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Conserved domains on  [gi|312445485|gb|ADQ81840|]
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RNA polymerase, sigma 70 subunit, RpoD subfamily [Riemerella anatipestifer ATCC 11845 = DSM 15868]

Protein Classification

RNA polymerase sigma factor RpoD/SigA( domain architecture ID 11426268)

RNA polymerase sigma factor RpoD/SigA is the primary sigma factor during exponential growth

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 21-287 1.61e-142

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: 401.35  E-value: 1.61e-142
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  21 YLQEIGKVDLITADEEVELAQKIRAGDKVALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGF 100
Cdd:COG0568    2 YLREIGRVPLLTAEEEVELARRIQAGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGF 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 101 KFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKINKAYAHLEQENERPPSPEELAEVLDMSEEDIKESMKNSGRHL 180
Cdd:COG0568   82 RFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPV 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 181 SMDAPLVEGEDSNLYDVLRSGESPSPDKELMLESLQIEIERALQTLTPREADLVRLYFGLNGKHPMTLEEIGETFDLTRE 260
Cdd:COG0568  162 SLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRE 241

                        250       260
                 ....*....|....*....|....*..
gi 312445485 261 RVRQIKEKAIKRLKHNSRSKILKSYLG 287
Cdd:COG0568  242 RVRQIEAKALRKLRHPLRSRKLRDYLD 268
 
Name Accession Description Interval E-value
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 21-287 1.61e-142

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: 401.35  E-value: 1.61e-142
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  21 YLQEIGKVDLITADEEVELAQKIRAGDKVALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGF 100
Cdd:COG0568    2 YLREIGRVPLLTAEEEVELARRIQAGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGF 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 101 KFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKINKAYAHLEQENERPPSPEELAEVLDMSEEDIKESMKNSGRHL 180
Cdd:COG0568   82 RFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPV 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 181 SMDAPLVEGEDSNLYDVLRSGESPSPDKELMLESLQIEIERALQTLTPREADLVRLYFGLNGKHPMTLEEIGETFDLTRE 260
Cdd:COG0568  162 SLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRE 241

                        250       260
                 ....*....|....*....|....*..
gi 312445485 261 RVRQIKEKAIKRLKHNSRSKILKSYLG 287
Cdd:COG0568  242 RVRQIEAKALRKLRHPLRSRKLRDYLD 268
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 21-286 3.21e-91

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 274.94  E-value: 3.21e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  21 YLQEIGKVDLITADEEVELAQKIRAGDKVALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGF 100
Cdd:PRK09210 101 YLKEIGRVPLLTAEEEIELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGF 180

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 101 KFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKINKAYAHLEQENERPPSPEELAEVLDMSEEDIKESMKNSGRHL 180
Cdd:PRK09210 181 KFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPV 260

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 181 SMDAPLVEGEDSNLYDVLRSGESPSPDKELMLESLQIEIERALQTLTPREADLVRLYFGLNGKHPMTLEEIGETFDLTRE 260
Cdd:PRK09210 261 SLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRE 340

                        250       260
                 ....*....|....*....|....*.
gi 312445485 261 RVRQIKEKAIKRLKHNSRSKILKSYL 286
Cdd:PRK09210 341 RIRQIEAKALRKLRHPSRSKQLKDFL 366
rpoH_proteo TIGR02392
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ...
 16-274 3.87e-48

alternative sigma factor RpoH; 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 RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors. [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]


