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Conserved domains on  [gi|215498598|gb|EEC08092|]
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transcription elongation factor SPT5, putative [Ixodes scapularis]

Protein Classification

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 ...
 129-216 3.92e-41

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: 145.37  E-value: 3.92e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598 129 NLWMVKCKIGEEKSTVLQMMRKFIAYQYSEEPLQIRSVVAPEGLKGYIYIEAYKHTHVKQVIQGVGNLRIGlyQQTMVPI 208
Cdd:cd09888    1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYLN--TIKLVPI 78


                 ....*...
gi 215498598 209 KEMTDVLR 216
Cdd:cd09888   79 KEMPDVLS 86
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 423-472 5.54e-27

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: 103.76  E-value: 5.54e-27
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 215498598 423 FKMGDHVKVIAGRFEGDTGLIVRVEDNMVVLFSDLTMHELKVLPRDLQLC 472
Cdd:cd06083    2 FKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 603-654 1.50e-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: 102.56  E-value: 1.50e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 215498598 603 RDSELIGETIKITQGPYKGHIGIVKDATESTARVELHTKCQTISVDRSRIAV 654
Cdd:cd06085    1 GRDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLAV 52
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 903-959 1.56e-25

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: 99.90  E-value: 1.56e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 215498598 903 EHLEPVVPVAKDKVKVILGEDREETGELLSIDHPEGVVKM-GNGKITMQPMRYLCKMH 959
Cdd:cd06086    1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMdSDGDIKILPMNFLAKLV 58
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 678-802 3.73e-23

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: 95.67  E-value: 3.73e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598   678 GSQTPMY-SSGSRTPMYGSQTPLYEAGSRT--PHFGGGQTPVHDG--SRTPVHGAWDPTTANTPARPELDDYQLEEASPS 752
Cdd:smart01104   1 GGRTPAWgASGSKTPAWGSRTPGTAAGGAPtaRGGSGSRTPAWGGagSRTPAWGGAGPTGSRTPAWGGASAWGNKSSEGS 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 215498598   753 YQPATPGYQAPETPQGPYTPQTPGMYGsdhgfspyqaSPSPTAYQPSPSP 802
Cdd:smart01104  81 ASSWAAGPGGAYGAPTPGYGGTPSAYG----------PATPGGGAMAGSA 120
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 371-421 1.83e-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: 88.33  E-value: 1.83e-21
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 215498598 371 FAPGDTVEVAEGELVHLQGKIISIDGNKITMLPRHEDLTEPLDFQAHELKK 421
Cdd:cd06082    1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 548-590 7.25e-21

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: 86.42  E-value: 7.25e-21
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 215498598 548 RDIVKVIDGPHSGSQGVVKHIFRSFAFLHSRMMLENGGIFVCK 590
Cdd:cd06084    1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 227-264 3.76e-17

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: 75.58  E-value: 3.76e-17
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 215498598 227 KQWVRLKRGIYRDDLAQVDYVDTAQSQVNLKLLPRVDY 264
Cdd:cd06081    1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 57-123 2.02e-07

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: 49.96  E-value: 2.02e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598   57 EGAETEEASSKELHSHRRL---QMMLTSQKEDEIEDYYRRKYADTTATEggYREADVElsdEIAQQTLLP 123
Cdd:pfam11942  33 EEDEDEEDGRRDDRRHRELdrrRELEEDEDAEEIAEYLKERYGRSSSDA--YRGDAEE---GVPQRLLLP 97
Med15 super family cl26621
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 759-850 1.71e-05

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.


The actual alignment was detected with superfamily member pfam09606:

Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 48.85  E-value: 1.71e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598  759 GYQAPETPQGPYtPQTPGMYGSDHGfsPYQASPSPtAYQPSPSPKgyvatpsPVAFQAGTPSPSTYGGYSPM-TPG---A 834
Cdd:pfam09606 392 FMRQSPQPSVPS-PQGPGSQPPQSH--PGGMIPSP-ALIPSPSPQ-------MSQQPAQQRTIGQDSPGGSLnTPGqsaV 460

                          90
                  ....*....|....*.
gi 215498598  835 PSPFNPQTPGAGMEAL 850
Cdd:pfam09606 461 NSPLNPQEEQLYREKY 476
 
Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
 129-216 3.92e-41

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: 145.37  E-value: 3.92e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598 129 NLWMVKCKIGEEKSTVLQMMRKFIAYQYSEEPLQIRSVVAPEGLKGYIYIEAYKHTHVKQVIQGVGNLRIGlyQQTMVPI 208
Cdd:cd09888    1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYLN--TIKLVPI 78


                 ....*...
gi 215498598 209 KEMTDVLR 216
Cdd:cd09888   79 KEMPDVLS 86
Spt5-NGN pfam03439
Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG ...
 129-215 1.16e-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: 109.98  E-value: 1.16e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598  129 NLWMVKCKIGEEKSTVLQMMRKFIAYQYSEEpLQIRSVVAPEGLKGYIYIEAYKHTHVKQVIQGVGNLRIGlyQQTMVPI 208
Cdd:pfam03439   1 KIWAVKCTPGQEREVALSLMRKILALAKTNN-LGIYSVFAPDGLKGYIYVEADRQAAVKRALEGIPNVRGL--VPGLVPI 77


                  ....*..
gi 215498598  209 KEMTDVL 215
Cdd:pfam03439  78 KEMEHLL 84
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 423-472 5.54e-27

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: 103.76  E-value: 5.54e-27
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 215498598 423 FKMGDHVKVIAGRFEGDTGLIVRVEDNMVVLFSDLTMHELKVLPRDLQLC 472
Cdd:cd06083    2 FKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 603-654 1.50e-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: 102.56  E-value: 1.50e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 215498598 603 RDSELIGETIKITQGPYKGHIGIVKDATESTARVELHTKCQTISVDRSRIAV 654
Cdd:cd06085    1 GRDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLAV 52
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 903-959 1.56e-25

