NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|447211046|ref|WP_001288302|]
View 

MULTISPECIES: transcription termination/antitermination protein NusG [Staphylococcus]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
1-182 4.11e-73

Transcription termination/antitermination protein NusG [Transcription];


:

Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 217.38  E-value: 4.11e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046   1 MSEEvgaKRWYAVHTYSGYENKVKKNLEKRVESMnmteqifRVVIPEEEETQVKDGKAKTTVKKTFPGYVLVELIMTDES 80
Cdd:COG0250    1 MSME---KRWYVVHTYSGYEKKVKENLERRIEGI-------EVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDES 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046  81 WYVVRNTPGVTGFVGSagaGSKPNPLLPEEVRFILKQM--GLKEKTIDVELEVGEQVRIKSGPFANQVGEVQEIETDKFK 158
Cdd:COG0250   71 WYLVRNTPGVTGFVGF---GGKPAPLPDEEVERILARLeeGEEKPRPKVDFEVGDRVRITDGPFAGFEGTVEEVDPEKGR 147

                        170       180
                 ....*....|....*....|....
gi 447211046 159 LTVLVDMFGRETPVEVEFDQIEKL 182
Cdd:COG0250  148 VKVLVSIFGRETPVELDFSQVEKI 171
 
Name Accession Description Interval E-value
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
1-182 4.11e-73

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 217.38  E-value: 4.11e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046   1 MSEEvgaKRWYAVHTYSGYENKVKKNLEKRVESMnmteqifRVVIPEEEETQVKDGKAKTTVKKTFPGYVLVELIMTDES 80
Cdd:COG0250    1 MSME---KRWYVVHTYSGYEKKVKENLERRIEGI-------EVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDES 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046  81 WYVVRNTPGVTGFVGSagaGSKPNPLLPEEVRFILKQM--GLKEKTIDVELEVGEQVRIKSGPFANQVGEVQEIETDKFK 158
Cdd:COG0250   71 WYLVRNTPGVTGFVGF---GGKPAPLPDEEVERILARLeeGEEKPRPKVDFEVGDRVRITDGPFAGFEGTVEEVDPEKGR 147

                        170       180
                 ....*....|....*....|....
gi 447211046 159 LTVLVDMFGRETPVEVEFDQIEKL 182
Cdd:COG0250  148 VKVLVSIFGRETPVELDFSQVEKI 171
nusG TIGR00922
transcription termination/antitermination factor NusG; NusG proteins are transcription factors ...
 10-181 1.24e-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: 208.69  E-value: 1.24e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046   10 WYAVHTYSGYENKVKKNLEKRVESMNMTEQIFRVVIPEEEETQVKDGKAKTTVKKTFPGYVLVELIMTDESWYVVRNTPG 89
Cdd:TIGR00922   1 WYVVQTYSGYEKKVKQNLEELIELLGMGDYIFEVIVPTEEVVEIKKGKKKVVERKIFPGYVLVKMDLTDVSWHLVKNTPG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046   90 VTGFVGSagaGSKPNPLLP-EEVR--FILKQMGLKEKTIDVELEVGEQVRIKSGPFANQVGEVQEIETDKFKLTVLVDMF 166
Cdd:TIGR00922  81 VTGFVGS---GGKPKALSEdEEVKniLNALEEGKDKPKPKIDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIF 157

                         170
                  ....*....|....*
gi 447211046  167 GRETPVEVEFDQIEK 181
Cdd:TIGR00922 158 GRETPVELEFSQVEK 172
NGN_Bact_1 cd09891
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The ...
 9-118 1.47e-52

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: 163.03  E-value: 1.47e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046   9 RWYAVHTYSGYENKVKKNLEKRVESMNMTEQIFRVVIPEEEETQVKDGKAKTTVKKTFPGYVLVELIMTDESWYVVRNTP 88
Cdd:cd09891    1 KWYVVHTYSGYENKVKENLEKRIESEGLEDYIGEVLVPTEEVVEVKNGKKKVKERKLFPGYVLVEMDMNDDTWHLVRNTP 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 447211046  89 GVTGFVGSagaGSKPNPLLPEEVRFILKQM 118
Cdd:cd09891   81 GVTGFVGS---GGKPVPLSEEEVERILGQV 107
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 9-117 1.27e-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: 125.18  E-value: 1.27e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046     9 RWYAVHTYSGYENKVKKNLEKRVESMNMTEQIFRVVIPEEEETQVKDGKAKTTVKKTFPGYVLVELIMTDESWYVVRNTP 88
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKAEALGLEDKIVSILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGTP 80

