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Conserved domains on  [gi|499873226|ref|WP_011553960|]
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MULTISPECIES: transcription termination/antitermination NusG family protein [Myxococcus]

Protein Classification

UpxY family transcription antiterminator( domain architecture ID 10177587)

UpxY family transcription antiterminator is a Specialized Paralog of NusG (NusG SP) that acts specifically in transcriptional antitermination of the operon from which it is encoded; UpxYs are necessary and specific for transcription regulation of the polysaccharide biosynthesis operon

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NGN_SP_TaA cd09893
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), TaA; ...
 10-100 1.90e-38

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: 126.65  E-value: 1.90e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226  10 DWVALLVRVNHEKVAAAQLGKHGYEFFLPTYTPP---KSSGVKAKLPLFPGYLFCRYQPLN-PYRIVRAPGVIRLLGGDA 85
Cdd:cd09893    1 SWYALYTRSRHEKKVADRLAKKGIESFLPLYEVLsrwKDRKKKIKVPLFPGYLFVRFQLDPeRLRILKTPGVVRIVGNSG 80

                         90
                 ....*....|....*
gi 499873226  86 GPEAVPAQELEAIRR 100
Cdd:cd09893   81 GPIPIPDEEIASLRI 95
KOW_NusG cd06091
NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif ...
 116-165 3.09e-07

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: 45.14  E-value: 3.09e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 499873226 116 VGQRVRIIEGPLTGLEGSLV---TSKSQLRfiVSVGLLQRSVSVEVSAEQLEP 165
Cdd:cd06091    6 VGDTVRIISGPFAGFEGKVEeidEEKGKVK--VLVEMFGRETPVELDFDQVEK 56
 
Name Accession Description Interval E-value
NGN_SP_TaA cd09893
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), TaA; ...
 10-100 1.90e-38

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: 126.65  E-value: 1.90e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226  10 DWVALLVRVNHEKVAAAQLGKHGYEFFLPTYTPP---KSSGVKAKLPLFPGYLFCRYQPLN-PYRIVRAPGVIRLLGGDA 85
Cdd:cd09893    1 SWYALYTRSRHEKKVADRLAKKGIESFLPLYEVLsrwKDRKKKIKVPLFPGYLFVRFQLDPeRLRILKTPGVVRIVGNSG 80

                         90
                 ....*....|....*
gi 499873226  86 GPEAVPAQELEAIRR 100
Cdd:cd09893   81 GPIPIPDEEIASLRI 95
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
8-166 3.49e-34

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 118.00  E-value: 3.49e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226   8 ENDWVALLVRVNHEKVAAAQLGK--HGYEFFLPTYT-PPKSSG--VKAKLPLFPGYLFCR--YQPLNPYRIVRAPGVIRL 80
Cdd:COG0250    4 EKRWYVVHTYSGYEKKVKENLERriEGIEVFVPTEEvVEIKNGkkKTVERPLFPGYVFVRmdLTDESWYLVRNTPGVTGF 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226  81 LGGDAGPEAVPAQELEAIRRVADSGVS-SNPCDYLRVGQRVRIIEGPLTGLEGSLVT-SKSQLRFIVSVGLLQRSVSVEV 158
Cdd:COG0250   84 VGFGGKPAPLPDEEVERILARLEEGEEkPRPKVDFEVGDRVRITDGPFAGFEGTVEEvDPEKGRVKVLVSIFGRETPVEL 163


                 ....*...
gi 499873226 159 SAEQLEPI 166
Cdd:COG0250  164 DFSQVEKI 171
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 11-163 1.85e-30

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: 108.33  E-value: 1.85e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226  11 WVALLVRVNHEKVAAAQLGKHGYEFFLPT-YTPPKSSGVKAK--LPLFPGYLFCRYQPLNPYRIV-RAPGVIRLL---GG 83
Cdd:NF033644   1 WYALYTRPRREKKVAELLEKKGIESFLPMqKEIRQWSDRKKRveVPLIPNLVFVHITEKELDEVLeQTPGVVRYIrddRG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226  84 DAGPEAVPAQELEAIRRVADSGVSSN--PCDYLRVGQRVRIIEGPLTGLEGSLVTSKSQLRFIVSVGLLQRSVSVEVSAE 161
Cdd:NF033644  81 KSKPAIIPDKQMERFRLMLDPSDEVVvyLEAPLKKGDKVRVIGGPLKGLEGELVRVKGKKRVVVRIPGLGAVATVEVPPS 160


