
gi 1066729447  923 ----------SPSPASFAGSPSPMGySPMTPAAPFTPQTPGTVMEP 958
Cdd:PHA03247  2882 pvrrlarpavSRSTESFALPPDQPE-RPPQPQAPPPPQPQPQPPPP 2926
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 193-279 5.15e-05

N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization Substance G (NusG) 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 in bacteria and archaea. 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. Spt5 forms a 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 being involved in RNA polymerase elongation and Rho-termination in bacteria. Orthologs of the NusG gene exist in all bacteria, but its functions and requirements are different. The diverse activities suggest that, after diverging from a common ancestor, NusG proteins became specialized in different bacteria.


Pssm-ID: 193574 [Multi-domain]  Cd Length: 99  Bit Score: 43.08  E-value: 5.15e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  193 NLWVVKCRMGEEKATVVHVMRKMI---------TYQFTEEPLQIKSIVAKEGLKGYIYIEAFKQTHVKQAIEGIGNLRmG 263
Cdd:cd08000      1 NWYVLFVKTGREEKVEKLLEKRFEandieafvpKKEVPERKRGKIEEVIKPLFPGYVFVETDLSPELYELIREVPGVI-G 79

                           90       100
                   ....*....|....*....|
gi 1066729447  264 FYK----QQMVPIREMTDVL 279
Cdd:cd08000     80 ILGngeePSPVSDEEIEMIL 99
NGN_Arch cd09887
Archaeal N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance ...
 194-261 6.07e-05

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: 42.53  E-value: 6.07e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1066729447  194 LWVVKCRMGEEKaTVVHVMRKMITyqftEEPLQIKSIVAKEGLKGYIYIEAFKQTHVKQAIEGIGNLR 261
Cdd:cd09887      2 IYAVKTTAGQER-NVADLLAMRAE----KENLDVYSILVPEELKGYVFVEAEDPDRVEELIRGIPHVR 64
PTZ00449 PTZ00449
104 kDa microneme/rhoptry antigen; Provisional
 721-1019 8.32e-05

104 kDa microneme/rhoptry antigen; Provisional


Pssm-ID: 185628 [Multi-domain]  Cd Length: 943  Bit Score: 46.99  E-value: 8.32e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  721 VRIVKGPFKGYIG-IVKDATETTARIELHSSCKtisvdrsHLNNLTGPKPAGAPASTYGARTPNYGGQTPmygsrtpmyl 799
Cdd:PTZ00449   474 TRISKIQFTQEIKkLIKKSKKKLAPIEEEDSDK-------HDEPPEGPEASGLPPKAPGDKEGEEGEHED---------- 536

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  800 gsqtplHDESRTPHYGGMTPSHESGGRTPSGGGSSVWDPSNANTPSRNNDFEFSYDDSPSPADFGTTPNPATPGYHADSP 879
Cdd:PTZ00449   537 ------SKESDEPKEGGKPGETKEGEVGKKPGPAKEHKPSKIPTLSKKPEFPKDPKHPKDPEEPKKPKRPRSAQRPTRPK 610

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  880 APMGPYTPQTPGSVYSPYPAASPggfdaQSPgyvgtPNPALMSSPSpasfagSPSpmgySPMTPAAPFTPQTPGTVMEPT 959
Cdd:PTZ00449   611 SPKLPELLDIPKSPKRPESPKSP-----KRP-----PPPQRPSSPE------RPE----GPKIIKSPKPPKSPKPPFDPK 670

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  960 MTDWHTTDIVVKVKATHESEQLVYQTGIIKSIngvmCALHLIEDEKTVSVSCEHLEPVLP 1019
Cdd:PTZ00449   671 FKEKFYDDYLDAAAKSKETKTTVVLDESFESI----LKETLPETPGTPFTTPRPLPPKLP 726
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 486-513 9.34e-05

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


Pssm-ID: 128978  Cd Length: 28  Bit Score: 40.39  E-value: 9.34e-05
                            10        20
                    ....*....|....*....|....*...
gi 1066729447   486 HFKMGDHVKVIAGRYEGDTGLIVRVEDN 513
Cdd:smart00739    1 KFEVGDTVRVIAGPFKGKVGKVLEVDGE 28
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 717-748 2.49e-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: 39.29  E-value: 2.49e-04
                           10        20        30
                   ....*....|....*....|....*....|..
gi 1066729447  717 IGQTVRIVKGPFKGYIGIVKDATETTARIELH 748
Cdd:pfam00467    1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
819-952 2.72e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 44.87  E-value: 2.72e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  819 PSHESGGRTPSgggSSVWDPSNANTPSRNndfefsyddSPSPADFGTTPNPATPGYHADSPAPMGPytPQTPGSVYSPYP 898
Cdd:PRK12323   365 PGQSGGGAGPA---TAAAAPVAQPAPAAA---------APAAAAPAPAAPPAAPAAAPAAAAAARA--VAAAPARRSPAP 430

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1066729447  899 AASPGGFDAQSPGYVGTPNPAlmSSPSPASFAGSPSPMGYSPMTPAAPFTPQTP 952
Cdd:PRK12323   431 EALAAARQASARGPGGAPAPA--PAPAAAPAAAARPAAAGPRPVAAAAAAAPAR 482
PHA03264 PHA03264
envelope glycoprotein D; Provisional
 850-959 4.45e-04

envelope glycoprotein D; Provisional


Pssm-ID: 223029 [Multi-domain]  Cd Length: 416  Bit Score: 43.84  E-value: 4.45e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  850 FEFSYDDSPSPADFGTTPNPatPGYHADSPAPM-GPYTPQTPGSVYSPYPAA-SPGGFDAQSPGYvGTPNPalmssPSPA 927
Cdd:PHA03264   258 FEESKGYEPPPAPSGGSPAP--PGDDRPEAKPEpGPVEDGAPGRETGGEGEGpEPAGRDGAAGGE-PKPGP-----PRPA 329

