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Conserved domains on  [gi|1084191150|gb|OGL83550|]
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transcription termination/antitermination protein NusG [Candidatus Uhrbacteria bacterium RIFCSPLOWO2_01_FULL_53_9]

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 Ontology:  GO:0006353|GO:0032784|GO:0031564|GO:0006354
PubMed:  12198166
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];
10-181 2.69e-75

Transcription termination/antitermination protein NusG [Transcription];


:

Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 223.16  E-value: 2.69e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  10 RRWYAVHAYSGYEENVAQNLRQRIESMDmeekiftVLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRNT 89
Cdd:COG0250     5 KRWYVVHTYSGYEKKVKENLERRIEGIE-------VFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLVRNT 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  90 PNVTGFIGTGVTPTPVSDEEIAMLQKRM--GIEEPEFNIDVSVNDPVRIIDGPFKNFEGKVSDIDETRGKVKVLVNMFGR 167
Cdd:COG0250    78 PGVTGFVGFGGKPAPLPDEEVERILARLeeGEEKPRPKVDFEVGDRVRITDGPFAGFEGTVEEVDPEKGRVKVLVSIFGR 157

                         170
                  ....*....|....
gi 1084191150 168 ETPVELDFLQISKI 181
Cdd:COG0250   158 ETPVELDFSQVEKI 171
 
Name Accession Description Interval E-value
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
10-181 2.69e-75

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 223.16  E-value: 2.69e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  10 RRWYAVHAYSGYEENVAQNLRQRIESMDmeekiftVLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRNT 89
Cdd:COG0250     5 KRWYVVHTYSGYEKKVKENLERRIEGIE-------VFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLVRNT 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  90 PNVTGFIGTGVTPTPVSDEEIAMLQKRM--GIEEPEFNIDVSVNDPVRIIDGPFKNFEGKVSDIDETRGKVKVLVNMFGR 167
Cdd:COG0250    78 PGVTGFVGFGGKPAPLPDEEVERILARLeeGEEKPRPKVDFEVGDRVRITDGPFAGFEGTVEEVDPEKGRVKVLVSIFGR 157

                         170
                  ....*....|....
gi 1084191150 168 ETPVELDFLQISKI 181
Cdd:COG0250   158 ETPVELDFSQVEKI 171
nusG TIGR00922
transcription termination/antitermination factor NusG; NusG proteins are transcription factors ...
 12-180 2.08e-69

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: 208.31  E-value: 2.08e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  12 WYAVHAYSGYEENVAQNLRQRIESMDMEEKIFTVLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRNTPN 91
Cdd:TIGR00922   1 WYVVQTYSGYEKKVKQNLEELIELLGMGDYIFEVIVPTEEVVEIKKGKKKVVERKIFPGYVLVKMDLTDVSWHLVKNTPG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  92 VTGFIGTGVTPTPVSD-EEI--AMLQKRMGIEEPEFNIDVSVNDPVRIIDGPFKNFEGKVSDIDETRGKVKVLVNMFGRE 168
Cdd:TIGR00922  81 VTGFVGSGGKPKALSEdEEVknILNALEEGKDKPKPKIDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFGRE 160

                         170
                  ....*....|..
gi 1084191150 169 TPVELDFLQISK 180
Cdd:TIGR00922 161 TPVELEFSQVEK 172
NGN_Bact_1 cd09891
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The ...
 11-115 2.30e-51

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: 160.33  E-value: 2.30e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  11 RWYAVHAYSGYEENVAQNLRQRIESMDMEEKIFTVLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRNTP 90
Cdd:cd09891     1 KWYVVHTYSGYENKVKENLEKRIESEGLEDYIGEVLVPTEEVVEVKNGKKKVKERKLFPGYVLVEMDMNDDTWHLVRNTP 80