                           90       100
                   ....*....|....*....|....*....
gi 447211046    89 GVTGFVGSagaGSKPNPLLPEEVRFILKQ 117
Cdd:smart00738  81 GVRGFVGG---GGKPTPVPDDEIEKILKP 106
NusG pfam02357
Transcription termination factor nusG;
8-115 8.07e-36

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 120.41  E-value: 8.07e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046    8 KRWYAVHTYSGYENKVKKNLEKrvesmnmteQIFRVVIPEEEETQVKDGKAKTTVKKTFPGYVLVELIMTDESWYVVRNT 87
Cdd:pfam02357   1 KKWYVLQTYSGKEKKVKENLER---------QGIEVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRST 71

                          90       100
                  ....*....|....*....|....*...
gi 447211046   88 PGVTGFVGSagaGSKPNPLLPEEVRFIL 115
Cdd:pfam02357  72 PGVTGFVGG---SGKPTPIPDEEVERIL 96
antiterm_LoaP NF033641
antiterminator LoaP; LoaP is a paralog of NusG with an extensive presence in Firmicutes. The ...
 10-181 1.49e-27

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: 101.31  E-value: 1.49e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046  10 WYAVHTYSGYENKVKKNLEKRVEsmnmtEQIFRVVIPEEEETQVKDGKAKTTVKKTFPGYVLVELIMTDESWYVVRNTPG 89
Cdd:NF033641   1 WYVLFVRTGKEEKVKKLLNKLFD-----KELLRCFVPKRKLPERKQGKWYKVIKPLFPGYVFIETDMNEELYYKLKKIPG 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046  90 VTGFVGSagAGSKPNPLLPEEVRFILKQMGlKEKTID---VELEvGEQVRIKSGPFANQVGEVQEIETDKFKLTVLVDMF 166
Cdd:NF033641  76 IIRLLGN--EGDEFSPIPEEEMEFLLKLLN-DDDIIEyskGYIE-GDKVIVISGPLKGLEGIIKKIDKRKRRAKIELNFM 151

                        170
                 ....*....|....*
gi 447211046 167 GRETPVEVEFDQIEK 181
Cdd:NF033641 152 GEERLVDVGIEIVSK 166
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 10-152 8.30e-13

UpxY family transcription antiterminator; The UpxY family of NusG-related transcription antiterminators was described originally from a paralogous family of eight members from Bacteriodes fragilis, UpaY to UphY, each of which was associated with a distinct capsular polysaccharide biosynthesis locus. There is no UpxY protein per se.


Pssm-ID: 468125 [Multi-domain]  Cd Length: 162  Bit Score: 62.87  E-value: 8.30e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046  10 WYAVHTYSGYENKVKKNLEKR-VESmnmteqiFrvvIPEEEETQVKDGKAKTTVKKTFPGYVLVElIMTDESWYVVRNTP 88
Cdd:NF033644   1 WYALYTRPRREKKVAELLEKKgIES-------F---LPMQKEIRQWSDRKKRVEVPLIPNLVFVH-ITEKELDEVLEQTP 69

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 447211046  89 GVTGFVGSAGAGSKPnPLLP----EEVRFILKQMGLKEKTIDVELEVGEQVRIKSGPFANQVGEVQEI 152
Cdd:NF033644  70 GVVRYIRDDRGKSKP-AIIPdkqmERFRLMLDPSDEVVVYLEAPLKKGDKVRVIGGPLKGLEGELVRV 136
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
8-182 7.48e-08