                 ..
gi 499873226 162 QL 163
Cdd:NF033644 161 YL 162
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 10-101 9.95e-16

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: 68.94  E-value: 9.95e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226    10 DWVALLVRVNHEKVAAAQLGKH---------GYEFFLPTYTPPK---SSGVKAKLPLFPGYLFCRYQPLN-PYRIVRA-P 75
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKaealgledkIVSILVPTEEVKEirrGKKKVVERKLFPGYIFVEADLEDeVWTAIRGtP 80

                           90       100
                   ....*....|....*....|....*.
gi 499873226    76 GVIRLLGGDAGPEAVPAQELEAIRRV 101
Cdd:smart00738  81 GVRGFVGGGGKPTPVPDDEIEKILKP 106
NusG pfam02357
Transcription termination factor nusG;
10-99 2.53e-14

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 64.94  E-value: 2.53e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226   10 DWVALLVRVNHEKVAAAQLGKHGYEFFLPTYTPPKSSG---VKAKLPLFPGYLFCRYQPLNP-YRIVRA-PGVIRLLGGD 84
Cdd:pfam02357   2 KWYVLQTYSGKEKKVKENLERQGIEVFLPTEEVVEIRNgkkKVVERPLFPGYVFVRMDMTDEtWHLVRStPGVTGFVGGS 81

                          90
                  ....*....|....*
gi 499873226   85 AGPEAVPAQELEAIR 99
Cdd:pfam02357  82 GKPTPIPDEEVERIL 96
RfaH TIGR01955
transcription elongation factor/antiterminator RfaH; This model represents the transcription ...
 11-164 8.21e-14

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: 65.18  E-value: 8.21e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226   11 WVALLVRVNHEKVAAAQLGKHGYEFFLPTYTPPKS-SGVKAKL--PLFPGYLFCRYQPLNP--YRIVRAPGVIRLLGGDA 85
Cdd:TIGR01955   1 WYLLYCKPRQEQRAQEHLERQAVECYLPMITVEKIvRGKRQAVsePLFPNYLFIEFDPEVDswTTIRSTRGVSRFVRFGG 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499873226   86 GPEAVPAQELEAIRRVADSGVSSNPCDYLRVGQRVRIIEGPLTGLEGSLVTSKSQLRFIVSVGLLQRSVSVEVSAEQLE 164
Cdd:TIGR01955  81 HPAPVPDDLIHQLRQYEPKDSVPPATTLPYKGDKVRITDGAFAGFEAIFLEPDGEKRSMLLLNMIGKQIKVSVPNTSVE 159
antiterm_LoaP NF033641
antiterminator LoaP; LoaP is a paralog of NusG with an extensive presence in Firmicutes. The ...
 11-132 1.08e-12

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: 62.40  E-value: 1.08e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226  11 WVALLVRVNHEKVAAAQL----GKHGYEFFLPTYT-PPKSSGV--KAKLPLFPGYLFCR-------YqplnpYRIVRAPG 76
Cdd:NF033641   1 WYVLFVRTGKEEKVKKLLnklfDKELLRCFVPKRKlPERKQGKwyKVIKPLFPGYVFIEtdmneelY-----YKLKKIPG 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499873226  77 VIRLLG-GDAGPEAVPAQELEAIRR-VADSGVssnpCDYLRV---GQRVRIIEGPLTGLEG 132
Cdd:NF033641  76 IIRLLGnEGDEFSPIPEEEMEFLLKlLNDDDI----IEYSKGyieGDKVIVISGPLKGLEG 132
KOW_NusG cd06091
NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif ...
 116-165 3.09e-07

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: 45.14  E-value: 3.09e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 499873226 116 VGQRVRIIEGPLTGLEGSLV---TSKSQLRfiVSVGLLQRSVSVEVSAEQLEP 165
Cdd:cd06091    6 VGDTVRIISGPFAGFEGKVEeidEEKGKVK--VLVEMFGRETPVELDFDQVEK 56
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
53-166 1.41e-05

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 42.96  E-value: 1.41e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226  53 PLFPGYLFCRYQPLN-PYRIVRAP-GVIRLLGGDAGPEAVPAQELEAIRRVADSGVSSnpCDYLRVGQRVRIIEGPLTGL 130
Cdd:PRK09014  49 PLFPNYLFVEFDPEViHTTTIRSTrGVSHFVRFGAQPAIVPSDVIYQLSVYKPEKIVD--PETPKPGDKVIITEGAFEGL 126

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 499873226 131 EGSLVTSKSQLRFIVSVGLLQRSVSVEVSAEQLEPI 166
Cdd:PRK09014 127 QAIYTEPDGEARSILLLNLLNKQVKHSVDNTQFRKI 162
 
Name Accession Description Interval E-value
NGN_SP_TaA cd09893
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), TaA; ...
 10-100 1.90e-38

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: 126.65  E-value: 1.90e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226  10 DWVALLVRVNHEKVAAAQLGKHGYEFFLPTYTPP---KSSGVKAKLPLFPGYLFCRYQPLN-PYRIVRAPGVIRLLGGDA 85
Cdd:cd09893    1 SWYALYTRSRHEKKVADRLAKKGIESFLPLYEVLsrwKDRKKKIKVPLFPGYLFVRFQLDPeRLRILKTPGVVRIVGNSG 80

                         90
                 ....*....|....*
gi 499873226  86 GPEAVPAQELEAIRR 100
Cdd:cd09893   81 GPIPIPDEEIASLRI 95
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
8-166 3.49e-34

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 118.00  E-value: 3.49e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226   8 ENDWVALLVRVNHEKVAAAQLGK--HGYEFFLPTYT-PPKSSG--VKAKLPLFPGYLFCR--YQPLNPYRIVRAPGVIRL 80
Cdd:COG0250    4 EKRWYVVHTYSGYEKKVKENLERriEGIEVFVPTEEvVEIKNGkkKTVERPLFPGYVFVRmdLTDESWYLVRNTPGVTGF 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226  81 LGGDAGPEAVPAQELEAIRRVADSGVS-SNPCDYLRVGQRVRIIEGPLTGLEGSLVT-SKSQLRFIVSVGLLQRSVSVEV 158
Cdd:COG0250   84 VGFGGKPAPLPDEEVERILARLEEGEEkPRPKVDFEVGDRVRITDGPFAGFEGTVEEvDPEKGRVKVLVSIFGRETPVEL 163


                 ....*...
gi 499873226 159 SAEQLEPI 166
Cdd:COG0250  164 DFSQVEKI 171
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 11-163 1.85e-30

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: 108.33  E-value: 1.85e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226  11 WVALLVRVNHEKVAAAQLGKHGYEFFLPT-YTPPKSSGVKAK--LPLFPGYLFCRYQPLNPYRIV-RAPGVIRLL---GG 83
Cdd:NF033644   1 WYALYTRPRREKKVAELLEKKGIESFLPMqKEIRQWSDRKKRveVPLIPNLVFVHITEKELDEVLeQTPGVVRYIrddRG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226  84 DAGPEAVPAQELEAIRRVADSGVSSN--PCDYLRVGQRVRIIEGPLTGLEGSLVTSKSQLRFIVSVGLLQRSVSVEVSAE 161
Cdd:NF033644  81 KSKPAIIPDKQMERFRLMLDPSDEVVvyLEAPLKKGDKVRVIGGPLKGLEGELVRVKGKKRVVVRIPGLGAVATVEVPPS 160


                 ..
gi 499873226 162 QL 163
Cdd:NF033644 161 YL 162
NGN_SP cd09886
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP); The ...
 10-100 4.58e-28

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: 100.14  E-value: 4.58e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226  10 DWVALLVRVNHEKVAAAQLGKHGYEFFLPTYTPPKSSG---VKAKLPLFPGYLFCRYQPL---NPYRIVRAPGVIRLLGG 83
Cdd:cd09886    1 SWYALRTNPGCEQRAEEALEARGVEAFLPMLTEERKRRrkkFDVERPLFPGYVFARLDRSkgqDTSTIRACDGVLGVVGF 80

                         90
                 ....*....|....*..
gi 499873226  84 DAGPEAVPAQELEAIRR 100
Cdd:cd09886   81 DGRPAPVPEQEMRDLRK 97
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 10-101 9.95e-16

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: 68.94  E-value: 9.95e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226    10 DWVALLVRVNHEKVAAAQLGKH---------GYEFFLPTYTPPK---SSGVKAKLPLFPGYLFCRYQPLN-PYRIVRA-P 75
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKaealgledkIVSILVPTEEVKEirrGKKKVVERKLFPGYIFVEADLEDeVWTAIRGtP 80

                           90       100
                   ....*....|....*....|....*.
gi 499873226    76 GVIRLLGGDAGPEAVPAQELEAIRRV 101
Cdd:smart00738  81 GVRGFVGGGGKPTPVPDDEIEKILKP 106
NGN_SP_RfaH cd09892
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; ...
 10-100 7.05e-15

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: 66.05  E-value: 7.05e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226  10 DWVALLVRVNHEKVAAAQLGKHGYEFFLPTYTPPKSSGVKAKL---PLFPGYLFCRYQPLN-PYRIVRA-PGVIRLLGGD 84
Cdd:cd09892    1 AWYLLYTKPRQEERAAENLERQGFEVFLPMIRVEKRRRGKRTVvtePLFPGYLFVRLDPEVqNWRPIRStRGVSRLVRFG 80

                         90
                 ....*....|....*.
gi 499873226  85 AGPEAVPAQELEAIRR 100
Cdd:cd09892   81 GEPAPVPDALIEALRA 96
NusG pfam02357
Transcription termination factor nusG;
10-99 2.53e-14

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 64.94  E-value: 2.53e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226   10 DWVALLVRVNHEKVAAAQLGKHGYEFFLPTYTPPKSSG---VKAKLPLFPGYLFCRYQPLNP-YRIVRA-PGVIRLLGGD 84
Cdd:pfam02357   2 KWYVLQTYSGKEKKVKENLERQGIEVFLPTEEVVEIRNgkkKVVERPLFPGYVFVRMDMTDEtWHLVRStPGVTGFVGGS 81

                          90
                  ....*....|....*
gi 499873226   85 AGPEAVPAQELEAIR 99
Cdd:pfam02357  82 GKPTPIPDEEVERIL 96
RfaH TIGR01955
transcription elongation factor/antiterminator RfaH; This model represents the transcription ...
 11-164 8.21e-14

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: 65.18  E-value: 8.21e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226   11 WVALLVRVNHEKVAAAQLGKHGYEFFLPTYTPPKS-SGVKAKL--PLFPGYLFCRYQPLNP--YRIVRAPGVIRLLGGDA 85
Cdd:TIGR01955   1 WYLLYCKPRQEQRAQEHLERQAVECYLPMITVEKIvRGKRQAVsePLFPNYLFIEFDPEVDswTTIRSTRGVSRFVRFGG 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499873226   86 GPEAVPAQELEAIRRVADSGVSSNPCDYLRVGQRVRIIEGPLTGLEGSLVTSKSQLRFIVSVGLLQRSVSVEVSAEQLE 164
Cdd:TIGR01955  81 HPAPVPDDLIHQLRQYEPKDSVPPATTLPYKGDKVRITDGAFAGFEAIFLEPDGEKRSMLLLNMIGKQIKVSVPNTSVE 159
antiterm_LoaP NF033641
antiterminator LoaP; LoaP is a paralog of NusG with an extensive presence in Firmicutes. The ...
 11-132 1.08e-12

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: 62.40  E-value: 1.08e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226  11 WVALLVRVNHEKVAAAQL----GKHGYEFFLPTYT-PPKSSGV--KAKLPLFPGYLFCR-------YqplnpYRIVRAPG 76
Cdd:NF033641   1 WYVLFVRTGKEEKVKKLLnklfDKELLRCFVPKRKlPERKQGKwyKVIKPLFPGYVFIEtdmneelY-----YKLKKIPG 75

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499873226  77 VIRLLG-GDAGPEAVPAQELEAIRR-VADSGVssnpCDYLRV---GQRVRIIEGPLTGLEG 132
Cdd:NF033641  76 IIRLLGnEGDEFSPIPEEEMEFLLKlLNDDDI----IEYSKGyieGDKVIVISGPLKGLEG 132
NGN_SP_UpxY cd09895
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; ...
 11-100 5.74e-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: 58.74  E-value: 5.74e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226  11 WVALLVRVNHEKVAAAQLGKHGYEFFLP-TYTPPKSSG--VKAKLPLFPGYLFCRYQPLNPYRIVRAPGVIRLLG-GDAG 86
Cdd:cd09895    2 WYALYTFPRREKKVAEYLEKKGIECFLPmQYEVRQWSGrkKRVEVPLFPNLVFVHITREELDEVLETPGVVRFVRyRGKE 81

                         90
                 ....*....|....
gi 499873226  87 PEAVPAQELEAIRR 100
Cdd:cd09895   82 PAIIPDKQMESFRL 95
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 11-99 2.20e-08

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: 49.24  E-value: 2.20e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226  11 WVALLVRVNHEKVAAAQLGKHG----YEFFLPTYTPP---KSSGVKAKLPLFPGYLF--CRYQPLNPYRIVRAPGVIRLL 81
Cdd:cd08000    2 WYVLFVKTGREEKVEKLLEKRFeandIEAFVPKKEVPerkRGKIEEVIKPLFPGYVFveTDLSPELYELIREVPGVIGIL 81

