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Conserved domains on  [gi|494650457|ref|WP_007408401|]
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MULTISPECIES: antiterminator LoaP [Bacillus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
antiterm_LoaP super family cl41362
antiterminator LoaP; LoaP is a paralog of NusG with an extensive presence in Firmicutes. The ...
 3-175 3.09e-79

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.


The actual alignment was detected with superfamily member NF033641:

Pssm-ID: 468124 [Multi-domain]  Cd Length: 166  Bit Score: 232.66  E-value: 3.09e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457   3 WYALFVESGKEETVQKFLRLQFDEQALYSIIPKKKVTERKAGIKYEALKKMFPGYVLFKTKMTERTFHKIKELPISCRIV 82
Cdd:NF033641   1 WYVLFVRTGKEEKVKKLLNKLFDKELLRCFVPKRKLPERKQGKWYKVIKPLFPGYVFIETDMNEELYYKLKKIPGIIRLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457  83 NNgayyskeRKTYFTTIKDEEILPIIRLIGEGDTVDYSKVYIENSKVTVASGPLKGMEGIIKKIDKRKRRAKICLSFMGL 162
Cdd:NF033641  81 GN-------EGDEFSPIPEEEMEFLLKLLNDDDIIEYSKGYIEGDKVIVISGPLKGLEGIIKKIDKRKRRAKIELNFMGE 153

                        170
                 ....*....|...
gi 494650457 163 DKMVNVGIEVLSK 175
Cdd:NF033641 154 ERLVDVGIEIVSK 166
 
Name Accession Description Interval E-value
antiterm_LoaP NF033641
antiterminator LoaP; LoaP is a paralog of NusG with an extensive presence in Firmicutes. The ...
 3-175 3.09e-79

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: 232.66  E-value: 3.09e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457   3 WYALFVESGKEETVQKFLRLQFDEQALYSIIPKKKVTERKAGIKYEALKKMFPGYVLFKTKMTERTFHKIKELPISCRIV 82
Cdd:NF033641   1 WYVLFVRTGKEEKVKKLLNKLFDKELLRCFVPKRKLPERKQGKWYKVIKPLFPGYVFIETDMNEELYYKLKKIPGIIRLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457  83 NNgayyskeRKTYFTTIKDEEILPIIRLIGEGDTVDYSKVYIENSKVTVASGPLKGMEGIIKKIDKRKRRAKICLSFMGL 162
Cdd:NF033641  81 GN-------EGDEFSPIPEEEMEFLLKLLNDDDIIEYSKGYIEGDKVIVISGPLKGLEGIIKKIDKRKRRAKIELNFMGE 153

                        170
                 ....*....|...
gi 494650457 163 DKMVNVGIEVLSK 175
Cdd:NF033641 154 ERLVDVGIEIVSK 166
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
1-175 1.75e-33

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 116.46  E-value: 1.75e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457   1 MKWYALFVESGKEETVQKFLRLQFDEqaLYSIIPKKKVTERKAGIKYEALKKMFPGYVLFKTKMTERTFHKIKELPISCR 80
Cdd:COG0250    5 KRWYVVHTYSGYEKKVKENLERRIEG--IEVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLVRNTPGVTG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457  81 IVNNGAYYskerktyfTTIKDEEILPIIRLIGEGDTVDYSKVYIE-NSKVTVASGPLKGMEGIIKKIDKRKRRAKICLSF 159
Cdd:COG0250   83 FVGFGGKP--------APLPDEEVERILARLEEGEEKPRPKVDFEvGDRVRITDGPFAGFEGTVEEVDPEKGRVKVLVSI 154

                        170
                 ....*....|....*.
gi 494650457 160 MGLDKMVNVGIEVLSK 175
Cdd:COG0250  155 FGRETPVELDFSQVEK 170
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 2-108 1.34e-29

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: 104.32  E-value: 1.34e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457   2 KWYALFVESGKEETVQKFLRLQFDEQALYSIIPKKKVTERKAGIKYEALKKMFPGYVLFKTKMTERTFHKIKELPISCRI 81
Cdd:cd08000    1 NWYVLFVKTGREEKVEKLLEKRFEANDIEAFVPKKEVPERKRGKIEEVIKPLFPGYVFVETDLSPELYELIREVPGVIGI 80

                         90       100
                 ....*....|....*....|....*..
gi 494650457  82 VNNGAYYSkerktyftTIKDEEILPII 108
Cdd:cd08000   81 LGNGEEPS--------PVSDEEIEMIL 99
NusG pfam02357
Transcription termination factor nusG;
1-104 6.56e-15