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: 99.90  E-value: 1.56e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 215498598 903 EHLEPVVPVAKDKVKVILGEDREETGELLSIDHPEGVVKM-GNGKITMQPMRYLCKMH 959
Cdd:cd06086    1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMdSDGDIKILPMNFLAKLV 58
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 678-802 3.73e-23

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: 95.67  E-value: 3.73e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598   678 GSQTPMY-SSGSRTPMYGSQTPLYEAGSRT--PHFGGGQTPVHDG--SRTPVHGAWDPTTANTPARPELDDYQLEEASPS 752
Cdd:smart01104   1 GGRTPAWgASGSKTPAWGSRTPGTAAGGAPtaRGGSGSRTPAWGGagSRTPAWGGAGPTGSRTPAWGGASAWGNKSSEGS 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 215498598   753 YQPATPGYQAPETPQGPYTPQTPGMYGsdhgfspyqaSPSPTAYQPSPSP 802
Cdd:smart01104  81 ASSWAAGPGGAYGAPTPGYGGTPSAYG----------PATPGGGAMAGSA 120
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 371-421 1.83e-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: 88.33  E-value: 1.83e-21
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 215498598 371 FAPGDTVEVAEGELVHLQGKIISIDGNKITMLPRHEDLTEPLDFQAHELKK 421
Cdd:cd06082    1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 548-590 7.25e-21

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: 86.42  E-value: 7.25e-21
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 215498598 548 RDIVKVIDGPHSGSQGVVKHIFRSFAFLHSRMMLENGGIFVCK 590
Cdd:cd06084    1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 227-264 3.76e-17

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: 75.58  E-value: 3.76e-17
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 215498598 227 KQWVRLKRGIYRDDLAQVDYVDTAQSQVNLKLLPRVDY 264
Cdd:cd06081    1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 678-737 2.12e-15

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: 71.71  E-value: 2.12e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598  678 GSQTPMYSS--GSRTPMY---GSQTPLY-EAGSRTPHFG-GGQTPVHD--GSRTPVH-GAWDPttANTPA 737
Cdd:pfam12815   1 GSRTPAYNSagGSRTPAWgadGSRTPAYgGAGGRTPAYNqGGKTPAWGgaGSRTPAYyGAWGG--SRTPA 68
nusG PRK08559
transcription antitermination protein NusG; Validated
 126-267 3.88e-11

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 62.19  E-value: 3.88e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598 126 KDPNLWMVKCKIGEEKSTVLQMMRKFiayqySEEPLQIRSVVAPEGLKGYIYIEAYKHTHVKQVIQGVGNLRiGLYQQTm 205
Cdd:PRK08559   4 EMSMIFAVKTTAGQERNVALMLAMRA-----KKENLPIYAILAPPELKGYVLVEAESKGAVEEAIRGIPHVR-GVVPGE- 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 215498598 206 VPIKEMTDVLRVTKEQAQLRPKQWVRLKRGIYRDDLAQVDYVDTAQSQVNLKLL----P-----RVDYTRL 267
Cdd:PRK08559  77 ISFEEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLeaavPipvtvRGDQVRV 147
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 129-217 1.20e-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: 59.31  E-value: 1.20e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598   129 NLWMVKCKIGEEKSTVLQMMRKFIAYQYseePLQIRSVVAP-EGLK----------------GYIYIEAYKHTHVKQVIQ 191
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKAEALGL---EDKIVSILVPtEEVKeirrgkkkvverklfpGYIFVEADLEDEVWTAIR 77

                           90       100
                   ....*....|....*....|....*....
gi 215498598   192 GVGNLRI---GLYQQTMVPIKEMTDVLRV 217
Cdd:smart00738  78 GTPGVRGfvgGGGKPTPVPDDEIEKILKP 106
KOW_elon_Spt5 TIGR00405
transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial ...
 133-259 1.07e-07

transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial NusG and the uL24 (previously L24p/L26e) family of ribosomal proteins. The most recent papers and crystal structures make this a transcription elongation factor rather than a ribosomal protein.


Pssm-ID: 129499 [Multi-domain]  Cd Length: 145  Bit Score: 52.20  E-value: 1.07e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598  133 VKCKIGEEKSTVLQMMRKfiayqYSEEPLQIRSVVAPEGLKGYIYIEAYKHTHVKQVIQGVGNLRiGLYQQTmVPIKEMT 212
Cdd:TIGR00405   3 VKTSVGQEKNVARLMARK-----ARKSGLEVYSILAPESLKGYILVEAETKIDMRNPIIGVPHVR-GVVEGE-IDFEEIE 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 215498598  213 DVLRVTKEQAQLRPKQWVRLKRGIYRDDLAQVDYVDTAQSQVNLKLL 259
Cdd:TIGR00405  76 RFLTPKKIIESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELI 122
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 57-123 2.02e-07

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: 49.96  E-value: 2.02e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598   57 EGAETEEASSKELHSHRRL---QMMLTSQKEDEIEDYYRRKYADTTATEggYREADVElsdEIAQQTLLP 123
Cdd:pfam11942  33 EEDEDEEDGRRDDRRHRELdrrRELEEDEDAEEIAEYLKERYGRSSSDA--YRGDAEE---GVPQRLLLP 97
PHA03247 PHA03247
large tegument protein UL36; Provisional
 715-844 7.20e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 50.32  E-value: 7.20e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598  715 PVHDGSRTPVHG--------AWDPTTANTP-ARPELDDYQLEEASPSYQPATPGYQA----PETPQGPYTPQTPgmyGSD 781
Cdd:PHA03247 2528 PVHPRMLTWIRGleelasddAGDPPPPLPPaAPPAAPDRSVPPPRPAPRPSEPAVTSrarrPDAPPQSARPRAP---VDD 2604

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 215498598  782 HGFSPYQASPS---PTAYQPSPSPKGyvatPSPVAFQAGTPSPSTyggyspmTPGAPSPFNPQTPG 844
Cdd:PHA03247 2605 RGDPRGPAPPSplpPDTHAPDPPPPS----PSPAANEPDPHPPPT-------VPPPERPRDDPAPG 2659
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 759-850 1.71e-05