Pssm-ID: 274107 [Multi-domain]  Cd Length: 270  Bit Score: 161.29  E-value: 3.87e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485   16 ASLDKYLQEIGKVDLITADEEVELAQKIR-AGDKVALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRY 94
Cdd:TIGR02392   1 GSLDAYIRAVNRIPMLTPEEEYQLAKRLReHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485   95 DETRGFKFISYAVWWIRQSILQALAEQSRIVrlplnKIGSINKINKAYAHLEQENERPP---SPEE---LAEVLDMSEED 168
Cdd:TIGR02392  81 DPERGVRLVSFAVHWIKAEIHEYILRNWRLV-----KVATTKAQRKLFFNLRKMKKRLQgwlNPEEveaIAEELGVSERE 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  169 IKEsMKN--SGRHLSMDAPLVEGEDSN--LYDVLrsgESPSPDKELMLESLQIE------IERALQTLTPREADLVRLYF 238
Cdd:TIGR02392 156 VRE-MESrlSGQDMSLNASIDDDEDDGgaPIAYL---VDKRSDPEDTLEEEQWEelqrqaLANALGSLDARSRRIIEARW 231

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 312445485  239 gLNGKhPMTLEEIGETFDLTRERVRQIKEKAIKRLK 274
Cdd:TIGR02392 232 -LDDD-KLTLQELAAEYGVSAERIRQIEKNAMKKLK 265
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 54-124 2.30e-17

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 74.55  E-value: 2.30e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 312445485   54 LIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQSRI 124
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 216-274 1.62e-09

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 52.88  E-value: 1.62e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 312445485 216 QIEIERALQTLTPREADLVRLYFGlngkHPMTLEEIGETFDLTRERVRQIKEKAIKRLK 274
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 21-287 1.61e-142

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: 401.35  E-value: 1.61e-142
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  21 YLQEIGKVDLITADEEVELAQKIRAGDKVALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGF 100
Cdd:COG0568    2 YLREIGRVPLLTAEEEVELARRIQAGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGF 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 101 KFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKINKAYAHLEQENERPPSPEELAEVLDMSEEDIKESMKNSGRHL 180
Cdd:COG0568   82 RFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPV 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 181 SMDAPLVEGEDSNLYDVLRSGESPSPDKELMLESLQIEIERALQTLTPREADLVRLYFGLNGKHPMTLEEIGETFDLTRE 260
Cdd:COG0568  162 SLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRE 241

                        250       260
                 ....*....|....*....|....*..
gi 312445485 261 RVRQIKEKAIKRLKHNSRSKILKSYLG 287
Cdd:COG0568  242 RVRQIEAKALRKLRHPLRSRKLRDYLD 268
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 21-286 3.21e-91

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 274.94  E-value: 3.21e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  21 YLQEIGKVDLITADEEVELAQKIRAGDKVALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGF 100
Cdd:PRK09210 101 YLKEIGRVPLLTAEEEIELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGF 180

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 101 KFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKINKAYAHLEQENERPPSPEELAEVLDMSEEDIKESMKNSGRHL 180
Cdd:PRK09210 181 KFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPV 260

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 181 SMDAPLVEGEDSNLYDVLRSGESPSPDKELMLESLQIEIERALQTLTPREADLVRLYFGLNGKHPMTLEEIGETFDLTRE 260
Cdd:PRK09210 261 SLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRE 340

                        250       260
                 ....*....|....*....|....*.
gi 312445485 261 RVRQIKEKAIKRLKHNSRSKILKSYL 286
Cdd:PRK09210 341 RIRQIEAKALRKLRHPSRSKQLKDFL 366
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 8-286 5.41e-89

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 273.79  E-value: 5.41e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485   8 KQVTNRETASLDK---YLQEIGKVDLITADEEVELAQKIRAG---------------------------DKVALEKLIKA 57
Cdd:PRK05901 200 ARKDAKLTATADPvkaYLKQIGKVKLLNAEEEVELAKRIEAGlyaeellaegekldpelrrdlqwigrdGKRAKNHLLEA 279

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  58 NLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINK 137
Cdd:PRK05901 280 NLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETINK 359

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 138 INKAYAHLEQENERPPSPEELAEVLDMSEEDIKEsMKNSGRH-LSMDAPLVEGEDSNLYDVLRSGESPSPDKELMLESLQ 216
Cdd:PRK05901 360 LGRIERELLQELGREPTPEELAKEMGFTPEKVRE-IQKYNREpISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFTLLQ 438

