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Conserved domains on  [gi|818621186|gb|KKS69419|]
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Transcription antitermination protein nusG [Candidatus Azambacteria bacterium GW2011_GWA2_42_62]

Protein Classification

transcription termination/antitermination protein NusG( domain architecture ID 11415705)

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 Symbol:  nusG
Gene Ontology:  GO:0006353|GO:0032784|GO:0031564|GO:0006354
PubMed:  12198166|27899640|29887376
SCOP:  4002609

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
2-168 4.30e-69

Transcription termination/antitermination protein NusG [Transcription];


:

Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 206.98  E-value: 4.30e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   2 LHTYSGYEDAVARNLKQRIESLDmqdkifsVLVPKEKKIRIKNGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRNTPRVTG 81
Cdd:COG0250   10 VHTYSGYEKKVKENLERRIEGIE-------VFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLVRNTPGVTG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186  82 FIGSGTVPIPVSLEEIKDLQKRM--GGTESKYTIEFSVGDPVKIIDGPFKDFDGKVNEVDENRGKVKVLISMFGRETAVE 159
Cdd:COG0250   83 FVGFGGKPAPLPDEEVERILARLeeGEEKPRPKVDFEVGDRVRITDGPFAGFEGTVEEVDPEKGRVKVLVSIFGRETPVE 162


                 ....*....
gi 818621186 160 LDSLQIKKL 168
Cdd:COG0250  163 LDFSQVEKI 171
 
Name Accession Description Interval E-value
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
2-168 4.30e-69

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 206.98  E-value: 4.30e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   2 LHTYSGYEDAVARNLKQRIESLDmqdkifsVLVPKEKKIRIKNGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRNTPRVTG 81
Cdd:COG0250   10 VHTYSGYEKKVKENLERRIEGIE-------VFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLVRNTPGVTG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186  82 FIGSGTVPIPVSLEEIKDLQKRM--GGTESKYTIEFSVGDPVKIIDGPFKDFDGKVNEVDENRGKVKVLISMFGRETAVE 159
Cdd:COG0250   83 FVGFGGKPAPLPDEEVERILARLeeGEEKPRPKVDFEVGDRVRITDGPFAGFEGTVEEVDPEKGRVKVLVSIFGRETPVE 162


                 ....*....
gi 818621186 160 LDSLQIKKL 168
Cdd:COG0250  163 LDFSQVEKI 171
nusG TIGR00922
transcription termination/antitermination factor NusG; NusG proteins are transcription factors ...
 2-167 3.01e-65

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: 197.14  E-value: 3.01e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186    2 LHTYSGYEDAVARNLKQRIESLDMQDKIFSVLVPKEKKIRIKNGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRNTPRVTG 81
Cdd:TIGR00922   4 VQTYSGYEKKVKQNLEELIELLGMGDYIFEVIVPTEEVVEIKKGKKKVVERKIFPGYVLVKMDLTDVSWHLVKNTPGVTG 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   82 FIGSGTVPIPVS-LEEIKDL--QKRMGGTESKYTIEFSVGDPVKIIDGPFKDFDGKVNEVDENRGKVKVLISMFGRETAV 158
Cdd:TIGR00922  84 FVGSGGKPKALSeDEEVKNIlnALEEGKDKPKPKIDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFGRETPV 163


                  ....*....
gi 818621186  159 ELDSLQIKK 167
Cdd:TIGR00922 164 ELEFSQVEK 172
NGN_Bact_1 cd09891
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The ...
 1-104 6.54e-49

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: 153.40  E-value: 6.54e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   1 MLHTYSGYEDAVARNLKQRIESLDMQDKIFSVLVPKEKKIRIKNGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRNTPRVT 80
Cdd:cd09891    4 VVHTYSGYENKVKENLEKRIESEGLEDYIGEVLVPTEEVVEVKNGKKKVKERKLFPGYVLVEMDMNDDTWHLVRNTPGVT 83

                         90       100
                 ....*....|....*....|....
gi 818621186  81 GFIGSGTVPIPVSLEEIKDLQKRM 104
Cdd:cd09891   84 GFVGSGGKPVPLSEEEVERILGQV 107
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 1-103 1.28e-37

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: 124.79  E-value: 1.28e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186     1 MLHTYSGYEDAVARNLKQRIESLDMQDKIFSVLVPKEKKIRIKNGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRNTPRVT 80
Cdd:smart00738   4 AVRTTSGQEKRVAENLERKAEALGLEDKIVSILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGTPGVR 83

