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Conserved domains on  [gi|1650117161|gb|QCQ36306|]
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UpxY family transcription antiterminator [Bacteroides fragilis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
antiterm_UpxY super family cl41364
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 13-179 3.60e-41

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.


The actual alignment was detected with superfamily member NF033644:

Pssm-ID: 468125 [Multi-domain]  Cd Length: 162  Bit Score: 136.06  E-value: 3.60e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1650117161  13 WYVMRdlKRVNAKQPAYMELKGMGMEVFVPMKQHLKMKKGVRVREEVPFIPDLLFVHEARTNLDLAVEKTPTLQyRWLRN 92
Cdd:NF033644    1 WYALY--TRPRREKKVAELLEKKGIESFLPMQKEIRQWSDRKKRVEVPLIPNLVFVHITEKELDEVLEQTPGVV-RYIRD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1650117161  93 --TWREPMTVADKDMERFIKAVSSTEFPQYYLPEEVTPemyRRRIRIVGGTLDGYEGRLLTTRGSKvrRLLVELKGFLA- 169
Cdd:NF033644   78 drGKSKPAIIPDKQMERFRLMLDPSDEVVVYLEAPLKK---GDKVRVIGGPLKGLEGELVRVKGKK--RVVVRIPGLGAv 152

                         170
                  ....*....|
gi 1650117161 170 VGVEVNPEYI 179
Cdd:NF033644  153 ATVEVPPSYL 162
 
Name Accession Description Interval E-value
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 13-179 3.60e-41

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: 136.06  E-value: 3.60e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1650117161  13 WYVMRdlKRVNAKQPAYMELKGMGMEVFVPMKQHLKMKKGVRVREEVPFIPDLLFVHEARTNLDLAVEKTPTLQyRWLRN 92
Cdd:NF033644    1 WYALY--TRPRREKKVAELLEKKGIESFLPMQKEIRQWSDRKKRVEVPLIPNLVFVHITEKELDEVLEQTPGVV-RYIRD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1650117161  93 --TWREPMTVADKDMERFIKAVSSTEFPQYYLPEEVTPemyRRRIRIVGGTLDGYEGRLLTTRGSKvrRLLVELKGFLA- 169
Cdd:NF033644   78 drGKSKPAIIPDKQMERFRLMLDPSDEVVVYLEAPLKK---GDKVRVIGGPLKGLEGELVRVKGKK--RVVVRIPGLGAv 152

                         170
                  ....*....|
gi 1650117161 170 VGVEVNPEYI 179
Cdd:NF033644  153 ATVEVPPSYL 162
NGN_SP_UpxY cd09895
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; ...
 12-110 3.61e-20

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: 80.31  E-value: 3.61e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1650117161  12 RWYVMRDLKRvnAKQPAYMELKGMGMEVFVPMKQHLKMKKGVRVREEVPFIPDLLFVHEARTNLDLAVEKTPTLQYRWLR 91
Cdd:cd09895     1 PWYALYTFPR--REKKVAEYLEKKGIECFLPMQYEVRQWSGRKKRVEVPLFPNLVFVHITREELDEVLETPGVVRFVRYR 78

                          90
                  ....*....|....*....
gi 1650117161  92 NtwREPMTVADKDMERFIK 110
Cdd:cd09895    79 G--KEPAIIPDKQMESFRL 95
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
8-182 5.69e-11

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 58.30  E-value: 5.69e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1650117161   8 DEDTRWYVMRDL----KRVNAkqpaYMELKGMGMEVFVPMKQHLKMKKGVRVREEVPFIPDLLFVHEARTNLDL-AVEKT 82
Cdd:COG0250     2 SMEKRWYVVHTYsgyeKKVKE----NLERRIEGIEVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWyLVRNT 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1650117161  83 PTLqYRWLRNTwREPMTVADKDMERFIKAVSSTEfpqyylPEEVTPEMYRR--RIRIVGGTLDGYEGRLLTTRGSKvRRL 160
Cdd:COG0250    78 PGV-TGFVGFG-GKPAPLPDEEVERILARLEEGE------EKPRPKVDFEVgdRVRITDGPFAGFEGTVEEVDPEK-GRV 148

                         170       180
                  ....*....|....*....|...
gi 1650117161 161 LVELKGF-LAVGVEVNPEYIKLL 182
Cdd:COG0250   149 KVLVSIFgRETPVELDFSQVEKI 171
NusG pfam02357
Transcription termination factor nusG;
12-109 1.41e-08