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: 48.85  E-value: 1.71e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598  759 GYQAPETPQGPYtPQTPGMYGSDHGfsPYQASPSPtAYQPSPSPKgyvatpsPVAFQAGTPSPSTYGGYSPM-TPG---A 834
Cdd:pfam09606 392 FMRQSPQPSVPS-PQGPGSQPPQSH--PGGMIPSP-ALIPSPSPQ-------MSQQPAQQRTIGQDSPGGSLnTPGqsaV 460

                          90
                  ....*....|....*.
gi 215498598  835 PSPFNPQTPGAGMEAL 850
Cdd:pfam09606 461 NSPLNPQEEQLYREKY 476
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 423-449 8.12e-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: 8.12e-05
                           10        20
                   ....*....|....*....|....*..
gi 215498598   423 FKMGDHVKVIAGRFEGDTGLIVRVEDN 449
Cdd:smart00739   2 FEVGDTVRVIAGPFKGKVGKVLEVDGE 28
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 426-451 2.68e-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: 38.91  E-value: 2.68e-04
                          10        20
                  ....*....|....*....|....*.
gi 215498598  426 GDHVKVIAGRFEGDTGLIVRVEDNMV 451
Cdd:pfam00467   2 GDVVRVIAGPFKGKVGKVVEVDDKKN 27
KREPA2 cd23959
Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of ...
 691-851 4.26e-04

Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of the parasitic protozoan's KREPA RNA editing catalytic complex (RECC). Kinetoplastid RNA editing (KRE) proteins occur as pairs or sets of related proteins in multiple complexes. KREPA complex is composed of six components (KREPA1-6), which share a conserved C-terminal region containing an oligonucleotide-binding (OB)-fold-like domain. KREPAs are responsible for the site-specific insertion and deletion of U nucleotides in the kinetoplastid mitochondria pre-messenger RNA. Apart from the conserved C-terminal OB-fold domain, KREPA1, KREPA2, and KREPA3 contain two conserved C2H2 zinc-finger domains. KREPA2 and kinetoplastid RNA editing ligase 1 (KREL1) are specific for ligation post-U-deletion and are paralogous to KREL2 and KREPA1 that are specific for ligation post-U-insertion. KREPA2, is critical for RECC stability and KREL1 integration into the complex.


Pssm-ID: 467780 [Multi-domain]  Cd Length: 424  Bit Score: 43.70  E-value: 4.26e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598 691 PMYGSQTPLYEAGSRTPHFGGGQT----PVHDGSRTPVH--GAWDPTTANT--PARPELDDYQLEEASPSYQPAT-PGYQ 761
Cdd:cd23959   56 PLYGAVSPEGENPFDGPGLVTASTvsdcYVGNANFYEVDmsDAFAMAPDESlgPFRAARVPNPFSASSSTQRETHkTAQV 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598 762 APETPQGPYTPQTP----GMYGSdhgfSPYQASPSPTAYQPSPSPKGYVATPSPVAFQAGTPSPstyggYSPMTPGAPSP 837
Cdd:cd23959  136 APPKAEPQTAPVTPfgqlPMFGQ----HPPPAKPLPAAAAAQQSSASPGEVASPFASGTVSASP-----FATATDTAPSS 206

                        170
                 ....*....|....
gi 215498598 838 FNPQTPGAGMEALS 851
Cdd:cd23959  207 GAPDGFPAEASAPS 220
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 608-639 4.51e-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: 38.52  E-value: 4.51e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 215498598  608 IGETIKITQGPYKGHIGIVKDATESTARVELH 639
Cdd:pfam00467   1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 549-576 4.21e-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: 35.44  E-value: 4.21e-03
                          10        20
                  ....*....|....*....|....*...
gi 215498598  549 DIVKVIDGPHSGSQGVVKHIFRSFAFLH 576
Cdd:pfam00467   3 DVVRVIAGPFKGKVGKVVEVDDKKNRVL 30
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 545-570 5.99e-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: 5.99e-03
                           10        20
                   ....*....|....*....|....*.
gi 215498598   545 IQIRDIVKVIDGPHSGSQGVVKHIFR 570
Cdd:smart00739   2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27
 
Name Accession Description Interval E-value
NGN_Euk cd09888
Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW ...
 129-216 3.92e-41

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: 145.37  E-value: 3.92e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598 129 NLWMVKCKIGEEKSTVLQMMRKFIAYQYSEEPLQIRSVVAPEGLKGYIYIEAYKHTHVKQVIQGVGNLRIGlyQQTMVPI 208
Cdd:cd09888    1 KLWAVKCKPGKEREIVISLMRKFLDLQRTGNPLGIKSVFARDGLKGYIYIEARKEAHVKDAIEGLRGVYLN--TIKLVPI 78


                 ....*...
gi 215498598 209 KEMTDVLR 216
Cdd:cd09888   79 KEMPDVLS 86
Spt5-NGN pfam03439
Early transcription elongation factor of RNA pol II, NGN section; Spt5p and prokaryotic NusG ...
 129-215 1.16e-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: 109.98  E-value: 1.16e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598  129 NLWMVKCKIGEEKSTVLQMMRKFIAYQYSEEpLQIRSVVAPEGLKGYIYIEAYKHTHVKQVIQGVGNLRIGlyQQTMVPI 208
Cdd:pfam03439   1 KIWAVKCTPGQEREVALSLMRKILALAKTNN-LGIYSVFAPDGLKGYIYVEADRQAAVKRALEGIPNVRGL--VPGLVPI 77


                  ....*..
gi 215498598  209 KEMTDVL 215
Cdd:pfam03439  78 KEMEHLL 84
KOW_Spt5_3 cd06083
KOW domain of Spt5, repeat 3; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 423-472 5.54e-27