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 217 IEIERALQTLTPREADLVRLYFGLNGKHPMTLEEIGETFDLTRERVRQIKEKAIKRLKHNSRSKILKSYL 286
Cdd:PRK05901 439 DQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFL 508
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 21-286 1.41e-80

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 247.77  E-value: 1.41e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  21 YLQEIGKVDLITADEEVELAQKI-------RAGDKV---------------------------------ALEKLIKANLR 60
Cdd:PRK07406  68 YLQEIGRIRLLRPDEEIELARKIadlleleELREQFeselgrepsdkewaelvdmplpkfrrrlmlgrrAKEKMVQSNLR 147

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  61 FVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKINK 140
Cdd:PRK07406 148 LVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKK 227

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 141 AYAHLEQENERPPSPEELAEVLDMSEEDIKESMKNSGRHLSMDAPLVEGEDSNLYDVLRS-GESPSPD--KELMLESLqi 217
Cdd:PRK07406 228 TTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEAdGETPEDDvaKNLLREDL-- 305

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 312445485 218 eiERALQTLTPREADLVRLYFGLNGKHPMTLEEIGETFDLTRERVRQIKEKAIKRLKHNSRSKILKSYL 286
Cdd:PRK07406 306 --EGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 372
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 21-285 6.81e-75

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 231.93  E-value: 6.81e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  21 YLQEIGKVDLITADEEVELAQKIRAG---------------------------DKVALEKLIKANLRFVVSVSKQYQNQG 73
Cdd:PRK07921  31 YLNGIGKTALLTAADEVELAKRIEAGlyaehlletrkrlsearkrdlaavvrdGEAARRHLLEANLRLVVSLAKRYTGRG 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  74 LSLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKINKAYAHLEQENERPP 153
Cdd:PRK07921 111 MPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQLGREA 190

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 154 SPEELAEVLDMSEEDIKESMKNSGRHLSMDAPLVEGEDSNLYDVLRSGESPSPDKELMLESLQIEIERALQTLTPREADL 233
Cdd:PRK07921 191 TDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLATLDEREQQV 270

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 312445485 234 VRLYFGLNGKHPMTLEEIGETFDLTRERVRQIKEKAIKRLKHNSRSKILKSY 285
Cdd:PRK07921 271 IRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSY 322
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 21-274 1.74e-73

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 228.30  E-value: 1.74e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  21 YLQEIGKVDLITADEEVELAQKIRAGDKVALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGF 100
Cdd:PRK05657  58 YLNEIGYSPLLTAEEEVYFARRALRGDFAARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGF 137

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 101 KFISYAVWWIRQSILQALAEQSRIVRLPLNKIGSINKINKAYAHLEQENERPPSPEELAEVLDMSEEDIKESMKNSGRHL 180
Cdd:PRK05657 138 RFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERIT 217

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 181 SMDAPLVEGEDSNLYDVLRSGESPSPDKELMLESLQIEIERALQTLTPREADLVRLYFGLNGKHPMTLEEIGETFDLTRE 260
Cdd:PRK05657 218 SLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRE 297

                        250
                 ....*....|....
gi 312445485 261 RVRQIKEKAIKRLK 274
Cdd:PRK05657 298 RVRQIQVEALRRLR 311
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 38-286 9.01e-70

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 226.60  E-value: 9.01e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  38 ELAQKIRAGDKVALE---KLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSI 114
Cdd:PRK05658 366 EINRQISKGEAKARRakkEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 445

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 115 LQALAEQSRIVRLPLNKIGSINKINKAYAHLEQENERPPSPEELAEVLDMSEEDIKESMKNSGRHLSMDAPLVEGEDSNL 194
Cdd:PRK05658 446 TRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHL 525

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 195 YDVLRSGESPSPDKELMLESLQIEIERALQTLTPREADLVRLYFGLNGKHPMTLEEIGETFDLTRERVRQIKEKAIKRLK 274
Cdd:PRK05658 526 GDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605

