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Conserved domains on  [gi|1889725830|ref|WP_182748059|]
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MULTISPECIES: transcription/translation regulatory transformer protein RfaH [unclassified Pseudoalteromonas]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
rfaH super family cl32338
transcription/translation regulatory transformer protein RfaH;
1-159 4.39e-75

transcription/translation regulatory transformer protein RfaH;


The actual alignment was detected with superfamily member PRK09014:

Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 221.30  E-value: 4.39e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830   1 MECWYLVVCKPKQEERAKTNLQNQGIEAFYPQLTTERLVKGRRTVKHTALFPNYLFVCLESKNGNFSAVKNTRGIGGFVS 80
Cdd:PRK09014    1 MKSWYLLYCKRGQLQRAQEHLERQGVECLYPMITLEKIVRGKRTEVSEPLFPNYLFVEFDPEVIHTTTIRSTRGVSHFVR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830  81 YGASYQLVSKHIIDHLK-NERAHTTESQIPKTGDVVNVNNDSFSNIQAIYKEPDGDLRSILLINLLNQKIEVSVDNKDIK 159
Cdd:PRK09014   81 FGAQPAIVPSDVIYQLSvYKPEKIVDPETPKPGDKVIITEGAFEGLQAIYTEPDGEARSILLLNLLNKQVKHSVDNTQFR 160
 
Name Accession Description Interval E-value
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
1-159 4.39e-75

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 221.30  E-value: 4.39e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830   1 MECWYLVVCKPKQEERAKTNLQNQGIEAFYPQLTTERLVKGRRTVKHTALFPNYLFVCLESKNGNFSAVKNTRGIGGFVS 80
Cdd:PRK09014    1 MKSWYLLYCKRGQLQRAQEHLERQGVECLYPMITLEKIVRGKRTEVSEPLFPNYLFVEFDPEVIHTTTIRSTRGVSHFVR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830  81 YGASYQLVSKHIIDHLK-NERAHTTESQIPKTGDVVNVNNDSFSNIQAIYKEPDGDLRSILLINLLNQKIEVSVDNKDIK 159
Cdd:PRK09014   81 FGAQPAIVPSDVIYQLSvYKPEKIVDPETPKPGDKVIITEGAFEGLQAIYTEPDGEARSILLLNLLNKQVKHSVDNTQFR 160
RfaH TIGR01955
transcription elongation factor/antiterminator RfaH; This model represents the transcription ...
 4-158 1.21e-45

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: 146.84  E-value: 1.21e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830   4 WYLVVCKPKQEERAKTNLQNQGIEAFYPQLTTERLVKGRRTVKHTALFPNYLFVCLESKNGNFSAVKNTRGIGGFVSYGA 83
Cdd:TIGR01955   1 WYLLYCKPRQEQRAQEHLERQAVECYLPMITVEKIVRGKRQAVSEPLFPNYLFIEFDPEVDSWTTIRSTRGVSRFVRFGG 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1889725830  84 SYQLVSKHIIDHLKNERAHTTES---QIPKTGDVVNVNNDSFSNIQAIYKEPDGDLRSILLINLLNQKIEVSVDNKDI 158
Cdd:TIGR01955  81 HPAPVPDDLIHQLRQYEPKDSVPpatTLPYKGDKVRITDGAFAGFEAIFLEPDGEKRSMLLLNMIGKQIKVSVPNTSV 158
NGN_SP_RfaH cd09892
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; ...
 3-98 8.30e-43

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: 137.31  E-value: 8.30e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830   3 CWYLVVCKPKQEERAKTNLQNQGIEAFYPQLTTERLVKGRRTVKHTALFPNYLFVCLESKNGNFSAVKNTRGIGGFVSYG 82
Cdd:cd09892     1 AWYLLYTKPRQEERAAENLERQGFEVFLPMIRVEKRRRGKRTVVTEPLFPGYLFVRLDPEVQNWRPIRSTRGVSRLVRFG 80

                          90
                  ....*....|....*.
gi 1889725830  83 ASYQLVSKHIIDHLKN 98
Cdd:cd09892    81 GEPAPVPDALIEALRA 96
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
4-159 7.89e-36

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 121.85  E-value: 7.89e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830   4 WYLVVCKPKQEERAKTNLQNQ--GIEAFYPQLTTERLVKGRRTVKHTALFPNYLFVCLESKNGNFSAVKNTRGIGGFVSY 81
Cdd:COG0250     7 WYVVHTYSGYEKKVKENLERRieGIEVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLVRNTPGVTGFVGF 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830  82 GASYQLVSKHIIDHLK----NERAHTTESQIPKTGDVVNVNNDSFSNIQAIYKEPD-GDLRSILLINLLNQKIEVSVDNK 156
Cdd:COG0250    87 GGKPAPLPDEEVERILarleEGEEKPRPKVDFEVGDRVRITDGPFAGFEGTVEEVDpEKGRVKVLVSIFGRETPVELDFS 166


