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Conserved domains on  [gi|521096181|ref|WP_020427084|]
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MULTISPECIES: transcription termination/antitermination protein NusG [Paenibacillus]

Protein Classification

transcription termination/antitermination protein NusG( domain architecture ID 11489978)

transcription termination/antitermination protein NusG (N-Utilization Substance G) is involved in transcription elongation and termination in bacteria

CATH:  2.30.30.30|3.30.70.940
Gene Ontology:  GO:0006353|GO:0032784|GO:0031564|GO:0006354
PubMed:  27899640|29887376
SCOP:  4002609

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
nusG TIGR00922
transcription termination/antitermination factor NusG; NusG proteins are transcription factors ...
 5-176 3.13e-77

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: 227.95  E-value: 3.13e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181    5 WYVVHTYSGYENKVKANLEKRVESMGMEDKIFRVLVPMEEELVNKDGKKKTVMRKVYPGYVLVEMVQTDDSWYVVRNTPG 84
Cdd:TIGR00922   1 WYVVQTYSGYEKKVKQNLEELIELLGMGDYIFEVIVPTEEVVEIKKGKKKVVERKIFPGYVLVKMDLTDVSWHLVKNTPG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   85 VTGFVGSTGSGSKPTalLPEEVEQIL--KHMGMVEPKAKIDFEIKESVRIMVGPFANFVGSVEEILADKSKIKVHVNMFG 162
Cdd:TIGR00922  81 VTGFVGSGGKPKALS--EDEEVKNILnaLEEGKDKPKPKIDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFG 158

                         170
                  ....*....|....
gi 521096181  163 RETPLELDFTQVEK 176
Cdd:TIGR00922 159 RETPVELEFSQVEK 172
 
Name Accession Description Interval E-value
nusG TIGR00922
transcription termination/antitermination factor NusG; NusG proteins are transcription factors ...
 5-176 3.13e-77

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: 227.95  E-value: 3.13e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181    5 WYVVHTYSGYENKVKANLEKRVESMGMEDKIFRVLVPMEEELVNKDGKKKTVMRKVYPGYVLVEMVQTDDSWYVVRNTPG 84
Cdd:TIGR00922   1 WYVVQTYSGYEKKVKQNLEELIELLGMGDYIFEVIVPTEEVVEIKKGKKKVVERKIFPGYVLVKMDLTDVSWHLVKNTPG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   85 VTGFVGSTGSGSKPTalLPEEVEQIL--KHMGMVEPKAKIDFEIKESVRIMVGPFANFVGSVEEILADKSKIKVHVNMFG 162
Cdd:TIGR00922  81 VTGFVGSGGKPKALS--EDEEVKNILnaLEEGKDKPKPKIDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFG 158

                         170
                  ....*....|....
gi 521096181  163 RETPLELDFTQVEK 176
Cdd:TIGR00922 159 RETPVELEFSQVEK 172
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
1-177 1.66e-75

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 223.55  E-value: 1.66e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   1 MEKRWYVVHTYSGYENKVKANLEKRVESMgmedkifRVLVPMEEELVNKDGKKKTVMRKVYPGYVLVEMVQTDDSWYVVR 80
Cdd:COG0250    3 MEKRWYVVHTYSGYEKKVKENLERRIEGI-------EVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLVR 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181  81 NTPGVTGFVgstGSGSKPTALLPEEVEQILKHM--GMVEPKAKIDFEIKESVRIMVGPFANFVGSVEEILADKSKIKVHV 158
Cdd:COG0250   76 NTPGVTGFV---GFGGKPAPLPDEEVERILARLeeGEEKPRPKVDFEVGDRVRITDGPFAGFEGTVEEVDPEKGRVKVLV 152

                        170
                 ....*....|....*....
gi 521096181 159 NMFGRETPLELDFTQVEKI 177
Cdd:COG0250  153 SIFGRETPVELDFSQVEKI 171
NGN_Bact_1 cd09891
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The ...
 4-110 9.94e-55

