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MULTISPECIES: transcription/translation regulatory transformer protein RfaH [Proteus]

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;
1-163 2.09e-107

transcription/translation regulatory transformer protein RfaH;


:

Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 303.35  E-value: 2.09e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450   1 MKNWHLLYCKRGQIARAIEHLERQQVICFTPMVTIEKLIRNKRTLVTEPLFPNYLFIQFDPEVIHTTTINSTRGVNAFVR 80
Cdd:PRK09014   1 MKSWYLLYCKRGQLQRAQEHLERQGVECLYPMITLEKIVRGKRTEVSEPLFPNYLFVEFDPEVIHTTTIRSTRGVSHFVR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450  81 FGRYPVTVPQEVIDTLQSPTPSSVIYSEenVPHSGDYVLITEGVFQGIKAIYQEPDGETRSILLLKILNNEVKKSVDNKE 160
Cdd:PRK09014  81 FGAQPAIVPSDVIYQLSVYKPEKIVDPE--TPKPGDKVIITEGAFEGLQAIYTEPDGEARSILLLNLLNKQVKHSVDNTQ 158


                 ...
gi 490366450 161 FKK 163
Cdd:PRK09014 159 FRK 161
 
Name Accession Description Interval E-value
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
1-163 2.09e-107

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 303.35  E-value: 2.09e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450   1 MKNWHLLYCKRGQIARAIEHLERQQVICFTPMVTIEKLIRNKRTLVTEPLFPNYLFIQFDPEVIHTTTINSTRGVNAFVR 80
Cdd:PRK09014   1 MKSWYLLYCKRGQLQRAQEHLERQGVECLYPMITLEKIVRGKRTEVSEPLFPNYLFVEFDPEVIHTTTIRSTRGVSHFVR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450  81 FGRYPVTVPQEVIDTLQSPTPSSVIYSEenVPHSGDYVLITEGVFQGIKAIYQEPDGETRSILLLKILNNEVKKSVDNKE 160
Cdd:PRK09014  81 FGAQPAIVPSDVIYQLSVYKPEKIVDPE--TPKPGDKVIITEGAFEGLQAIYTEPDGEARSILLLNLLNKQVKHSVDNTQ 158


                 ...
gi 490366450 161 FKK 163
Cdd:PRK09014 159 FRK 161
RfaH TIGR01955
transcription elongation factor/antiterminator RfaH; This model represents the transcription ...
 4-161 4.81e-64

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: 193.45  E-value: 4.81e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450    4 WHLLYCKRGQIARAIEHLERQQVICFTPMVTIEKLIRNKRTLVTEPLFPNYLFIQFDPEVIHTTTINSTRGVNAFVRFGR 83
Cdd:TIGR01955   1 WYLLYCKPRQEQRAQEHLERQAVECYLPMITVEKIVRGKRQAVSEPLFPNYLFIEFDPEVDSWTTIRSTRGVSRFVRFGG 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490366450   84 YPVTVPQEVIDTLQSPTPSSVIYSEENVPHSGDYVLITEGVFQGIKAIYQEPDGETRSILLLKILNNEVKKSVDNKEF 161
Cdd:TIGR01955  81 HPAPVPDDLIHQLRQYEPKDSVPPATTLPYKGDKVRITDGAFAGFEAIFLEPDGEKRSMLLLNMIGKQIKVSVPNTSV 158
NGN_SP_RfaH cd09892
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; ...
 3-97 2.80e-46

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: 146.17  E-value: 2.80e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450   3 NWHLLYCKRGQIARAIEHLERQQVICFTPMVTIEKLIRNKRTLVTEPLFPNYLFIQFDPEVIHTTTINSTRGVNAFVRFG 82
Cdd:cd09892    1 AWYLLYTKPRQEERAAENLERQGFEVFLPMIRVEKRRRGKRTVVTEPLFPGYLFVRLDPEVQNWRPIRSTRGVSRLVRFG 80

                         90
                 ....*....|....*
gi 490366450  83 RYPVTVPQEVIDTLQ 97
Cdd:cd09892   81 GEPAPVPDALIEALR 95
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
1-163 4.63e-41