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: 103.76  E-value: 5.54e-27
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 215498598 423 FKMGDHVKVIAGRFEGDTGLIVRVEDNMVVLFSDLTMHELKVLPRDLQLC 472
Cdd:cd06083    2 FKVGDHVKVISGRHEGETGLVVKVEDDVVTVFSDLTMRELKVFPRDLQLS 51
KOW_Spt5_5 cd06085
KOW domain of Spt5, repeat 5; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 603-654 1.50e-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: 102.56  E-value: 1.50e-26
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 215498598 603 RDSELIGETIKITQGPYKGHIGIVKDATESTARVELHTKCQTISVDRSRIAV 654
Cdd:cd06085    1 GRDPLIGKTVRIRKGPYKGYIGIVKDATGTTARVELHSKNKTITVDRSRLAV 52
KOW_Spt5_6 cd06086
KOW domain of Spt5, repeat 6; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 903-959 1.56e-25

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: 99.90  E-value: 1.56e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 215498598 903 EHLEPVVPVAKDKVKVILGEDREETGELLSIDHPEGVVKM-GNGKITMQPMRYLCKMH 959
Cdd:cd06086    1 EHLEPVPPEKGDRVKVIKGEDRGSTGELISIDGADGIVKMdSDGDIKILPMNFLAKLV 58
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 678-802 3.73e-23

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: 95.67  E-value: 3.73e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598   678 GSQTPMY-SSGSRTPMYGSQTPLYEAGSRT--PHFGGGQTPVHDG--SRTPVHGAWDPTTANTPARPELDDYQLEEASPS 752
Cdd:smart01104   1 GGRTPAWgASGSKTPAWGSRTPGTAAGGAPtaRGGSGSRTPAWGGagSRTPAWGGAGPTGSRTPAWGGASAWGNKSSEGS 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 215498598   753 YQPATPGYQAPETPQGPYTPQTPGMYGsdhgfspyqaSPSPTAYQPSPSP 802
Cdd:smart01104  81 ASSWAAGPGGAYGAPTPGYGGTPSAYG----------PATPGGGAMAGSA 120
KOW_Spt5_2 cd06082
KOW domain of Spt5, repeat 2; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 371-421 1.83e-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: 88.33  E-value: 1.83e-21
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 215498598 371 FAPGDTVEVAEGELVHLQGKIISIDGNKITMLPRHEDLTEPLDFQAHELKK 421
Cdd:cd06082    1 FQPGDNVEVIEGELKGLQGKVESVDGDIVTIMPKHEDLKEPLEFPAKELRK 51
KOW_Spt5_4 cd06084
KOW domain of Spt5, repeat 4; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 548-590 7.25e-21

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: 86.42  E-value: 7.25e-21
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 215498598 548 RDIVKVIDGPHSGSQGVVKHIFRSFAFLHSRMMLENGGIFVCK 590
Cdd:cd06084    1 GDTVKVVDGPYKGRQGTVLHIYRGTLFLHSREVTENGGIFVVR 43
KOW_Spt5_1 cd06081
KOW domain of Spt5, repeat 1; Spt5, an eukaryotic ortholog of NusG, contains multiple KOW ...
 227-264 3.76e-17

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: 75.58  E-value: 3.76e-17
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 215498598 227 KQWVRLKRGIYRDDLAQVDYVDTAQSQVNLKLLPRVDY 264
Cdd:cd06081    1 GSWVRIKRGIYKGDLAQVDEVDENGNRVVVKLIPRIDY 38
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 678-737 2.12e-15

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: 71.71  E-value: 2.12e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598  678 GSQTPMYSS--GSRTPMY---GSQTPLY-EAGSRTPHFG-GGQTPVHD--GSRTPVH-GAWDPttANTPA 737
Cdd:pfam12815   1 GSRTPAYNSagGSRTPAWgadGSRTPAYgGAGGRTPAYNqGGKTPAWGgaGSRTPAYyGAWGG--SRTPA 68
nusG PRK08559
transcription antitermination protein NusG; Validated
 126-267 3.88e-11

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 62.19  E-value: 3.88e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598 126 KDPNLWMVKCKIGEEKSTVLQMMRKFiayqySEEPLQIRSVVAPEGLKGYIYIEAYKHTHVKQVIQGVGNLRiGLYQQTm 205
Cdd:PRK08559   4 EMSMIFAVKTTAGQERNVALMLAMRA-----KKENLPIYAILAPPELKGYVLVEAESKGAVEEAIRGIPHVR-GVVPGE- 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 215498598 206 VPIKEMTDVLRVTKEQAQLRPKQWVRLKRGIYRDDLAQVDYVDTAQSQVNLKLL----P-----RVDYTRL 267
Cdd:PRK08559  77 ISFEEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLeaavPipvtvRGDQVRV 147
CTD smart01104
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 671-781 5.58e-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 characteristic TPA motif.


Pssm-ID: 215026 [Multi-domain]  Cd Length: 121  Bit Score: 60.61  E-value: 5.58e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598   671 RTPMYG-SGSQTPMYSS---------------------------GSRTPMYGSQTPlyeAGSRTPHFGGGQTPvhdgsrt 722
Cdd:smart01104   3 RTPAWGaSGSKTPAWGSrtpgtaaggaptarggsgsrtpawggaGSRTPAWGGAGP---TGSRTPAWGGASAW------- 72

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 215498598   723 pvHGAWDPTTANTPARPElddyqleeaSPSYQPATPGYQAPETPQGPYTPQTPGMYGSD 781
Cdd:smart01104  73 --GNKSSEGSASSWAAGP---------GGAYGAPTPGYGGTPSAYGPATPGGGAMAGSA 120
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 687-755 9.29e-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: 58.61  E-value: 9.29e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 215498598  687 GSRTPMY----GSQTPLYEA-GSRTPHFG--GGQTPV-HDGSRTPvhgAWDPTTANTPARPELDDyqlEEASPSYQP 755
Cdd:pfam12815   1 GSRTPAYnsagGSRTPAWGAdGSRTPAYGgaGGRTPAyNQGGKTP---AWGGAGSRTPAYYGAWG---GSRTPAYGG 71
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 129-217 1.20e-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: 59.31  E-value: 1.20e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598   129 NLWMVKCKIGEEKSTVLQMMRKFIAYQYseePLQIRSVVAP-EGLK----------------GYIYIEAYKHTHVKQVIQ 191
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKAEALGL---EDKIVSILVPtEEVKeirrgkkkvverklfpGYIFVEADLEDEVWTAIR 77

