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Conserved domains on  [gi|82407773|pdb|2AHQ|A]
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Chain A, RNA polymerase sigma factor RpoN

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoN super family cl46833
DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]; ...
 1-75 1.87e-33

DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog is part of the Pathway/BioSystem: RNA polymerase


The actual alignment was detected with superfamily member COG1508:

Pssm-ID: 481173  Cd Length: 413  Bit Score: 117.87  E-value: 1.87e-33
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
2AHQ_A        1 TYSLRTFFVR----ESAEGLTQGELMKLIKEIVENEDKRKPYSDQEIANILKEKGFKVARRTVAKYREMLGIPSSRERR 75
Cdd:COG1508 333 IFELKYFFSSgvstDDGEEVSSTAIKALIKELIAAEDKKKPLSDQKIAELLKEQGINIARRTVAKYREQLGIPSSSQRK 411
 
Name Accession Description Interval E-value
RpoN COG1508
DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]; ...
 1-75 1.87e-33

DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441117  Cd Length: 413  Bit Score: 117.87  E-value: 1.87e-33
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
2AHQ_A        1 TYSLRTFFVR----ESAEGLTQGELMKLIKEIVENEDKRKPYSDQEIANILKEKGFKVARRTVAKYREMLGIPSSRERR 75
Cdd:COG1508 333 IFELKYFFSSgvstDDGEEVSSTAIKALIKELIAAEDKKKPLSDQKIAELLKEQGINIARRTVAKYREQLGIPSSSQRK 411
rpoN_sigma TIGR02395
RNA polymerase sigma-54 factor; A sigma factor is a DNA-binding protein protein that binds to ...
 1-75 4.59e-32

RNA polymerase sigma-54 factor; A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., ). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations [Transcription, Transcription factors]


Pssm-ID: 274109  Cd Length: 429  Bit Score: 114.31  E-value: 4.59e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2AHQ_A          1 TYSLRTFFVR----ESAEG-LTQGELMKLIKEIVENEDKRKPYSDQEIANILKEKGFKVARRTVAKYREMLGIPSSRERR 75
Cdd:TIGR02395 350 VFELKYFFSRgvstDSAEGeVSSTAIKALIKELIAAEDKRKPLSDQKIAELLKEKGIKIARRTVAKYREELGIPSSSKRK 429
Sigma54_DBD pfam04552
Sigma-54, DNA binding domain; This DNA binding domain is based on peptide fragmentation data. ...
 1-75 1.17e-30

Sigma-54, DNA binding domain; This DNA binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore this region contains a putative helix-turn-helix motif. At the C-terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins.


Pssm-ID: 428004 [Multi-domain]  Cd Length: 159  Bit Score: 105.04  E-value: 1.17e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
2AHQ_A          1 TYSLRTFFVRESAEGLTQGE----LMKLIKEIVENEDKRKPYSDQEIANILKEKGFKVARRTVAKYREMLGIPSSRERR 75
Cdd:pfam04552  80 TFELKYFFSSSVSTAGGGEAsataIRALIKKLIEAEDKAKPLSDDKIVELLKEQGIDIARRTVAKYREALNIPSSSQRR 158
PRK05932 PRK05932
RNA polymerase factor sigma-54; Reviewed
 24-75 1.27e-25

RNA polymerase factor sigma-54; Reviewed


Pssm-ID: 235648 [Multi-domain]  Cd Length: 455  Bit Score: 97.19  E-value: 1.27e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
2AHQ_A        24 LIKEIVENEDKRKPYSDQEIANILKEKGFKVARRTVAKYREMLGIPSSRERR 75
Cdd:PRK05932 402 LIKKLIAAENPKKPLSDSKIAELLKEQGIDVARRTVAKYREALNIPSSSQRK 453
 
Name Accession Description Interval E-value
RpoN COG1508
DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]; ...
 1-75 1.87e-33

DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441117  Cd Length: 413  Bit Score: 117.87  E-value: 1.87e-33
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
2AHQ_A        1 TYSLRTFFVR----ESAEGLTQGELMKLIKEIVENEDKRKPYSDQEIANILKEKGFKVARRTVAKYREMLGIPSSRERR 75
Cdd:COG1508 333 IFELKYFFSSgvstDDGEEVSSTAIKALIKELIAAEDKKKPLSDQKIAELLKEQGINIARRTVAKYREQLGIPSSSQRK 411
rpoN_sigma TIGR02395
RNA polymerase sigma-54 factor; A sigma factor is a DNA-binding protein protein that binds to ...
 1-75 4.59e-32

RNA polymerase sigma-54 factor; A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., ). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations [Transcription, Transcription factors]


Pssm-ID: 274109  Cd Length: 429  Bit Score: 114.31  E-value: 4.59e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2AHQ_A          1 TYSLRTFFVR----ESAEG-LTQGELMKLIKEIVENEDKRKPYSDQEIANILKEKGFKVARRTVAKYREMLGIPSSRERR 75
Cdd:TIGR02395 350 VFELKYFFSRgvstDSAEGeVSSTAIKALIKELIAAEDKRKPLSDQKIAELLKEKGIKIARRTVAKYREELGIPSSSKRK 429
Sigma54_DBD pfam04552
Sigma-54, DNA binding domain; This DNA binding domain is based on peptide fragmentation data. ...
 1-75 1.17e-30

Sigma-54, DNA binding domain; This DNA binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore this region contains a putative helix-turn-helix motif. At the C-terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins.


Pssm-ID: 428004 [Multi-domain]  Cd Length: 159  Bit Score: 105.04  E-value: 1.17e-30
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
2AHQ_A          1 TYSLRTFFVRESAEGLTQGE----LMKLIKEIVENEDKRKPYSDQEIANILKEKGFKVARRTVAKYREMLGIPSSRERR 75
Cdd:pfam04552  80 TFELKYFFSSSVSTAGGGEAsataIRALIKKLIEAEDKAKPLSDDKIVELLKEQGIDIARRTVAKYREALNIPSSSQRR 158
PRK05932 PRK05932
RNA polymerase factor sigma-54; Reviewed
 24-75 1.27e-25

RNA polymerase factor sigma-54; Reviewed


Pssm-ID: 235648 [Multi-domain]  Cd Length: 455  Bit Score: 97.19  E-value: 1.27e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
2AHQ_A        24 LIKEIVENEDKRKPYSDQEIANILKEKGFKVARRTVAKYREMLGIPSSRERR 75
Cdd:PRK05932 402 LIKKLIAAENPKKPLSDSKIAELLKEQGIDVARRTVAKYREALNIPSSSQRK 453
PRK12469 PRK12469
RNA polymerase factor sigma-54; Provisional
 1-75 6.73e-17

RNA polymerase factor sigma-54; Provisional


Pssm-ID: 237109  Cd Length: 481  Bit Score: 72.93  E-value: 6.73e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2AHQ_A         1 TYSLRTFFVREsAEGLTQGE-----LMKLIKEIVENEDKRKPYSDQEIANILKEKGFKVARRTVAKYREMLGIPSSRERR 75
Cdd:PRK12469 401 TFEFKHFFPRK-LEAAGGGEcsaaaVRALIKEMIAAEQAGDPLSDVALAEMLAGRGVLIARRTVAKYREAMKIPPAELRR 479
 
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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