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 49.50  E-value: 7.48e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046   8 KRWYAVHTYSGYENKVKKNLEKR-VES---MNMTEQIFRvvipeeeetqvkdGKAKTTVKKTFPGYVLVELIMTDESWYV 83
Cdd:PRK09014   2 KSWYLLYCKRGQLQRAQEHLERQgVEClypMITLEKIVR-------------GKRTEVSEPLFPNYLFVEFDPEVIHTTT 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046  84 VRNTPGVTGFVGsagAGSKPNpLLPEEVRFILKQMGlKEKTIDVEL-EVGEQVRIKSGPFAN-------QVGEVQEIetd 155
Cdd:PRK09014  69 IRSTRGVSHFVR---FGAQPA-IVPSDVIYQLSVYK-PEKIVDPETpKPGDKVIITEGAFEGlqaiytePDGEARSI--- 140

                        170       180
                 ....*....|....*....|....*..
gi 447211046 156 kfkltVLVDMFGRETPVEVEFDQIEKL 182
Cdd:PRK09014 141 -----LLLNLLNKQVKHSVDNTQFRKI 162
 
Name Accession Description Interval E-value
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
1-182 4.11e-73

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 217.38  E-value: 4.11e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046   1 MSEEvgaKRWYAVHTYSGYENKVKKNLEKRVESMnmteqifRVVIPEEEETQVKDGKAKTTVKKTFPGYVLVELIMTDES 80
Cdd:COG0250    1 MSME---KRWYVVHTYSGYEKKVKENLERRIEGI-------EVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDES 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046  81 WYVVRNTPGVTGFVGSagaGSKPNPLLPEEVRFILKQM--GLKEKTIDVELEVGEQVRIKSGPFANQVGEVQEIETDKFK 158
Cdd:COG0250   71 WYLVRNTPGVTGFVGF---GGKPAPLPDEEVERILARLeeGEEKPRPKVDFEVGDRVRITDGPFAGFEGTVEEVDPEKGR 147

                        170       180
                 ....*....|....*....|....
gi 447211046 159 LTVLVDMFGRETPVEVEFDQIEKL 182
Cdd:COG0250  148 VKVLVSIFGRETPVELDFSQVEKI 171
nusG TIGR00922
transcription termination/antitermination factor NusG; NusG proteins are transcription factors ...
 10-181 1.24e-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: 208.69  E-value: 1.24e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046   10 WYAVHTYSGYENKVKKNLEKRVESMNMTEQIFRVVIPEEEETQVKDGKAKTTVKKTFPGYVLVELIMTDESWYVVRNTPG 89
Cdd:TIGR00922   1 WYVVQTYSGYEKKVKQNLEELIELLGMGDYIFEVIVPTEEVVEIKKGKKKVVERKIFPGYVLVKMDLTDVSWHLVKNTPG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046   90 VTGFVGSagaGSKPNPLLP-EEVR--FILKQMGLKEKTIDVELEVGEQVRIKSGPFANQVGEVQEIETDKFKLTVLVDMF 166
Cdd:TIGR00922  81 VTGFVGS---GGKPKALSEdEEVKniLNALEEGKDKPKPKIDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIF 157

                         170
                  ....*....|....*
gi 447211046  167 GRETPVEVEFDQIEK 181
Cdd:TIGR00922 158 GRETPVELEFSQVEK 172
NGN_Bact_1 cd09891
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The ...
 9-118 1.47e-52

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: 163.03  E-value: 1.47e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046   9 RWYAVHTYSGYENKVKKNLEKRVESMNMTEQIFRVVIPEEEETQVKDGKAKTTVKKTFPGYVLVELIMTDESWYVVRNTP 88
Cdd:cd09891    1 KWYVVHTYSGYENKVKENLEKRIESEGLEDYIGEVLVPTEEVVEVKNGKKKVKERKLFPGYVLVEMDMNDDTWHLVRNTP 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 447211046  89 GVTGFVGSagaGSKPNPLLPEEVRFILKQM 118
Cdd:cd09891   81 GVTGFVGS---GGKPVPLSEEEVERILGQV 107
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 9-117 1.27e-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: 125.18  E-value: 1.27e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046     9 RWYAVHTYSGYENKVKKNLEKRVESMNMTEQIFRVVIPEEEETQVKDGKAKTTVKKTFPGYVLVELIMTDESWYVVRNTP 88
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLERKAEALGLEDKIVSILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGTP 80