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 66.48  E-value: 6.56e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457    1 MKWYALFVESGKEETVQKflrlQFDEQALYSIIPKKKVTERKAGIKYEALKKMFPGYVLFKTKMTERTFHKIKELPISCR 80
Cdd:pfam02357   1 KKWYVLQTYSGKEKKVKE----NLERQGIEVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRSTPGVTG 76

                          90       100
                  ....*....|....*....|....
gi 494650457   81 IVNNGAYYskerktyfTTIKDEEI 104
Cdd:pfam02357  77 FVGGSGKP--------TPIPDEEV 92
nusG TIGR00922
transcription termination/antitermination factor NusG; NusG proteins are transcription factors ...
 3-161 8.60e-15

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: 68.10  E-value: 8.60e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457    3 WYALFVESGKEETVQKFLR-----LQFDEQALYSIIPKKKVTERKAGIKYEALKKMFPGYVLFKTKMTERTFHKIKELPI 77
Cdd:TIGR00922   1 WYVVQTYSGYEKKVKQNLEelielLGMGDYIFEVIVPTEEVVEIKKGKKKVVERKIFPGYVLVKMDLTDVSWHLVKNTPG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457   78 SCRIVNNGayySKERKtyftTIKDEEILPIIRLIGEG-DTVDYSKVYIENSKVTVASGPLKGMEGIIKKIDKRKRRAKIC 156
Cdd:TIGR00922  81 VTGFVGSG---GKPKA----LSEDEEVKNILNALEEGkDKPKPKIDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVS 153


                  ....*
gi 494650457  157 LSFMG 161
Cdd:TIGR00922 154 VSIFG 158
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 3-168 8.92e-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: 62.49  E-value: 8.92e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457   3 WYALFVESGKEETVQKFLrlqfDEQALYSIIPKKKVTERKAGIKYEALKKMFPGYVLFKTkmTERTFHKIK-ELPISCRI 81
Cdd:NF033644   1 WYALYTRPRREKKVAELL----EKKGIESFLPMQKEIRQWSDRKKRVEVPLIPNLVFVHI--TEKELDEVLeQTPGVVRY 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457  82 VnngaYYSKERKTYfTTIKDEEILPIIRLIGEGDTVdysKVYIENS-----KVTVASGPLKGMEGIIKKIdKRKRRAKIC 156
Cdd:NF033644  75 I----RDDRGKSKP-AIIPDKQMERFRLMLDPSDEV---VVYLEAPlkkgdKVRVIGGPLKGLEGELVRV-KGKKRVVVR 145

                        170
                 ....*....|..
gi 494650457 157 LSFMGLDKMVNV 168
Cdd:NF033644 146 IPGLGAVATVEV 157
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 2-76 3.34e-10

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: 54.69  E-value: 3.34e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457     2 KWYALFVESGKEETVQKFLR-----LQFDEQALYSIIPKKKVTERKAGIKYEALKKMFPGYVLFKTKMTERTFHKIKELP 76
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLErkaeaLGLEDKIVSILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGTP 80
 
Name Accession Description Interval E-value
antiterm_LoaP NF033641
antiterminator LoaP; LoaP is a paralog of NusG with an extensive presence in Firmicutes. The ...
 3-175 3.09e-79

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: 232.66  E-value: 3.09e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457   3 WYALFVESGKEETVQKFLRLQFDEQALYSIIPKKKVTERKAGIKYEALKKMFPGYVLFKTKMTERTFHKIKELPISCRIV 82
Cdd:NF033641   1 WYVLFVRTGKEEKVKKLLNKLFDKELLRCFVPKRKLPERKQGKWYKVIKPLFPGYVFIETDMNEELYYKLKKIPGIIRLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457  83 NNgayyskeRKTYFTTIKDEEILPIIRLIGEGDTVDYSKVYIENSKVTVASGPLKGMEGIIKKIDKRKRRAKICLSFMGL 162
Cdd:NF033641  81 GN-------EGDEFSPIPEEEMEFLLKLLNDDDIIEYSKGYIEGDKVIVISGPLKGLEGIIKKIDKRKRRAKIELNFMGE 153

                        170
                 ....*....|...
gi 494650457 163 DKMVNVGIEVLSK 175
Cdd:NF033641 154 ERLVDVGIEIVSK 166
NusG COG0250
Transcription termination/antitermination protein NusG [Transcription];
1-175 1.75e-33

Transcription termination/antitermination protein NusG [Transcription];