                           90       100
                   ....*....|....*....|....*....
gi 215498598   192 GVGNLRI---GLYQQTMVPIKEMTDVLRV 217
Cdd:smart00738  78 GTPGVRGfvgGGGKPTPVPDDEIEKILKP 106
CTD pfam12815
Spt5 C-terminal nonapeptide repeat binding Spt4; The C-terminal domain of the transcription ...
 669-711 4.90e-08

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: 50.91  E-value: 4.90e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 215498598  669 YNRTPMYG-SGSQTPMYSSGSRTPMY---GSQTPLYEA---GSRTPHFGG 711
Cdd:pfam12815  22 GSRTPAYGgAGGRTPAYNQGGKTPAWggaGSRTPAYYGawgGSRTPAYGG 71
NGN_Arch cd09887
Archaeal N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance ...
 130-200 8.17e-08

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: 50.62  E-value: 8.17e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 215498598 130 LWMVKCKIGEEKsTVLQMMRKFIAyqysEEPLQIRSVVAPEGLKGYIYIEAYKHTHVKQVIQGVGNLRIGL 200
Cdd:cd09887    2 IYAVKTTAGQER-NVADLLAMRAE----KENLDVYSILVPEELKGYVFVEAEDPDRVEELIRGIPHVRGVV 67
KOW_elon_Spt5 TIGR00405
transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial ...
 133-259 1.07e-07

transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial NusG and the uL24 (previously L24p/L26e) family of ribosomal proteins. The most recent papers and crystal structures make this a transcription elongation factor rather than a ribosomal protein.


Pssm-ID: 129499 [Multi-domain]  Cd Length: 145  Bit Score: 52.20  E-value: 1.07e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598  133 VKCKIGEEKSTVLQMMRKfiayqYSEEPLQIRSVVAPEGLKGYIYIEAYKHTHVKQVIQGVGNLRiGLYQQTmVPIKEMT 212
Cdd:TIGR00405   3 VKTSVGQEKNVARLMARK-----ARKSGLEVYSILAPESLKGYILVEAETKIDMRNPIIGVPHVR-GVVEGE-IDFEEIE 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 215498598  213 DVLRVTKEQAQLRPKQWVRLKRGIYRDDLAQVDYVDTAQSQVNLKLL 259
Cdd:TIGR00405  76 RFLTPKKIIESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELI 122
Spt5_N pfam11942
Spt5 transcription elongation factor, acidic N-terminal; This is the very acidic N-terminal ...
 57-123 2.02e-07

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: 49.96  E-value: 2.02e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598   57 EGAETEEASSKELHSHRRL---QMMLTSQKEDEIEDYYRRKYADTTATEggYREADVElsdEIAQQTLLP 123
Cdd:pfam11942  33 EEDEDEEDGRRDDRRHRELdrrRELEEDEDAEEIAEYLKERYGRSSSDA--YRGDAEE---GVPQRLLLP 97
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 426-470 1.15e-06

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: 46.06  E-value: 1.15e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 215498598 426 GDHVKVIAGRFEGDTGLIVRVED----NMVVLFSDLTMHELKVLPRDLQ 470
Cdd:cd00380    1 GDVVRVLRGPYKGREGVVVDIDPrfgiVTVKGATGSKGAELKVRFDDVD 49
PHA03247 PHA03247
large tegument protein UL36; Provisional
 715-844 7.20e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 50.32  E-value: 7.20e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598  715 PVHDGSRTPVHG--------AWDPTTANTP-ARPELDDYQLEEASPSYQPATPGYQA----PETPQGPYTPQTPgmyGSD 781
Cdd:PHA03247 2528 PVHPRMLTWIRGleelasddAGDPPPPLPPaAPPAAPDRSVPPPRPAPRPSEPAVTSrarrPDAPPQSARPRAP---VDD 2604

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 215498598  782 HGFSPYQASPS---PTAYQPSPSPKGyvatPSPVAFQAGTPSPSTyggyspmTPGAPSPFNPQTPG 844
Cdd:PHA03247 2605 RGDPRGPAPPSplpPDTHAPDPPPPS----PSPAANEPDPHPPPT-------VPPPERPRDDPAPG 2659
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 759-850 1.71e-05

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: 48.85  E-value: 1.71e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598  759 GYQAPETPQGPYtPQTPGMYGSDHGfsPYQASPSPtAYQPSPSPKgyvatpsPVAFQAGTPSPSTYGGYSPM-TPG---A 834
Cdd:pfam09606 392 FMRQSPQPSVPS-PQGPGSQPPQSH--PGGMIPSP-ALIPSPSPQ-------MSQQPAQQRTIGQDSPGGSLnTPGqsaV 460

                          90
                  ....*....|....*.
gi 215498598  835 PSPFNPQTPGAGMEAL 850
Cdd:pfam09606 461 NSPLNPQEEQLYREKY 476
PHA03291 PHA03291
envelope glycoprotein I; Provisional
 722-837 1.84e-05

envelope glycoprotein I; Provisional


Pssm-ID: 223033 [Multi-domain]  Cd Length: 401  Bit Score: 48.03  E-value: 1.84e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598 722 TPVHGAWDPttANTPARPELddyqleeaSPS--YQPATPgYQAPETPQGPYTPQTPgmygsdhgfspyqASPSPTAYQPS 799
Cdd:PHA03291 180 GSADGSCDP--ALPLSAPRL--------GPAdvFVPATP-RPTPRTTASPETTPTP-------------STTTSPPSTTI 235

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 215498598 800 PSPKGYVATPSP--VAFQAGTPSPSTYG-GYSPMTPGAPSP 837
Cdd:PHA03291 236 PAPSTTIAAPQAgtTPEAEGTPAPPTPGgGEAPPANATPAP 276
PHA03247 PHA03247
large tegument protein UL36; Provisional
 653-845 2.00e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 48.78  E-value: 2.00e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598  653 AVVGSASKGGGGGVSTYNRTPMYGSGSqtpmyssgSRTPMYGSQTPLYEAGSRTPHFGGGQTPVHDGSRTPVHGAWDPTT 732
Cdd:PHA03247 2581 AVTSRARRPDAPPQSARPRAPVDDRGD--------PRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERP 2652

