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Conserved domains on  [gi|1082930764|gb|OGC38222|]
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transcription termination/antitermination factor NusG [candidate division WS6 bacterium RIFOXYC1_FULL_33_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 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];
7-181 1.51e-58

Transcription termination/antitermination protein NusG [Transcription];


:

Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 180.79  E-value: 1.51e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764   7 NPKAKWYVLNIRTGYENSIKKELQQRIEatGLqdkieEILIPTQKKIIVKKGKQNVMADKLFPGYVLIKMELDAYTWDIV 86
Cdd:COG0250     2 SMEKRWYVVHTYSGYEKKVKENLERRIE--GI-----EVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLV 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  87 KNTEGVRGFVKTDKYPRPLPESEVKAIMKFME--VEQPSYQTSFSVGEAVKITDGAFADFIGSVQEIDTTKGKIKVLISF 164
Cdd:COG0250    75 RNTPGVTGFVGFGGKPAPLPDEEVERILARLEegEEKPRPKVDFEVGDRVRITDGPFAGFEGTVEEVDPEKGRVKVLVSI 154

                         170
                  ....*....|....*..
gi 1082930764 165 LGREAPVELDLSQVSKL 181
Cdd:COG0250   155 FGRETPVELDFSQVEKI 171
 
Name Accession Description Interval E-value
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
7-181 1.51e-58

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 180.79  E-value: 1.51e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764   7 NPKAKWYVLNIRTGYENSIKKELQQRIEatGLqdkieEILIPTQKKIIVKKGKQNVMADKLFPGYVLIKMELDAYTWDIV 86
Cdd:COG0250     2 SMEKRWYVVHTYSGYEKKVKENLERRIE--GI-----EVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLV 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  87 KNTEGVRGFVKTDKYPRPLPESEVKAIMKFME--VEQPSYQTSFSVGEAVKITDGAFADFIGSVQEIDTTKGKIKVLISF 164
Cdd:COG0250    75 RNTPGVTGFVGFGGKPAPLPDEEVERILARLEegEEKPRPKVDFEVGDRVRITDGPFAGFEGTVEEVDPEKGRVKVLVSI 154

                         170
                  ....*....|....*..
gi 1082930764 165 LGREAPVELDLSQVSKL 181
Cdd:COG0250   155 FGRETPVELDFSQVEKI 171
nusG TIGR00922
transcription termination/antitermination factor NusG; NusG proteins are transcription factors ...
 12-180 6.34e-56

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: 174.03  E-value: 6.34e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  12 WYVLNIRTGYENSIKKELQQRIEATGLQDKIEEILIPTQKKIIVKKGKQNVMADKLFPGYVLIKMELDAYTWDIVKNTEG 91
Cdd:TIGR00922   1 WYVVQTYSGYEKKVKQNLEELIELLGMGDYIFEVIVPTEEVVEIKKGKKKVVERKIFPGYVLVKMDLTDVSWHLVKNTPG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  92 VRGFVKTDKYPRPLPES-EVKAIMKFMEVEQ--PSYQTSFSVGEAVKITDGAFADFIGSVQEIDTTKGKIKVLISFLGRE 168
Cdd:TIGR00922  81 VTGFVGSGGKPKALSEDeEVKNILNALEEGKdkPKPKIDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFGRE 160

                         170
                  ....*....|..
gi 1082930764 169 APVELDLSQVSK 180
Cdd:TIGR00922 161 TPVELEFSQVEK 172
NGN_Bact_1 cd09891
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The ...
 11-117 2.10e-38

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: 127.21  E-value: 2.10e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  11 KWYVLNIRTGYENSIKKELQQRIEATGLQDKIEEILIPTQKKIIVKKGKQNVMADKLFPGYVLIKMELDAYTWDIVKNTE 90
Cdd:cd09891     1 KWYVVHTYSGYENKVKENLEKRIESEGLEDYIGEVLVPTEEVVEVKNGKKKVKERKLFPGYVLVEMDMNDDTWHLVRNTP 80

                          90       100
                  ....*....|....*....|....*..
gi 1082930764  91 GVRGFVKTDKYPRPLPESEVKAIMKFM 117
Cdd:cd09891    81 GVTGFVGSGGKPVPLSEEEVERILGQV 107
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 11-115 1.03e-28