Pssm-ID: 440020 [Multi-domain]  Cd Length: 171  Bit Score: 116.46  E-value: 1.75e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457   1 MKWYALFVESGKEETVQKFLRLQFDEqaLYSIIPKKKVTERKAGIKYEALKKMFPGYVLFKTKMTERTFHKIKELPISCR 80
Cdd:COG0250    5 KRWYVVHTYSGYEKKVKENLERRIEG--IEVFVPTEEVVEIKNGKKKTVERPLFPGYVFVRMDLTDESWYLVRNTPGVTG 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457  81 IVNNGAYYskerktyfTTIKDEEILPIIRLIGEGDTVDYSKVYIE-NSKVTVASGPLKGMEGIIKKIDKRKRRAKICLSF 159
Cdd:COG0250   83 FVGFGGKP--------APLPDEEVERILARLEEGEEKPRPKVDFEvGDRVRITDGPFAGFEGTVEEVDPEKGRVKVLVSI 154

                        170
                 ....*....|....*.
gi 494650457 160 MGLDKMVNVGIEVLSK 175
Cdd:COG0250  155 FGRETPVELDFSQVEK 170
NGN cd08000
N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily; The N-Utilization ...
 2-108 1.34e-29

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: 104.32  E-value: 1.34e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457   2 KWYALFVESGKEETVQKFLRLQFDEQALYSIIPKKKVTERKAGIKYEALKKMFPGYVLFKTKMTERTFHKIKELPISCRI 81
Cdd:cd08000    1 NWYVLFVKTGREEKVEKLLEKRFEANDIEAFVPKKEVPERKRGKIEEVIKPLFPGYVFVETDLSPELYELIREVPGVIGI 80

                         90       100
                 ....*....|....*....|....*..
gi 494650457  82 VNNGAYYSkerktyftTIKDEEILPII 108
Cdd:cd08000   81 LGNGEEPS--------PVSDEEIEMIL 99
NusG pfam02357
Transcription termination factor nusG;
1-104 6.56e-15

Transcription termination factor nusG;


Pssm-ID: 426736 [Multi-domain]  Cd Length: 96  Bit Score: 66.48  E-value: 6.56e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457    1 MKWYALFVESGKEETVQKflrlQFDEQALYSIIPKKKVTERKAGIKYEALKKMFPGYVLFKTKMTERTFHKIKELPISCR 80
Cdd:pfam02357   1 KKWYVLQTYSGKEKKVKE----NLERQGIEVFLPTEEVVEIRNGKKKVVERPLFPGYVFVRMDMTDETWHLVRSTPGVTG 76

                          90       100
                  ....*....|....*....|....
gi 494650457   81 IVNNGAYYskerktyfTTIKDEEI 104
Cdd:pfam02357  77 FVGGSGKP--------TPIPDEEV 92
nusG TIGR00922
transcription termination/antitermination factor NusG; NusG proteins are transcription factors ...
 3-161 8.60e-15

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: 68.10  E-value: 8.60e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457    3 WYALFVESGKEETVQKFLR-----LQFDEQALYSIIPKKKVTERKAGIKYEALKKMFPGYVLFKTKMTERTFHKIKELPI 77
Cdd:TIGR00922   1 WYVVQTYSGYEKKVKQNLEelielLGMGDYIFEVIVPTEEVVEIKKGKKKVVERKIFPGYVLVKMDLTDVSWHLVKNTPG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457   78 SCRIVNNGayySKERKtyftTIKDEEILPIIRLIGEG-DTVDYSKVYIENSKVTVASGPLKGMEGIIKKIDKRKRRAKIC 156
Cdd:TIGR00922  81 VTGFVGSG---GKPKA----LSEDEEVKNILNALEEGkDKPKPKIDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVS 153


                  ....*
gi 494650457  157 LSFMG 161
Cdd:TIGR00922 154 VSIFG 158
NGN_Bact_1 cd09891
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; The ...
 2-76 1.67e-13

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: 63.26  E-value: 1.67e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457   2 KWYALFVESGKEETVQKFL-----RLQFDEQALYSIIPKKKVTERKAGIKYEALKKMFPGYVLFKTKMTERTFHKIKELP 76
Cdd:cd09891    1 KWYVVHTYSGYENKVKENLekrieSEGLEDYIGEVLVPTEEVVEVKNGKKKVKERKLFPGYVLVEMDMNDDTWHLVRNTP 80
antiterm_UpxY NF033644
UpxY family transcription antiterminator; The UpxY family of NusG-related transcription ...
 3-168 8.92e-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: 62.49  E-value: 8.92e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457   3 WYALFVESGKEETVQKFLrlqfDEQALYSIIPKKKVTERKAGIKYEALKKMFPGYVLFKTkmTERTFHKIK-ELPISCRI 81
Cdd:NF033644   1 WYALYTRPRREKKVAELL----EKKGIESFLPMQKEIRQWSDRKKRVEVPLIPNLVFVHI--TEKELDEVLeQTPGVVRY 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457  82 VnngaYYSKERKTYfTTIKDEEILPIIRLIGEGDTVdysKVYIENS-----KVTVASGPLKGMEGIIKKIdKRKRRAKIC 156
Cdd:NF033644  75 I----RDDRGKSKP-AIIPDKQMERFRLMLDPSDEV---VVYLEAPlkkgdKVRVIGGPLKGLEGELVRV-KGKKRVVVR 145