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: 168.42  E-value: 9.94e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   4 RWYVVHTYSGYENKVKANLEKRVESMGMEDKIFRVLVPMEEELVNKDGKKKTVMRKVYPGYVLVEMVQTDDSWYVVRNTP 83
Cdd:cd09891    1 KWYVVHTYSGYENKVKENLEKRIESEGLEDYIGEVLVPTEEVVEVKNGKKKVKERKLFPGYVLVEMDMNDDTWHLVRNTP 80

                         90       100
                 ....*....|....*....|....*..
gi 521096181  84 GVTGFVgstGSGSKPTALLPEEVEQIL 110
Cdd:cd09891   81 GVTGFV---GSGGKPVPLSEEEVERIL 104
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 4-112 2.58e-39

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: 129.42  E-value: 2.58e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181     4 RWYVVHTYSGYENKVKANLEKRVESMGMEDKIFRVLVPMEEELVNKDGKKKTVMRKVYPGYVLVEMVQTDDSWYVVRNTP 83
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKAEALGLEDKIVSILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGTP 80

                           90       100
                   ....*....|....*....|....*....
gi 521096181    84 GVTGFVgstGSGSKPTALLPEEVEQILKH 112
Cdd:smart00738  81 GVRGFV---GGGGKPTPVPDDEIEKILKP 106
NusG pfam02357
Transcription termination factor nusG;
3-110 7.90e-37

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 122.72  E-value: 7.90e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181    3 KRWYVVHTYSGYENKVKANLEKRvesmGMEdkifrVLVPMEEELVNKDGKKKTVMRKVYPGYVLVEMVQTDDSWYVVRNT 82
Cdd:pfam02357   1 KKWYVLQTYSGKEKKVKENLERQ----GIE-----VFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRST 71

                          90       100
                  ....*....|....*....|....*...
gi 521096181   83 PGVTGFVgstGSGSKPTALLPEEVEQIL 110
Cdd:pfam02357  72 PGVTGFV---GGSGKPTPIPDEEVERIL 96
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 5-162 4.35e-13

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: 63.64  E-value: 4.35e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   5 WYVVHTYSGYENKVKANLEKrvesMGMEdkifrVLVPMEEELVNKDGKKKTVMRKVYPGYVLVEMVQTdDSWYVVRNTPG 84
Cdd:NF033644   1 WYALYTRPRREKKVAELLEK----KGIE-----SFLPMQKEIRQWSDRKKRVEVPLIPNLVFVHITEK-ELDEVLEQTPG 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181  85 VTGFVGSTGSGSKPtALLPEEVEQILKHMGMVEPKAKIDFEIK----ESVRIMVGPFANFVGSVEEIlADKSKIKVHVNM 160
Cdd:NF033644  71 VVRYIRDDRGKSKP-AIIPDKQMERFRLMLDPSDEVVVYLEAPlkkgDKVRVIGGPLKGLEGELVRV-KGKKRVVVRIPG 148


                 ..
gi 521096181 161 FG 162
Cdd:NF033644 149 LG 150
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
3-177 6.51e-05

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 41.03  E-value: 6.51e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   3 KRWYVVHTYSGYENKVKANLEKR-VES---MGMEDKIFRvlvpmeeelvnkdGKKKTVMRKVYPGYVLVEMVQTDDSWYV 78
Cdd:PRK09014   2 KSWYLLYCKRGQLQRAQEHLERQgVEClypMITLEKIVR-------------GKRTEVSEPLFPNYLFVEFDPEVIHTTT 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181  79 VRNTPGVTGFVgstGSGSKPtALLPEEVEQILKhmgMVEPKAKIDFEIKE---SVRIMVGPFANFVGSVEEILADKSKIK 155
Cdd:PRK09014  69 IRSTRGVSHFV---RFGAQP-AIVPSDVIYQLS---VYKPEKIVDPETPKpgdKVIITEGAFEGLQAIYTEPDGEARSIL 141