                           90       100
                   ....*....|....*....|...
gi 818621186    81 GFIGSGTVPIPVSLEEIKDLQKR 103
Cdd:smart00738  84 GFVGGGGKPTPVPDDEIEKILKP 106
NusG pfam02357
Transcription termination factor nusG;
2-101 1.33e-32

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 111.55  E-value: 1.33e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186    2 LHTYSGYEDAVARNLKQriesldmqdKIFSVLVPKEKKIRIKNGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRNTPRVTG 81
Cdd:pfam02357   6 LQTYSGKEKKVKENLER---------QGIEVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRSTPGVTG 76

                          90       100
                  ....*....|....*....|
gi 818621186   82 FIGSGTVPIPVSLEEIKDLQ 101
Cdd:pfam02357  77 FVGGSGKPTPIPDEEVERIL 96
antiterm_LoaP NF033641
antiterminator LoaP; LoaP is a paralog of NusG with an extensive presence in Firmicutes. The ...
 2-160 6.34e-24

antiterminator LoaP; LoaP is a paralog of NusG with an extensive presence in Firmicutes. The founding member, from Bacillus amyloliquefaciens, was shown to serve as an antiterminator for the transcription of genes involved in antibiotic biosynthesis.


Pssm-ID: 468124 [Multi-domain]  Cd Length: 166  Bit Score: 91.68  E-value: 6.34e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   2 LHTYSGYEDAVARNLKQRIEsldmqDKIFSVLVPKEKKIRIKNGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRNTPRVTG 81
Cdd:NF033641   4 LFVRTGKEEKVKKLLNKLFD-----KELLRCFVPKRKLPERKQGKWYKVIKPLFPGYVFIETDMNEELYYKLKKIPGIIR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186  82 FIGS-GTVPIPVSLEEIKDLQKRMGGTEskyTIEFS----VGDPVKIIDGPFKDFDGKVNEVDENRGKVKVLISMFGRET 156
Cdd:NF033641  79 LLGNeGDEFSPIPEEEMEFLLKLLNDDD---IIEYSkgyiEGDKVIVISGPLKGLEGIIKKIDKRKRRAKIELNFMGEER 155


                 ....
gi 818621186 157 AVEL 160
Cdd:NF033641 156 LVDV 159
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 2-149 3.05e-11

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: 58.25  E-value: 3.05e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   2 LHTYSGYEDAVARNLKQR-IESldmqdkiFsvlVPKEKKIRIKNGKRRTIEEKIYPGYVLVEmIVTDDSWYVVRNTP--- 77
Cdd:NF033644   4 LYTRPRREKKVAELLEKKgIES-------F---LPMQKEIRQWSDRKKRVEVPLIPNLVFVH-ITEKELDEVLEQTPgvv 72

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 818621186  78 RVTGFIGSGTVPIPVSLEEIKDLQKRMGGTES--KYTIE-FSVGDPVKIIDGPFKDFDGKVNEVdenRGKVKVLI 149
Cdd:NF033644  73 RYIRDDRGKSKPAIIPDKQMERFRLMLDPSDEvvVYLEApLKKGDKVRVIGGPLKGLEGELVRV---KGKKRVVV 144
nusG PRK08559
transcription antitermination protein NusG; Validated
 4-147 2.37e-10

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 55.64  E-value: 2.37e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   4 TYSGYEDAVARNLKQRIESLDMqdKIFSVLVPKEKKirikngkrrtieekiypGYVLVEMIVTDDSWYVVRNTPRVtgfi 83
Cdd:PRK08559  13 TTAGQERNVALMLAMRAKKENL--PIYAILAPPELK-----------------GYVLVEAESKGAVEEAIRGIPHV---- 69

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 818621186  84 gSGTVPIPVSLEEIKDLQKrmggtESKYTIEFSVGDPVKIIDGPFKDFDGKVNEVDENRGKVKV 147
Cdd:PRK08559  70 -RGVVPGEISFEEVEHFLK-----PKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTV 127
 
Name Accession Description Interval E-value
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
2-168 4.30e-69