                          90       100
                  ....*....|....*....|....*.
gi 1084191150  91 NVTGFIGTGVTPTPVSDEEI-AMLQK 115
Cdd:cd09891    81 GVTGFVGSGGKPVPLSEEEVeRILGQ 106
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 11-116 1.66e-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: 130.19  E-value: 1.66e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150   11 RWYAVHAYSGYEENVAQNLRQRIESMDMEEKIFTVLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRNTP 90
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKAEALGLEDKIVSILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGTP 80

                           90       100
                   ....*....|....*....|....*.
gi 1084191150   91 NVTGFIGTGVTPTPVSDEEIAMLQKR 116
Cdd:smart00738  81 GVRGFVGGGGKPTPVPDDEIEKILKP 106
NusG pfam02357
Transcription termination factor nusG;
11-114 3.43e-37

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 123.88  E-value: 3.43e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  11 RWYAVHAYSGYEENVAQNLrqriesmdmEEKIFTVLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRNTP 90
Cdd:pfam02357   2 KWYVLQTYSGKEKKVKENL---------ERQGIEVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRSTP 72

                          90       100
                  ....*....|....*....|....
gi 1084191150  91 NVTGFIGTGVTPTPVSDEEIAMLQ 114
Cdd:pfam02357  73 GVTGFVGGSGKPTPIPDEEVERIL 96
antiterm_LoaP NF033641
antiterminator LoaP; LoaP is a paralog of NusG with an extensive presence in Firmicutes. The ...
 12-173 8.07e-35

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: 120.18  E-value: 8.07e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  12 WYAVHAYSGYEENVAQNLRQRIEsmdmeEKIFTVLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRNTPN 91
Cdd:NF033641    1 WYVLFVRTGKEEKVKKLLNKLFD-----KELLRCFVPKRKLPERKQGKWYKVIKPLFPGYVFIETDMNEELYYKLKKIPG 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  92 VTGFIGT-GVTPTPVSDEEIAMLQKRMGIEEpefNIDVS----VNDPVRIIDGPFKNFEGKVSDIDETRGKVKVLVNMFG 166
Cdd:NF033641   76 IIRLLGNeGDEFSPIPEEEMEFLLKLLNDDD---IIEYSkgyiEGDKVIVISGPLKGLEGIIKKIDKRKRRAKIELNFMG 152


                  ....*..
gi 1084191150 167 RETPVEL 173
Cdd:NF033641  153 EERLVDV 159
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 12-162 8.12e-18

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: 75.97  E-value: 8.12e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  12 WYAVHAYSGYEENVAQnlrqRIESMDMEekiftVLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEmVVDDDSWYVVRNTPN 91
Cdd:NF033644    1 WYALYTRPRREKKVAE----LLEKKGIE-----SFLPMQKEIRQWSDRKKRVEVPLIPNLVFVH-ITEKELDEVLEQTPG 70

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1084191150  92 VTGFI---GTGVTPTPVSDEEIAMLQKRMGIEEP---EFNIDVSVNDPVRIIDGPFKNFEGKVSDIdetRGKVKVLV 162
Cdd:NF033644   71 VVRYIrddRGKSKPAIIPDKQMERFRLMLDPSDEvvvYLEAPLKKGDKVRVIGGPLKGLEGELVRV---KGKKRVVV 144
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
10-181 1.18e-13

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 64.91  E-value: 1.18e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  10 RRWYAVHAYSGYEENVAQNL-RQRIESmdmeekiFTVLVPKEKKIKiknGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRN 88
Cdd:PRK09014    2 KSWYLLYCKRGQLQRAQEHLeRQGVEC-------LYPMITLEKIVR---GKRTEVSEPLFPNYLFVEFDPEVIHTTTIRS 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  89 TPNVTGFIGTGVTPTPVSDEEIAMLQKRmgieEPEFNIDVSV---NDPVRIIDGPFKNFEGKVSDID-ETRGkvKVLVNM 164
Cdd:PRK09014   72 TRGVSHFVRFGAQPAIVPSDVIYQLSVY----KPEKIVDPETpkpGDKVIITEGAFEGLQAIYTEPDgEARS--ILLLNL 145