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 49.92  E-value: 1.41e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1650117161  12 RWYVMRdlKRVNAKQPAYMELKGMGMEVFVPMKQHLKMKKGVRVREEVPFIPDLLFVHEARTNLDLA-VEKTPTLqYRWL 90
Cdd:pfam02357   2 KWYVLQ--TYSGKEKKVKENLERQGIEVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHlVRSTPGV-TGFV 78

                          90
                  ....*....|....*....
gi 1650117161  91 RNTwREPMTVADKDMERFI 109
Cdd:pfam02357  79 GGS-GKPTPIPDEEVERIL 96
 
Name Accession Description Interval E-value
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 13-179 3.60e-41

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: 136.06  E-value: 3.60e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1650117161  13 WYVMRdlKRVNAKQPAYMELKGMGMEVFVPMKQHLKMKKGVRVREEVPFIPDLLFVHEARTNLDLAVEKTPTLQyRWLRN 92
Cdd:NF033644    1 WYALY--TRPRREKKVAELLEKKGIESFLPMQKEIRQWSDRKKRVEVPLIPNLVFVHITEKELDEVLEQTPGVV-RYIRD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1650117161  93 --TWREPMTVADKDMERFIKAVSSTEFPQYYLPEEVTPemyRRRIRIVGGTLDGYEGRLLTTRGSKvrRLLVELKGFLA- 169
Cdd:NF033644   78 drGKSKPAIIPDKQMERFRLMLDPSDEVVVYLEAPLKK---GDKVRVIGGPLKGLEGELVRVKGKK--RVVVRIPGLGAv 152

                         170
                  ....*....|
gi 1650117161 170 VGVEVNPEYI 179
Cdd:NF033644  153 ATVEVPPSYL 162
NGN_SP_UpxY cd09895
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; ...
 12-110 3.61e-20

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: 80.31  E-value: 3.61e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1650117161  12 RWYVMRDLKRvnAKQPAYMELKGMGMEVFVPMKQHLKMKKGVRVREEVPFIPDLLFVHEARTNLDLAVEKTPTLQYRWLR 91
Cdd:cd09895     1 PWYALYTFPR--REKKVAEYLEKKGIECFLPMQYEVRQWSGRKKRVEVPLFPNLVFVHITREELDEVLETPGVVRFVRYR 78

                          90
                  ....*....|....*....
gi 1650117161  92 NtwREPMTVADKDMERFIK 110
Cdd:cd09895    79 G--KEPAIIPDKQMESFRL 95
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
8-182 5.69e-11

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 58.30  E-value: 5.69e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1650117161   8 DEDTRWYVMRDL----KRVNAkqpaYMELKGMGMEVFVPMKQHLKMKKGVRVREEVPFIPDLLFVHEARTNLDL-AVEKT 82
Cdd:COG0250     2 SMEKRWYVVHTYsgyeKKVKE----NLERRIEGIEVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWyLVRNT 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1650117161  83 PTLqYRWLRNTwREPMTVADKDMERFIKAVSSTEfpqyylPEEVTPEMYRR--RIRIVGGTLDGYEGRLLTTRGSKvRRL 160
Cdd:COG0250    78 PGV-TGFVGFG-GKPAPLPDEEVERILARLEEGE------EKPRPKVDFEVgdRVRITDGPFAGFEGTVEEVDPEK-GRV 148

                         170       180
                  ....*....|....*....|...
gi 1650117161 161 LVELKGF-LAVGVEVNPEYIKLL 182
Cdd:COG0250   149 KVLVSIFgRETPVELDFSQVEKI 171
NusG pfam02357
Transcription termination factor nusG;
12-109 1.41e-08

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 49.92  E-value: 1.41e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1650117161  12 RWYVMRdlKRVNAKQPAYMELKGMGMEVFVPMKQHLKMKKGVRVREEVPFIPDLLFVHEARTNLDLA-VEKTPTLqYRWL 90
Cdd:pfam02357   2 KWYVLQ--TYSGKEKKVKENLERQGIEVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHlVRSTPGV-TGFV 78

                          90
                  ....*....|....*....
gi 1650117161  91 RNTwREPMTVADKDMERFI 109
Cdd:pfam02357  79 GGS-GKPTPIPDEEVERIL 96
NGN_SP cd09886
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP); The ...
 12-68 1.37e-03

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: 36.58  E-value: 1.37e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1650117161  12 RWYVMRdlKRVNAKQPAYMELKGMGMEVFVPMKQHLKMKKGVRVREEVPFIPDLLFV 68
Cdd:cd09886     1 SWYALR--TNPGCEQRAEEALEARGVEAFLPMLTEERKRRRKKFDVERPLFPGYVFA 55
 
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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