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Conserved domains on  [gi|486247130|ref|WP_001562941|]
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transcription termination/antitermination NusG family protein [Escherichia coli]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NGN super family cl02766
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 9-101 6.45e-30

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.


The actual alignment was detected with superfamily member cd09894:

Pssm-ID: 445911 [Multi-domain]  Cd Length: 99  Bit Score: 104.29  E-value: 6.45e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130   9 NWYVLEFCSARTARVFSHLERLGVTFWCPLTCSHYRRSDKNCFRRKEVPLFPGYVFIKIDFNKTHSTTVTSVPWVKSFVS 88
Cdd:cd09894    2 RWYLLRCKSGKIQSVIFSLERLGVEVFCPMIRTRRKRTDCKSYREKIEPLFPGYLFVRFDPEVVHTSKITLASGVSGFVR 81

                         90
                 ....*....|...
gi 486247130  89 FGGEPVPVCEEII 101
Cdd:cd09894   82 FGGEPCPVPDAVI 94
 
Name Accession Description Interval E-value
NGN_SP_AnfA1 cd09894
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1; ...
 9-101 6.45e-30

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: 104.29  E-value: 6.45e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130   9 NWYVLEFCSARTARVFSHLERLGVTFWCPLTCSHYRRSDKNCFRRKEVPLFPGYVFIKIDFNKTHSTTVTSVPWVKSFVS 88
Cdd:cd09894    2 RWYLLRCKSGKIQSVIFSLERLGVEVFCPMIRTRRKRTDCKSYREKIEPLFPGYLFVRFDPEVVHTSKITLASGVSGFVR 81

                         90
                 ....*....|...
gi 486247130  89 FGGEPVPVCEEII 101
Cdd:cd09894   82 FGGEPCPVPDAVI 94
RfaH TIGR01955
transcription elongation factor/antiterminator RfaH; This model represents the transcription ...
 10-149 4.34e-18

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: 75.96  E-value: 4.34e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130   10 WYVLeFCSART-ARVFSHLERLGVTFWCPLTCSHYRRSdkNCFRRKEVPLFPGYVFIKIDFNKTHSTTVTSVPWVKSFVS 88
Cdd:TIGR01955   1 WYLL-YCKPRQeQRAQEHLERQAVECYLPMITVEKIVR--GKRQAVSEPLFPNYLFIEFDPEVDSWTTIRSTRGVSRFVR 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 486247130   89 FGGEPVPVCEEIILGLRRRETN----------YWGEYSPI-RGIPHELAEILLENNPMKRSFLFFKYLSNTQ 149
Cdd:TIGR01955  78 FGGHPAPVPDDLIHQLRQYEPKdsvppattlpYKGDKVRItDGAFAGFEAIFLEPDGEKRSMLLLNMIGKQI 149
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
1-108 5.38e-18

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 75.63  E-value: 5.38e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130   1 MTTRKsgfNWYVLEFCSARTARVFSHLERL--GVTFWCPLTCSHYRRSDKncFRRKEVPLFPGYVFIKIDFNKTHSTTVT 78
Cdd:COG0250    1 MSMEK---RWYVVHTYSGYEKKVKENLERRieGIEVFVPTEEVVEIKNGK--KKTVERPLFPGYVFVRMDLTDESWYLVR 75

                         90       100       110
                 ....*....|....*....|....*....|
gi 486247130  79 SVPWVKSFVSFGGEPVPVCEEIILGLRRRE 108
Cdd:COG0250   76 NTPGVTGFVGFGGKPAPLPDEEVERILARL 105
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 9-107 4.91e-17

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: 71.64  E-value: 4.91e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130     9 NWYVLEFCSARTARVFSHLERLGVT---------FWCPL-TCSHYRRSDKncfRRKEVPLFPGYVFIKIDFNKTHSTTVT 78
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKAEAlgledkivsILVPTeEVKEIRRGKK---KVVERKLFPGYIFVEADLEDEVWTAIR 77

                           90       100
                   ....*....|....*....|....*....
gi 486247130    79 SVPWVKSFVSFGGEPVPVCEEIILGLRRR 107
Cdd:smart00738  78 GTPGVRGFVGGGGKPTPVPDDEIEKILKP 106
NusG pfam02357
Transcription termination factor nusG;
8-105 1.58e-15

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 67.25  E-value: 1.58e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130    8 FNWYVLEFCSARTARVFSHLERLGVTFWCPLTCSHYRRSDKNcfRRKEVPLFPGYVFIKIDFNKTHSTTVTSVPWVKSFV 87
Cdd:pfam02357   1 KKWYVLQTYSGKEKKVKENLERQGIEVFLPTEEVVEIRNGKK--KVVERPLFPGYVFVRMDMTDETWHLVRSTPGVTGFV 78