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598  733 ANTPARPElddyqleeASPSYQPATPGY--QAPETPQGPYTPQTPGMYGSDHGFspyqASPSPTAYQPSPSPKGYV-ATP 809
Cdd:PHA03247 2653 RDDPAPGR--------VSRPRRARRLGRaaQASSPPQRPRRRAARPTVGSLTSL----ADPPPPPPTPEPAPHALVsATP 2720

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 215498598  810 SPvafqagtPSPSTYGGYSPMTPGAP----SPFNPQTPGA 845
Cdd:PHA03247 2721 LP-------PGPAAARQASPALPAAPappaVPAGPATPGG 2753
DUF3432 pfam11914
Domain of unknown function (DUF3432); This presumed domain is functionally uncharacterized. ...
 785-837 2.97e-05

Domain of unknown function (DUF3432); This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 100 amino acids in length. This domain is found associated with pfam00096. This domain has two conserved sequence motifs: YPSPV and PSP.


Pssm-ID: 403204 [Multi-domain]  Cd Length: 98  Bit Score: 43.94  E-value: 2.97e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 215498598  785 SPYQASPSP--TAYqPSPSPKGYvatPSPVAFQAGTPSPSTYGgySPMTPGAPSP 837
Cdd:pfam11914  10 SSISSYSSSvtTSY-PSPITTSY---PSPVSTSYSSPVPSSYP--SPVHTSFPSP 58
PHA03247 PHA03247
large tegument protein UL36; Provisional
 688-847 3.52e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 48.01  E-value: 3.52e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598  688 SRTPMYGSQTPLyEAGSRTPHFGGGQTPVHDGSRTPVHGAWDPTTANTPARPELDDYQLEEASPSYQPATPGYQAPETPQ 767
Cdd:PHA03247 2710 PAPHALVSATPL-PPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAV 2788

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598  768 GPYTPQTPGMYgsdhgfSPYQASPSPTAYQPSPSPKGYVATPSPvafqaGTPSPSTYGGYSPMTPGAPSPfNPQTPGAGM 847
Cdd:PHA03247 2789 ASLSESRESLP------SPWDPADPPAAVLAPAAALPPAASPAG-----PLPPPTSAQPTAPPPPPGPPP-PSLPLGGSV 2856
PHA03247 PHA03247
large tegument protein UL36; Provisional
 681-839 3.80e-05

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 48.01  E-value: 3.80e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598  681 TPMYSSGSRTPMYGSQTPLYEAGSRTPhfGGGQTPVHDGSRTPVHGAwDPTTANTPARPELDDYQLEEASPSYQPATpgy 760
Cdd:PHA03247 2826 GPLPPPTSAQPTAPPPPPGPPPPSLPL--GGSVAPGGDVRRRPPSRS-PAAKPAAPARPPVRRLARPAVSRSTESFA--- 2899

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 215498598  761 QAPETPQGPYTPQTPGmygsdhgfSPYQASPSPTAYQPSPSPKGYVATPSPVAfqagtPSPSTYGGYSPmTPGAPSPFN 839
Cdd:PHA03247 2900 LPPDQPERPPQPQAPP--------PPQPQPQPPPPPQPQPPPPPPPRPQPPLA-----PTTDPAGAGEP-SGAVPQPWL 2964
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 549-586 6.39e-05

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: 41.05  E-value: 6.39e-05
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 215498598 549 DIVKVIDGPHSGSQGVVKHIFRSFAFLHsrMMLENGGI 586
Cdd:cd00380    2 DVVRVLRGPYKGREGVVVDIDPRFGIVT--VKGATGSK 37
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 423-449 8.12e-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: 8.12e-05
                           10        20
                   ....*....|....*....|....*..
gi 215498598   423 FKMGDHVKVIAGRFEGDTGLIVRVEDN 449
Cdd:smart00739   2 FEVGDTVRVIAGPFKGKVGKVLEVDGE 28
PHA03378 PHA03378
EBNA-3B; Provisional
 687-862 8.32e-05

EBNA-3B; Provisional


Pssm-ID: 223065 [Multi-domain]  Cd Length: 991  Bit Score: 46.60  E-value: 8.32e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598 687 GSRTPMYGSQ---TPLYEAGSRTPHFGGGQTPV-HDGSRTPvhgAWDPTTANTPAR-------PELDDYQLEEASPSYQP 755
Cdd:PHA03378 647 VFPTPHQPPQveiTPYKPTWTQIGHIPYQPSPTgANTMLPI---QWAPGTMQPPPRaptpmrpPAAPPGRAQRPAAATGR 723

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598 756 ATPGYQAPETPQGPYTPQTPGMYGSDhgfSPYQASPSPTAYQPSPSPKGYVATPSPVAFQAGTPSPST--YGGYSPMTP- 832
Cdd:PHA03378 724 ARPPAAAPGRARPPAAAPGRARPPAA---APGRARPPAAAPGRARPPAAAPGAPTPQPPPQAPPAPQQrpRGAPTPQPPp 800

                        170       180       190
                 ....*....|....*....|....*....|....
gi 215498598 833 -GAPSPFN---PQTPGAGMEALSVEWQTMDLEVR 862
Cdd:PHA03378 801 qAGPTSMQlmpRAAPGQQGPTKQILRQLLTGGVK 834
PHA03379 PHA03379
EBNA-3A; Provisional
 702-843 1.20e-04

EBNA-3A; Provisional


Pssm-ID: 223066 [Multi-domain]  Cd Length: 935  Bit Score: 46.20  E-value: 1.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598 702 AGSRTPHFGGGQTPV--------HDGSRTPVHGAWD----PTTANTPARPELDDYQLE-----EASPS-YQPATPGYQAP 763
Cdd:PHA03379 406 EKASEPTYGTPRPPVekprpevpQSLETATSHGSAQvpepPPVHDLEPGPLHDQHSMApcpvaQLPPGpLQDLEPGDQLP 485