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 206.98  E-value: 4.30e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   2 LHTYSGYEDAVARNLKQRIESLDmqdkifsVLVPKEKKIRIKNGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRNTPRVTG 81
Cdd:COG0250   10 VHTYSGYEKKVKENLERRIEGIE-------VFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLVRNTPGVTG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186  82 FIGSGTVPIPVSLEEIKDLQKRM--GGTESKYTIEFSVGDPVKIIDGPFKDFDGKVNEVDENRGKVKVLISMFGRETAVE 159
Cdd:COG0250   83 FVGFGGKPAPLPDEEVERILARLeeGEEKPRPKVDFEVGDRVRITDGPFAGFEGTVEEVDPEKGRVKVLVSIFGRETPVE 162


                 ....*....
gi 818621186 160 LDSLQIKKL 168
Cdd:COG0250  163 LDFSQVEKI 171
nusG TIGR00922
transcription termination/antitermination factor NusG; NusG proteins are transcription factors ...
 2-167 3.01e-65

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: 197.14  E-value: 3.01e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186    2 LHTYSGYEDAVARNLKQRIESLDMQDKIFSVLVPKEKKIRIKNGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRNTPRVTG 81
Cdd:TIGR00922   4 VQTYSGYEKKVKQNLEELIELLGMGDYIFEVIVPTEEVVEIKKGKKKVVERKIFPGYVLVKMDLTDVSWHLVKNTPGVTG 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   82 FIGSGTVPIPVS-LEEIKDL--QKRMGGTESKYTIEFSVGDPVKIIDGPFKDFDGKVNEVDENRGKVKVLISMFGRETAV 158
Cdd:TIGR00922  84 FVGSGGKPKALSeDEEVKNIlnALEEGKDKPKPKIDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFGRETPV 163


                  ....*....
gi 818621186  159 ELDSLQIKK 167
Cdd:TIGR00922 164 ELEFSQVEK 172
NGN_Bact_1 cd09891
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The ...
 1-104 6.54e-49

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: 153.40  E-value: 6.54e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   1 MLHTYSGYEDAVARNLKQRIESLDMQDKIFSVLVPKEKKIRIKNGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRNTPRVT 80
Cdd:cd09891    4 VVHTYSGYENKVKENLEKRIESEGLEDYIGEVLVPTEEVVEVKNGKKKVKERKLFPGYVLVEMDMNDDTWHLVRNTPGVT 83

                         90       100
                 ....*....|....*....|....
gi 818621186  81 GFIGSGTVPIPVSLEEIKDLQKRM 104
Cdd:cd09891   84 GFVGSGGKPVPLSEEEVERILGQV 107
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 1-103 1.28e-37

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: 124.79  E-value: 1.28e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186     1 MLHTYSGYEDAVARNLKQRIESLDMQDKIFSVLVPKEKKIRIKNGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRNTPRVT 80
Cdd:smart00738   4 AVRTTSGQEKRVAENLERKAEALGLEDKIVSILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGTPGVR 83

                           90       100
                   ....*....|....*....|...
gi 818621186    81 GFIGSGTVPIPVSLEEIKDLQKR 103
Cdd:smart00738  84 GFVGGGGKPTPVPDDEIEKILKP 106
NusG pfam02357
Transcription termination factor nusG;
2-101 1.33e-32

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 111.55  E-value: 1.33e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186    2 LHTYSGYEDAVARNLKQriesldmqdKIFSVLVPKEKKIRIKNGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRNTPRVTG 81
Cdd:pfam02357   6 LQTYSGKEKKVKENLER---------QGIEVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRSTPGVTG 76

                          90       100
                  ....*....|....*....|
gi 818621186   82 FIGSGTVPIPVSLEEIKDLQ 101
Cdd:pfam02357  77 FVGGSGKPTPIPDEEVERIL 96
antiterm_LoaP NF033641
antiterminator LoaP; LoaP is a paralog of NusG with an extensive presence in Firmicutes. The ...
 2-160 6.34e-24

antiterminator LoaP; LoaP is a paralog of NusG with an extensive presence in Firmicutes. The founding member, from Bacillus amyloliquefaciens, was shown to serve as an antiterminator for the transcription of genes involved in antibiotic biosynthesis.