                          90
                  ....*....|....*...
gi 486247130   88 SFGGEPVPVCEEIILGLR 105
Cdd:pfam02357  79 GGSGKPTPIPDEEVERIL 96
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
9-109 4.86e-13

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 62.60  E-value: 4.86e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130   9 NWYVLeFCSART-ARVFSHLERLGVTFWCPL-TCSHYRRSdkncfRRKEV--PLFPGYVFIKIDFNKTHSTTVTSVPWVK 84
Cdd:PRK09014   3 SWYLL-YCKRGQlQRAQEHLERQGVECLYPMiTLEKIVRG-----KRTEVsePLFPNYLFVEFDPEVIHTTTIRSTRGVS 76

                         90       100
                 ....*....|....*....|....*
gi 486247130  85 SFVSFGGEPVPVCEEIILGLRRRET 109
Cdd:PRK09014  77 HFVRFGAQPAIVPSDVIYQLSVYKP 101
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 10-92 1.88e-07

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: 47.85  E-value: 1.88e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130  10 WYVLefcsaRTA-----RVFSHLERLGVTFWCPLTCSHYRRSDKncFRRKEVPLFPGYVFIKIDfNKTHSTTVTSVPWVK 84
Cdd:NF033644   1 WYAL-----YTRprrekKVAELLEKKGIESFLPMQKEIRQWSDR--KKRVEVPLIPNLVFVHIT-EKELDEVLEQTPGVV 72


                 ....*...
gi 486247130  85 SFVSFGGE 92
Cdd:NF033644  73 RYIRDDRG 80
 
Name Accession Description Interval E-value
NGN_SP_AnfA1 cd09894
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1; ...
 9-101 6.45e-30

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: 104.29  E-value: 6.45e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130   9 NWYVLEFCSARTARVFSHLERLGVTFWCPLTCSHYRRSDKNCFRRKEVPLFPGYVFIKIDFNKTHSTTVTSVPWVKSFVS 88
Cdd:cd09894    2 RWYLLRCKSGKIQSVIFSLERLGVEVFCPMIRTRRKRTDCKSYREKIEPLFPGYLFVRFDPEVVHTSKITLASGVSGFVR 81

                         90
                 ....*....|...
gi 486247130  89 FGGEPVPVCEEII 101
Cdd:cd09894   82 FGGEPCPVPDAVI 94
NGN_SP_RfaH cd09892
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; ...
 9-106 5.56e-20

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: 78.76  E-value: 5.56e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130   9 NWYVLEFCSARTARVFSHLERLGVTFWCPLTCshYRRSDKNCFRRKEVPLFPGYVFIKIDFNKTHSTTVTSVPWVKSFVS 88
Cdd:cd09892    1 AWYLLYTKPRQEERAAENLERQGFEVFLPMIR--VEKRRRGKRTVVTEPLFPGYLFVRLDPEVQNWRPIRSTRGVSRLVR 78

                         90
                 ....*....|....*...
gi 486247130  89 FGGEPVPVCEEIILGLRR 106
Cdd:cd09892   79 FGGEPAPVPDALIEALRA 96
RfaH TIGR01955
transcription elongation factor/antiterminator RfaH; This model represents the transcription ...
 10-149 4.34e-18

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: 75.96  E-value: 4.34e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130   10 WYVLeFCSART-ARVFSHLERLGVTFWCPLTCSHYRRSdkNCFRRKEVPLFPGYVFIKIDFNKTHSTTVTSVPWVKSFVS 88
Cdd:TIGR01955   1 WYLL-YCKPRQeQRAQEHLERQAVECYLPMITVEKIVR--GKRQAVSEPLFPNYLFIEFDPEVDSWTTIRSTRGVSRFVR 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 486247130   89 FGGEPVPVCEEIILGLRRRETN----------YWGEYSPI-RGIPHELAEILLENNPMKRSFLFFKYLSNTQ 149
Cdd:TIGR01955  78 FGGHPAPVPDDLIHQLRQYEPKdsvppattlpYKGDKVRItDGAFAGFEAIFLEPDGEKRSMLLLNMIGKQI 149
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
1-108 5.38e-18

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 75.63  E-value: 5.38e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130   1 MTTRKsgfNWYVLEFCSARTARVFSHLERL--GVTFWCPLTCSHYRRSDKncFRRKEVPLFPGYVFIKIDFNKTHSTTVT 78
Cdd:COG0250    1 MSMEK---RWYVVHTYSGYEKKVKENLERRieGIEVFVPTEEVVEIKNGK--KKTVERPLFPGYVFVRMDLTDESWYLVR 75