                        170       180
                 ....*....|....*....|..
gi 521096181 156 VhVNMFGRETPLELDFTQVEKI 177
Cdd:PRK09014 142 L-LNLLNKQVKHSVDNTQFRKI 162
 
Name Accession Description Interval E-value
nusG TIGR00922
transcription termination/antitermination factor NusG; NusG proteins are transcription factors ...
 5-176 3.13e-77

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: 227.95  E-value: 3.13e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181    5 WYVVHTYSGYENKVKANLEKRVESMGMEDKIFRVLVPMEEELVNKDGKKKTVMRKVYPGYVLVEMVQTDDSWYVVRNTPG 84
Cdd:TIGR00922   1 WYVVQTYSGYEKKVKQNLEELIELLGMGDYIFEVIVPTEEVVEIKKGKKKVVERKIFPGYVLVKMDLTDVSWHLVKNTPG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   85 VTGFVGSTGSGSKPTalLPEEVEQIL--KHMGMVEPKAKIDFEIKESVRIMVGPFANFVGSVEEILADKSKIKVHVNMFG 162
Cdd:TIGR00922  81 VTGFVGSGGKPKALS--EDEEVKNILnaLEEGKDKPKPKIDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFG 158

                         170
                  ....*....|....
gi 521096181  163 RETPLELDFTQVEK 176
Cdd:TIGR00922 159 RETPVELEFSQVEK 172
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
1-177 1.66e-75

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 223.55  E-value: 1.66e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   1 MEKRWYVVHTYSGYENKVKANLEKRVESMgmedkifRVLVPMEEELVNKDGKKKTVMRKVYPGYVLVEMVQTDDSWYVVR 80
Cdd:COG0250    3 MEKRWYVVHTYSGYEKKVKENLERRIEGI-------EVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLVR 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181  81 NTPGVTGFVgstGSGSKPTALLPEEVEQILKHM--GMVEPKAKIDFEIKESVRIMVGPFANFVGSVEEILADKSKIKVHV 158
Cdd:COG0250   76 NTPGVTGFV---GFGGKPAPLPDEEVERILARLeeGEEKPRPKVDFEVGDRVRITDGPFAGFEGTVEEVDPEKGRVKVLV 152

                        170
                 ....*....|....*....
gi 521096181 159 NMFGRETPLELDFTQVEKI 177
Cdd:COG0250  153 SIFGRETPVELDFSQVEKI 171
NGN_Bact_1 cd09891
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The ...
 4-110 9.94e-55

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: 168.42  E-value: 9.94e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   4 RWYVVHTYSGYENKVKANLEKRVESMGMEDKIFRVLVPMEEELVNKDGKKKTVMRKVYPGYVLVEMVQTDDSWYVVRNTP 83
Cdd:cd09891    1 KWYVVHTYSGYENKVKENLEKRIESEGLEDYIGEVLVPTEEVVEVKNGKKKVKERKLFPGYVLVEMDMNDDTWHLVRNTP 80

                         90       100
                 ....*....|....*....|....*..
gi 521096181  84 GVTGFVgstGSGSKPTALLPEEVEQIL 110
Cdd:cd09891   81 GVTGFV---GSGGKPVPLSEEEVERIL 104
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 4-112 2.58e-39

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: 129.42  E-value: 2.58e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181     4 RWYVVHTYSGYENKVKANLEKRVESMGMEDKIFRVLVPMEEELVNKDGKKKTVMRKVYPGYVLVEMVQTDDSWYVVRNTP 83
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKAEALGLEDKIVSILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGTP 80

                           90       100
                   ....*....|....*....|....*....
gi 521096181    84 GVTGFVgstGSGSKPTALLPEEVEQILKH 112
Cdd:smart00738  81 GVRGFV---GGGGKPTPVPDDEIEKILKP 106
NusG pfam02357
Transcription termination factor nusG;
3-110 7.90e-37