Pssm-ID: 468124 [Multi-domain]  Cd Length: 166  Bit Score: 91.68  E-value: 6.34e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   2 LHTYSGYEDAVARNLKQRIEsldmqDKIFSVLVPKEKKIRIKNGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRNTPRVTG 81
Cdd:NF033641   4 LFVRTGKEEKVKKLLNKLFD-----KELLRCFVPKRKLPERKQGKWYKVIKPLFPGYVFIETDMNEELYYKLKKIPGIIR 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186  82 FIGS-GTVPIPVSLEEIKDLQKRMGGTEskyTIEFS----VGDPVKIIDGPFKDFDGKVNEVDENRGKVKVLISMFGRET 156
Cdd:NF033641  79 LLGNeGDEFSPIPEEEMEFLLKLLNDDD---IIEYSkgyiEGDKVIVISGPLKGLEGIIKKIDKRKRRAKIELNFMGEER 155


                 ....
gi 818621186 157 AVEL 160
Cdd:NF033641 156 LVDV 159
KOW_NusG cd06091
NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif ...
 113-167 1.80e-23

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: 87.13  E-value: 1.80e-23
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 818621186 113 IEFSVGDPVKIIDGPFKDFDGKVNEVDENRGKVKVLISMFGRETAVELDSLQIKK 167
Cdd:cd06091    2 VDFEVGDTVRIISGPFAGFEGKVEEIDEEKGKVKVLVEMFGRETPVELDFDQVEK 56
NusG_myco TIGR01956
NusG family protein; This model represents a family of Mycoplasma proteins orthologous to the ...
 1-167 1.05e-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: 88.10  E-value: 1.05e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186    1 MLHTYSGYEDAVARNLKQRIESLDMQDKIFSVLVPKEKKIRIK-------------------------NGKRRTI---EE 52
Cdd:TIGR01956   4 IATTINGNEDEVIENIKAKVRALGLENYISDFKILKEREIEEKvfepkngqaprsmkntattkwetldETKYKKTkisEK 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   53 KIYPGYVLVEMIVTDDSWYVVRNTPRVTGFIGS---GTVPIPVSLEEIKDLQKRM------------------------- 104
Cdd:TIGR01956  84 NKYNGYIYIKMIMTEDAWFLIRNTENVTGLVGSsgkGAKPIPISADADKLKMLKGisentkkrvlvtntaivemeenkfd 163

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186  105 --------------------------------GGTESKYTIEFSVGDPVKIIDGPFKDFDGKVNEVDENRGKVKVLISMF 152
Cdd:TIGR01956 164 ekcqyilkhkqvkpeaiaqvsesgeiideiveEFQLVDNLSKFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEVEIL 243

                         250
                  ....*....|....*
gi 818621186  153 GRETAVELDSLQIKK 167
Cdd:TIGR01956 244 GKSVDVDLNFKHLKL 258
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 2-100 1.59e-17

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: 73.12  E-value: 1.59e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   2 LHTYSGYEDAVARNLKQRIESldmqdKIFSVLVPKEKKIRIKNGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRNTPRVTG 81
Cdd:cd08000    5 LFVKTGREEKVEKLLEKRFEA-----NDIEAFVPKKEVPERKRGKIEEVIKPLFPGYVFVETDLSPELYELIREVPGVIG 79

                         90
                 ....*....|....*....
gi 818621186  82 FIGSGTVPIPVSLEEIKDL 100
Cdd:cd08000   80 ILGNGEEPSPVSDEEIEMI 98
RfaH TIGR01955
transcription elongation factor/antiterminator RfaH; This model represents the transcription ...
 21-160 1.34e-16

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: 72.49  E-value: 1.34e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   21 ESLDMQDkiFSVLVPKEKKIRIKNGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRNTPRVTGFIGSGTVPIPVSLEEIKDL 100
Cdd:TIGR01955  16 EHLERQA--VECYLPMITVEKIVRGKRQAVSEPLFPNYLFIEFDPEVDSWTTIRSTRGVSRFVRFGGHPAPVPDDLIHQL 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818621186  101 -QKRMGGTESKYTIEFSVGDPVKIIDGPFKDFDGKVNEVDENRgKVKVLISMFGRETAVEL 160
Cdd:TIGR01955  94 rQYEPKDSVPPATTLPYKGDKVRITDGAFAGFEAIFLEPDGEK-RSMLLLNMIGKQIKVSV 153
NGN_SP_RfaH cd09892
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; ...
 21-101 4.02e-12

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: 59.11  E-value: 4.02e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186  21 ESLDMQDkiFSVLVPKEKKIRIKNGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRNTPRVTGFIGSGTVPIPVSLEEIKDL 100
Cdd:cd09892   17 ENLERQG--FEVFLPMIRVEKRRRGKRTVVTEPLFPGYLFVRLDPEVQNWRPIRSTRGVSRLVRFGGEPAPVPDALIEAL 94


                 .
gi 818621186 101 Q 101
Cdd:cd09892   95 R 95
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 2-149 3.05e-11