                        250
                 ....*....|..
gi 312445485 275 HNSRSKILKSYL 286
Cdd:PRK05658 606 HPSRSRKLRSFL 617
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 38-286 1.13e-69

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 221.28  E-value: 1.13e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  38 ELAQKIRAGDKvALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQA 117
Cdd:PRK07598 165 ELEQIQKQGLR-AKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRA 243

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 118 LAEQSRIVRLPLNKIGSINKINKAYAHLEQENERPPSPEELAEVLDMSEEDIKESMKNSGRHLSMDAPLVEGEDSNLYDV 197
Cdd:PRK07598 244 IATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDL 323

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 198 LRSgESPSPDKELMLESLQIEIERALQTLTPREADLVRLYFGLNGKHPMTLEEIGETFDLTRERVRQIKEKAIKRLKHNS 277
Cdd:PRK07598 324 LET-DDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQPK 402


                 ....*....
gi 312445485 278 RSKILKSYL 286
Cdd:PRK07598 403 RRNRIRDYL 411
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 7-286 7.52e-57

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 185.43  E-value: 7.52e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485   7 TKQVTNRETASLD---KYLQEIGKVDLITADEEV-----------------------------------------ELAQK 42
Cdd:PRK05949   6 TNTKTKQPTFSADmvrTYLHEIGRVPLLTHEQEIvygkqvqqmmslleakealakklgrepslpewaeavnlsetELKQT 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  43 IRAGDKvALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQS 122
Cdd:PRK05949  86 LKQGKR-AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQA 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 123 RIVRLPLNKIGSINKINKAYAHLEQENERPPSPEELAEVLDMSEEDIKESMKNSGRHLSMDAPLVEGEDSNLYDVLRSgE 202
Cdd:PRK05949 165 RTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLED-E 243

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 203 SPSPDKELMLESLQIEIERALQTLTPREADLVRLYFGLNGKHPMTLEEIGETFDLTRERVRQIKEKAIKRLKHnsRSKIL 282
Cdd:PRK05949 244 GPSPDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR--RRANV 321


                 ....
gi 312445485 283 KSYL 286
Cdd:PRK05949 322 KEYL 325
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 35-274 2.78e-55

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 181.11  E-value: 2.78e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  35 EEVELAQKIRAGDkVALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSI 114
Cdd:PRK07405  68 SEEELRSAIAEGE-AAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAI 146

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 115 LQALAEQSRIVRLPLNKIGSINKINKAYAHLEQENERPPSPEELAEVLDMSEEDIKESMKNSGRHLSMDAPLVEGEDSNL 194
Cdd:PRK07405 147 TRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTEL 226

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 195 YDVLRSgESPSPDKELMLESLQIEIERALQTLTPREADLVRLYFGLNGKHPMTLEEIGETFDLTRERVRQIKEKAIKRLK 274
Cdd:PRK07405 227 GELLED-TGASPEDFATQSSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLR 305
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 35-274 2.21e-48

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


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 160.76  E-value: 2.21e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  35 EEVELAQKIRAGDKVALEKLIKANLRFVVSVSKQYQNQGLS-LPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQS 113
Cdd:COG1191    1 DLEELLRRYQEGDEEAREELIEEYLPLVKKIASRLAGRLPAeLDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 114 ILQALAEQ---SRIVRLplnkigSINKINKAYAHLEQENERPPSPEELAEVLDMSEEDIKESMK--NSGRHLSMDAPLVE 188
Cdd:COG1191   81 ILDYLRDEdwvPRSVRE------LARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEaaNAYQLLSLDEPLED 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 189 GEDsnLYDVLrsgESPSPDKELMLESLQIEIERALQTLTPREADLVRLYFglngKHPMTLEEIGETFDLTRERVRQIKEK 268
Cdd:COG1191  155 GDD--LLDLL---ESGDPEEELEHEELREALAEAIEQLPERERLVLSLYY----FEELTLKEIAEVLGVSESRVSRLHKK 225


