NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|188090700|gb|ACD49584|]
View 

RNA polymerase sigma factor, partial [Xanthomonas sacchari]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 1000435)

sigma-70 family RNA polymerase sigma factor similar to RNA polymerase sigma factor RpoD/SigA, which is the primary sigma factor during exponential growth; preferentially transcribes genes associated with fast growth, such as ribosomal operons, other protein-synthesis related genes, rRNA- and tRNA-encoding genes and prfB

CATH:  1.10.601.10
Gene Ontology:  GO:0016987|GO:0006352|GO:0003700|GO:0003677|GO:0006355
SCOP:  4003741

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK05658 super family cl35358
RNA polymerase sigma factor RpoD; Validated
 1-286 6.82e-87

RNA polymerase sigma factor RpoD; Validated


The actual alignment was detected with superfamily member PRK05658:

Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 271.28  E-value: 6.82e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188090700   1 YAEVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLNDGNTGNrEVDDTAAEEAAAALTALDTEGGRTTDPV 80
Cdd:PRK05658  28 YAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEAPDADDLLLAENEADA-QTDEDAEEEAAAALSSVESEIGRTDDPV 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188090700  81 RMYMREMGTVELLTREGEIAIAKRIEEGLGQVQAALGAFPLAVETLLEDYEQHKEGKKRLAEIVVGFNDLIEEEPAPPVA 160
Cdd:PRK05658 107 RMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLENGERRLRELIDGFVDPNAEEDPAHVG 186

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188090700 161 vsdDDSATDADADEDDDEDVDTAEEDAGPTGPDPAEVARRMEVLATEYAKFKKAHAKNG----AEHKLVTKLRNDIAEVF 236
Cdd:PRK05658 187 ---SELEELDDDEDEEEEEDENDDSLAADESELPEKVLEKFKALAKQYKKLRKAQEKKVegrlAQHKKYAKLREKLKEEL 263

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 188090700 237 VTLKLPLPLTDVLVRKLRDTMAQVKDHERRVLHLAThVARVPRKDFIRSW 286
Cdd:PRK05658 264 KSLRLTSKQIDELVEQLRDINKRVRGQERELLRLVE-RLKMPRKDFLKLF 312
 
Name Accession Description Interval E-value
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 1-286 6.82e-87

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 271.28  E-value: 6.82e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188090700   1 YAEVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLNDGNTGNrEVDDTAAEEAAAALTALDTEGGRTTDPV 80
Cdd:PRK05658  28 YAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEAPDADDLLLAENEADA-QTDEDAEEEAAAALSSVESEIGRTDDPV 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188090700  81 RMYMREMGTVELLTREGEIAIAKRIEEGLGQVQAALGAFPLAVETLLEDYEQHKEGKKRLAEIVVGFNDLIEEEPAPPVA 160
Cdd:PRK05658 107 RMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLENGERRLRELIDGFVDPNAEEDPAHVG 186

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188090700 161 vsdDDSATDADADEDDDEDVDTAEEDAGPTGPDPAEVARRMEVLATEYAKFKKAHAKNG----AEHKLVTKLRNDIAEVF 236
Cdd:PRK05658 187 ---SELEELDDDEDEEEEEDENDDSLAADESELPEKVLEKFKALAKQYKKLRKAQEKKVegrlAQHKKYAKLREKLKEEL 263

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 188090700 237 VTLKLPLPLTDVLVRKLRDTMAQVKDHERRVLHLAThVARVPRKDFIRSW 286
Cdd:PRK05658 264 KSLRLTSKQIDELVEQLRDINKRVRGQERELLRLVE-RLKMPRKDFLKLF 312
Sigma70_ner pfam04546
Sigma-70, non-essential region; The domain is found in the primary vegetative sigma factor. ...
 120-286 1.29e-27

Sigma-70, non-essential region; The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function.