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: 58.25  E-value: 3.05e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   2 LHTYSGYEDAVARNLKQR-IESldmqdkiFsvlVPKEKKIRIKNGKRRTIEEKIYPGYVLVEmIVTDDSWYVVRNTP--- 77
Cdd:NF033644   4 LYTRPRREKKVAELLEKKgIES-------F---LPMQKEIRQWSDRKKRVEVPLIPNLVFVH-ITEKELDEVLEQTPgvv 72

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 818621186  78 RVTGFIGSGTVPIPVSLEEIKDLQKRMGGTES--KYTIE-FSVGDPVKIIDGPFKDFDGKVNEVdenRGKVKVLI 149
Cdd:NF033644  73 RYIRDDRGKSKPAIIPDKQMERFRLMLDPSDEvvVYLEApLKKGDKVRVIGGPLKGLEGELVRV---KGKKRVVV 144
nusG PRK08559
transcription antitermination protein NusG; Validated
 4-147 2.37e-10

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 55.64  E-value: 2.37e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   4 TYSGYEDAVARNLKQRIESLDMqdKIFSVLVPKEKKirikngkrrtieekiypGYVLVEMIVTDDSWYVVRNTPRVtgfi 83
Cdd:PRK08559  13 TTAGQERNVALMLAMRAKKENL--PIYAILAPPELK-----------------GYVLVEAESKGAVEEAIRGIPHV---- 69

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 818621186  84 gSGTVPIPVSLEEIKDLQKrmggtESKYTIEFSVGDPVKIIDGPFKDFDGKVNEVDENRGKVKV 147
Cdd:PRK08559  70 -RGVVPGEISFEEVEHFLK-----PKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTV 127
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
20-168 2.95e-10

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 55.67  E-value: 2.95e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186  20 IESLDMQD-KIFSVLVPKEKKIRiknGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRNTPRVTGFIGSGTVPIPVSLEEIK 98
Cdd:PRK09014  18 QEHLERQGvECLYPMITLEKIVR---GKRTEVSEPLFPNYLFVEFDPEVIHTTTIRSTRGVSHFVRFGAQPAIVPSDVIY 94

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 818621186  99 DLQKRmggTESKYtIEFSV---GDPVKIIDGPFKDFDGKVNEVD-ENRGkvKVLISMFGRETAVELDSLQIKKL 168
Cdd:PRK09014  95 QLSVY---KPEKI-VDPETpkpGDKVIITEGAFEGLQAIYTEPDgEARS--ILLLNLLNKQVKHSVDNTQFRKI 162
KOW_elon_Spt5 TIGR00405
transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial ...
 2-147 5.78e-09

transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial NusG and the uL24 (previously L24p/L26e) family of ribosomal proteins. The most recent papers and crystal structures make this a transcription elongation factor rather than a ribosomal protein.


Pssm-ID: 129499 [Multi-domain]  Cd Length: 145  Bit Score: 51.82  E-value: 5.78e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186    2 LHTYSGYEDAVARNLKQRIEslDMQDKIFSVLVPKEKKirikngkrrtieekiypGYVLVEMIVTDDSWYVVRNTPRVtg 81
Cdd:TIGR00405   3 VKTSVGQEKNVARLMARKAR--KSGLEVYSILAPESLK-----------------GYILVEAETKIDMRNPIIGVPHV-- 61

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 818621186   82 figSGTVPIPVSLEEIKDLQkrmggTESKYTIEFSVGDPVKIIDGPFKDFDGKVNEVDENRGKVKV 147
Cdd:TIGR00405  62 ---RGVVEGEIDFEEIERFL-----TPKKIIESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTL 119
NGN_plant cd09890
Plant N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance G ...
 1-100 3.82e-08

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: 48.89  E-value: 3.82e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   1 MLHTYSGYEDAVARNLkQRIESLDMQDKIFSVLVPK-EKKIRIKNGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRNTPRV 79
Cdd:cd09890    4 MLRVPAGRENQAAEAL-ERALATEFPDREFEVWVPSiPVDRKLKNGSISVKEKPLFPGYVLLRCVLNKEVYDFIRDNDSV 82

                         90       100       110
                 ....*....|....*....|....*....|
gi 818621186  80 TGFIGSGT---------VPIPVSLEEIKDL 100
Cdd:cd09890   83 YGFVGSKVgktgkrqieIPRPVPVEEIEAI 112
NGN_SP_TaA cd09893
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), TaA; ...
 2-102 1.43e-07