                           90       100
                   ....*....|....*....|....*....
gi 447211046    89 GVTGFVGSagaGSKPNPLLPEEVRFILKQ 117
Cdd:smart00738  81 GVRGFVGG---GGKPTPVPDDEIEKILKP 106
NusG pfam02357
Transcription termination factor nusG;
8-115 8.07e-36

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 120.41  E-value: 8.07e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046    8 KRWYAVHTYSGYENKVKKNLEKrvesmnmteQIFRVVIPEEEETQVKDGKAKTTVKKTFPGYVLVELIMTDESWYVVRNT 87
Cdd:pfam02357   1 KKWYVLQTYSGKEKKVKENLER---------QGIEVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRST 71

                          90       100
                  ....*....|....*....|....*...
gi 447211046   88 PGVTGFVGSagaGSKPNPLLPEEVRFIL 115
Cdd:pfam02357  72 PGVTGFVGG---SGKPTPIPDEEVERIL 96
antiterm_LoaP NF033641
antiterminator LoaP; LoaP is a paralog of NusG with an extensive presence in Firmicutes. The ...
 10-181 1.49e-27

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: 101.31  E-value: 1.49e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046  10 WYAVHTYSGYENKVKKNLEKRVEsmnmtEQIFRVVIPEEEETQVKDGKAKTTVKKTFPGYVLVELIMTDESWYVVRNTPG 89
Cdd:NF033641   1 WYVLFVRTGKEEKVKKLLNKLFD-----KELLRCFVPKRKLPERKQGKWYKVIKPLFPGYVFIETDMNEELYYKLKKIPG 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046  90 VTGFVGSagAGSKPNPLLPEEVRFILKQMGlKEKTID---VELEvGEQVRIKSGPFANQVGEVQEIETDKFKLTVLVDMF 166
Cdd:NF033641  76 IIRLLGN--EGDEFSPIPEEEMEFLLKLLN-DDDIIEyskGYIE-GDKVIVISGPLKGLEGIIKKIDKRKRRAKIELNFM 151

                        170
                 ....*....|....*
gi 447211046 167 GRETPVEVEFDQIEK 181
Cdd:NF033641 152 GEERLVDVGIEIVSK 166
KOW_NusG cd06091
NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif ...
 126-181 5.91e-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: 88.67  E-value: 5.91e-24
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 447211046 126 DVELEVGEQVRIKSGPFANQVGEVQEIETDKFKLTVLVDMFGRETPVEVEFDQIEK 181
Cdd:cd06091    1 EVDFEVGDTVRIISGPFAGFEGKVEEIDEEKGKVKVLVEMFGRETPVELDFDQVEK 56
NusG_myco TIGR01956
NusG family protein; This model represents a family of Mycoplasma proteins orthologous to the ...
 9-181 4.08e-22

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: 89.64  E-value: 4.08e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046    9 RWYAVHTYSGYENKVKKNLEKRVESMNMTEQI--FRVV---IPEEEETQVKDGKAKTTVKKT------------------ 65
Cdd:TIGR01956   1 QWYIATTINGNEDEVIENIKAKVRALGLENYIsdFKILkerEIEEKVFEPKNGQAPRSMKNTattkwetldetkykktki 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046   66 -----FPGYVLVELIMTDESWYVVRNTPGVTGFVGSAGAGSKPNPL---------------------------------- 106
Cdd:TIGR01956  81 seknkYNGYIYIKMIMTEDAWFLIRNTENVTGLVGSSGKGAKPIPIsadadklkmlkgisentkkrvlvtntaivemeen 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046  107 -LPEEVRFILKQMGLKEKTID----------------------VELEVGEQVRIKSGPFANQVGEVQEIETDKFKLTVLV 163
Cdd:TIGR01956 161 kFDEKCQYILKHKQVKPEAIAqvsesgeiideiveefqlvdnlSKFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEV 240

                         250
                  ....*....|....*...
gi 447211046  164 DMFGRETPVEVEFDQIEK 181
Cdd:TIGR01956 241 EILGKSVDVDLNFKHLKL 258
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 10-115 8.72e-21