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 135.72  E-value: 4.63e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450   1 MKNWHLLYCKRGQIARAIEHLERQ--QVICFTPMVTIEKLIRNKRTLVTEPLFPNYLFIQFDPEVIHTTTINSTRGVNAF 78
Cdd:COG0250    4 EKRWYVVHTYSGYEKKVKENLERRieGIEVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLVRNTPGVTGF 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450  79 VRFGRYPVTVPQEVIDTLQSPTPSSVIYSEENVP-HSGDYVLITEGVFQGIKAIYQEPD-GETRSILLLKILNNEVKKSV 156
Cdd:COG0250   84 VGFGGKPAPLPDEEVERILARLEEGEEKPRPKVDfEVGDRVRITDGPFAGFEGTVEEVDpEKGRVKVLVSIFGRETPVEL 163


                 ....*..
gi 490366450 157 DNKEFKK 163
Cdd:COG0250  164 DFSQVEK 170
NusG pfam02357
Transcription termination factor nusG;
2-97 2.90e-24

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 90.36  E-value: 2.90e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450    2 KNWHLLYCKRGQIARAIEHLERQQVICFTPMVTIEKLIRNKRTLVTEPLFPNYLFIQFDPEVIHTTTINSTRGVNAFVRF 81
Cdd:pfam02357   1 KKWYVLQTYSGKEKKVKENLERQGIEVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRSTPGVTGFVGG 80

                          90
                  ....*....|....*.
gi 490366450   82 GRYPVTVPQEVIDTLQ 97
Cdd:pfam02357  81 SGKPTPIPDEEVERIL 96
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 3-99 1.21e-22

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: 86.66  E-value: 1.21e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450     3 NWHLLYCKRGQIARAIEHLERQQ---------VICFTPMVTIEKLIRNKRTLVTEPLFPNYLFIQFDPEVIHTTTINSTR 73
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKAealgledkiVSILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGTP 80

                           90       100
                   ....*....|....*....|....*.
gi 490366450    74 GVNAFVRFGRYPVTVPQEVIDTLQSP 99
Cdd:smart00738  81 GVRGFVGGGGKPTPVPDDEIEKILKP 106
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 19-147 1.41e-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: 74.81  E-value: 1.41e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450  19 EHLERQQVICFTPMVTIEKLIRNKRTLVTEPLFPNYLFIQFDPEVIHtTTINSTRGVNAFVRFGR---YPVTVPQEVIDT 95
Cdd:NF033644  16 ELLEKKGIESFLPMQKEIRQWSDRKKRVEVPLIPNLVFVHITEKELD-EVLEQTPGVVRYIRDDRgksKPAIIPDKQMER 94

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 490366450  96 LQ---SPTPSSVIYSEENVPhSGDYVLITEGVFQGIKAIYQEPDGETRsiLLLKI 147
Cdd:NF033644  95 FRlmlDPSDEVVVYLEAPLK-KGDKVRVIGGPLKGLEGELVRVKGKKR--VVVRI 146
 
Name Accession Description Interval E-value
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
1-163 2.09e-107

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 303.35  E-value: 2.09e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450   1 MKNWHLLYCKRGQIARAIEHLERQQVICFTPMVTIEKLIRNKRTLVTEPLFPNYLFIQFDPEVIHTTTINSTRGVNAFVR 80
Cdd:PRK09014   1 MKSWYLLYCKRGQLQRAQEHLERQGVECLYPMITLEKIVRGKRTEVSEPLFPNYLFVEFDPEVIHTTTIRSTRGVSHFVR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450  81 FGRYPVTVPQEVIDTLQSPTPSSVIYSEenVPHSGDYVLITEGVFQGIKAIYQEPDGETRSILLLKILNNEVKKSVDNKE 160
Cdd:PRK09014  81 FGAQPAIVPSDVIYQLSVYKPEKIVDPE--TPKPGDKVIITEGAFEGLQAIYTEPDGEARSILLLNLLNKQVKHSVDNTQ 158


                 ...
gi 490366450 161 FKK 163
Cdd:PRK09014 159 FRK 161
RfaH TIGR01955
transcription elongation factor/antiterminator RfaH; This model represents the transcription ...
 4-161 4.81e-64

