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Conserved domains on  [gi|496138476|ref|WP_008862983|]
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MULTISPECIES: UpxY family transcription antiterminator [Barnesiella]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 11-176 1.68e-62

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: 190.37  E-value: 1.68e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496138476  11 WFAIRVTYSREMALKEYLDRCRMESFIPMSYKEVIKGERKVRKLVPVIHNLVFVRSTREKLDEIKRDISLKVpiRYIMD- 89
Cdd:NF033644   1 WYALYTRPRREKKVAELLEKKGIESFLPMQKEIRQWSDRKKRVEVPLIPNLVFVHITEKELDEVLEQTPGVV--RYIRDd 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496138476  90 RETRRPLVVPDRQMHSFIAVAGAYDEQIVYLdptIVSLREGDRVRIVGGVFSGVEGIFIRIKGDRRVVVSIEGVMAVATA 169
Cdd:NF033644  79 RGKSKPAIIPDKQMERFRLMLDPSDEVVVYL---EAPLKKGDKVRVIGGPLKGLEGELVRVKGKKRVVVRIPGLGAVATV 155


                 ....*..
gi 496138476 170 FVHPSLI 176
Cdd:NF033644 156 EVPPSYL 162
 
Name Accession Description Interval E-value
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 11-176 1.68e-62

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: 190.37  E-value: 1.68e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496138476  11 WFAIRVTYSREMALKEYLDRCRMESFIPMSYKEVIKGERKVRKLVPVIHNLVFVRSTREKLDEIKRDISLKVpiRYIMD- 89
Cdd:NF033644   1 WYALYTRPRREKKVAELLEKKGIESFLPMQKEIRQWSDRKKRVEVPLIPNLVFVHITEKELDEVLEQTPGVV--RYIRDd 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496138476  90 RETRRPLVVPDRQMHSFIAVAGAYDEQIVYLdptIVSLREGDRVRIVGGVFSGVEGIFIRIKGDRRVVVSIEGVMAVATA 169
Cdd:NF033644  79 RGKSKPAIIPDKQMERFRLMLDPSDEVVVYL---EAPLKKGDKVRVIGGPLKGLEGELVRVKGKKRVVVRIPGLGAVATV 155


                 ....*..
gi 496138476 170 FVHPSLI 176
Cdd:NF033644 156 EVPPSYL 162
NGN_SP_UpxY cd09895
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; ...
 10-108 2.80e-24

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: 90.71  E-value: 2.80e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496138476  10 QWFAIRVTYSREMALKEYLDRCRMESFIPMSYKEVIKGERKVRKLVPVIHNLVFVRSTREKLDEIKRDISlkvPIRYIMD 89
Cdd:cd09895    1 PWYALYTFPRREKKVAEYLEKKGIECFLPMQYEVRQWSGRKKRVEVPLFPNLVFVHITREELDEVLETPG---VVRFVRY 77

                         90
                 ....*....|....*....
gi 496138476  90 REtRRPLVVPDRQMHSFIA 108
Cdd:cd09895   78 RG-KEPAIIPDKQMESFRL 95
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
7-179 6.35e-19

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 79.10  E-value: 6.35e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496138476   7 EAKQWFAIRVTYSREMALKEYLDR--CRMESFIPMSYKEVIKGERKVRKLVPVIHNLVFVRSTREklDEIKRDIsLKVP- 83
Cdd:COG0250    3 MEKRWYVVHTYSGYEKKVKENLERriEGIEVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLT--DESWYLV-RNTPg 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496138476  84 -IRYImdRETRRPLVVPDRQMHSFIAVAGAYDEQIVyldpTIVSLREGDRVRIVGGVFSGVEGIFIRIKGDR-RVVVSIE 161
Cdd:COG0250   80 vTGFV--GFGGKPAPLPDEEVERILARLEEGEEKPR----PKVDFEVGDRVRITDGPFAGFEGTVEEVDPEKgRVKVLVS 153

                        170
                 ....*....|....*...
gi 496138476 162 GVMAVATAFVHPSLIEPV 179
Cdd:COG0250  154 IFGRETPVELDFSQVEKI 171
NusG pfam02357
Transcription termination factor nusG;
9-107 2.83e-12

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 59.93  E-value: 2.83e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496138476    9 KQWFAIRVTYSREMALKEYLDRCRMESFIPMSYKEVIKGERKVRKLVPVIHNLVFVRSTREklDEIKRDI-SLKVPIRYI 87
Cdd:pfam02357   1 KKWYVLQTYSGKEKKVKENLERQGIEVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMT--DETWHLVrSTPGVTGFV 78

                          90       100
                  ....*....|....*....|
gi 496138476   88 mdRETRRPLVVPDRQMHSFI 107
Cdd:pfam02357  79 --GGSGKPTPIPDEEVERIL 96
 