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: 81.98  E-value: 8.72e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046  10 WYAVHTYSGYENKVKKNLEKRVEsmnmtEQIFRVVIPEEEETQVKDGKAKTTVKKTFPGYVLVELIMTDESWYVVRNTPG 89
Cdd:cd08000    2 WYVLFVKTGREEKVEKLLEKRFE-----ANDIEAFVPKKEVPERKRGKIEEVIKPLFPGYVFVETDLSPELYELIREVPG 76

                         90       100
                 ....*....|....*....|....*.
gi 447211046  90 VTGFVGSagaGSKPNPLLPEEVRFIL 115
Cdd:cd08000   77 VIGILGN---GEEPSPVSDEEIEMIL 99
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 10-152 8.30e-13

UpxY family transcription antiterminator; The UpxY family of NusG-related transcription antiterminators was described originally from a paralogous family of eight members from Bacteriodes fragilis, UpaY to UphY, each of which was associated with a distinct capsular polysaccharide biosynthesis locus. There is no UpxY protein per se.


Pssm-ID: 468125 [Multi-domain]  Cd Length: 162  Bit Score: 62.87  E-value: 8.30e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046  10 WYAVHTYSGYENKVKKNLEKR-VESmnmteqiFrvvIPEEEETQVKDGKAKTTVKKTFPGYVLVElIMTDESWYVVRNTP 88
Cdd:NF033644   1 WYALYTRPRREKKVAELLEKKgIES-------F---LPMQKEIRQWSDRKKRVEVPLIPNLVFVH-ITEKELDEVLEQTP 69

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 447211046  89 GVTGFVGSAGAGSKPnPLLP----EEVRFILKQMGLKEKTIDVELEVGEQVRIKSGPFANQVGEVQEI 152
Cdd:NF033644  70 GVVRYIRDDRGKSKP-AIIPdkqmERFRLMLDPSDEVVVYLEAPLKKGDKVRVIGGPLKGLEGELVRV 136
NGN_SP_RfaH cd09892
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH; ...
 9-111 2.26e-11

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: 57.57  E-value: 2.26e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046   9 RWYAVHTYSGYENKVKKNLEKrvesmnmteQIFRVVIPEEEETQVKDGKAKTTVKKTFPGYVLVELIMTDESWYVVRNTP 88
Cdd:cd09892    1 AWYLLYTKPRQEERAAENLER---------QGFEVFLPMIRVEKRRRGKRTVVTEPLFPGYLFVRLDPEVQNWRPIRSTR 71

                         90       100
                 ....*....|....*....|...
gi 447211046  89 GVTGFVGSagaGSKPNPlLPEEV 111
Cdd:cd09892   72 GVSRLVRF---GGEPAP-VPDAL 90
NGN_SP_TaA cd09893
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), TaA; ...
 9-112 2.82e-09

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: 51.92  E-value: 2.82e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046   9 RWYAVHTYSGYENKVKKNLEKR-VESMNMTEQIFRvvipeeeetQVKDGKAKTTVkKTFPGYVLVELIMTDESWYVVRnT 87
Cdd:cd09893    1 SWYALYTRSRHEKKVADRLAKKgIESFLPLYEVLS---------RWKDRKKKIKV-PLFPGYLFVRFQLDPERLRILK-T 69

                         90       100
                 ....*....|....*....|....*
gi 447211046  88 PGVTGFVGSAGAgskPNPLLPEEVR 112
Cdd:cd09893   70 PGVVRIVGNSGG---PIPIPDEEIA 91
NGN_plant cd09890
Plant N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance G ...
 10-111 9.87e-09

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: 50.81  E-value: 9.87e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046  10 WYAVHTYSGYENKVKKNLEKRVESMnMTEQIFRVVIPE-EEETQVKDGKAKTTVKKTFPGYVLVELIMTDESWYVVRNTP 88
Cdd:cd09890    2 WYMLRVPAGRENQAAEALERALATE-FPDREFEVWVPSiPVDRKLKNGSISVKEKPLFPGYVLLRCVLNKEVYDFIRDND 80

                         90       100       110
                 ....*....|....*....|....*....|
gi 447211046  89 GVTGFVGSaGAGS-------KPNPLLPEEV 111
Cdd:cd09890   81 SVYGFVGS-KVGKtgkrqieIPRPVPVEEI 109
NGN_Bact_2 cd09889
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 2; The ...
 9-115 2.88e-08