                 ....*.
gi 312445485 269 AIKRLK 274
Cdd:COG1191  226 ALARLR 231
rpoH_proteo TIGR02392
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ...
 16-274 3.87e-48

alternative sigma factor RpoH; 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 RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors. [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]


Pssm-ID: 274107 [Multi-domain]  Cd Length: 270  Bit Score: 161.29  E-value: 3.87e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485   16 ASLDKYLQEIGKVDLITADEEVELAQKIR-AGDKVALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRY 94
Cdd:TIGR02392   1 GSLDAYIRAVNRIPMLTPEEEYQLAKRLReHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485   95 DETRGFKFISYAVWWIRQSILQALAEQSRIVrlplnKIGSINKINKAYAHLEQENERPP---SPEE---LAEVLDMSEED 168
Cdd:TIGR02392  81 DPERGVRLVSFAVHWIKAEIHEYILRNWRLV-----KVATTKAQRKLFFNLRKMKKRLQgwlNPEEveaIAEELGVSERE 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  169 IKEsMKN--SGRHLSMDAPLVEGEDSN--LYDVLrsgESPSPDKELMLESLQIE------IERALQTLTPREADLVRLYF 238
Cdd:TIGR02392 156 VRE-MESrlSGQDMSLNASIDDDEDDGgaPIAYL---VDKRSDPEDTLEEEQWEelqrqaLANALGSLDARSRRIIEARW 231

                         250       260       270
                  ....*....|....*....|....*....|....*.
gi 312445485  239 gLNGKhPMTLEEIGETFDLTRERVRQIKEKAIKRLK 274
Cdd:TIGR02392 232 -LDDD-KLTLQELAAEYGVSAERIRQIEKNAMKKLK 265
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 16-274 4.64e-46

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 156.49  E-value: 4.64e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  16 ASLDKYLQEIGKVDLITADEEVELAQKIRA-GDKVALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRY 94
Cdd:PRK06596  14 GNLDAYIQAVNKIPMLTAEEEYMLAKRLREhGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRF 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  95 DETRGFKFISYAVWWIRQSILQALAEQSRIVrlplnKIG----------SINKINKAYAHLEQENerppsPEELAEVLDM 164
Cdd:PRK06596  94 DPEVGVRLVSFAVHWIKAEIHEYILRNWRIV-----KVAttkaqrklffNLRKAKKRLGWLNPEE-----VEMVAEELGV 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 165 SEEDIKEsMKN--SGRHLSMDAPLV--EGEDSNLYDVLrsgESPSPDKELMLESLQIE------IERALQTLTPREADLV 234
Cdd:PRK06596 164 SEEEVRE-MESrlSGQDASLDAPIDddDEESGAPQDYL---EDKSSDPADVLEEDNWEdqrralLADALEGLDERSRDII 239

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 312445485 235 ---RLyfglnGKHPMTLEEIGETFDLTRERVRQIKEKAIKRLK 274
Cdd:PRK06596 240 earWL-----DDDKSTLQELAAEYGVSAERVRQIEKNAMKKLK 277
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 75-274 2.75e-38

RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.


Pssm-ID: 274153 [Multi-domain]  Cd Length: 224  Bit Score: 134.32  E-value: 2.75e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485   75 SLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKigsINKINKAYAHLEQENERPPS 154
Cdd:TIGR02479  25 ELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLDWVPRSLRQK---ARKLERAIRELEARLGREPT 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  155 PEELAEVLDMSEEDIKESMK--NSGRHLSMDAPLVEGEDS-NLYDVLRSGESPSPDKELMLESLQIEIERALQTLTPREA 231
Cdd:TIGR02479 102 EEEIAEELGMDLKEYRQALNeiNALSLVSLDELLESGDDGgSLIDRIEDDKSEDPEEELEREELREALAEAIESLSEREQ 181

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 312445485  232 DLVRLYFglngKHPMTLEEIGETFDLTRERVRQIKEKAIKRLK 274
Cdd:TIGR02479 182 LVLSLYY----YEELNLKEIGEVLGLTESRVSQIHSQALKKLR 220
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 27-274 6.14e-36

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 130.16  E-value: 6.14e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  27 KVDLITADEEVELAQKIR-AGDKVALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGFKFISY 105
Cdd:PRK07500  17 KAPYLEREEEHALAYRWKdHRDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTY 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 106 AVWWIRQSILQALAEQSRIVRlplnkiGSINKINKAY--------AHLEQENERPPSPE---ELAEVLDMSEEDIkESMK 174
Cdd:PRK07500  97 ATWWIRASIQDYILRNWSIVR------GGTSSAQKALffnlrrlrARLAQADEELTKQEihrEIATALGVSLSDV-EMMD 169

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 175 N--SGRHLSMDAPLVEGED--SNLYDVLRSgESPSPDkELMLESLQIEIER-----ALQTLTPREADLVRLYfGLNgKHP 245
Cdd:PRK07500 170 ArlSGPDASLNAPQSEEDEgrSERMDFLVD-DSPLPD-EQVESSIDGERRRrwltqALQTLNERELRIIRER-RLR-EDG 245

                        250       260
                 ....*....|....*....|....*....
gi 312445485 246 MTLEEIGETFDLTRERVRQIKEKAIKRLK 274
Cdd:PRK07500 246 ATLEALGEELGISKERVRQIEARALEKLR 274
SigBFG TIGR02980
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
 47-274 2.17e-33

RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.


Pssm-ID: 274373 [Multi-domain]  Cd Length: 227  Bit Score: 121.56  E-value: 2.17e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485   47 DKVALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQSRIVR 126
Cdd:TIGR02980   1 DKEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  127 LP--LNKIGsiNKINKAYAHLEQENERPPSPEELAEVLDMSEEDIKESM--KNSGRHLSMDAPLVEGEDSNLYdVLRSGE 202
Cdd:TIGR02980  81 VPrrLKELG--VKINKATEELTQRLGRSPTIAEIAERLGVSEEEVVEALeaGNAYQALSLDASIEDDDGDPIA-LLDTLG 157

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 312445485  203 SPSPDKELMLEslQIEIERALQTLTPREADLVRLYFGLNgkhpMTLEEIGETFDLTRERVRQIKEKAIKRLK 274
Cdd:TIGR02980 158 DEDDALETVED--RLALKPLLAALPERERRILLLRFFED----KTQSEIAERLGISQMHVSRLLRRALKKLR 223
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 74-274 4.39e-28

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 108.01  E-value: 4.39e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  74 LSLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQ---SRIVRLplnkigSINKINKAYAHLEQENE 150
Cdd:PRK06986  36 VDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLdwvPRSVRR------NAREVAQAIRQLEQELG 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 151 RPPSPEELAEVLDMSEEDIKESMK--NSGRHLSMDAPLVEGEDSNLYDVLRSGESPSpdKELMLESLQIEIERALQTLTP 228
Cdd:PRK06986 110 REPTDTEVAEKLGLSLEEYREMLLdtNISQLFSIDELRGEHGDSILVTEDHQDEDPL--QQLEDEELREALVEAIESLPE 187

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 312445485 229 READLVRLYFglngKHPMTLEEIGETFDLTRERVRQIKEKAIKRLK 274
Cdd:PRK06986 188 REQLVLSLYY----QEELNLKEIGAVLGVSESRVSQIHSQAIKRLR 229
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
47-275 3.18e-26

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 103.59  E-value: 3.18e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  47 DKVALEKLIKanlRFVVSVSKQYQNQGLSLP------DLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAE 120
Cdd:PRK07670  20 DPDAADELIR---RYMPLVHYHVQRISVGLPksvskdDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRK 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 121 QSRIVRLPLNKIgsiNKINKAYAHLEQENERPPSPEELAEVLDMSEEDIKESMKNS--GRHLSMDAPLVEGEDSNLYDV- 197
Cdd:PRK07670  97 EDWLPRSMREKT---KKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGffANLLSIDEKTHDQDDGENVSVt 173