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: 193.45  E-value: 4.81e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450    4 WHLLYCKRGQIARAIEHLERQQVICFTPMVTIEKLIRNKRTLVTEPLFPNYLFIQFDPEVIHTTTINSTRGVNAFVRFGR 83
Cdd:TIGR01955   1 WYLLYCKPRQEQRAQEHLERQAVECYLPMITVEKIVRGKRQAVSEPLFPNYLFIEFDPEVDSWTTIRSTRGVSRFVRFGG 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490366450   84 YPVTVPQEVIDTLQSPTPSSVIYSEENVPHSGDYVLITEGVFQGIKAIYQEPDGETRSILLLKILNNEVKKSVDNKEF 161
Cdd:TIGR01955  81 HPAPVPDDLIHQLRQYEPKDSVPPATTLPYKGDKVRITDGAFAGFEAIFLEPDGEKRSMLLLNMIGKQIKVSVPNTSV 158
NGN_SP_RfaH cd09892
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; ...
 3-97 2.80e-46

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: 146.17  E-value: 2.80e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450   3 NWHLLYCKRGQIARAIEHLERQQVICFTPMVTIEKLIRNKRTLVTEPLFPNYLFIQFDPEVIHTTTINSTRGVNAFVRFG 82
Cdd:cd09892    1 AWYLLYTKPRQEERAAENLERQGFEVFLPMIRVEKRRRGKRTVVTEPLFPGYLFVRLDPEVQNWRPIRSTRGVSRLVRFG 80

                         90
                 ....*....|....*
gi 490366450  83 RYPVTVPQEVIDTLQ 97
Cdd:cd09892   81 GEPAPVPDALIEALR 95
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
1-163 4.63e-41

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 135.72  E-value: 4.63e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450   1 MKNWHLLYCKRGQIARAIEHLERQ--QVICFTPMVTIEKLIRNKRTLVTEPLFPNYLFIQFDPEVIHTTTINSTRGVNAF 78
Cdd:COG0250    4 EKRWYVVHTYSGYEKKVKENLERRieGIEVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLVRNTPGVTGF 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450  79 VRFGRYPVTVPQEVIDTLQSPTPSSVIYSEENVP-HSGDYVLITEGVFQGIKAIYQEPD-GETRSILLLKILNNEVKKSV 156
Cdd:COG0250   84 VGFGGKPAPLPDEEVERILARLEEGEEKPRPKVDfEVGDRVRITDGPFAGFEGTVEEVDpEKGRVKVLVSIFGRETPVEL 163


                 ....*..
gi 490366450 157 DNKEFKK 163
Cdd:COG0250  164 DFSQVEK 170
NGN_SP_AnfA1 cd09894
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1; ...
 2-97 1.48e-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: 108.91  E-value: 1.48e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450   2 KNWHLLYCKRGQIARAIEHLERQQVICFTPMVTIEKL---IRNKRTlVTEPLFPNYLFIQFDPEVIHTTTINSTRGVNAF 78
Cdd:cd09894    1 KRWYLLRCKSGKIQSVIFSLERLGVEVFCPMIRTRRKrtdCKSYRE-KIEPLFPGYLFVRFDPEVVHTSKITLASGVSGF 79

                         90
                 ....*....|....*....
gi 490366450  79 VRFGRYPVTVPQEVIDTLQ 97
Cdd:cd09894   80 VRFGGEPCPVPDAVIRALM 98
NGN_SP cd09886
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP); The ...
 4-93 1.42e-27

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: 98.98  E-value: 1.42e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450   4 WHLLYCKRGQIARAIEHLERQQVICFTPMVTIEKLIRNKRTLVTEPLFPNYLFIQFDPE-VIHTTTINSTRGVNAFVRFG 82
Cdd:cd09886    2 WYALRTNPGCEQRAEEALEARGVEAFLPMLTEERKRRRKKFDVERPLFPGYVFARLDRSkGQDTSTIRACDGVLGVVGFD 81

                         90
                 ....*....|.
gi 490366450  83 RYPVTVPQEVI 93
Cdd:cd09886   82 GRPAPVPEQEM 92
NusG pfam02357
Transcription termination factor nusG;
2-97 2.90e-24

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 90.36  E-value: 2.90e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450    2 KNWHLLYCKRGQIARAIEHLERQQVICFTPMVTIEKLIRNKRTLVTEPLFPNYLFIQFDPEVIHTTTINSTRGVNAFVRF 81
Cdd:pfam02357   1 KKWYVLQTYSGKEKKVKENLERQGIEVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRSTPGVTGFVGG 80