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: 49.24  E-value: 2.88e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046   9 RWYAVHTYSGYENKVKKnlekRVESMNMTEQIFRVVIPEEEETQVKDGKAKTTVKKTFPGYVLVELIMTDESWYVVRNTP 88
Cdd:cd09889    1 MWYVVQVRTGREKAVLE----LLEKLVGPDVLQECFIPQYERKKRSQGVWRERKYTLFPGYVFVVTDDIDELYYELKRVP 76

                         90       100
                 ....*....|....*....|....*..
gi 447211046  89 GVTGFVgsaGAGSKPNPLLPEEVRFIL 115
Cdd:cd09889   77 GFTRLL---GNDGSFFPLTPEEADFIR 100
NGN_SP cd09886
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP); The ...
 9-117 4.51e-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: 48.90  E-value: 4.51e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046   9 RWYAVHTYSGYENKVKKNLEKR-VEsmnmteqifrVVIPEEEETQVKDGKAKTTVKKTFPGYVLVEL-IMTDESWYVVRN 86
Cdd:cd09886    1 SWYALRTNPGCEQRAEEALEARgVE----------AFLPMLTEERKRRRKKFDVERPLFPGYVFARLdRSKGQDTSTIRA 70

                         90       100       110
                 ....*....|....*....|....*....|.
gi 447211046  87 TPGVTGFVGSAGagsKPNPlLPEEVRFILKQ 117
Cdd:cd09886   71 CDGVLGVVGFDG---RPAP-VPEQEMRDLRK 97
rfaH PRK09014
transcription/translation regulatory transformer protein RfaH;
8-182 7.48e-08

transcription/translation regulatory transformer protein RfaH;


Pssm-ID: 181611 [Multi-domain]  Cd Length: 162  Bit Score: 49.50  E-value: 7.48e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046   8 KRWYAVHTYSGYENKVKKNLEKR-VES---MNMTEQIFRvvipeeeetqvkdGKAKTTVKKTFPGYVLVELIMTDESWYV 83
Cdd:PRK09014   2 KSWYLLYCKRGQLQRAQEHLERQgVEClypMITLEKIVR-------------GKRTEVSEPLFPNYLFVEFDPEVIHTTT 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046  84 VRNTPGVTGFVGsagAGSKPNpLLPEEVRFILKQMGlKEKTIDVEL-EVGEQVRIKSGPFAN-------QVGEVQEIetd 155
Cdd:PRK09014  69 IRSTRGVSHFVR---FGAQPA-IVPSDVIYQLSVYK-PEKIVDPETpKPGDKVIITEGAFEGlqaiytePDGEARSI--- 140

                        170       180
                 ....*....|....*....|....*..
gi 447211046 156 kfkltVLVDMFGRETPVEVEFDQIEKL 182
Cdd:PRK09014 141 -----LLLNLLNKQVKHSVDNTQFRKI 162
NGN_SP_UpxY cd09895
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; ...
 9-94 3.43e-05

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: 41.02  E-value: 3.43e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046   9 RWYAVHTYSGYENKVKKNLEKR-VESmnmteqiFrvvIPEEEETQVKDGKAKTTVKKTFPGYVLVELimTDESWYVVRNT 87
Cdd:cd09895    1 PWYALYTFPRREKKVAEYLEKKgIEC-------F---LPMQYEVRQWSGRKKRVEVPLFPNLVFVHI--TREELDEVLET 68


                 ....*..
gi 447211046  88 PGVTGFV 94
Cdd:cd09895   69 PGVVRFV 75
KOW cd00380
KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese); KOW domain is known ...
 132-180 9.60e-05

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: 38.35  E-value: 9.60e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 447211046 132 GEQVRIKSGPFANQVGEVQEIETDKFKLTVLVDMFGRETPVEVEFDQIE 180
Cdd:cd00380    1 GDVVRVLRGPYKGREGVVVDIDPRFGIVTVKGATGSKGAELKVRFDDVD 49
NGN_SP_AnfA1 cd09894
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1; ...
 8-111 5.72e-04

N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1; Regulation of the afp, antifeeding prophage, gene cluster is mediated by AnFA1, a RfaH-like transcriptional antiterminator. RfaH is an operon-specific virulence regulator, thought to arisen from an early duplication of N-Utilization Substance G (NusG). NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination in bacteria. Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS biosynthesis genes. NusG SP family members are operon-specific transcriptional antitermination factors. Orthologs of the NusG gene exist in all bacteria, but their functions and requirements are different. The NusG N-terminal domain (NGN) is similar in all NusG orthologs, but its C-terminal domain and the linker that separate these two domains are different. The domain organization of NusG and its orthologs suggests that the common properties of NusG and its orthologs and paralogs are due to their similar NGN domains.