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: 102.45  E-value: 1.03e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764   11 KWYVLNIRTGYENSIKKELQQRIEATGLQDKIEEILIPTQKKIIVKKGKQNVMADKLFPGYVLIKMELDAYTWDIVKNTE 90
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKAEALGLEDKIVSILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGTP 80

                           90       100
                   ....*....|....*....|....*
gi 1082930764   91 GVRGFVKTDKYPRPLPESEVKAIMK 115
Cdd:smart00738  81 GVRGFVGGGGKPTPVPDDEIEKILK 105
NusG pfam02357
Transcription termination factor nusG;
11-114 1.44e-25

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 94.21  E-value: 1.44e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  11 KWYVLNIRTGYENSIKKELQQRieatGLqdkieEILIPTQKKIIVKKGKQNVMADKLFPGYVLIKMELDAYTWDIVKNTE 90
Cdd:pfam02357   2 KWYVLQTYSGKEKKVKENLERQ----GI-----EVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRSTP 72

                          90       100
                  ....*....|....*....|....
gi 1082930764  91 GVRGFVKTDKYPRPLPESEVKAIM 114
Cdd:pfam02357  73 GVTGFVGGSGKPTPIPDEEVERIL 96
antiterm_LoaP NF033641
antiterminator LoaP; LoaP is a paralog of NusG with an extensive presence in Firmicutes. The ...
 12-180 3.57e-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: 92.45  E-value: 3.57e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  12 WYVLNIRTGYENSIKKELQQRIEatglqDKIEEILIPTQKKIIVKKGKQNVMADKLFPGYVLIKMELDAYTWDIVKNTEG 91
Cdd:NF033641    1 WYVLFVRTGKEEKVKKLLNKLFD-----KELLRCFVPKRKLPERKQGKWYKVIKPLFPGYVFIETDMNEELYYKLKKIPG 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  92 VRGFVKT-DKYPRPLPESEVKAIMKFMEVEQP-SYQTSFSVGEAVKITDGAFADFIGSVQEIDTTKGKIKVLISFLGREA 169
Cdd:NF033641   76 IIRLLGNeGDEFSPIPEEEMEFLLKLLNDDDIiEYSKGYIEGDKVIVISGPLKGLEGIIKKIDKRKRRAKIELNFMGEER 155

                         170
                  ....*....|.
gi 1082930764 170 PVELDLSQVSK 180
Cdd:NF033641  156 LVDVGIEIVSK 166
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
52-181 2.30e-09

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 53.74  E-value: 2.30e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  52 KIIvkKGKQNVMADKLFPGYVLIKMELDAYTWDIVKNTEGVRGFVKTDKYPRPLPESEVKAIMKFmEVEQPSYQTSFSVG 131
Cdd:PRK09014   37 KIV--RGKRTEVSEPLFPNYLFVEFDPEVIHTTTIRSTRGVSHFVRFGAQPAIVPSDVIYQLSVY-KPEKIVDPETPKPG 113

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1082930764 132 EAVKITDGAFADFIGSVQEIDTTKGKIkVLISFLGREAPVELDLSQVSKL 181
Cdd:PRK09014  114 DKVIITEGAFEGLQAIYTEPDGEARSI-LLLNLLNKQVKHSVDNTQFRKI 162
 
Name Accession Description Interval E-value
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
7-181 1.51e-58

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 180.79  E-value: 1.51e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764   7 NPKAKWYVLNIRTGYENSIKKELQQRIEatGLqdkieEILIPTQKKIIVKKGKQNVMADKLFPGYVLIKMELDAYTWDIV 86
Cdd:COG0250     2 SMEKRWYVVHTYSGYEKKVKENLERRIE--GI-----EVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLV 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  87 KNTEGVRGFVKTDKYPRPLPESEVKAIMKFME--VEQPSYQTSFSVGEAVKITDGAFADFIGSVQEIDTTKGKIKVLISF 164
Cdd:COG0250    75 RNTPGVTGFVGFGGKPAPLPDEEVERILARLEegEEKPRPKVDFEVGDRVRITDGPFAGFEGTVEEVDPEKGRVKVLVSI 154

                         170
                  ....*....|....*..
gi 1082930764 165 LGREAPVELDLSQVSKL 181
Cdd:COG0250   155 FGRETPVELDFSQVEKI 171
nusG TIGR00922
transcription termination/antitermination factor NusG; NusG proteins are transcription factors ...
 12-180 6.34e-56

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: 174.03  E-value: 6.34e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  12 WYVLNIRTGYENSIKKELQQRIEATGLQDKIEEILIPTQKKIIVKKGKQNVMADKLFPGYVLIKMELDAYTWDIVKNTEG 91
Cdd:TIGR00922   1 WYVVQTYSGYEKKVKQNLEELIELLGMGDYIFEVIVPTEEVVEIKKGKKKVVERKIFPGYVLVKMDLTDVSWHLVKNTPG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  92 VRGFVKTDKYPRPLPES-EVKAIMKFMEVEQ--PSYQTSFSVGEAVKITDGAFADFIGSVQEIDTTKGKIKVLISFLGRE 168
Cdd:TIGR00922  81 VTGFVGSGGKPKALSEDeEVKNILNALEEGKdkPKPKIDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFGRE 160

                         170
                  ....*....|..
gi 1082930764 169 APVELDLSQVSK 180
Cdd:TIGR00922 161 TPVELEFSQVEK 172
NGN_Bact_1 cd09891
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The ...
 11-117 2.10e-38

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: 127.21  E-value: 2.10e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  11 KWYVLNIRTGYENSIKKELQQRIEATGLQDKIEEILIPTQKKIIVKKGKQNVMADKLFPGYVLIKMELDAYTWDIVKNTE 90
Cdd:cd09891     1 KWYVVHTYSGYENKVKENLEKRIESEGLEDYIGEVLVPTEEVVEVKNGKKKVKERKLFPGYVLVEMDMNDDTWHLVRNTP 80

                          90       100
                  ....*....|....*....|....*..
gi 1082930764  91 GVRGFVKTDKYPRPLPESEVKAIMKFM 117
Cdd:cd09891    81 GVTGFVGSGGKPVPLSEEEVERILGQV 107
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 11-115 1.03e-28

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: 102.45  E-value: 1.03e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764   11 KWYVLNIRTGYENSIKKELQQRIEATGLQDKIEEILIPTQKKIIVKKGKQNVMADKLFPGYVLIKMELDAYTWDIVKNTE 90
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKAEALGLEDKIVSILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGTP 80

                           90       100
                   ....*....|....*....|....*
gi 1082930764   91 GVRGFVKTDKYPRPLPESEVKAIMK 115
Cdd:smart00738  81 GVRGFVGGGGKPTPVPDDEIEKILK 105
NusG pfam02357
Transcription termination factor nusG;
11-114 1.44e-25

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 94.21  E-value: 1.44e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  11 KWYVLNIRTGYENSIKKELQQRieatGLqdkieEILIPTQKKIIVKKGKQNVMADKLFPGYVLIKMELDAYTWDIVKNTE 90
Cdd:pfam02357   2 KWYVLQTYSGKEKKVKENLERQ----GI-----EVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRSTP 72

                          90       100
                  ....*....|....*....|....
gi 1082930764  91 GVRGFVKTDKYPRPLPESEVKAIM 114
Cdd:pfam02357  73 GVTGFVGGSGKPTPIPDEEVERIL 96
antiterm_LoaP NF033641
antiterminator LoaP; LoaP is a paralog of NusG with an extensive presence in Firmicutes. The ...
 12-180 3.57e-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: 92.45  E-value: 3.57e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  12 WYVLNIRTGYENSIKKELQQRIEatglqDKIEEILIPTQKKIIVKKGKQNVMADKLFPGYVLIKMELDAYTWDIVKNTEG 91
Cdd:NF033641    1 WYVLFVRTGKEEKVKKLLNKLFD-----KELLRCFVPKRKLPERKQGKWYKVIKPLFPGYVFIETDMNEELYYKLKKIPG 75

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  92 VRGFVKT-DKYPRPLPESEVKAIMKFMEVEQP-SYQTSFSVGEAVKITDGAFADFIGSVQEIDTTKGKIKVLISFLGREA 169
Cdd:NF033641   76 IIRLLGNeGDEFSPIPEEEMEFLLKLLNDDDIiEYSKGYIEGDKVIVISGPLKGLEGIIKKIDKRKRRAKIELNFMGEER 155

                         170
                  ....*....|.
gi 1082930764 170 PVELDLSQVSK 180
Cdd:NF033641  156 LVDVGIEIVSK 166
KOW_NusG cd06091
NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif ...
 128-180 1.34e-20

NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif is one of the two domains of N-Utilization Substance G (NusG) a transcription elongation and Rho-termination factor in bacteria and archaea. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The eukaryotic ortholog of NusG is Spt5 with multiple KOW motifs at its C-terminus.


Pssm-ID: 240515 [Multi-domain]  Cd Length: 56  Bit Score: 80.19  E-value: 1.34e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1082930764 128 FSVGEAVKITDGAFADFIGSVQEIDTTKGKIKVLISFLGREAPVELDLSQVSK 180
Cdd:cd06091     4 FEVGDTVRIISGPFAGFEGKVEEIDEEKGKVKVLVEMFGRETPVELDFDQVEK 56
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 11-113 4.72e-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: 72.35  E-value: 4.72e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  11 KWYVLNIRTGYENSIKKELQQRIEAtglqdKIEEILIPTQKKIIVKKGKQNVMADKLFPGYVLIKMELDAYTWDIVKNTE 90
Cdd:cd08000     1 NWYVLFVKTGREEKVEKLLEKRFEA-----NDIEAFVPKKEVPERKRGKIEEVIKPLFPGYVFVETDLSPELYELIREVP 75

                          90       100
                  ....*....|....*....|...
gi 1082930764  91 GVRGFVKTDKYPRPLPESEVKAI 113
Cdd:cd08000    76 GVIGILGNGEEPSPVSDEEIEMI 98
NGN_plant cd09890
Plant N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance G ...
 12-114 5.83e-15

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: 67.38  E-value: 5.83e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  12 WYVLNIRTGYENSIKKELQqRIEATGLQDKIEEILIPT-QKKIIVKKGKQNVMADKLFPGYVLIKMELDAYTWDIVKNTE 90
Cdd:cd09890     2 WYMLRVPAGRENQAAEALE-RALATEFPDREFEVWVPSiPVDRKLKNGSISVKEKPLFPGYVLLRCVLNKEVYDFIRDND 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1082930764  91 GVRGFV--KTDKY-------PRPLPESEVKAIM 114
Cdd:cd09890    81 SVYGFVgsKVGKTgkrqieiPRPVPVEEIEAIF 113
NusG_myco TIGR01956
NusG family protein; This model represents a family of Mycoplasma proteins orthologous to the ...
 11-180 1.41e-11

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: 61.13  E-value: 1.41e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  11 KWYVLNIRTGYENSIKKELQQRIEATGLQDKIEEILIPTQKKIIV----------------------------KKGKQNV 62
Cdd:TIGR01956   1 QWYIATTINGNEDEVIENIKAKVRALGLENYISDFKILKEREIEEkvfepkngqaprsmkntattkwetldetKYKKTKI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  63 MADKLFPGYVLIKMELDAYTWDIVKNTEGVRGFVKTD---KYPRPLPESEVKAIMKFMEVEQPSYQ-------------- 125
Cdd:TIGR01956  81 SEKNKYNGYIYIKMIMTEDAWFLIRNTENVTGLVGSSgkgAKPIPISADADKLKMLKGISENTKKRvlvtntaivemeen 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764 126 -------------------------------------------TSFSVGEAVKITDGAFADFIGSVQEIDTTKGKIKVLI 162
Cdd:TIGR01956 161 kfdekcqyilkhkqvkpeaiaqvsesgeiideiveefqlvdnlSKFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEV 240

                         250
                  ....*....|....*...
gi 1082930764 163 SFLGREAPVELDLSQVSK 180
Cdd:TIGR01956 241 EILGKSVDVDLNFKHLKL 258
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
52-181 2.30e-09