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 122.72  E-value: 7.90e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181    3 KRWYVVHTYSGYENKVKANLEKRvesmGMEdkifrVLVPMEEELVNKDGKKKTVMRKVYPGYVLVEMVQTDDSWYVVRNT 82
Cdd:pfam02357   1 KKWYVLQTYSGKEKKVKENLERQ----GIE-----VFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRST 71

                          90       100
                  ....*....|....*....|....*...
gi 521096181   83 PGVTGFVgstGSGSKPTALLPEEVEQIL 110
Cdd:pfam02357  72 PGVTGFV---GGSGKPTPIPDEEVERIL 96
NusG_myco TIGR01956
NusG family protein; This model represents a family of Mycoplasma proteins orthologous to the ...
 4-176 2.04e-21

NusG family protein; This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.


Pssm-ID: 273895 [Multi-domain]  Cd Length: 258  Bit Score: 87.71  E-value: 2.04e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181    4 RWYVVHTYSGYENKVKANLEKRVESMGMEDKI--FRVL----VPMEE--------------------ELVNKDGKKKTVM 57
Cdd:TIGR01956   1 QWYIATTINGNEDEVIENIKAKVRALGLENYIsdFKILkereIEEKVfepkngqaprsmkntattkwETLDETKYKKTKI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   58 RKV--YPGYVLVEMVQTDDSWYVVRNTPGVTGFVGSTGSGSKPTALLPEEVEQILKHMGMVEPKAKI------------- 122
Cdd:TIGR01956  81 SEKnkYNGYIYIKMIMTEDAWFLIRNTENVTGLVGSSGKGAKPIPISADADKLKMLKGISENTKKRVlvtntaivemeen 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181  123 --------------------------------------------DFEIKESVRIMVGPFANFVGSVEEILADKSKIKVHV 158
Cdd:TIGR01956 161 kfdekcqyilkhkqvkpeaiaqvsesgeiideiveefqlvdnlsKFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEV 240

                         250
                  ....*....|....*...
gi 521096181  159 NMFGRETPLELDFTQVEK 176
Cdd:TIGR01956 241 EILGKSVDVDLNFKHLKL 258
KOW_NusG cd06091
NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif ...
 121-176 1.34e-20

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: 80.19  E-value: 1.34e-20
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 521096181 121 KIDFEIKESVRIMVGPFANFVGSVEEILADKSKIKVHVNMFGRETPLELDFTQVEK 176
Cdd:cd06091    1 EVDFEVGDTVRIISGPFAGFEGKVEEIDEEKGKVKVLVEMFGRETPVELDFDQVEK 56
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 5-110 2.62e-20

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: 80.83  E-value: 2.62e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   5 WYVVHTYSGYENKVKANLEKRVESmgmedKIFRVLVPMEEELVNKDGKKKTVMRKVYPGYVLVEMVQTDDSWYVVRNTPG 84
Cdd:cd08000    2 WYVLFVKTGREEKVEKLLEKRFEA-----NDIEAFVPKKEVPERKRGKIEEVIKPLFPGYVFVETDLSPELYELIREVPG 76

                         90       100
                 ....*....|....*....|....*.
gi 521096181  85 VTGFVgstGSGSKPTALLPEEVEQIL 110
Cdd:cd08000   77 VIGIL---GNGEEPSPVSDEEIEMIL 99
RfaH TIGR01955
transcription elongation factor/antiterminator RfaH; This model represents the transcription ...
 5-175 5.15e-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: 76.35  E-value: 5.15e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181    5 WYVVHTYSGYENKVKANLEKRVesmgmedkiFRVLVPMEEELVNKDGKKKTVMRKVYPGYVLVEMVQTDDSWYVVRNTPG 84
Cdd:TIGR01955   1 WYLLYCKPRQEQRAQEHLERQA---------VECYLPMITVEKIVRGKRQAVSEPLFPNYLFIEFDPEVDSWTTIRSTRG 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   85 VTGFVgstGSGSKPTALLPEEVEQI-LKHMGMVEPKAKIDFEIKESVRIMVGPFANFVGSVEEILADKSKIkVHVNMFGR 163
Cdd:TIGR01955  72 VSRFV---RFGGHPAPVPDDLIHQLrQYEPKDSVPPATTLPYKGDKVRITDGAFAGFEAIFLEPDGEKRSM-LLLNMIGK 147