                           90       100       110
                   ....*....|....*....|....*....|..
gi 1066729447  928 SFAGSPSpmGYsPMTPAAPFTPQTPGTVMEPT 959
Cdd:PHA03264   330 PDADRPE--GW-PSLEAITFPPPTPATPAVPR 358
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 490-513 6.08e-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: 38.14  E-value: 6.08e-04
                           10        20
                   ....*....|....*....|....
gi 1066729447  490 GDHVKVIAGRYEGDTGLIVRVEDN 513
Cdd:pfam00467    2 GDVVRVIAGPFKGKVGKVVEVDDK 25
KOW_NusG cd06091
NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif ...
 717-747 8.14e-04

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: 38.59  E-value: 8.14e-04
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1066729447  717 IGQTVRIVKGPFKGYIGIVK--DATETTARIEL 747
Cdd:cd06091      6 VGDTVRIISGPFAGFEGKVEeiDEEKGKVKVLV 38
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 857-955 1.35e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 42.67  E-value: 1.35e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  857 SPSPADFGTTPNPATPGYHADSPAPMGPYTPQTPGSVYSPYPAASPGGFDAQSPGYVGTPNPALMSSPSPASFAGSPSPM 936
Cdd:PRK07764   409 APAPAAAAPAAAAAPAPAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSPPPAAAPSAQPAPAPAAAPEPTAAPAPAPPAAP 488

                           90       100
                   ....*....|....*....|.
gi 1066729447  937 --GYSPMTPAAPFTPQTPGTV 955
Cdd:PRK07764   489 apAAAPAAPAAPAAPAGADDA 509
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 765-946 1.40e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 42.85  E-value: 1.40e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  765 TGPKPAGAPASTYGARTPNYGGQTPMYGSRTPMylgSQTPLHDESRTPHYGGMTPSHESGGRTPSGGGSSVWDPSNANTP 844
Cdd:PHA03307    64 RFEPPTGPPPGPGTEAPANESRSTPTWSLSTLA---PASPAREGSPTPPGPSSPDPPPPTPPPASPPPSPAPDLSEMLRP 140

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  845 SRNNDFEFSYDDSPSPADFGTTPNPATPGYHADSPAPMGPYTPQTPGSVYSPYPAASPGGFDAQSPGYVGTPNPALMSSP 924
Cdd:PHA03307   141 VGSPGPPPAASPPAAGASPAAVASDAASSRQAALPLSSPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASSP 220

                          170       180
                   ....*....|....*....|..
gi 1066729447  925 SPASFAGSPSPMGYSPMTPAAP 946
Cdd:PHA03307   221 APAPGRSAADDAGASSSDSSSS 242
Drf_FH1 pfam06346
Formin Homology Region 1; This region is found in some of the Diaphanous related formins (Drfs) ...
 858-958 2.16e-03

Formin Homology Region 1; This region is found in some of the Diaphanous related formins (Drfs). It consists of low complexity repeats of around 12 residues.


Pssm-ID: 461881 [Multi-domain]  Cd Length: 157  Bit Score: 39.85  E-value: 2.16e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1066729447  858 PSPADFGTTPNPatPGYHADSPAPM-----GPYTPQTPGSVYSPYPAASPGGFDAQSPgyvgTPNPALMSSPSPASFAGS 932
Cdd:pfam06346    5 PLPGDSSTIPLP--PGACIPTPPPLpggggPPPPPPLPGSAAIPPPPPLPGGTSIPPP----PPLPGAASIPPPPPLPGS 78

                           90       100       110
                   ....*....|....*....|....*....|.
gi 1066729447  933 -----PSPMGYSPMTPAAPftPQTPGTVMEP 958
Cdd:pfam06346   79 tgippPPPLPGGAGIPPPP--PPLPGGAGVP 107
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 718-761 4.42e-03

KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); 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 KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues.


Pssm-ID: 240504  Cd Length: 49  Bit Score: 36.04  E-value: 4.42e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1066729447  718 GQTVRIVKGPFKGYIGIVKDATETT--ARIELH--SSCKTISVDRSHL 761
Cdd:cd00380      1 GDVVRVLRGPYKGREGVVVDIDPRFgiVTVKGAtgSKGAELKVRFDDV 48
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 613-650 7.99e-03

KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); 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 KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues.


Pssm-ID: 240504  Cd Length: 49  Bit Score: 35.27  E-value: 7.99e-03
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1066729447  613 DIVNVIEGPHSGRTGEIKHLYRNFAFLNSRLMTDNGGY 650
Cdd:cd00380      2 DVVRVLRGPYKGREGVVVDIDPRFGIVTVKGATGSKGA 39
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 438-484 8.82e-03

KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); 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 KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues.


Pssm-ID: 240504  Cd Length: 49  Bit Score: 35.27  E-value: 8.82e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1066729447  438 GDVVVVAEGELQHLQGKVIRVDG--NKITIMPKHEDLKDPLEFPYTELR 484
Cdd:cd00380      1 GDVVRVLRGPYKGREGVVVDIDPrfGIVTVKGATGSKGAELKVRFDDVD 49
 
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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