                        170
                 ....*....|..
gi 494650457 157 LSFMGLDKMVNV 168
Cdd:NF033644 146 IPGLGAVATVEV 157
NGN smart00738
In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold; In Spt5p, ...
 2-76 3.34e-10

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: 54.69  E-value: 3.34e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457     2 KWYALFVESGKEETVQKFLR-----LQFDEQALYSIIPKKKVTERKAGIKYEALKKMFPGYVLFKTKMTERTFHKIKELP 76
Cdd:smart00738   1 NWYAVRTTSGQEKRVAENLErkaeaLGLEDKIVSILVPTEEVKEIRRGKKKVVERKLFPGYIFVEADLEDEVWTAIRGTP 80
KOW_NusG cd06091
NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; KOW_NusG motif ...
 123-161 3.30e-08

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: 47.84  E-value: 3.30e-08
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 494650457 123 YIENSKVTVASGPLKGMEGIIKKIDKRKRRAKICLSFMG 161
Cdd:cd06091    4 FEVGDTVRIISGPFAGFEGKVEEIDEEKGKVKVLVEMFG 42
NGN_SP cd09886
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP); The ...
 2-58 6.41e-06

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: 42.74  E-value: 6.41e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 494650457   2 KWYALFVESGKEETVQKFLrlqfDEQALYSIIPKKKVTERKAGIKYEALKKMFPGYV 58
Cdd:cd09886    1 SWYALRTNPGCEQRAEEAL----EARGVEAFLPMLTEERKRRRKKFDVERPLFPGYV 53
NGN_Bact_2 cd09889
Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 2; The ...
 2-104 7.90e-05

Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 2; The N-Utilization Substance G (NusG) protein is involved in transcription elongation and termination. NusG is essential in Escherichia coli and associates with RNA polymerase elongation and Rho-termination. Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS biosynthesis genes. NusG SP family members are operon-specific transcriptional antitermination factors. The NusG N-terminal domain (NGN) is quite similar in all NusG orthologs, but its C-terminal domain and the linker that separates these two domains are different. The domain organization of NusG and its orthologs suggests that the common properties of NusG and its orthologs and paralogs are due to their similar NGN domains.


Pssm-ID: 193578 [Multi-domain]  Cd Length: 100  Bit Score: 40.00  E-value: 7.90e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457   2 KWYALFVESGKEETVQKFLRLQFDEQALYSI-IPKKKVTERKAGIKYEALKKMFPGYVLFKTKMTERTFHKIKELPISCR 80
Cdd:cd09889    1 MWYVVQVRTGREKAVLELLEKLVGPDVLQECfIPQYERKKRSQGVWRERKYTLFPGYVFVVTDDIDELYYELKRVPGFTR 80

                         90       100
                 ....*....|....*....|....
gi 494650457  81 IVNNGAyyskerktYFTTIKDEEI 104
Cdd:cd09889   81 LLGNDG--------SFFPLTPEEA 96
NGN_SP_UpxY cd09895
N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY; ...
 2-109 9.89e-04

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: 36.79  E-value: 9.89e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457   2 KWYALFVESGKEETVQKflrlQFDEQALYSIIPKKKVTERKAGIKYEALKKMFPGYVLFKTKMTERTFHKIKELPISCRI 81
Cdd:cd09895    1 PWYALYTFPRREKKVAE----YLEKKGIECFLPMQYEVRQWSGRKKRVEVPLFPNLVFVHITREELDEVLETPGVVRFVR 76

                         90       100
                 ....*....|....*....|....*...
gi 494650457  82 VNNGAYYskerktyftTIKDEEILPIIR 109
Cdd:cd09895   77 YRGKEPA---------IIPDKQMESFRL 95
NGN_plant cd09890
Plant N-Utilization Substance G (NusG) N-terminal (NGN) domain; The N-Utilization Substance G ...
 3-76 8.63e-03

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: 34.64  E-value: 8.63e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494650457   3 WYALFVESGKEETVQKFLRLQF-------DEQALYSIIPKKKVTerKAGIKYEALKKMFPGYVLFKTKMTERTFHKIKEL 75
Cdd:cd09890    2 WYMLRVPAGRENQAAEALERALatefpdrEFEVWVPSIPVDRKL--KNGSISVKEKPLFPGYVLLRCVLNKEVYDFIRDN 79


                 .
gi 494650457  76 P 76
Cdd:cd09890   80 D 80
 
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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