                  ...
gi 1889725830 157 DIK 159
Cdd:COG0250   167 QVE 169
NusG pfam02357
Transcription termination factor nusG;
3-97 1.32e-24

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 91.13  E-value: 1.32e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830   3 CWYLVVCKPKQEERAKTNLQNQGIEAFYPQLTTERLVKGRRTVKHTALFPNYLFVCLESKNGNFSAVKNTRGIGGFVSYG 82
Cdd:pfam02357   2 KWYVLQTYSGKEKKVKENLERQGIEVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRSTPGVTGFVGGS 81

                          90
                  ....*....|....*
gi 1889725830  83 ASYQLVSKHIIDHLK 97
Cdd:pfam02357  82 GKPTPIPDEEVERIL 96
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 4-99 1.11e-14

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: 65.86  E-value: 1.11e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830    4 WYLVVCKPKQEERAKTNL---------QNQGIEAFYPQLTTERLVKGRRTVKHTALFPNYLFVCLESKNGNFSAVKNTRG 74
Cdd:smart00738   2 WYAVRTTSGQEKRVAENLerkaealglEDKIVSILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGTPG 81

                           90       100
                   ....*....|....*....|....*
gi 1889725830   75 IGGFVSYGASYQLVSKHIIDHLKNE 99
Cdd:smart00738  82 VRGFVGGGGKPTPVPDDEIEKILKP 106
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 4-158 1.05e-11

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: 59.41  E-value: 1.05e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830   4 WYLVVCKPKQEERAKTNLQNQGIEAFYPQLTTERLVKGRRTVKHTALFPNYLFVCLeSKNGNFSAVKNTRGIGGFVSYG- 82
Cdd:NF033644    1 WYALYTRPRREKKVAELLEKKGIESFLPMQKEIRQWSDRKKRVEVPLIPNLVFVHI-TEKELDEVLEQTPGVVRYIRDDr 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830  83 --ASYQLVSKHIIDHLK----NERAHTTESQIP-KTGDVVNVNNDSFSNIQAIYKEPDGDLRSILLINLLNQKIEVSVDN 155
Cdd:NF033644   80 gkSKPAIIPDKQMERFRlmldPSDEVVVYLEAPlKKGDKVRVIGGPLKGLEGELVRVKGKKRVVVRIPGLGAVATVEVPP 159


                  ...
gi 1889725830 156 KDI 158
Cdd:NF033644  160 SYL 162
 
Name Accession Description Interval E-value
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
1-159 4.39e-75

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 221.30  E-value: 4.39e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830   1 MECWYLVVCKPKQEERAKTNLQNQGIEAFYPQLTTERLVKGRRTVKHTALFPNYLFVCLESKNGNFSAVKNTRGIGGFVS 80
Cdd:PRK09014    1 MKSWYLLYCKRGQLQRAQEHLERQGVECLYPMITLEKIVRGKRTEVSEPLFPNYLFVEFDPEVIHTTTIRSTRGVSHFVR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830  81 YGASYQLVSKHIIDHLK-NERAHTTESQIPKTGDVVNVNNDSFSNIQAIYKEPDGDLRSILLINLLNQKIEVSVDNKDIK 159
Cdd:PRK09014   81 FGAQPAIVPSDVIYQLSvYKPEKIVDPETPKPGDKVIITEGAFEGLQAIYTEPDGEARSILLLNLLNKQVKHSVDNTQFR 160
RfaH TIGR01955
transcription elongation factor/antiterminator RfaH; This model represents the transcription ...
 4-158 1.21e-45

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: 146.84  E-value: 1.21e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830   4 WYLVVCKPKQEERAKTNLQNQGIEAFYPQLTTERLVKGRRTVKHTALFPNYLFVCLESKNGNFSAVKNTRGIGGFVSYGA 83
Cdd:TIGR01955   1 WYLLYCKPRQEQRAQEHLERQAVECYLPMITVEKIVRGKRQAVSEPLFPNYLFIEFDPEVDSWTTIRSTRGVSRFVRFGG 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1889725830  84 SYQLVSKHIIDHLKNERAHTTES---QIPKTGDVVNVNNDSFSNIQAIYKEPDGDLRSILLINLLNQKIEVSVDNKDI 158
Cdd:TIGR01955  81 HPAPVPDDLIHQLRQYEPKDSVPpatTLPYKGDKVRITDGAFAGFEAIFLEPDGEKRSMLLLNMIGKQIKVSVPNTSV 158
NGN_SP_RfaH cd09892
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; ...
 3-98 8.30e-43