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 53.74  E-value: 2.30e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  52 KIIvkKGKQNVMADKLFPGYVLIKMELDAYTWDIVKNTEGVRGFVKTDKYPRPLPESEVKAIMKFmEVEQPSYQTSFSVG 131
Cdd:PRK09014   37 KIV--RGKRTEVSEPLFPNYLFVEFDPEVIHTTTIRSTRGVSHFVRFGAQPAIVPSDVIYQLSVY-KPEKIVDPETPKPG 113

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1082930764 132 EAVKITDGAFADFIGSVQEIDTTKGKIkVLISFLGREAPVELDLSQVSKL 181
Cdd:PRK09014  114 DKVIITEGAFEGLQAIYTEPDGEARSI-LLLNLLNKQVKHSVDNTQFRKI 162
NGN_SP_RfaH cd09892
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; ...
 12-114 4.86e-09

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: 51.41  E-value: 4.86e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  12 WYVLNIRTGYENSIKKELQQRieatGLqdkieEILIPTQKKIIVKKGKQNVMADKLFPGYVLIKMELDAYTWDIVKNTEG 91
Cdd:cd09892     2 WYLLYTKPRQEERAAENLERQ----GF-----EVFLPMIRVEKRRRGKRTVVTEPLFPGYLFVRLDPEVQNWRPIRSTRG 72

                          90       100
                  ....*....|....*....|...
gi 1082930764  92 VRGFVKTDKYPRPLPESEVKAIM 114
Cdd:cd09892    73 VSRLVRFGGEPAPVPDALIEALR 95
NGN_SP_TaA cd09893
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), TaA; ...
 12-115 2.46e-08

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: 49.23  E-value: 2.46e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  12 WYVLNIRTGYENSIkkelqqrieATGLQDKIEEILIPTQKKIIVKKGkQNVMAD-KLFPGYVLIKMELDAYTWDIVKnTE 90
Cdd:cd09893     2 WYALYTRSRHEKKV---------ADRLAKKGIESFLPLYEVLSRWKD-RKKKIKvPLFPGYLFVRFQLDPERLRILK-TP 70

                          90       100
                  ....*....|....*....|....*
gi 1082930764  91 GVRGFVKTDKYPRPLPESEVKAIMK 115
Cdd:cd09893    71 GVVRIVGNSGGPIPIPDEEIASLRI 95
NGN_SP cd09886
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP); The ...
 11-115 2.67e-08

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: 49.29  E-value: 2.67e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  11 KWYVLNIRTGYEnsikKELQQRIEATGLqdkieEILIPTQKKIIVKKGKQNVMADKLFPGYVLIKM-ELDAYTWDIVKNT 89
Cdd:cd09886     1 SWYALRTNPGCE----QRAEEALEARGV-----EAFLPMLTEERKRRRKKFDVERPLFPGYVFARLdRSKGQDTSTIRAC 71

                          90       100
                  ....*....|....*....|....*.
gi 1082930764  90 EGVRGFVKTDKYPRPLPESEVKAIMK 115
Cdd:cd09886    72 DGVLGVVGFDGRPAPVPEQEMRDLRK 97
NGN_SP_AnfA1 cd09894
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1; ...
 10-115 9.92e-08

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: 47.66  E-value: 9.92e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1082930764  10 AKWYVLNIRTGYENSIKKEL-QQRIEAtgLQDKIEEILIPTQKKIIVKKGKQnvmadkLFPGYVLIKMELDAYTWDIVKN 88
Cdd:cd09894     1 KRWYLLRCKSGKIQSVIFSLeRLGVEV--FCPMIRTRRKRTDCKSYREKIEP------LFPGYLFVRFDPEVVHTSKITL 72

                          90       100
                  ....*....|....*....|....*..
gi 1082930764  89 TEGVRGFVKTDKYPRPLPESEVKAIMK 115
Cdd:cd09894    73 ASGVSGFVRFGGEPCPVPDAVIRALML 99
NGN_Bact_2 cd09889
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 2; The ...
 11-77 1.98e-04

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: 38.84  E-value: 1.98e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1082930764  11 KWYVLNIRTGYENSIKkelqQRIEATGLQDKIEEILIPTQKKIIVKKGKQNVMADKLFPGYVLIKME 77
Cdd:cd09889     1 MWYVVQVRTGREKAVL----ELLEKLVGPDVLQECFIPQYERKKRSQGVWRERKYTLFPGYVFVVTD 63
 
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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