                         90       100       110
                 ....*....|....*....|....*....|
gi 486247130  79 SVPWVKSFVSFGGEPVPVCEEIILGLRRRE 108
Cdd:COG0250   76 NTPGVTGFVGFGGKPAPLPDEEVERILARL 105
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 9-107 4.91e-17

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: 71.64  E-value: 4.91e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130     9 NWYVLEFCSARTARVFSHLERLGVT---------FWCPL-TCSHYRRSDKncfRRKEVPLFPGYVFIKIDFNKTHSTTVT 78
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKAEAlgledkivsILVPTeEVKEIRRGKK---KVVERKLFPGYIFVEADLEDEVWTAIR 77

                           90       100
                   ....*....|....*....|....*....
gi 486247130    79 SVPWVKSFVSFGGEPVPVCEEIILGLRRR 107
Cdd:smart00738  78 GTPGVRGFVGGGGKPTPVPDDEIEKILKP 106
NGN_SP cd09886
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP); The ...
 10-106 1.03e-16

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: 70.47  E-value: 1.03e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130  10 WYVLEFCSARTARVFSHLERLGVTFWCPLTCSHYRRSDKNcfRRKEVPLFPGYVFIKIDFNKTHST-TVTSVPWVKSFVS 88
Cdd:cd09886    2 WYALRTNPGCEQRAEEALEARGVEAFLPMLTEERKRRRKK--FDVERPLFPGYVFARLDRSKGQDTsTIRACDGVLGVVG 79

                         90
                 ....*....|....*...
gi 486247130  89 FGGEPVPVCEEIILGLRR 106
Cdd:cd09886   80 FDGRPAPVPEQEMRDLRK 97
NusG pfam02357
Transcription termination factor nusG;
8-105 1.58e-15

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 67.25  E-value: 1.58e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130    8 FNWYVLEFCSARTARVFSHLERLGVTFWCPLTCSHYRRSDKNcfRRKEVPLFPGYVFIKIDFNKTHSTTVTSVPWVKSFV 87
Cdd:pfam02357   1 KKWYVLQTYSGKEKKVKENLERQGIEVFLPTEEVVEIRNGKK--KVVERPLFPGYVFVRMDMTDETWHLVRSTPGVTGFV 78

                          90
                  ....*....|....*...
gi 486247130   88 SFGGEPVPVCEEIILGLR 105
Cdd:pfam02357  79 GGSGKPTPIPDEEVERIL 96
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
9-109 4.86e-13

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 62.60  E-value: 4.86e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130   9 NWYVLeFCSART-ARVFSHLERLGVTFWCPL-TCSHYRRSdkncfRRKEV--PLFPGYVFIKIDFNKTHSTTVTSVPWVK 84
Cdd:PRK09014   3 SWYLL-YCKRGQlQRAQEHLERQGVECLYPMiTLEKIVRG-----KRTEVsePLFPNYLFVEFDPEVIHTTTIRSTRGVS 76

                         90       100
                 ....*....|....*....|....*
gi 486247130  85 SFVSFGGEPVPVCEEIILGLRRRET 109
Cdd:PRK09014  77 HFVRFGAQPAIVPSDVIYQLSVYKP 101
NGN_SP_TaA cd09893
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), TaA; ...
 9-106 9.40e-12

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: 57.70  E-value: 9.40e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130   9 NWYVLEFCSARTARVFSHLERLGVTFWCPLTCSHYRRSDkncfRRKE--VPLFPGYVFIKIDFNKTHsTTVTSVPWVKSF 86
Cdd:cd09893    1 SWYALYTRSRHEKKVADRLAKKGIESFLPLYEVLSRWKD----RKKKikVPLFPGYLFVRFQLDPER-LRILKTPGVVRI 75

                         90       100
                 ....*....|....*....|
gi 486247130  87 VSFGGEPVPVCEEIILGLRR 106
Cdd:cd09893   76 VGNSGGPIPIPDEEIASLRI 95
NGN_SP_UpxY cd09895
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; ...
 9-93 1.25e-08

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: 49.50  E-value: 1.25e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130   9 NWYVLEFCSARTARVFSHLERLGVTFWCPLTCSHYRRSDKncFRRKEVPLFPGYVFIKIDFnkTHSTTVTSVPWVKSFVS 88
Cdd:cd09895    1 PWYALYTFPRREKKVAEYLEKKGIECFLPMQYEVRQWSGR--KKRVEVPLFPNLVFVHITR--EELDEVLETPGVVRFVR 76