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: 137.31  E-value: 8.30e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830   3 CWYLVVCKPKQEERAKTNLQNQGIEAFYPQLTTERLVKGRRTVKHTALFPNYLFVCLESKNGNFSAVKNTRGIGGFVSYG 82
Cdd:cd09892     1 AWYLLYTKPRQEERAAENLERQGFEVFLPMIRVEKRRRGKRTVVTEPLFPGYLFVRLDPEVQNWRPIRSTRGVSRLVRFG 80

                          90
                  ....*....|....*.
gi 1889725830  83 ASYQLVSKHIIDHLKN 98
Cdd:cd09892    81 GEPAPVPDALIEALRA 96
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
4-159 7.89e-36

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 121.85  E-value: 7.89e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830   4 WYLVVCKPKQEERAKTNLQNQ--GIEAFYPQLTTERLVKGRRTVKHTALFPNYLFVCLESKNGNFSAVKNTRGIGGFVSY 81
Cdd:COG0250     7 WYVVHTYSGYEKKVKENLERRieGIEVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLVRNTPGVTGFVGF 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830  82 GASYQLVSKHIIDHLK----NERAHTTESQIPKTGDVVNVNNDSFSNIQAIYKEPD-GDLRSILLINLLNQKIEVSVDNK 156
Cdd:COG0250    87 GGKPAPLPDEEVERILarleEGEEKPRPKVDFEVGDRVRITDGPFAGFEGTVEEVDpEKGRVKVLVSIFGRETPVELDFS 166


                  ...
gi 1889725830 157 DIK 159
Cdd:COG0250   167 QVE 169
NusG pfam02357
Transcription termination factor nusG;
3-97 1.32e-24

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 91.13  E-value: 1.32e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830   3 CWYLVVCKPKQEERAKTNLQNQGIEAFYPQLTTERLVKGRRTVKHTALFPNYLFVCLESKNGNFSAVKNTRGIGGFVSYG 82
Cdd:pfam02357   2 KWYVLQTYSGKEKKVKENLERQGIEVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRSTPGVTGFVGGS 81

                          90
                  ....*....|....*
gi 1889725830  83 ASYQLVSKHIIDHLK 97
Cdd:pfam02357  82 GKPTPIPDEEVERIL 96
NGN_SP cd09886
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP); The ...
 4-97 2.01e-20

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: 80.49  E-value: 2.01e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830   4 WYLVVCKPKQEERAKTNLQNQGIEAFYPQLTTERLVKGRRTVKHTALFPNYLFVCL-ESKNGNFSAVKNTRGIGGFVSYG 82
Cdd:cd09886     2 WYALRTNPGCEQRAEEALEARGVEAFLPMLTEERKRRRKKFDVERPLFPGYVFARLdRSKGQDTSTIRACDGVLGVVGFD 81

                          90
                  ....*....|....*
gi 1889725830  83 ASYQLVSKHIIDHLK 97
Cdd:cd09886    82 GRPAPVPEQEMRDLR 96
NGN_SP_AnfA1 cd09894
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1; ...
 4-98 6.12e-15

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: 66.15  E-value: 6.12e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830   4 WYLVVCKPKQEERAKTNLQNQGIEAFYPQLTTERL---VKGRRTVKHtALFPNYLFVCLESKNGNFSAVKNTRGIGGFVS 80
Cdd:cd09894     3 WYLLRCKSGKIQSVIFSLERLGVEVFCPMIRTRRKrtdCKSYREKIE-PLFPGYLFVRFDPEVVHTSKITLASGVSGFVR 81

                          90
                  ....*....|....*...
gi 1889725830  81 YGASYQLVSKHIIDHLKN 98
Cdd:cd09894    82 FGGEPCPVPDAVIRALML 99
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 4-99 1.11e-14

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: 65.86  E-value: 1.11e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830    4 WYLVVCKPKQEERAKTNL---------QNQGIEAFYPQLTTERLVKGRRTVKHTALFPNYLFVCLESKNGNFSAVKNTRG 74
Cdd:smart00738   2 WYAVRTTSGQEKRVAENLerkaealglEDKIVSILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGTPG 81