Name Accession Description Interval E-value
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 11-176 1.68e-62

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: 190.37  E-value: 1.68e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496138476  11 WFAIRVTYSREMALKEYLDRCRMESFIPMSYKEVIKGERKVRKLVPVIHNLVFVRSTREKLDEIKRDISLKVpiRYIMD- 89
Cdd:NF033644   1 WYALYTRPRREKKVAELLEKKGIESFLPMQKEIRQWSDRKKRVEVPLIPNLVFVHITEKELDEVLEQTPGVV--RYIRDd 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496138476  90 RETRRPLVVPDRQMHSFIAVAGAYDEQIVYLdptIVSLREGDRVRIVGGVFSGVEGIFIRIKGDRRVVVSIEGVMAVATA 169
Cdd:NF033644  79 RGKSKPAIIPDKQMERFRLMLDPSDEVVVYL---EAPLKKGDKVRVIGGPLKGLEGELVRVKGKKRVVVRIPGLGAVATV 155


                 ....*..
gi 496138476 170 FVHPSLI 176
Cdd:NF033644 156 EVPPSYL 162
NGN_SP_UpxY cd09895
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; ...
 10-108 2.80e-24

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: 90.71  E-value: 2.80e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496138476  10 QWFAIRVTYSREMALKEYLDRCRMESFIPMSYKEVIKGERKVRKLVPVIHNLVFVRSTREKLDEIKRDISlkvPIRYIMD 89
Cdd:cd09895    1 PWYALYTFPRREKKVAEYLEKKGIECFLPMQYEVRQWSGRKKRVEVPLFPNLVFVHITREELDEVLETPG---VVRFVRY 77

                         90
                 ....*....|....*....
gi 496138476  90 REtRRPLVVPDRQMHSFIA 108
Cdd:cd09895   78 RG-KEPAIIPDKQMESFRL 95
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
7-179 6.35e-19

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 79.10  E-value: 6.35e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496138476   7 EAKQWFAIRVTYSREMALKEYLDR--CRMESFIPMSYKEVIKGERKVRKLVPVIHNLVFVRSTREklDEIKRDIsLKVP- 83
Cdd:COG0250    3 MEKRWYVVHTYSGYEKKVKENLERriEGIEVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLT--DESWYLV-RNTPg 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496138476  84 -IRYImdRETRRPLVVPDRQMHSFIAVAGAYDEQIVyldpTIVSLREGDRVRIVGGVFSGVEGIFIRIKGDR-RVVVSIE 161
Cdd:COG0250   80 vTGFV--GFGGKPAPLPDEEVERILARLEEGEEKPR----PKVDFEVGDRVRITDGPFAGFEGTVEEVDPEKgRVKVLVS 153

                        170
                 ....*....|....*...
gi 496138476 162 GVMAVATAFVHPSLIEPV 179
Cdd:COG0250  154 IFGRETPVELDFSQVEKI 171
NGN_SP cd09886
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP); The ...
 10-108 7.19e-15

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: 66.62  E-value: 7.19e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496138476  10 QWFAIRVTYSREMALKEYLDRCRMESFIPMSYKEVIKGERKVRKLVPVIHNLVFVRstrekLDEIKRDISLKV----PIR 85
Cdd:cd09886    1 SWYALRTNPGCEQRAEEALEARGVEAFLPMLTEERKRRRKKFDVERPLFPGYVFAR-----LDRSKGQDTSTIracdGVL 75

                         90       100
                 ....*....|....*....|...
gi 496138476  86 YIMDREtRRPLVVPDRQMHSFIA 108
Cdd:cd09886   76 GVVGFD-GRPAPVPEQEMRDLRK 97
NusG pfam02357
Transcription termination factor nusG;
9-107 2.83e-12

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 59.93  E-value: 2.83e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496138476    9 KQWFAIRVTYSREMALKEYLDRCRMESFIPMSYKEVIKGERKVRKLVPVIHNLVFVRSTREklDEIKRDI-SLKVPIRYI 87
Cdd:pfam02357   1 KKWYVLQTYSGKEKKVKENLERQGIEVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMT--DETWHLVrSTPGVTGFV 78

                          90       100
                  ....*....|....*....|
gi 496138476   88 mdRETRRPLVVPDRQMHSFI 107
Cdd:pfam02357  79 --GGSGKPTPIPDEEVERIL 96
KOW_NusG cd06091
NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif ...
 124-161 2.63e-03

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: 34.74  E-value: 2.63e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 496138476 124 IVSLREGDRVRIVGGVFSGVEGIFIRIKGDR-RVVVSIE 161
Cdd:cd06091    1 EVDFEVGDTVRIISGPFAGFEGKVEEIDEEKgKVKVLVE 39
 
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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