                 ....*
gi 486247130  89 FGGEP 93
Cdd:cd09895   77 YRGKE 81
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 9-101 1.53e-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: 1.53e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130   9 NWYVLEFCSARTARVFSHLERLGVTFWC----PLTCSHYRRSDKNcfRRKEVPLFPGYVFIKIDFNKTHSTTVTSVPWVK 84
Cdd:cd08000    1 NWYVLFVKTGREEKVEKLLEKRFEANDIeafvPKKEVPERKRGKI--EEVIKPLFPGYVFVETDLSPELYELIREVPGVI 78

                         90
                 ....*....|....*..
gi 486247130  85 SFVSFGGEPVPVCEEII 101
Cdd:cd08000   79 GILGNGEEPSPVSDEEI 95
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 10-92 1.88e-07

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: 47.85  E-value: 1.88e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130  10 WYVLefcsaRTA-----RVFSHLERLGVTFWCPLTCSHYRRSDKncFRRKEVPLFPGYVFIKIDfNKTHSTTVTSVPWVK 84
Cdd:NF033644   1 WYAL-----YTRprrekKVAELLEKKGIESFLPMQKEIRQWSDR--KKRVEVPLIPNLVFVHIT-EKELDEVLEQTPGVV 72


                 ....*...
gi 486247130  85 SFVSFGGE 92
Cdd:NF033644  73 RYIRDDRG 80
NGN_Bact_1 cd09891
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The ...
 48-99 3.09e-07

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: 45.93  E-value: 3.09e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 486247130  48 KNCFRRKEVPLFPGYVFIKIDFNKTHSTTVTSVPWVKSFVSFGGEPVPVCEE 99
Cdd:cd09891   47 NGKKKVKERKLFPGYVLVEMDMNDDTWHLVRNTPGVTGFVGSGGKPVPLSEE 98
nusG TIGR00922
transcription termination/antitermination factor NusG; NusG proteins are transcription factors ...
 10-95 2.28e-04

transcription termination/antitermination factor NusG; NusG proteins are transcription factors which are aparrently universal in prokaryotes (archaea and eukaryotes have homologs that may have related functions). The essential components of these factors include an N-terminal RNP-like (ribonucleoprotein) domain and a C-terminal KOW motif (pfam00467) believed to be a nucleic acid binding domain. In E. coli, NusA has been shown to interact with RNA polymerase and termination factor Rho. This model covers a wide variety of bacterial species but excludes mycoplasmas which are covered by a separate model (TIGR01956).The function of all of these NusG proteins is likely to be the same at the level of interaction with RNA and other protein factors to affect termination; however different species may utilize NusG towards different processes and in combination with different suites of affector proteins.In E. coli, NusG promotes rho-dependent termination. It is an essential gene. In Streptomyces virginiae and related species, an additional N-terminal sequence is also present and is suggested to play a role in butyrolactone-mediated autoregulation. In Thermotoga maritima, NusG has a long insert, fails to substitute for E. coli NusG (with or without the long insert), is a large 0.7 % of total cellular protein, and has a general, sequence non-specific DNA and RNA binding activity that blocks ethidium staining, yet permits transcription.Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405). [Transcription, Transcription factors]


Pssm-ID: 273341 [Multi-domain]  Cd Length: 172  Bit Score: 39.21  E-value: 2.28e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130   10 WYVLEFCSARTARVFSHLE----RLGVT-----FWCPLT-CSHYRRSDKNCFRRKevpLFPGYVFIKIDFNKTHSTTVTS 79
Cdd:TIGR00922   1 WYVVQTYSGYEKKVKQNLEelieLLGMGdyifeVIVPTEeVVEIKKGKKKVVERK---IFPGYVLVKMDLTDVSWHLVKN 77

                          90
                  ....*....|....*.
gi 486247130   80 VPWVKSFVSFGGEPVP 95
Cdd:TIGR00922  78 TPGVTGFVGSGGKPKA 93
NGN_plant cd09890
Plant N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance G ...
 10-88 6.99e-03

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: 34.25  E-value: 6.99e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 486247130  10 WYVLEFCSARTARVFSHLERLGVT--------FWCPlTCSHYRRSDKNCFRRKEVPLFPGYVFIKIDFNKTHSTTVTSVP 81
Cdd:cd09890    2 WYMLRVPAGRENQAAEALERALATefpdrefeVWVP-SIPVDRKLKNGSISVKEKPLFPGYVLLRCVLNKEVYDFIRDND 80


                 ....*..
gi 486247130  82 WVKSFVS 88
Cdd:cd09890   81 SVYGFVG 87
 
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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