Pssm-ID: 193583 [Multi-domain]  Cd Length: 99  Bit Score: 37.65  E-value: 5.72e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046   8 KRWYAVHTYSGYENKVKKNLEkrvesmnmTEQIfRVVIPEE-EETQVKDGKAKTTVKKT-FPGYVLVELIMTDESWYVVR 85
Cdd:cd09894    1 KRWYLLRCKSGKIQSVIFSLE--------RLGV-EVFCPMIrTRRKRTDCKSYREKIEPlFPGYLFVRFDPEVVHTSKIT 71

                         90       100
                 ....*....|....*....|....*.
gi 447211046  86 NTPGVTGFVGSAGagsKPNPlLPEEV 111
Cdd:cd09894   72 LASGVSGFVRFGG---EPCP-VPDAV 93
KOW_elon_Spt5 TIGR00405
transcription elongation factor Spt5; This protein contains a KOW domain, shared by bacterial ...
 11-179 8.77e-04

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: 37.95  E-value: 8.77e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046   11 YAVHTYSGYENKVKKNLEKRVESMNMteQIFRVVIPEEeetqvkdgkakttvkktFPGYVLVELIMTDESWYVVRNTPGV 90
Cdd:TIGR00405   1 FAVKTSVGQEKNVARLMARKARKSGL--EVYSILAPES-----------------LKGYILVEAETKIDMRNPIIGVPHV 61

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046   91 TGFVgsagagskpnpllPEEVRFILKQMGLKEKTIDVELEVGEQVRIKSGPFANQVGEVQEIETDKFKLTVLVDMFGRET 170
Cdd:TIGR00405  62 RGVV-------------EGEIDFEEIERFLTPKKIIESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIEAAVPI 128


                  ....*....
gi 447211046  171 PVEVEFDQI 179
Cdd:TIGR00405 129 PVTVKGDQV 137
KOW pfam00467
KOW motif; This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, ...
 131-161 3.85e-03

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: 33.51  E-value: 3.85e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 447211046  131 VGEQVRIKSGPFANQVGEVQEIETDKFKLTV 161
Cdd:pfam00467   1 KGDVVRVIAGPFKGKVGKVVEVDDKKNRVLV 31
nusG PRK08559
transcription antitermination protein NusG; Validated
 11-161 4.92e-03

transcription antitermination protein NusG; Validated


Pssm-ID: 181467 [Multi-domain]  Cd Length: 153  Bit Score: 36.00  E-value: 4.92e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447211046  11 YAVHTYSGYENKVKKNLEKRVESMNMteQIFRVVIPEEeetqvkdgkakttVKktfpGYVLVELIMTDESWYVVRNTPGV 90
Cdd:PRK08559   9 FAVKTTAGQERNVALMLAMRAKKENL--PIYAILAPPE-------------LK----GYVLVEAESKGAVEEAIRGIPHV 69

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 447211046  91 TGFVgsagagskpnpllPEEVRFILKQMGLKEKTIDVELEVGEQVRIKSGPFANQVGEVQEIETDKFKLTV 161
Cdd:PRK08559  70 RGVV-------------PGEISFEEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTV 127
KOW smart00739
KOW (Kyprides, Ouzounis, Woese) motif; Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
 128-153 7.55e-03

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


Pssm-ID: 128978  Cd Length: 28  Bit Score: 32.69  E-value: 7.55e-03
                           10        20
                   ....*....|....*....|....*.
gi 447211046   128 ELEVGEQVRIKSGPFANQVGEVQEIE 153
Cdd:smart00739   1 KFEVGDTVRVIAGPFKGKVGKVLEVD 26
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH