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Conserved domains on  [gi|447115140|ref|WP_001192396|]
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MULTISPECIES: transcription/translation regulatory transformer protein RfaH [Enterobacteriaceae]

Protein Classification

transcriptional activator RfaH( domain architecture ID 11483492)

transcriptional activator RfaH controls general transcriptional pausing and termination in prokaryotes

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
1-162 6.69e-123

transcription/translation regulatory transformer protein RfaH;


:

Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 342.26  E-value: 6.69e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140   1 MQSWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVR 80
Cdd:PRK09014   1 MKSWYLLYCKRGQLQRAQEHLERQGVECLYPMITLEKIVRGKRTEVSEPLFPNYLFVEFDPEVIHTTTIRSTRGVSHFVR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140  81 FGASPAIVPSAVIHQLSVYKPKDIVDPATPYPGDKVIITEGAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKNTEFR 160
Cdd:PRK09014  81 FGAQPAIVPSDVIYQLSVYKPEKIVDPETPKPGDKVIITEGAFEGLQAIYTEPDGEARSILLLNLLNKQVKHSVDNTQFR 160


                 ..
gi 447115140 161 KL 162
Cdd:PRK09014 161 KI 162
 
Name Accession Description Interval E-value
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
1-162 6.69e-123

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 342.26  E-value: 6.69e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140   1 MQSWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVR 80
Cdd:PRK09014   1 MKSWYLLYCKRGQLQRAQEHLERQGVECLYPMITLEKIVRGKRTEVSEPLFPNYLFVEFDPEVIHTTTIRSTRGVSHFVR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140  81 FGASPAIVPSAVIHQLSVYKPKDIVDPATPYPGDKVIITEGAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKNTEFR 160
Cdd:PRK09014  81 FGAQPAIVPSDVIYQLSVYKPEKIVDPETPKPGDKVIITEGAFEGLQAIYTEPDGEARSILLLNLLNKQVKHSVDNTQFR 160


                 ..
gi 447115140 161 KL 162
Cdd:PRK09014 161 KI 162
RfaH TIGR01955
transcription elongation factor/antiterminator RfaH; This model represents the transcription ...
 4-160 2.24e-92

transcription elongation factor/antiterminator RfaH; This model represents the transcription elongation factor/antiterminator, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes. [Transcription, Transcription factors]


Pssm-ID: 131010 [Multi-domain]  Cd Length: 159  Bit Score: 265.09  E-value: 2.24e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140    4 WYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVRFGA 83
Cdd:TIGR01955   1 WYLLYCKPRQEQRAQEHLERQAVECYLPMITVEKIVRGKRQAVSEPLFPNYLFIEFDPEVDSWTTIRSTRGVSRFVRFGG 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 447115140   84 SPAIVPSAVIHQLSVYKPKDIVDPAT--PYPGDKVIITEGAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKNTEFR 160
Cdd:TIGR01955  81 HPAPVPDDLIHQLRQYEPKDSVPPATtlPYKGDKVRITDGAFAGFEAIFLEPDGEKRSMLLLNMIGKQIKVSVPNTSVE 159
NGN_SP_RfaH cd09892
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; ...
 3-96 1.02e-50

N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; RfaH is an operon-specific virulence regulator, thought to have arisen from an early duplication of N-Utilization Substance G (NusG). Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS biosynthesis genes. NusG SP family members are operon-specific transcriptional antitermination factors. NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination in bacteria. In contrast, RfaH is a non-essential protein that controls expression of operons containing an ops (operon polarity suppressor) element in their transcribed DNA. RfaH and NusG are different in their response to Rho-dependent terminators and regulatory targets. The NusG N-terminal (NGN) domain is quite similar in all NusG orthologs, but its C-terminal domains and the linker that separate these two domains are different. The domain organization of NusG and its homologs suggest that the common properties of NusG and RfaH are due to their similar NGN domains.


Pssm-ID: 193581 [Multi-domain]  Cd Length: 96  Bit Score: 157.34  E-value: 1.02e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140   3 SWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVRFG 82
Cdd:cd09892    1 AWYLLYTKPRQEERAAENLERQGFEVFLPMIRVEKRRRGKRTVVTEPLFPGYLFVRLDPEVQNWRPIRSTRGVSRLVRFG 80

                         90
                 ....*....|....
gi 447115140  83 ASPAIVPSAVIHQL 96
Cdd:cd09892   81 GEPAPVPDALIEAL 94
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
1-162 5.96e-47

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 150.36  E-value: 5.96e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140   1 MQSWYLLYCKRGQLQRAQEHLERQAVN--CLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHF 78
Cdd:COG0250    4 EKRWYVVHTYSGYEKKVKENLERRIEGieVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLVRNTPGVTGF 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140  79 VRFGASPAIVPSAVIHQL--SVYKPKDIVDPATPY-PGDKVIITEGAFEGFQAIFTEPD-GEARSMLLLNLINKEIKHSV 154
Cdd:COG0250   84 VGFGGKPAPLPDEEVERIlaRLEEGEEKPRPKVDFeVGDRVRITDGPFAGFEGTVEEVDpEKGRVKVLVSIFGRETPVEL 163


                 ....*...
gi 447115140 155 KNTEFRKL 162
Cdd:COG0250  164 DFSQVEKI 171
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 3-96 2.47e-30

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: 105.92  E-value: 2.47e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140     3 SWYLLYCKRGQLQRAQEHLERQAVN---------CLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATR 73
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKAEAlgledkivsILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGTP 80

                           90       100
                   ....*....|....*....|...
gi 447115140    74 GVSHFVRFGASPAIVPSAVIHQL 96
Cdd:smart00738  81 GVRGFVGGGGKPTPVPDDEIEKI 103
NusG pfam02357
Transcription termination factor nusG;
4-96 1.52e-29

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 103.84  E-value: 1.52e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140    4 WYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVRFGA 83
Cdd:pfam02357   3 WYVLQTYSGKEKKVKENLERQGIEVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRSTPGVTGFVGGSG 82

                          90
                  ....*....|...
gi 447115140   84 SPAIVPSAVIHQL 96
Cdd:pfam02357  83 KPTPIPDEEVERI 95
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 4-130 5.87e-17

UpxY family transcription antiterminator; The UpxY family of NusG-related transcription antiterminators was described originally from a paralogous family of eight members from Bacteriodes fragilis, UpaY to UphY, each of which was associated with a distinct capsular polysaccharide biosynthesis locus. There is no UpxY protein per se.


Pssm-ID: 468125 [Multi-domain]  Cd Length: 162  Bit Score: 73.27  E-value: 5.87e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140   4 WYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHtTTINATRGVSHFVRFG- 82
Cdd:NF033644   1 WYALYTRPRREKKVAELLEKKGIESFLPMQKEIRQWSDRKKRVEVPLIPNLVFVHITEKELD-EVLEQTPGVVRYIRDDr 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 447115140  83 --ASPAIVPSAVIHQ----LSVYKPKDIVDPATPYPGDKVIITEGAFEGFQAIF 130
Cdd:NF033644  80 gkSKPAIIPDKQMERfrlmLDPSDEVVVYLEAPLKKGDKVRVIGGPLKGLEGEL 133
antiterm_LoaP NF033641
antiterminator LoaP; LoaP is a paralog of NusG with an extensive presence in Firmicutes. The ...
 4-129 6.15e-06

antiterminator LoaP; LoaP is a paralog of NusG with an extensive presence in Firmicutes. The founding member, from Bacillus amyloliquefaciens, was shown to serve as an antiterminator for the transcription of genes involved in antibiotic biosynthesis.


Pssm-ID: 468124 [Multi-domain]  Cd Length: 166  Bit Score: 43.91  E-value: 6.15e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140   4 WYLLYCKRGQLQRAQEHLERQA----VNCLAP-MITLEKIvRGKRTAVSEPLFPNYLFVEfdpevihtTTINAT-----R 73
Cdd:NF033641   1 WYVLFVRTGKEEKVKKLLNKLFdkelLRCFVPkRKLPERK-QGKWYKVIKPLFPGYVFIE--------TDMNEElyyklK 71

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 447115140  74 GVSHFVRF----GASPAIVPS---AVIHQLSvyKPKDIVDPATPY-PGDKVIITEGAFEGFQAI 129
Cdd:NF033641  72 KIPGIIRLlgneGDEFSPIPEeemEFLLKLL--NDDDIIEYSKGYiEGDKVIVISGPLKGLEGI 133
 
Name Accession Description Interval E-value
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
1-162 6.69e-123

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 342.26  E-value: 6.69e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140   1 MQSWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVR 80
Cdd:PRK09014   1 MKSWYLLYCKRGQLQRAQEHLERQGVECLYPMITLEKIVRGKRTEVSEPLFPNYLFVEFDPEVIHTTTIRSTRGVSHFVR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140  81 FGASPAIVPSAVIHQLSVYKPKDIVDPATPYPGDKVIITEGAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKNTEFR 160
Cdd:PRK09014  81 FGAQPAIVPSDVIYQLSVYKPEKIVDPETPKPGDKVIITEGAFEGLQAIYTEPDGEARSILLLNLLNKQVKHSVDNTQFR 160


                 ..
gi 447115140 161 KL 162
Cdd:PRK09014 161 KI 162
RfaH TIGR01955
transcription elongation factor/antiterminator RfaH; This model represents the transcription ...
 4-160 2.24e-92

transcription elongation factor/antiterminator RfaH; This model represents the transcription elongation factor/antiterminator, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes. [Transcription, Transcription factors]


Pssm-ID: 131010 [Multi-domain]  Cd Length: 159  Bit Score: 265.09  E-value: 2.24e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140    4 WYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVRFGA 83
Cdd:TIGR01955   1 WYLLYCKPRQEQRAQEHLERQAVECYLPMITVEKIVRGKRQAVSEPLFPNYLFIEFDPEVDSWTTIRSTRGVSRFVRFGG 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 447115140   84 SPAIVPSAVIHQLSVYKPKDIVDPAT--PYPGDKVIITEGAFEGFQAIFTEPDGEARSMLLLNLINKEIKHSVKNTEFR 160
Cdd:TIGR01955  81 HPAPVPDDLIHQLRQYEPKDSVPPATtlPYKGDKVRITDGAFAGFEAIFLEPDGEKRSMLLLNMIGKQIKVSVPNTSVE 159
NGN_SP_RfaH cd09892
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; ...
 3-96 1.02e-50

N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; RfaH is an operon-specific virulence regulator, thought to have arisen from an early duplication of N-Utilization Substance G (NusG). Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS biosynthesis genes. NusG SP family members are operon-specific transcriptional antitermination factors. NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination in bacteria. In contrast, RfaH is a non-essential protein that controls expression of operons containing an ops (operon polarity suppressor) element in their transcribed DNA. RfaH and NusG are different in their response to Rho-dependent terminators and regulatory targets. The NusG N-terminal (NGN) domain is quite similar in all NusG orthologs, but its C-terminal domains and the linker that separate these two domains are different. The domain organization of NusG and its homologs suggest that the common properties of NusG and RfaH are due to their similar NGN domains.


Pssm-ID: 193581 [Multi-domain]  Cd Length: 96  Bit Score: 157.34  E-value: 1.02e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140   3 SWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVRFG 82
Cdd:cd09892    1 AWYLLYTKPRQEERAAENLERQGFEVFLPMIRVEKRRRGKRTVVTEPLFPGYLFVRLDPEVQNWRPIRSTRGVSRLVRFG 80

                         90
                 ....*....|....
gi 447115140  83 ASPAIVPSAVIHQL 96
Cdd:cd09892   81 GEPAPVPDALIEAL 94
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
1-162 5.96e-47

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 150.36  E-value: 5.96e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140   1 MQSWYLLYCKRGQLQRAQEHLERQAVN--CLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHF 78
Cdd:COG0250    4 EKRWYVVHTYSGYEKKVKENLERRIEGieVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLVRNTPGVTGF 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140  79 VRFGASPAIVPSAVIHQL--SVYKPKDIVDPATPY-PGDKVIITEGAFEGFQAIFTEPD-GEARSMLLLNLINKEIKHSV 154
Cdd:COG0250   84 VGFGGKPAPLPDEEVERIlaRLEEGEEKPRPKVDFeVGDRVRITDGPFAGFEGTVEEVDpEKGRVKVLVSIFGRETPVEL 163


                 ....*...
gi 447115140 155 KNTEFRKL 162
Cdd:COG0250  164 DFSQVEKI 171
NGN_SP cd09886
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP); The ...
 3-96 1.07e-37

N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP); The N-Utilization Substance G (NusG) protein is involved in transcription elongation and termination. NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination in bacteria. Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS biosynthesis genes. NusG SP family members are operon-specific transcriptional antitermination factors. The NusG N-terminal (NGN) domain is quite similar in all NusG orthologs, but its C-terminal domains and the linker that separate these two domains are different. The domain organization of NusG and its orthologs suggest that the common properties of NusG and its orthologs and paralogs are due to their similar NGN domains.


Pssm-ID: 193575 [Multi-domain]  Cd Length: 97  Bit Score: 124.40  E-value: 1.07e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140   3 SWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPE-VIHTTTINATRGVSHFVRF 81
Cdd:cd09886    1 SWYALRTNPGCEQRAEEALEARGVEAFLPMLTEERKRRRKKFDVERPLFPGYVFARLDRSkGQDTSTIRACDGVLGVVGF 80

                         90
                 ....*....|....*
gi 447115140  82 GASPAIVPSAVIHQL 96
Cdd:cd09886   81 DGRPAPVPEQEMRDL 95
NGN_SP_AnfA1 cd09894
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1; ...
 2-96 5.56e-31

N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1; Regulation of the afp, antifeeding prophage, gene cluster is mediated by AnFA1, a RfaH-like transcriptional antiterminator. RfaH is an operon-specific virulence regulator, thought to arisen from an early duplication of N-Utilization Substance G (NusG). NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination in bacteria. Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS biosynthesis genes. NusG SP family members are operon-specific transcriptional antitermination factors. Orthologs of the NusG gene exist in all bacteria, but their functions and requirements are different. The NusG N-terminal domain (NGN) is similar in all NusG orthologs, but its C-terminal domain and the linker that separate these two domains are different. The domain organization of NusG and its orthologs suggests that the common properties of NusG and its orthologs and paralogs are due to their similar NGN domains.


Pssm-ID: 193583 [Multi-domain]  Cd Length: 99  Bit Score: 107.37  E-value: 5.56e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140   2 QSWYLLYCKRGQLQRAQEHLERQAVNCLAPMI---TLEKIVRGKRTaVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHF 78
Cdd:cd09894    1 KRWYLLRCKSGKIQSVIFSLERLGVEVFCPMIrtrRKRTDCKSYRE-KIEPLFPGYLFVRFDPEVVHTSKITLASGVSGF 79

                         90
                 ....*....|....*...
gi 447115140  79 VRFGASPAIVPSAVIHQL 96
Cdd:cd09894   80 VRFGGEPCPVPDAVIRAL 97
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 3-96 2.47e-30

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: 105.92  E-value: 2.47e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140     3 SWYLLYCKRGQLQRAQEHLERQAVN---------CLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATR 73
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKAEAlgledkivsILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGTP 80

                           90       100
                   ....*....|....*....|...
gi 447115140    74 GVSHFVRFGASPAIVPSAVIHQL 96
Cdd:smart00738  81 GVRGFVGGGGKPTPVPDDEIEKI 103
NusG pfam02357
Transcription termination factor nusG;
4-96 1.52e-29

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 103.84  E-value: 1.52e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140    4 WYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHFVRFGA 83
Cdd:pfam02357   3 WYVLQTYSGKEKKVKENLERQGIEVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRSTPGVTGFVGGSG 82

                          90
                  ....*....|...
gi 447115140   84 SPAIVPSAVIHQL 96
Cdd:pfam02357  83 KPTPIPDEEVERI 95
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 3-89 1.01e-23

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: 88.91  E-value: 1.01e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140   3 SWYLLYCKRGQLQRAQEHLERQA----VNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHTTTINATRGVSHF 78
Cdd:cd08000    1 NWYVLFVKTGREEKVEKLLEKRFeandIEAFVPKKEVPERKRGKIEEVIKPLFPGYVFVETDLSPELYELIREVPGVIGI 80

                         90
                 ....*....|.
gi 447115140  79 VRFGASPAIVP 89
Cdd:cd08000   81 LGNGEEPSPVS 91
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 4-130 5.87e-17

UpxY family transcription antiterminator; The UpxY family of NusG-related transcription antiterminators was described originally from a paralogous family of eight members from Bacteriodes fragilis, UpaY to UphY, each of which was associated with a distinct capsular polysaccharide biosynthesis locus. There is no UpxY protein per se.


Pssm-ID: 468125 [Multi-domain]  Cd Length: 162  Bit Score: 73.27  E-value: 5.87e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140   4 WYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHtTTINATRGVSHFVRFG- 82
Cdd:NF033644   1 WYALYTRPRREKKVAELLEKKGIESFLPMQKEIRQWSDRKKRVEVPLIPNLVFVHITEKELD-EVLEQTPGVVRYIRDDr 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 447115140  83 --ASPAIVPSAVIHQ----LSVYKPKDIVDPATPYPGDKVIITEGAFEGFQAIF 130
Cdd:NF033644  80 gkSKPAIIPDKQMERfrlmLDPSDEVVVYLEAPLKKGDKVRVIGGPLKGLEGEL 133
NGN_SP_UpxY cd09895
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; ...
 4-91 2.18e-13

N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; The N-Utilization Substance G (NusG) proteins are involved in transcription elongation and termination. NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination. Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS (lipopolysaccharide) biosynthesis genes. NusG SP family members are operon-specific transcriptional antitermination factors. UpxY proteins, UpxY proteins, where the x is replaced by the letter designation of the specific polysaccharide (UpaY to UphY), are a family of NusG SP factors that act specifically in transcriptional antitermination of operons from which they are encoded. UpxYs are necessary and specific for transcription regulation of the polysaccharide biosynthesis operon. Orthologs of the NusG gene exist in all bacteria, but their functions and requirements are different. The NusG N-terminal (NGN) domain is similar in all NusG orthologs, but its C-terminal domain and the linker that separate these two domains are different. The domain organization of NusG and its orthologs suggests that the common properties of NusG and its orthologs and paralogs are due to their similar NGN domains.


Pssm-ID: 193584 [Multi-domain]  Cd Length: 95  Bit Score: 62.21  E-value: 2.18e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140   4 WYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIhtTTINATRGVSHFVRFGA 83
Cdd:cd09895    2 WYALYTFPRREKKVAEYLEKKGIECFLPMQYEVRQWSGRKKRVEVPLFPNLVFVHITREEL--DEVLETPGVVRFVRYRG 79


                 ....*....
gi 447115140  84 -SPAIVPSA 91
Cdd:cd09895   80 kEPAIIPDK 88
NGN_SP_TaA cd09893
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), TaA; ...
 3-96 2.23e-08

N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), TaA; The N-Utilization Substance G (NusG) protein is involved in transcription elongation and termination. NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination in bacteria. Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS biosynthesis genes. NusG SP family members are operon-specific transcriptional antiterminationn factors. TaA is a NusG SP factor that is required for synthesis of a polyketide antibiotic TA in Myxococcus xanthus. Orthologs of the NusG gene exist in all bacteria, but its functions and requirements are different. The NusG N-terminal (NGN) domain is quite similar in all NusG orthologs, but its C-terminal domains and the linker that separate these two domains are different. The domain organization of NusG and its orthologs suggest that the common properties of NusG and its orthologs and paralogs are due to their similar NGN domains.


Pssm-ID: 193582 [Multi-domain]  Cd Length: 95  Bit Score: 49.23  E-value: 2.23e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140   3 SWYLLYCKRGQLQRAQEHLERQAVNCLAPMITLEKIVRGKRTAVSEPLFPNYLFVEFDPEVIHtTTINATRGVSHFVRFG 82
Cdd:cd09893    1 SWYALYTRSRHEKKVADRLAKKGIESFLPLYEVLSRWKDRKKKIKVPLFPGYLFVRFQLDPER-LRILKTPGVVRIVGNS 79

                         90
                 ....*....|....
gi 447115140  83 ASPAIVPSAVIHQL 96
Cdd:cd09893   80 GGPIPIPDEEIASL 93
NGN_Bact_1 cd09891
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The ...
 4-85 6.21e-08

Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The N-Utilization Substance G (NusG) protein is involved in transcription elongation and termination in bacteria. NusG is essential in Escherichia coli and associates with RNA polymerase elongation and Rho-termination. Homologs of the NusG gene exist in all bacteria. The NusG N-terminal domain (NGN) is similar in all NusG homologs, but its C-terminal domain and the linker that separates these two domains are different. The domain organization of NusG suggests that the common properties of NusG and its homologs are due to their similar NGN domains.


Pssm-ID: 193580 [Multi-domain]  Cd Length: 107  Bit Score: 48.24  E-value: 6.21e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140   4 WYLLYCKRGQLQRAQEHLERQAVN---------CLAPMITLEKIVRGKRTAVSEPLFPNYLFVE--FDPEVIHttTINAT 72
Cdd:cd09891    2 WYVVHTYSGYENKVKENLEKRIESegledyigeVLVPTEEVVEVKNGKKKVKERKLFPGYVLVEmdMNDDTWH--LVRNT 79

                         90
                 ....*....|...
gi 447115140  73 RGVSHFVRFGASP 85
Cdd:cd09891   80 PGVTGFVGSGGKP 92
antiterm_LoaP NF033641
antiterminator LoaP; LoaP is a paralog of NusG with an extensive presence in Firmicutes. The ...
 4-129 6.15e-06

antiterminator LoaP; LoaP is a paralog of NusG with an extensive presence in Firmicutes. The founding member, from Bacillus amyloliquefaciens, was shown to serve as an antiterminator for the transcription of genes involved in antibiotic biosynthesis.


Pssm-ID: 468124 [Multi-domain]  Cd Length: 166  Bit Score: 43.91  E-value: 6.15e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140   4 WYLLYCKRGQLQRAQEHLERQA----VNCLAP-MITLEKIvRGKRTAVSEPLFPNYLFVEfdpevihtTTINAT-----R 73
Cdd:NF033641   1 WYVLFVRTGKEEKVKKLLNKLFdkelLRCFVPkRKLPERK-QGKWYKVIKPLFPGYVFIE--------TDMNEElyyklK 71

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 447115140  74 GVSHFVRF----GASPAIVPS---AVIHQLSvyKPKDIVDPATPY-PGDKVIITEGAFEGFQAI 129
Cdd:NF033641  72 KIPGIIRLlgneGDEFSPIPEeemEFLLKLL--NDDDIIEYSKGYiEGDKVIVISGPLKGLEGI 133
NGN_plant cd09890
Plant N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance G ...
 4-92 3.92e-04

Plant 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. NusG contains a 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 comprising an acidic N-terminus, an NGN domain, and multiple KOW motifs at its C-terminus. Spt5 forms an Spt4-Spt5 complex that is an essential RNA polymerase II elongation factor. The bacterial infected plants contain bacterial DNA, such as NGN sequences, that can be used to clone the DNA of uncultured organisms.


Pssm-ID: 193579  Cd Length: 113  Bit Score: 38.10  E-value: 3.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447115140   4 WYLLYCKRGQLQRAQEHLERQAVNCL--------APMITLEKIVR-GKRTAVSEPLFPNYLFVE--FDPEVIhtTTINAT 72
Cdd:cd09890    2 WYMLRVPAGRENQAAEALERALATEFpdrefevwVPSIPVDRKLKnGSISVKEKPLFPGYVLLRcvLNKEVY--DFIRDN 79

                         90       100
                 ....*....|....*....|....*
gi 447115140  73 RGVSHFV-----RFGASPAIVPSAV 92
Cdd:cd09890   80 DSVYGFVgskvgKTGKRQIEIPRPV 104
KOW_NusG cd06091
NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif ...
 112-136 6.85e-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: 35.90  E-value: 6.85e-04
                         10        20
                 ....*....|....*....|....*
gi 447115140 112 PGDKVIITEGAFEGFQAIFTEPDGE 136
Cdd:cd06091    6 VGDTVRIISGPFAGFEGKVEEIDEE 30
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 112-136 4.03e-03

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


Pssm-ID: 128978  Cd Length: 28  Bit Score: 33.46  E-value: 4.03e-03
                           10        20
                   ....*....|....*....|....*
gi 447115140   112 PGDKVIITEGAFEGFQAIFTEPDGE 136
Cdd:smart00739   4 VGDTVRVIAGPFKGKVGKVLEVDGE 28
 
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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