Pssm-ID: 461348  Cd Length: 169  Bit Score: 104.94  E-value: 1.29e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188090700  120 PLAVETLLEDYEQHKEGkkrlaeivvgfndliEEEpappvavsdddsatdadadedddeDVDTAEEDAGPTGPDPAEVAR 199
Cdd:pfam04546   1 PLTIAEILEWYDRVEAG---------------DDD------------------------DDDDSESLAADEGPDPEEALE 41

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188090700  200 RMEVLATEYAKFKKAHAKNGAEHKLVTKLRNDIAEVFVTLKLPLPLTDVLVRKLRDTMAQVKDHERRVLHLATHVARVPR 279
Cdd:pfam04546  42 RFEELREQYEKLRKAIEKHGRSSKKYLKLREELSEEFMQFRLVPKQFDRLVDQLREMVDRVRAQEREIMRLCVERAKMPR 121


                  ....*..
gi 188090700  280 KDFIRSW 286
Cdd:pfam04546 122 KDFIKSF 128
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 82-108 1.09e-03

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 39.65  E-value: 1.09e-03
                         10        20
                 ....*....|....*....|....*..
gi 188090700  82 MYMREMGTVELLTREGEIAIAKRIEEG 108
Cdd:COG0568    1 AYLREIGRVPLLTAEEEVELARRIQAG 27
 
Name Accession Description Interval E-value
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 1-286 6.82e-87

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 271.28  E-value: 6.82e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188090700   1 YAEVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLNDGNTGNrEVDDTAAEEAAAALTALDTEGGRTTDPV 80
Cdd:PRK05658  28 YAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEAPDADDLLLAENEADA-QTDEDAEEEAAAALSSVESEIGRTDDPV 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188090700  81 RMYMREMGTVELLTREGEIAIAKRIEEGLGQVQAALGAFPLAVETLLEDYEQHKEGKKRLAEIVVGFNDLIEEEPAPPVA 160
Cdd:PRK05658 107 RMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLENGERRLRELIDGFVDPNAEEDPAHVG 186

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188090700 161 vsdDDSATDADADEDDDEDVDTAEEDAGPTGPDPAEVARRMEVLATEYAKFKKAHAKNG----AEHKLVTKLRNDIAEVF 236
Cdd:PRK05658 187 ---SELEELDDDEDEEEEEDENDDSLAADESELPEKVLEKFKALAKQYKKLRKAQEKKVegrlAQHKKYAKLREKLKEEL 263

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 188090700 237 VTLKLPLPLTDVLVRKLRDTMAQVKDHERRVLHLAThVARVPRKDFIRSW 286
Cdd:PRK05658 264 KSLRLTSKQIDELVEQLRDINKRVRGQERELLRLVE-RLKMPRKDFLKLF 312
Sigma70_ner pfam04546
Sigma-70, non-essential region; The domain is found in the primary vegetative sigma factor. ...
 120-286 1.29e-27

Sigma-70, non-essential region; The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function.


Pssm-ID: 461348  Cd Length: 169  Bit Score: 104.94  E-value: 1.29e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188090700  120 PLAVETLLEDYEQHKEGkkrlaeivvgfndliEEEpappvavsdddsatdadadedddeDVDTAEEDAGPTGPDPAEVAR 199
Cdd:pfam04546   1 PLTIAEILEWYDRVEAG---------------DDD------------------------DDDDSESLAADEGPDPEEALE 41

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188090700  200 RMEVLATEYAKFKKAHAKNGAEHKLVTKLRNDIAEVFVTLKLPLPLTDVLVRKLRDTMAQVKDHERRVLHLATHVARVPR 279
Cdd:pfam04546  42 RFEELREQYEKLRKAIEKHGRSSKKYLKLREELSEEFMQFRLVPKQFDRLVDQLREMVDRVRAQEREIMRLCVERAKMPR 121


                  ....*..
gi 188090700  280 KDFIRSW 286
Cdd:pfam04546 122 KDFIKSF 128
Sigma70_r1_1 pfam03979
Sigma-70 factor, region 1.1; Region 1.1 modulates DNA binding by region 2 and 4 when sigma is ...
 1-48 2.00e-19

Sigma-70 factor, region 1.1; Region 1.1 modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase. Region 1.1 is also involved in promoter binding