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598 764 ETPQGPYTPQTPGMYGSDHGFSPYQASPS------PTAYQPSPSPKGYVATPSPVAFQAGTPSPSTYGGYSPMTPG---- 833
Cdd:PHA03379 486 GVVQDGRPACAPVPAPAGPIVRPWEASLSqvpgvaFAPVMPQPMPVEPVPVPTVALERPVCPAPPLIAMQGPGETSgivr 565

                        170
                 ....*....|....*
gi 215498598 834 -----APSPFNPQTP 843
Cdd:PHA03379 566 vrerwRPAPWTPNPP 580
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 129-215 1.35e-04

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: 41.92  E-value: 1.35e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598 129 NLWMVKCKIGEEKSTVLQMMRKFIA---------YQYSEEPLQIRSVVAPEGLKGYIYIEAYKHTHVKQVIQGVGNLR-- 197
Cdd:cd08000    1 NWYVLFVKTGREEKVEKLLEKRFEAndieafvpkKEVPERKRGKIEEVIKPLFPGYVFVETDLSPELYELIREVPGVIgi 80

                         90
                 ....*....|....*....
gi 215498598 198 -IGLYQQTMVPIKEMTDVL 215
Cdd:cd08000   81 lGNGEEPSPVSDEEIEMIL 99
PHA03247 PHA03247
large tegument protein UL36; Provisional
 737-849 1.69e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 45.70  E-value: 1.69e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598  737 ARPELDDYQLEEASPSYQPATP--------GYQAPETPQGPYTPQTPGMYGSDHGFSPyQASPSPTAYQPSPSPKGYVAT 808
Cdd:PHA03247 2699 ADPPPPPPTPEPAPHALVSATPlppgpaaaRQASPALPAAPAPPAVPAGPATPGGPAR-PARPPTTAGPPAPAPPAAPAA 2777

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 215498598  809 PSPVAFQAGTPSPStyggySPMTPGAPSPFNPQTPGAGMEA 849
Cdd:PHA03247 2778 GPPRRLTRPAVASL-----SESRESLPSPWDPADPPAAVLA 2813
DUF1373 pfam07117
Protein of unknown function (DUF1373); This family consists of several hypothetical proteins ...
 691-802 2.40e-04

Protein of unknown function (DUF1373); This family consists of several hypothetical proteins which seem to be specific to Oryzias latipes (Japanese ricefish). Members of this family are typically around 200 residues in length. The function of this family is unknown.


Pssm-ID: 462093 [Multi-domain]  Cd Length: 212  Bit Score: 43.63  E-value: 2.40e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598  691 PMYGSQTPLYEAGSrtPHFGGGQTPVHDGSRTPvhgawDPTTANTPARPelddYQLEEASPSYQPATPGYQAPETPQGPY 770
Cdd:pfam07117  36 PGQEPEPPRPEEEE--GQGGGGGTFPFPGSPEP-----EPGGGGSGPMP----MSASAPEPEPAKAKPQRPAPAQGHGHG 104

                          90       100       110
                  ....*....|....*....|....*....|..
gi 215498598  771 tpqtpGMYGSDHGFSPYQASPSPTAYQPSPSP 802
Cdd:pfam07117 105 -----GGGDSDSSGSGSGHQGSGGAGAGAGAP 131
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 426-451 2.68e-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: 38.91  E-value: 2.68e-04
                          10        20
                  ....*....|....*....|....*.
gi 215498598  426 GDHVKVIAGRFEGDTGLIVRVEDNMV 451
Cdd:pfam00467   2 GDVVRVIAGPFKGKVGKVVEVDDKKN 27
PRK12323 PRK12323
DNA polymerase III subunit gamma/tau;
673-849 3.62e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237057 [Multi-domain]  Cd Length: 700  Bit Score: 44.48  E-value: 3.62e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598 673 PMYGSGSQTPMYSSGSRTPMYGSQTPLYEAGSRTPhfGGGQTPVHDGSRTPVhGAWDPTTANTPARPELDDYQLEEASPS 752
Cdd:PRK12323 410 PAAAAAARAVAAAPARRSPAPEALAAARQASARGP--GGAPAPAPAPAAAPA-AAARPAAAGPRPVAAAAAAAPARAAPA 486

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598 753 YQPATPGYQAPETPQGPYTPQTPGMYGSDHGFSPYQASPSPTAYQPSPSPKGYVATPSPVAFQAgtpspstyggysPMTP 832
Cdd:PRK12323 487 AAPAPADDDPPPWEELPPEFASPAPAQPDAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPA------------PRAA 554

                        170
                 ....*....|....*..
gi 215498598 833 GAPSPFNPQTPGAGMEA 849
Cdd:PRK12323 555 AATEPVVAPRPPRASAS 571
dnaA PRK14086
chromosomal replication initiator protein DnaA;
729-858 3.97e-04

chromosomal replication initiator protein DnaA;


Pssm-ID: 237605 [Multi-domain]  Cd Length: 617  Bit Score: 44.05  E-value: 3.97e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598 729 DPTTANTPARPELDDYQLEEASPSYQPAT-PGYQAPE-TPQGPYTPQTPGMYGSDHGFSPYQASPSPTAYQPSPSPKGYV 806
Cdd:PRK14086  89 DPSAGEPAPPPPHARRTSEPELPRPGRRPyEGYGGPRaDDRPPGLPRQDQLPTARPAYPAYQQRPEPGAWPRAADDYGWQ 168

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 215498598 807 ATPspvafqAGTPSPSTYGgySPMTPGAPSPFNPQTPGAGMEALSVEWQTMD 858
Cdd:PRK14086 169 QQR------LGFPPRAPYA--SPASYAPEQERDREPYDAGRPEYDQRRRDYD 212
KREPA2 cd23959
Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of ...
 691-851 4.26e-04

Kinetoplastid RNA Editing Protein A2 (KREPA2); The KREPA2 (TbMP63) protein is a component of the parasitic protozoan's KREPA RNA editing catalytic complex (RECC). Kinetoplastid RNA editing (KRE) proteins occur as pairs or sets of related proteins in multiple complexes. KREPA complex is composed of six components (KREPA1-6), which share a conserved C-terminal region containing an oligonucleotide-binding (OB)-fold-like domain. KREPAs are responsible for the site-specific insertion and deletion of U nucleotides in the kinetoplastid mitochondria pre-messenger RNA. Apart from the conserved C-terminal OB-fold domain, KREPA1, KREPA2, and KREPA3 contain two conserved C2H2 zinc-finger domains. KREPA2 and kinetoplastid RNA editing ligase 1 (KREL1) are specific for ligation post-U-deletion and are paralogous to KREL2 and KREPA1 that are specific for ligation post-U-insertion. KREPA2, is critical for RECC stability and KREL1 integration into the complex.