                         170
                  ....*....|....*..
gi 1084191150 165 FGRETPVELDFLQISKI 181
Cdd:PRK09014  146 LNKQVKHSVDNTQFRKI 162
 
Name Accession Description Interval E-value
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
10-181 2.69e-75

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 223.16  E-value: 2.69e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  10 RRWYAVHAYSGYEENVAQNLRQRIESMDmeekiftVLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRNT 89
Cdd:COG0250     5 KRWYVVHTYSGYEKKVKENLERRIEGIE-------VFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLVRNT 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  90 PNVTGFIGTGVTPTPVSDEEIAMLQKRM--GIEEPEFNIDVSVNDPVRIIDGPFKNFEGKVSDIDETRGKVKVLVNMFGR 167
Cdd:COG0250    78 PGVTGFVGFGGKPAPLPDEEVERILARLeeGEEKPRPKVDFEVGDRVRITDGPFAGFEGTVEEVDPEKGRVKVLVSIFGR 157

                         170
                  ....*....|....
gi 1084191150 168 ETPVELDFLQISKI 181
Cdd:COG0250   158 ETPVELDFSQVEKI 171
nusG TIGR00922
transcription termination/antitermination factor NusG; NusG proteins are transcription factors ...
 12-180 2.08e-69

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: 208.31  E-value: 2.08e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  12 WYAVHAYSGYEENVAQNLRQRIESMDMEEKIFTVLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRNTPN 91
Cdd:TIGR00922   1 WYVVQTYSGYEKKVKQNLEELIELLGMGDYIFEVIVPTEEVVEIKKGKKKVVERKIFPGYVLVKMDLTDVSWHLVKNTPG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  92 VTGFIGTGVTPTPVSD-EEI--AMLQKRMGIEEPEFNIDVSVNDPVRIIDGPFKNFEGKVSDIDETRGKVKVLVNMFGRE 168
Cdd:TIGR00922  81 VTGFVGSGGKPKALSEdEEVknILNALEEGKDKPKPKIDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFGRE 160

                         170
                  ....*....|..
gi 1084191150 169 TPVELDFLQISK 180
Cdd:TIGR00922 161 TPVELEFSQVEK 172
NGN_Bact_1 cd09891
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The ...
 11-115 2.30e-51

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: 160.33  E-value: 2.30e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  11 RWYAVHAYSGYEENVAQNLRQRIESMDMEEKIFTVLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRNTP 90
Cdd:cd09891     1 KWYVVHTYSGYENKVKENLEKRIESEGLEDYIGEVLVPTEEVVEVKNGKKKVKERKLFPGYVLVEMDMNDDTWHLVRNTP 80

                          90       100
                  ....*....|....*....|....*.
gi 1084191150  91 NVTGFIGTGVTPTPVSDEEI-AMLQK 115
Cdd:cd09891    81 GVTGFVGSGGKPVPLSEEEVeRILGQ 106
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 11-116 1.66e-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: 130.19  E-value: 1.66e-39
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150   11 RWYAVHAYSGYEENVAQNLRQRIESMDMEEKIFTVLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRNTP 90
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKAEALGLEDKIVSILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGTP 80

                           90       100
                   ....*....|....*....|....*.
gi 1084191150   91 NVTGFIGTGVTPTPVSDEEIAMLQKR 116
Cdd:smart00738  81 GVRGFVGGGGKPTPVPDDEIEKILKP 106
NusG pfam02357
Transcription termination factor nusG;
11-114 3.43e-37

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 123.88  E-value: 3.43e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  11 RWYAVHAYSGYEENVAQNLrqriesmdmEEKIFTVLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRNTP 90
Cdd:pfam02357   2 KWYVLQTYSGKEKKVKENL---------ERQGIEVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRSTP 72

                          90       100
                  ....*....|....*....|....
gi 1084191150  91 NVTGFIGTGVTPTPVSDEEIAMLQ 114
Cdd:pfam02357  73 GVTGFVGGSGKPTPIPDEEVERIL 96
antiterm_LoaP NF033641
antiterminator LoaP; LoaP is a paralog of NusG with an extensive presence in Firmicutes. The ...
 12-173 8.07e-35

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: 120.18  E-value: 8.07e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  12 WYAVHAYSGYEENVAQNLRQRIEsmdmeEKIFTVLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRNTPN 91
Cdd:NF033641    1 WYVLFVRTGKEEKVKKLLNKLFD-----KELLRCFVPKRKLPERKQGKWYKVIKPLFPGYVFIETDMNEELYYKLKKIPG 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  92 VTGFIGT-GVTPTPVSDEEIAMLQKRMGIEEpefNIDVS----VNDPVRIIDGPFKNFEGKVSDIDETRGKVKVLVNMFG 166
Cdd:NF033641   76 IIRLLGNeGDEFSPIPEEEMEFLLKLLNDDD---IIEYSkgyiEGDKVIVISGPLKGLEGIIKKIDKRKRRAKIELNFMG 152


                  ....*..
gi 1084191150 167 RETPVEL 173
Cdd:NF033641  153 EERLVDV 159
KOW_NusG cd06091
NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif ...
 126-180 1.16e-24

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: 90.59  E-value: 1.16e-24
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1084191150 126 IDVSVNDPVRIIDGPFKNFEGKVSDIDETRGKVKVLVNMFGRETPVELDFLQISK 180
Cdd:cd06091     2 VDFEVGDTVRIISGPFAGFEGKVEEIDEEKGKVKVLVEMFGRETPVELDFDQVEK 56
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 12-113 1.49e-22

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: 86.60  E-value: 1.49e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  12 WYAVHAYSGYEENVAQNLRQRIEsmdmeEKIFTVLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRNTPN 91
Cdd:cd08000     2 WYVLFVKTGREEKVEKLLEKRFE-----ANDIEAFVPKKEVPERKRGKIEEVIKPLFPGYVFVETDLSPELYELIREVPG 76

                          90       100
                  ....*....|....*....|..
gi 1084191150  92 VTGFIGTGVTPTPVSDEEIAML 113
Cdd:cd08000    77 VIGILGNGEEPSPVSDEEIEMI 98
NusG_myco TIGR01956
NusG family protein; This model represents a family of Mycoplasma proteins orthologous to the ...
 11-180 2.21e-20

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: 85.01  E-value: 2.21e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  11 RWYAVHAYSGYEENVAQNLRQRIESMDMEEKIFTVLVPKEKKIKI----------------------------KNGKRKI 62
Cdd:TIGR01956   1 QWYIATTINGNEDEVIENIKAKVRALGLENYISDFKILKEREIEEkvfepkngqaprsmkntattkwetldetKYKKTKI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  63 IEEKIFPGYVLVEMVVDDDSWYVVRNTPNVTGFIGT---GVTPTPVSDEEIAMLQKRMGIEEPEFNIDVS---------- 129
Cdd:TIGR01956  81 SEKNKYNGYIYIKMIMTEDAWFLIRNTENVTGLVGSsgkGAKPIPISADADKLKMLKGISENTKKRVLVTntaivemeen 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150 130 -----------------------------------------------VNDPVRIIDGPFKNFEGKVSDIDETRGKVKVLV 162
Cdd:TIGR01956 161 kfdekcqyilkhkqvkpeaiaqvsesgeiideiveefqlvdnlskfrVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEV 240

                         250
                  ....*....|....*...
gi 1084191150 163 NMFGRETPVELDFLQISK 180
Cdd:TIGR01956 241 EILGKSVDVDLNFKHLKL 258
RfaH TIGR01955
transcription elongation factor/antiterminator RfaH; This model represents the transcription ...
 12-173 2.96e-20

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: 82.51  E-value: 2.96e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  12 WYAVHAYSGYEENVAQNL-RQRIEsmdmeekiftVLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRNTP 90
Cdd:TIGR01955   1 WYLLYCKPRQEQRAQEHLeRQAVE----------CYLPMITVEKIVRGKRQAVSEPLFPNYLFIEFDPEVDSWTTIRSTR 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  91 NVTGFIGTGVTPTPVSDEEIAMLQKRmgieEPEFNIDVSVNDP-----VRIIDGPFKNFEGKVSDIDETRgKVKVLVNMF 165
Cdd:TIGR01955  71 GVSRFVRFGGHPAPVPDDLIHQLRQY----EPKDSVPPATTLPykgdkVRITDGAFAGFEAIFLEPDGEK-RSMLLLNMI 145


                  ....*...
gi 1084191150 166 GRETPVEL 173
Cdd:TIGR01955 146 GKQIKVSV 153
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 12-162 8.12e-18

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: 75.97  E-value: 8.12e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  12 WYAVHAYSGYEENVAQnlrqRIESMDMEekiftVLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEmVVDDDSWYVVRNTPN 91
Cdd:NF033644    1 WYALYTRPRREKKVAE----LLEKKGIE-----SFLPMQKEIRQWSDRKKRVEVPLIPNLVFVH-ITEKELDEVLEQTPG 70

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1084191150  92 VTGFI---GTGVTPTPVSDEEIAMLQKRMGIEEP---EFNIDVSVNDPVRIIDGPFKNFEGKVSDIdetRGKVKVLV 162
Cdd:NF033644   71 VVRYIrddRGKSKPAIIPDKQMERFRLMLDPSDEvvvYLEAPLKKGDKVRVIGGPLKGLEGELVRV---KGKKRVVV 144
NGN_SP_RfaH cd09892
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; ...
 11-114 5.72e-17

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: 71.82  E-value: 5.72e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  11 RWYAVHAYSGYEENVAQNL-RQRiesmdmeekiFTVLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRNT 89
Cdd:cd09892     1 AWYLLYTKPRQEERAAENLeRQG----------FEVFLPMIRVEKRRRGKRTVVTEPLFPGYLFVRLDPEVQNWRPIRST 70

                          90       100
                  ....*....|....*....|....*
gi 1084191150  90 PNVTGFIGTGVTPTPVSDEEIAMLQ 114
Cdd:cd09892    71 RGVSRLVRFGGEPAPVPDALIEALR 95
NGN_SP_TaA cd09893
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), TaA; ...
 11-115 2.17e-14

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: 65.41  E-value: 2.17e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  11 RWYAVHAYSGYEENVAQNLRQR-IESmdmeekiftvLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRnT 89
Cdd:cd09893     1 SWYALYTRSRHEKKVADRLAKKgIES----------FLPLYEVLSRWKDRKKKIKVPLFPGYLFVRFQLDPERLRILK-T 69

                          90       100
                  ....*....|....*....|....*.
gi 1084191150  90 PNVTGFIGTGVTPTPVSDEEIAMLQK 115
Cdd:cd09893    70 PGVVRIVGNSGGPIPIPDEEIASLRI 95
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
10-181 1.18e-13

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 64.91  E-value: 1.18e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  10 RRWYAVHAYSGYEENVAQNL-RQRIESmdmeekiFTVLVPKEKKIKiknGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRN 88
Cdd:PRK09014    2 KSWYLLYCKRGQLQRAQEHLeRQGVEC-------LYPMITLEKIVR---GKRTEVSEPLFPNYLFVEFDPEVIHTTTIRS 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  89 TPNVTGFIGTGVTPTPVSDEEIAMLQKRmgieEPEFNIDVSV---NDPVRIIDGPFKNFEGKVSDID-ETRGkvKVLVNM 164
Cdd:PRK09014   72 TRGVSHFVRFGAQPAIVPSDVIYQLSVY----KPEKIVDPETpkpGDKVIITEGAFEGLQAIYTEPDgEARS--ILLLNL 145

                         170
                  ....*....|....*..
gi 1084191150 165 FGRETPVELDFLQISKI 181
Cdd:PRK09014  146 LNKQVKHSVDNTQFRKI 162
NGN_plant cd09890
Plant N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance G ...
 12-110 6.22e-12

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: 59.29  E-value: 6.22e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  12 WYAVHAYSGYEENVAQNLRQRIESMDMEEKiFTVLVPK-EKKIKIKNGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRNTP 90
Cdd:cd09890     2 WYMLRVPAGRENQAAEALERALATEFPDRE-FEVWVPSiPVDRKLKNGSISVKEKPLFPGYVLLRCVLNKEVYDFIRDND 80

                          90       100
                  ....*....|....*....|....*....
gi 1084191150  91 NVTGFIGTGVT---------PTPVSDEEI 110
Cdd:cd09890    81 SVYGFVGSKVGktgkrqieiPRPVPVEEI 109
NGN_Bact_2 cd09889
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 2; The ...
 11-114 4.27e-10

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: 54.25  E-value: 4.27e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  11 RWYAVHAYSGYEENVAQnlrqRIESMDMEEKIFTVLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEMVVDDDSWYVVRNTP 90
Cdd:cd09889     1 MWYVVQVRTGREKAVLE----LLEKLVGPDVLQECFIPQYERKKRSQGVWRERKYTLFPGYVFVVTDDIDELYYELKRVP 76

                          90       100
                  ....*....|....*....|....
gi 1084191150  91 NVTGFIGTGVTPTPVSDEEIAMLQ 114
Cdd:cd09889    77 GFTRLLGNDGSFFPLTPEEADFIR 100
NGN_SP cd09886
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP); The ...
 11-115 1.06e-09

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: 53.14  E-value: 1.06e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  11 RWYAVHAYSGYEENVAQNL-RQRIEsmdmeekiftVLVPKEKKIKIKNGKRKIIEEKIFPGYVLVEMVVDDD-SWYVVRN 88
Cdd:cd09886     1 SWYALRTNPGCEQRAEEALeARGVE----------AFLPMLTEERKRRRKKFDVERPLFPGYVFARLDRSKGqDTSTIRA 70

                          90       100
                  ....*....|....*....|....*..
gi 1084191150  89 TPNVTGFIGTGVTPTPVSDEEIAMLQK 115
Cdd:cd09886    71 CDGVLGVVGFDGRPAPVPEQEMRDLRK 97
nusG PRK08559
transcription antitermination protein NusG; Validated
 13-160 2.21e-09

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 53.33  E-value: 2.21e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  13 YAVHAYSGYEENVAQNLRQRIESMDMEekIFTVLVPKEKKikikngkrkiieekifpGYVLVEMVVDDDSWYVVRNTPNV 92
Cdd:PRK08559    9 FAVKTTAGQERNVALMLAMRAKKENLP--IYAILAPPELK-----------------GYVLVEAESKGAVEEAIRGIPHV 69

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1084191150  93 TGfigtgVTPTPVSDEEI-AMLQKRMGIEEpefnidVSVNDPVRIIDGPFKNFEGKVSDIDETRGKVKV 160
Cdd:PRK08559   70 RG-----VVPGEISFEEVeHFLKPKPIVEG------IKEGDIVELIAGPFKGEKARVVRVDESKEEVTV 127
NGN_SP_UpxY cd09895
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; ...
 11-115 1.05e-07

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: 47.57  E-value: 1.05e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  11 RWYAVHAYSGYEENVAQNLRQR-IESmdmeekiFtvlVPKEKKIKIKNGKRKIIEEKIFPGYVLVEMvvDDDSWYVVRNT 89
Cdd:cd09895     1 PWYALYTFPRREKKVAEYLEKKgIEC-------F---LPMQYEVRQWSGRKKRVEVPLFPNLVFVHI--TREELDEVLET 68

                          90       100
                  ....*....|....*....|....*..
gi 1084191150  90 PNVTGFIGT-GVTPTPVSDEEIAMLQK 115
Cdd:cd09895    69 PGVVRFVRYrGKEPAIIPDKQMESFRL 95
KOW_elon_Spt5 TIGR00405
transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial ...
 13-160 1.71e-07

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: 48.35  E-value: 1.71e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  13 YAVHAYSGYEENVAQNLRQRIESMDMEekIFTVLVPKEKKikikngkrkiieekifpGYVLVEMVVDDDSWYVVRNTPNV 92
Cdd:TIGR00405   1 FAVKTSVGQEKNVARLMARKARKSGLE--VYSILAPESLK-----------------GYILVEAETKIDMRNPIIGVPHV 61

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1084191150  93 TGfigtgVTPTPVSDEEIAMLQKRMGIEEpefniDVSVNDPVRIIDGPFKNFEGKVSDIDETRGKVKV 160
Cdd:TIGR00405  62 RG-----VVEGEIDFEEIERFLTPKKIIE-----SIKKGDIVEIISGPFKGERAKVIRVDESKEEVTL 119
NGN_SP_AnfA1 cd09894
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1; ...
 10-115 5.00e-05

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: 40.35  E-value: 5.00e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  10 RRWY-AVHAYSGYEENVAQNLRQRIESmdmeekiFTVLVPKEKKIKIKNGKRKIIEeKIFPGYVLVEMVVDDDSWYVVRN 88
Cdd:cd09894     1 KRWYlLRCKSGKIQSVIFSLERLGVEV-------FCPMIRTRRKRTDCKSYREKIE-PLFPGYLFVRFDPEVVHTSKITL 72

                          90       100
                  ....*....|....*....|....*..
gi 1084191150  89 TPNVTGFIGTGVTPTPVSDEEIAMLQK 115
Cdd:cd09894    73 ASGVSGFVRFGGEPCPVPDAVIRALML 99
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 131-178 5.33e-04

KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); 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 KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues.


Pssm-ID: 240504  Cd Length: 49  Bit Score: 36.43  E-value: 5.33e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1084191150 131 NDPVRIIDGPFKNFEGKVSDIDETRGKVKVLVNMFGRETPVELDFLQI 178
Cdd:cd00380     1 GDVVRVLRGPYKGREGVVVDIDPRFGIVTVKGATGSKGAELKVRFDDV 48
NGN_Arch cd09887
Archaeal N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance ...
 11-110 6.22e-04

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: 37.14  E-value: 6.22e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084191150  11 RWYAVHAYSGYEENVAQNLRQRIESMDMEekIFTVLVPKEKKikikngkrkiieekifpGYVLVEMVVDDDSWYVVRNTP 90
Cdd:cd09887     1 RIYAVKTTAGQERNVADLLAMRAEKENLD--VYSILVPEELK-----------------GYVFVEAEDPDRVEELIRGIP 61

                          90       100
                  ....*....|....*....|
gi 1084191150  91 NVtgfigTGVTPTPVSDEEI 110
Cdd:cd09887    62 HV-----RGVVPGEISLEEI 76
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 130-160 9.16e-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: 35.44  E-value: 9.16e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1084191150 130 VNDPVRIIDGPFKNFEGKVSDIDETRGKVKV 160
Cdd:pfam00467   1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLV 31
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 127-153 1.27e-03

KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.


Pssm-ID: 128978  Cd Length: 28  Bit Score: 35.00  E-value: 1.27e-03
                           10        20
                   ....*....|....*....|....*..
gi 1084191150  127 DVSVNDPVRIIDGPFKNFEGKVSDIDE 153
Cdd:smart00739   1 KFEVGDTVRVIAGPFKGKVGKVLEVDG 27
 
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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