Pssm-ID: 461117 [Multi-domain]  Cd Length: 69  Bit Score: 79.92  E-value: 2.00e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 188090700    1 YAEVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLNDGN 48
Cdd:pfam03979  18 YDEINDALPDDILDSEQIEDIIEMLNDMGIDVVEEAPDADELLLSDEA 65
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 1-153 6.52e-14

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 70.78  E-value: 6.52e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188090700   1 YAEVNDHLPDDLVDPEQIEDIIGMINGMGIDVHEVAPDAETLLLNDgntgnrevddtAAEEAAAALTALDTEGGRTTDPV 80
Cdd:PRK09210  30 YDEIAEKLIPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQVVE-----------EEEEEELDNDLSVPPGVKINDPV 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188090700  81 RMYMREMGTVELLTREGEIAIAKRIEEGlgqvqaalgafplavetlledyeqHKEGKKRLAE----IVVG---------- 146
Cdd:PRK09210  99 RMYLKEIGRVPLLTAEEEIELAKRIEEG------------------------DEEAKQRLAEanlrLVVSiakryvgrgm 154


                 ....*...
gi 188090700 147 -FNDLIEE 153
Cdd:PRK09210 155 lFLDLIQE 162
Sigma70_r1_2 pfam00140
Sigma-70 factor, region 1.2;
78-108 5.81e-10

Sigma-70 factor, region 1.2;


Pssm-ID: 425482 [Multi-domain]  Cd Length: 34  Bit Score: 53.47  E-value: 5.81e-10
                          10        20        30
                  ....*....|....*....|....*....|.
gi 188090700   78 DPVRMYMREMGTVELLTREGEIAIAKRIEEG 108
Cdd:pfam00140   1 DSVRLYLKEIGRIPLLTAEEEVELAKRIEAG 31
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 74-153 9.47e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 58.85  E-value: 9.47e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 188090700  74 GRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLGQVQAALGAFPLAVETLLEDYEQHKEGKK----------RLaei 143
Cdd:PRK05901 207 TATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEELLAEGEKLDPELRRDLQWIGRDGKRaknhlleanlRL--- 283

                         90       100
                 ....*....|....*....|.
gi 188090700 144 VV-----------GFNDLIEE 153
Cdd:PRK05901 284 VVslakrytnrglSFLDLIQE 304
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 76-106 3.27e-04

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 41.67  E-value: 3.27e-04
                         10        20        30
                 ....*....|....*....|....*....|.
gi 188090700  76 TTDPVRMYMREMGTVELLTREGEIAIAKRIE 106
Cdd:PRK07405   6 STDLVRTYLREIGRVPLLTHEEEILYGKQVQ 36
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 82-108 1.09e-03

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 39.65  E-value: 1.09e-03
                         10        20
                 ....*....|....*....|....*..
gi 188090700  82 MYMREMGTVELLTREGEIAIAKRIEEG 108
Cdd:COG0568    1 AYLREIGRVPLLTAEEEVELARRIQAG 27
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 74-145 1.14e-03

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 39.71  E-value: 1.14e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 188090700  74 GRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGlgqvqaalgafpLAVETLLEDYEQHKEGKKRLAEIVV 145
Cdd:PRK07921  22 SPAADLVRVYLNGIGKTALLTAADEVELAKRIEAG------------LYAEHLLETRKRLSEARKRDLAAVV 81
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 74-141 3.54e-03

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 38.70  E-value: 3.54e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 188090700  74 GRTTDPVRMYMREMGTVELLTREGEIAIAKRIEEGLGQVqaALGAFPLAVETLLEDYEQHKEGKKRLA 141
Cdd:PRK07598  56 RRSTDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLI--VLANAAKEGDEVIKPYLRLIEVRERLT 121
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 76-107 5.23e-03

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 37.90  E-value: 5.23e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 188090700  76 TTDPVRMYMREMGTVELLTREGEIAIAKRIEE 107
Cdd:PRK05949  16 SADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQ 47
 
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