                           90       100
                   ....*....|....*....|....*
gi 1889725830   75 IGGFVSYGASYQLVSKHIIDHLKNE 99
Cdd:smart00738  82 VRGFVGGGGKPTPVPDDEIEKILKP 106
NGN_SP_UpxY cd09895
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; ...
 3-82 5.29e-14

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: 63.75  E-value: 5.29e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830   3 CWYLVVCKPKQEERAKTNLQNQGIEAFYPQLTTERLVKGRRTVKHTALFPNYLFVCLESKngNFSAVKNTRGIGGFVSYG 82
Cdd:cd09895     1 PWYALYTFPRREKKVAEYLEKKGIECFLPMQYEVRQWSGRKKRVEVPLFPNLVFVHITRE--ELDEVLETPGVVRFVRYR 78
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 4-158 1.05e-11

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: 59.41  E-value: 1.05e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830   4 WYLVVCKPKQEERAKTNLQNQGIEAFYPQLTTERLVKGRRTVKHTALFPNYLFVCLeSKNGNFSAVKNTRGIGGFVSYG- 82
Cdd:NF033644    1 WYALYTRPRREKKVAELLEKKGIESFLPMQKEIRQWSDRKKRVEVPLIPNLVFVHI-TEKELDEVLEQTPGVVRYIRDDr 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830  83 --ASYQLVSKHIIDHLK----NERAHTTESQIP-KTGDVVNVNNDSFSNIQAIYKEPDGDLRSILLINLLNQKIEVSVDN 155
Cdd:NF033644   80 gkSKPAIIPDKQMERFRlmldPSDEVVVYLEAPlKKGDKVRVIGGPLKGLEGELVRVKGKKRVVVRIPGLGAVATVEVPP 159


                  ...
gi 1889725830 156 KDI 158
Cdd:NF033644  160 SYL 162
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 4-97 3.46e-11

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: 56.56  E-value: 3.46e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830   4 WYLVVCKPKQEERAKTNLQNQG----IEAFYPQLTTERLVKGRRTVKHTALFPNYLFVCLESKNGNFSAVKNTRGIGGFV 79
Cdd:cd08000     2 WYVLFVKTGREEKVEKLLEKRFeandIEAFVPKKEVPERKRGKIEEVIKPLFPGYVFVETDLSPELYELIREVPGVIGIL 81

                          90
                  ....*....|....*...
gi 1889725830  80 SYGASYQLVSKHIIDHLK 97
Cdd:cd08000    82 GNGEEPSPVSDEEIEMIL 99
NGN_SP_TaA cd09893
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), TaA; ...
 4-98 1.84e-10

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: 54.62  E-value: 1.84e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830   4 WYLVVCKPKQEERAKTNLQNQGIEAFYPQLTTERLVKGRRTVKHTALFPNYLFVCLESKNGNFSAVKnTRGIGGFVSYGA 83
Cdd:cd09893     2 WYALYTRSRHEKKVADRLAKKGIESFLPLYEVLSRWKDRKKKIKVPLFPGYLFVRFQLDPERLRILK-TPGVVRIVGNSG 80

                          90
                  ....*....|....*
gi 1889725830  84 SYQLVSKHIIDHLKN 98
Cdd:cd09893    81 GPIPIPDEEIASLRI 95
NGN_plant cd09890
Plant N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance G ...
 4-93 2.58e-06

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: 43.88  E-value: 2.58e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830   4 WYLVVCKPKQEERAKTNLQNQG--------IEAFYPQLTTER-LVKGRRTVKHTALFPNYLFV-CLESKNgNFSAVKNTR 73
Cdd:cd09890     2 WYMLRVPAGRENQAAEALERALatefpdreFEVWVPSIPVDRkLKNGSISVKEKPLFPGYVLLrCVLNKE-VYDFIRDND 80

                          90       100
                  ....*....|....*....|
gi 1889725830  74 GIGGFVSyGASYQLVSKHII 93
Cdd:cd09890    81 SVYGFVG-SKVGKTGKRQIE 99
NGN_Bact_1 cd09891
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The ...
 4-83 6.12e-06

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: 42.85  E-value: 6.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889725830   4 WYLVVCKPKQEERAKTNL----QNQGIEAFYPQLT--TERLV---KGRRTVKHTALFPNYLFVCLESKNGNFSAVKNTRG 74
Cdd:cd09891     2 WYVVHTYSGYENKVKENLekriESEGLEDYIGEVLvpTEEVVevkNGKKKVKERKLFPGYVLVEMDMNDDTWHLVRNTPG 81


                  ....*....
gi 1889725830  75 IGGFVSYGA 83
Cdd:cd09891    82 VTGFVGSGG 90
 
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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