                         90
                 ....*....|....*...
gi 499873226  82 GGDAGPEAVPAQELEAIR 99
Cdd:cd08000   82 GNGEEPSPVSDEEIEMIL 99
KOW_NusG cd06091
NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif ...
 116-165 3.09e-07

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: 45.14  E-value: 3.09e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 499873226 116 VGQRVRIIEGPLTGLEGSLV---TSKSQLRfiVSVGLLQRSVSVEVSAEQLEP 165
Cdd:cd06091    6 VGDTVRIISGPFAGFEGKVEeidEEKGKVK--VLVEMFGRETPVELDFDQVEK 56
NGN_Bact_2 cd09889
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 2; The ...
 10-99 2.10e-06

Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 2; The N-Utilization Substance G (NusG) protein is involved in transcription elongation and termination. NusG is essential in Escherichia coli and associates 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 biosynthesis genes. NusG SP family members are operon-specific transcriptional antitermination factors. The NusG N-terminal domain (NGN) is quite similar in all NusG orthologs, but its C-terminal domain and the linker that separates 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: 193578 [Multi-domain]  Cd Length: 100  Bit Score: 43.85  E-value: 2.10e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226  10 DWVALLVRVNHEKVAAAQLGKHG-----YEFFLPTYTPPKSSG---VKAKLPLFPGYLF--CRYQPLNPYRIVRAPGVIR 79
Cdd:cd09889    1 MWYVVQVRTGREKAVLELLEKLVgpdvlQECFIPQYERKKRSQgvwRERKYTLFPGYVFvvTDDIDELYYELKRVPGFTR 80

                         90       100
                 ....*....|....*....|
gi 499873226  80 LLGGDAGPEAVPAQELEAIR 99
Cdd:cd09889   81 LLGNDGSFFPLTPEEADFIR 100
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
53-166 1.41e-05

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 42.96  E-value: 1.41e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226  53 PLFPGYLFCRYQPLN-PYRIVRAP-GVIRLLGGDAGPEAVPAQELEAIRRVADSGVSSnpCDYLRVGQRVRIIEGPLTGL 130
Cdd:PRK09014  49 PLFPNYLFVEFDPEViHTTTIRSTrGVSHFVRFGAQPAIVPSDVIYQLSVYKPEKIVD--PETPKPGDKVIITEGAFEGL 126

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 499873226 131 EGSLVTSKSQLRFIVSVGLLQRSVSVEVSAEQLEPI 166
Cdd:PRK09014 127 QAIYTEPDGEARSILLLNLLNKQVKHSVDNTQFRKI 162
NGN_plant cd09890
Plant N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance G ...
 11-99 1.53e-05

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: 41.95  E-value: 1.53e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499873226  11 WVALLVRVNHEKVAAAQLGKHGYEFF----LPTYTPPKSSGVKAKL--------PLFPGYLFCRYqPLNP--YRIVRA-P 75
Cdd:cd09890    2 WYMLRVPAGRENQAAEALERALATEFpdreFEVWVPSIPVDRKLKNgsisvkekPLFPGYVLLRC-VLNKevYDFIRDnD 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 499873226  76 GVIRLLGGDAG---------PEAVPAQELEAIR 99
Cdd:cd09890   81 SVYGFVGSKVGktgkrqieiPRPVPVEEIEAIF 113
NGN_SP_AnfA1 cd09894
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1; ...
 26-91 2.79e-04

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: 38.42  E-value: 2.79e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499873226  26 AQLGKHGYEFFLP---TYTPPK-SSGVKAKL-PLFPGYLFCRYQPLN--PYRIVRAPGVIRLLGGDAGPEAVP 91
Cdd:cd09894   18 FSLERLGVEVFCPmirTRRKRTdCKSYREKIePLFPGYLFVRFDPEVvhTSKITLASGVSGFVRFGGEPCPVP 90
NGN_Bact_1 cd09891
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The ...
 54-100 6.26e-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: 34.76  E-value: 6.26e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 499873226  54 LFPGYLFCRYQpLNP--YRIVR-APGVIRLLGGDAGPEAVPAQELEAIRR 100
Cdd:cd09891   57 LFPGYVLVEMD-MNDdtWHLVRnTPGVTGFVGSGGKPVPLSEEEVERILG 105
 
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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