Pssm-ID: 467780 [Multi-domain]  Cd Length: 424  Bit Score: 43.70  E-value: 4.26e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598 691 PMYGSQTPLYEAGSRTPHFGGGQT----PVHDGSRTPVH--GAWDPTTANT--PARPELDDYQLEEASPSYQPAT-PGYQ 761
Cdd:cd23959   56 PLYGAVSPEGENPFDGPGLVTASTvsdcYVGNANFYEVDmsDAFAMAPDESlgPFRAARVPNPFSASSSTQRETHkTAQV 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598 762 APETPQGPYTPQTP----GMYGSdhgfSPYQASPSPTAYQPSPSPKGYVATPSPVAFQAGTPSPstyggYSPMTPGAPSP 837
Cdd:cd23959  136 APPKAEPQTAPVTPfgqlPMFGQ----HPPPAKPLPAAAAAQQSSASPGEVASPFASGTVSASP-----FATATDTAPSS 206

                        170
                 ....*....|....
gi 215498598 838 FNPQTPGAGMEALS 851
Cdd:cd23959  207 GAPDGFPAEASAPS 220
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 608-639 4.51e-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: 38.52  E-value: 4.51e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 215498598  608 IGETIKITQGPYKGHIGIVKDATESTARVELH 639
Cdd:pfam00467   1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLVE 32
RCR pfam12273
Chitin synthesis regulation, resistance to Congo red; RCR proteins are ER membrane proteins ...
 751-811 4.73e-04

Chitin synthesis regulation, resistance to Congo red; RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5.


Pssm-ID: 432443 [Multi-domain]  Cd Length: 113  Bit Score: 40.86  E-value: 4.73e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 215498598  751 PSYQPATPGYQAPETPQGPYTPQTpGMYGSDHGFSP--YQASPSPTAYQPSPSPKG---YVATPSP 811
Cdd:pfam12273  47 PSYGQSQQDPQPTGTYVPTYTPND-GYYDQQGNFHNagSGLQPPQQAYQPPTSSEGdpdYAPPAGP 111
PHA03247 PHA03247
large tegument protein UL36; Provisional
 697-852 5.06e-04

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 44.16  E-value: 5.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598  697 TPLYEAGSRTPhfGGGQTPVHDGSRTPVHGAWDPTTANTPARPELDDY---QLEEASPSYQPATPgyQAPETPQGPYTPQ 773
Cdd:PHA03247 2646 VPPPERPRDDP--APGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTvgsLTSLADPPPPPPTP--EPAPHALVSATPL 2721

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 215498598  774 TPGMYGSDHGFSPYQASPSPTAYQPSPSPKGYVATPSPVAFQAGTPSPStyggySPMTPGAPSPfnPQTPGAGMEALSV 852
Cdd:PHA03247 2722 PPGPAAARQASPALPAAPAPPAVPAGPATPGGPARPARPPTTAGPPAPA-----PPAAPAAGPP--RRLTRPAVASLSE 2793
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 710-846 2.39e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 41.90  E-value: 2.39e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598 710 GGGQTPVHDGSRTPVHGAWDPTTANTPARpelddyqleeASPSYQPATPGYQAPETPQGPYTPQTPGMYGSDhgfspyQA 789
Cdd:PRK07764 395 AAAAPSAAAAAPAAAPAPAAAAPAAAAAP----------APAAAPQPAPAPAPAPAPPSPAGNAPAGGAPSP------PP 458

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 215498598 790 SPSPTAyQPSPSPkgyVATPSPVAFQAGTPSPSTYGGYSPMTPGAPSPFNPQTPGAG 846
Cdd:PRK07764 459 AAAPSA-QPAPAP---AAAPEPTAAPAPAPPAAPAPAAAPAAPAAPAAPAGADDAAT 511
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 549-576 4.21e-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: 35.44  E-value: 4.21e-03
                          10        20
                  ....*....|....*....|....*...
gi 215498598  549 DIVKVIDGPHSGSQGVVKHIFRSFAFLH 576
Cdd:pfam00467   3 DVVRVIAGPFKGKVGKVVEVDDKKNRVL 30
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 545-570 5.99e-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: 5.99e-03
                           10        20
                   ....*....|....*....|....*.
gi 215498598   545 IQIRDIVKVIDGPHSGSQGVVKHIFR 570
Cdd:smart00739   2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27
PRK07764 PRK07764
DNA polymerase III subunits gamma and tau; Validated
 710-845 6.29e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236090 [Multi-domain]  Cd Length: 824  Bit Score: 40.35  E-value: 6.29e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 215498598 710 GGGQTPVHDGSRTPVHGAWDPTTANTPARPELDDYQLEEASPSYQPATPGYQAPETPQGPYTPQTPGMYGSDHGFSPYQA 789
Cdd:PRK07764 595 AGGEGPPAPASSGPPEEAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAG 674

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 215498598 790 SPSPTAYQPSPSPKGyVATPSPVAFQAGTPSPSTyggySPMTPGAPSPFNPQTPGA 845
Cdd:PRK07764 675 GAAPAAPPPAPAPAA-PAAPAGAAPAQPAPAPAA----TPPAGQADDPAAQPPQAA 725
 
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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