                         170
                  ....*....|..
gi 521096181  164 ETPLELDFTQVE 175
Cdd:TIGR01955 148 QIKVSVPNTSVE 159
NGN_SP_RfaH cd09892
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; ...
 4-109 7.03e-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: 66.43  E-value: 7.03e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   4 RWYVVHTYSGYENKVKANLEKRVesmgmedkiFRVLVPMEEELVNKDGKKKTVMRKVYPGYVLVEMVQTDDSWYVVRNTP 83
Cdd:cd09892    1 AWYLLYTKPRQEERAAENLERQG---------FEVFLPMIRVEKRRRGKRTVVTEPLFPGYLFVRLDPEVQNWRPIRSTR 71

                         90       100
                 ....*....|....*....|....*.
gi 521096181  84 GVTGFVgstGSGSKPTALLPEEVEQI 109
Cdd:cd09892   72 GVSRLV---RFGGEPAPVPDALIEAL 94
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 5-162 4.35e-13

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: 63.64  E-value: 4.35e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   5 WYVVHTYSGYENKVKANLEKrvesMGMEdkifrVLVPMEEELVNKDGKKKTVMRKVYPGYVLVEMVQTdDSWYVVRNTPG 84
Cdd:NF033644   1 WYALYTRPRREKKVAELLEK----KGIE-----SFLPMQKEIRQWSDRKKRVEVPLIPNLVFVHITEK-ELDEVLEQTPG 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181  85 VTGFVGSTGSGSKPtALLPEEVEQILKHMGMVEPKAKIDFEIK----ESVRIMVGPFANFVGSVEEIlADKSKIKVHVNM 160
Cdd:NF033644  71 VVRYIRDDRGKSKP-AIIPDKQMERFRLMLDPSDEVVVYLEAPlkkgDKVRVIGGPLKGLEGELVRV-KGKKRVVVRIPG 148


                 ..
gi 521096181 161 FG 162
Cdd:NF033644 149 LG 150
NGN_SP cd09886
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP); The ...
 4-111 2.10e-12

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: 60.07  E-value: 2.10e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   4 RWYVVHTysgyenkvKANLEKRVEsMGMEDKIFRVLVPMEEELVNKDGKKKTVMRKVYPGYVLVEM-VQTDDSWYVVRNT 82
Cdd:cd09886    1 SWYALRT--------NPGCEQRAE-EALEARGVEAFLPMLTEERKRRRKKFDVERPLFPGYVFARLdRSKGQDTSTIRAC 71

                         90       100
                 ....*....|....*....|....*....
gi 521096181  83 PGVTGFVGSTGSgskpTALLPEEVEQILK 111
Cdd:cd09886   72 DGVLGVVGFDGR----PAPVPEQEMRDLR 96
NGN_Bact_2 cd09889
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 2; The ...
 4-110 2.85e-12

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: 59.64  E-value: 2.85e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   4 RWYVVHTYSGYENKVKAnlekRVESMGMEDKIFRVLVPMEEELVNKDGKKKTVMRKVYPGYVLVEMVQTDDSWYVVRNTP 83
Cdd:cd09889    1 MWYVVQVRTGREKAVLE----LLEKLVGPDVLQECFIPQYERKKRSQGVWRERKYTLFPGYVFVVTDDIDELYYELKRVP 76

                         90       100
                 ....*....|....*....|....*..
gi 521096181  84 GVTGFVGSTGSgskPTALLPEEVEQIL 110
Cdd:cd09889   77 GFTRLLGNDGS---FFPLTPEEADFIR 100
NGN_SP_TaA cd09893
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), TaA; ...
 4-109 1.98e-10