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: 46.92  E-value: 1.43e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   2 LHTYSGYEDAVARNLKQR-IESLdmqdkifsvlVPKEKKIRIKNGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRnTPRVT 80
Cdd:cd09893    5 LYTRSRHEKKVADRLAKKgIESF----------LPLYEVLSRWKDRKKKIKVPLFPGYLFVRFQLDPERLRILK-TPGVV 73

                         90       100
                 ....*....|....*....|..
gi 818621186  81 GFIGSGTVPIPVSLEEIKDLQK 102
Cdd:cd09893   74 RIVGNSGGPIPIPDEEIASLRI 95
NGN_SP cd09886
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP); The ...
 2-102 2.83e-07

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: 46.21  E-value: 2.83e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   2 LHTYSGYEDAVARNL-KQRIEsldmqdkifsVLVPKEKKIRIKNGKRRTIEEKIYPGYVLVEM-IVTDDSWYVVRNTPRV 79
Cdd:cd09886    5 LRTNPGCEQRAEEALeARGVE----------AFLPMLTEERKRRRKKFDVERPLFPGYVFARLdRSKGQDTSTIRACDGV 74

                         90       100
                 ....*....|....*....|...
gi 818621186  80 TGFIGSGTVPIPVSLEEIKDLQK 102
Cdd:cd09886   75 LGVVGFDGRPAPVPEQEMRDLRK 97
NGN_Bact_2 cd09889
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 2; The ...
 2-98 1.59e-05

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: 41.54  E-value: 1.59e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   2 LHTYSGYEDAVArnlkQRIESLDMQDKIFSVLVPKEKKIRIKNGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRNTPRVTG 81
Cdd:cd09889    5 VQVRTGREKAVL----ELLEKLVGPDVLQECFIPQYERKKRSQGVWRERKYTLFPGYVFVVTDDIDELYYELKRVPGFTR 80

                         90
                 ....*....|....*..
gi 818621186  82 FIGSGTVPIPVSLEEIK 98
Cdd:cd09889   81 LLGNDGSFFPLTPEEAD 97
NGN_Arch cd09887
Archaeal N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance ...
 4-98 2.17e-05

Archaeal 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. Transcription in archaea has a eukaryotic-type transcription apparatus, but contains bacterial-type transcription factors. NusG is one of the few archaeal transcription factors that has orthologs in both bacteria and eukaryotes. Archaeal NusG is similar to bacterial NusG, composed of an NGN domain and a Kyrpides Ouzounis and Woese (KOW) repeat. 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. NusG was originally discovered as a 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. Archaeal NusG forms a complex with DNA-directed RNA polymerase subunit E (rpoE) that is similar to the Spt5-Spt4 complex in eukaryotes.


Pssm-ID: 193576  Cd Length: 82  Bit Score: 40.99  E-value: 2.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186   4 TYSGYEDAVARNLKQRIESLDMqdKIFSVLVPKEKKirikngkrrtieekiypGYVLVEMIVTDDSWYVVRNTPRVTGFi 83
Cdd:cd09887    7 TTAGQERNVADLLAMRAEKENL--DVYSILVPEELK-----------------GYVFVEAEDPDRVEELIRGIPHVRGV- 66

                         90
                 ....*....|....*
gi 818621186  84 gsgtVPIPVSLEEIK 98
Cdd:cd09887   67 ----VPGEISLEEIE 77
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 117-147 9.50e-04

KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and NusG.


Pssm-ID: 425698 [Multi-domain]  Cd Length: 32  Bit Score: 35.06  E-value: 9.50e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 818621186  117 VGDPVKIIDGPFKDFDGKVNEVDENRGKVKV 147
Cdd:pfam00467   1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLV 31
NGN_SP_AnfA1 cd09894
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1; ...
 16-102 7.54e-03

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: 34.18  E-value: 7.54e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818621186  16 LKQRIESLDMqdkifSVLVPKEKKI--RIKNGKRRTIEEKIYPGYVLVEMIVTDDSWYVVRNTPRVTGFIGSGTVPIPVS 93
Cdd:cd09894   16 VIFSLERLGV-----EVFCPMIRTRrkRTDCKSYREKIEPLFPGYLFVRFDPEVVHTSKITLASGVSGFVRFGGEPCPVP 90


                 ....*....
gi 818621186  94 LEEIKDLQK 102
Cdd:cd09894   91 DAVIRALML 99
 
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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