                          90
                  ....*....|....*.
gi 490366450   82 GRYPVTVPQEVIDTLQ 97
Cdd:pfam02357  81 SGKPTPIPDEEVERIL 96
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 3-99 1.21e-22

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: 86.66  E-value: 1.21e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450     3 NWHLLYCKRGQIARAIEHLERQQ---------VICFTPMVTIEKLIRNKRTLVTEPLFPNYLFIQFDPEVIHTTTINSTR 73
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKAealgledkiVSILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGTP 80

                           90       100
                   ....*....|....*....|....*.
gi 490366450    74 GVNAFVRFGRYPVTVPQEVIDTLQSP 99
Cdd:smart00738  81 GVRGFVGGGGKPTPVPDDEIEKILKP 106
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 19-147 1.41e-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: 74.81  E-value: 1.41e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450  19 EHLERQQVICFTPMVTIEKLIRNKRTLVTEPLFPNYLFIQFDPEVIHtTTINSTRGVNAFVRFGR---YPVTVPQEVIDT 95
Cdd:NF033644  16 ELLEKKGIESFLPMQKEIRQWSDRKKRVEVPLIPNLVFVHITEKELD-EVLEQTPGVVRYIRDDRgksKPAIIPDKQMER 94

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 490366450  96 LQ---SPTPSSVIYSEENVPhSGDYVLITEGVFQGIKAIYQEPDGETRsiLLLKI 147
Cdd:NF033644  95 FRlmlDPSDEVVVYLEAPLK-KGDKVRVIGGPLKGLEGELVRVKGKKR--VVVRI 146
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 3-91 9.75e-16

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: 68.50  E-value: 9.75e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450   3 NWHLLYCKRGQIARAIEHLERQ----QVICFTPMVTIEKLIRNKRTLVTEPLFPNYLFIQFDPEVIHTTTINSTRGVNAF 78
Cdd:cd08000    1 NWYVLFVKTGREEKVEKLLEKRfeanDIEAFVPKKEVPERKRGKIEEVIKPLFPGYVFVETDLSPELYELIREVPGVIGI 80

                         90
                 ....*....|...
gi 490366450  79 VRFGRYPVTVPQE 91
Cdd:cd08000   81 LGNGEEPSPVSDE 93
NGN_SP_UpxY cd09895
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; ...
 3-97 2.00e-12

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: 59.90  E-value: 2.00e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450   3 NWHLLYCKRGQIARAIEHLERQQVICFTPMVTIEKLIRNKRTLVTEPLFPNYLFIQFDPEVIhtTTINSTRGVNAFVRF- 81
Cdd:cd09895    1 PWYALYTFPRREKKVAEYLEKKGIECFLPMQYEVRQWSGRKKRVEVPLFPNLVFVHITREEL--DEVLETPGVVRFVRYr 78

                         90
                 ....*....|....*.
gi 490366450  82 GRYPVTVPQEVIDTLQ 97
Cdd:cd09895   79 GKEPAIIPDKQMESFR 94
NGN_SP_TaA cd09893
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), TaA; ...
 3-97 2.22e-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: 2.22e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450   3 NWHLLYCKRGQIARAIEHLERQQVICFTPMVTIEKLIRNKRTLVTEPLFPNYLFIQFDPEVIHtTTINSTRGVNAFVRFG 82
Cdd:cd09893    1 SWYALYTRSRHEKKVADRLAKKGIESFLPLYEVLSRWKDRKKKIKVPLFPGYLFVRFQLDPER-LRILKTPGVVRIVGNS 79

                         90
                 ....*....|....*
gi 490366450  83 RYPVTVPQEVIDTLQ 97
Cdd:cd09893   80 GGPIPIPDEEIASLR 94
NGN_Bact_1 cd09891
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The ...
 14-96 2.44e-03

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: 35.91  E-value: 2.44e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490366450  14 IARAIEHLERQQVI--CFTPMVTIEKLIRNKRTLVTEPLFPNYLFIQ--FDPEVIHttTINSTRGVNAFVRFGRYPVTVP 89
Cdd:cd09891   19 LEKRIESEGLEDYIgeVLVPTEEVVEVKNGKKKVKERKLFPGYVLVEmdMNDDTWH--LVRNTPGVTGFVGSGGKPVPLS 96


                 ....*..
gi 490366450  90 QEVIDTL 96
Cdd:cd09891   97 EEEVERI 103
 
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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