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: 55.01  E-value: 1.98e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   4 RWYVVHTYSGYENKVKANLEKRvesmGMEdkifrVLVPMEEELVNKDGKKKTVMRKVYPGYVLVEMVQTDDSWYVVRnTP 83
Cdd:cd09893    1 SWYALYTRSRHEKKVADRLAKK----GIE-----SFLPLYEVLSRWKDRKKKIKVPLFPGYLFVRFQLDPERLRILK-TP 70

                         90       100
                 ....*....|....*....|....*.
gi 521096181  84 GVTGFVGSTGSgskPTALLPEEVEQI 109
Cdd:cd09893   71 GVVRIVGNSGG---PIPIPDEEIASL 93
NGN_plant cd09890
Plant N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance G ...
 5-109 3.74e-10

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: 54.67  E-value: 3.74e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   5 WYVVHTYSGYENKVKANLEKRVESM--GMEDKIFRVLVPMEEELVNkdGKKKTVMRKVYPGYVLVEMVQTDDSWYVVRNT 82
Cdd:cd09890    2 WYMLRVPAGRENQAAEALERALATEfpDREFEVWVPSIPVDRKLKN--GSISVKEKPLFPGYVLLRCVLNKEVYDFIRDN 79

                         90       100
                 ....*....|....*....|....*...
gi 521096181  83 PGVTGFVGST-GSGSKPTALLPEEVEQI 109
Cdd:cd09890   80 DSVYGFVGSKvGKTGKRQIEIPRPVPVE 107
NGN_SP_UpxY cd09895
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; ...
 4-89 3.98e-09

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: 51.42  E-value: 3.98e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   4 RWYVVHTYSGYENKVKANLEKRvesmgmedKIfRVLVPMEEELVNKDGKKKTVMRKVYPGYVLVEMvqTDDSWYVVRNTP 83
Cdd:cd09895    1 PWYALYTFPRREKKVAEYLEKK--------GI-ECFLPMQYEVRQWSGRKKRVEVPLFPNLVFVHI--TREELDEVLETP 69


                 ....*.
gi 521096181  84 GVTGFV 89
Cdd:cd09895   70 GVVRFV 75
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
3-177 6.51e-05

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 41.03  E-value: 6.51e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   3 KRWYVVHTYSGYENKVKANLEKR-VES---MGMEDKIFRvlvpmeeelvnkdGKKKTVMRKVYPGYVLVEMVQTDDSWYV 78
Cdd:PRK09014   2 KSWYLLYCKRGQLQRAQEHLERQgVEClypMITLEKIVR-------------GKRTEVSEPLFPNYLFVEFDPEVIHTTT 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181  79 VRNTPGVTGFVgstGSGSKPtALLPEEVEQILKhmgMVEPKAKIDFEIKE---SVRIMVGPFANFVGSVEEILADKSKIK 155
Cdd:PRK09014  69 IRSTRGVSHFV---RFGAQP-AIVPSDVIYQLS---VYKPEKIVDPETPKpgdKVIITEGAFEGLQAIYTEPDGEARSIL 141

                        170       180
                 ....*....|....*....|..
gi 521096181 156 VhVNMFGRETPLELDFTQVEKI 177
Cdd:PRK09014 142 L-LNLLNKQVKHSVDNTQFRKI 162
NGN_SP_AnfA1 cd09894
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1; ...
 3-111 8.42e-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: 36.88  E-value: 8.42e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 521096181   3 KRWYVVHTYSGYENKVKanleKRVESMGMEdkifrVLVPMEEELVNK-DGKKK-TVMRKVYPGYVLVEMVQTDDSWYVVR 80
Cdd:cd09894    1 KRWYLLRCKSGKIQSVI----FSLERLGVE-----VFCPMIRTRRKRtDCKSYrEKIEPLFPGYLFVRFDPEVVHTSKIT 71

                         90       100       110
                 ....*....|....*....|....*....|.
gi 521096181  81 NTPGVTGFVgstGSGSKPtALLPEEVEQILK 111
Cdd:cd09894   72 LASGVSGFV---RFGGEP-CPVPDAVIRALM 98
 
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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