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 312445485 198 LRSGESPSPDKELMLESLQIEIERALQTLTPREADLVRLYFglngKHPMTLEEIGETFDLTRERVRQIKEKAIKRLKH 275
Cdd:PRK07670 174 IRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFY----KEELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
27-274 1.35e-21

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 91.16  E-value: 1.35e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  27 KVDLITADEEVELAQKIRAGDKVALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGFKFISYA 106
Cdd:PRK08215  15 KLPVLKNEEMRELFERMQNGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYA 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 107 VWWIRQSILQALAEQSRI-VRLPLNKIGSinKINKAYAHLEQENERPPSPEELAEVLDMSEEDIKESMKNSGRHLSMDAP 185
Cdd:PRK08215  95 VPMIIGEIRRYLRDNNPIrVSRSLRDIAY--KALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEP 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 186 LVEGEDSNLYDVLRSGESPSPDkELMLEslQIEIERALQTLTPREADLVRLYFgLNGKHPMTL-EEIGetfdLTRERVRQ 264
Cdd:PRK08215 173 IYHDGGDPIYVMDQISDEKNKD-ENWLE--EIALKEAMKKLNDREKLILNLRF-FQGKTQMEVaEEIG----ISQAQVSR 244

                        250
                 ....*....|
gi 312445485 265 IKEKAIKRLK 274
Cdd:PRK08215 245 LEKAALKHMR 254
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 78-274 1.59e-21

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 91.29  E-value: 1.59e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  78 DLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSI---LQALAEQSRIVRLplnkigSINKINKAYAHLEQENERPPS 154
Cdd:PRK06288  63 DLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIfdeLRSIDWIPRSVRQ------KARQIERAIAMLEARLGRTPS 136

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 155 PEELAEVLDMSEEDIKESM-KNSGRHL-SMDAPLVEGEDSN---LYDVLRSGESPSPDKELMLESLQIEIERALQTLTPR 229
Cdd:PRK06288 137 DEEIADELGISLEEYNSLLsKLSGTSVvSLNDLWFGGDEGDevsLMDTLESPAALNPDEIAEREEIKRVIVEAIKTLPER 216

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 312445485 230 EADLVRLYFglngKHPMTLEEIGETFDLTRERVRQIKEKAIKRLK 274
Cdd:PRK06288 217 EKKVLILYY----YEDLTLKEIGKVLGVTESRISQLHTKAVLQLR 257
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 46-274 5.16e-21

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 89.75  E-value: 5.16e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  46 GDKVALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQSRIV 125
Cdd:PRK08583  26 QDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSV 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 126 RLP--LNKIGSinKINKAYAHLEQENERPPSPEELAEVLDMSEEDIKESM--KNSGRHLSMDAPL---VEGEDSNLYDVL 198
Cdd:PRK08583 106 HVPrrIKELGP--KIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMemGKSYQALSVDHSIeadSDGSTVTLLDIV 183

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 312445485 199 RSGES--PSPDKELMLeslqieiERALQTLTPREADLVRLYFGLNgkhpMTLEEIGETFDLTRERVRQIKEKAIKRLK 274
Cdd:PRK08583 184 GQQEDgyELTEQRMIL-------EKILPVLSDREKSIIQCTFIEN----LSQKETGERLGISQMHVSRLQRQAIKKLR 250
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 54-124 2.30e-17

Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 74.55  E-value: 2.30e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 312445485   54 LIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQSRI 124
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
34-169 5.64e-17

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 78.47  E-value: 5.64e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  34 DEEV-ELAQKIRAGDKVALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQ 112
Cdd:PRK05572  16 DEENkELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIG 95

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 312445485 113 SILQALAEQSRI-VRLPLNKIGsiNKINKAYAHLEQENERPPSPEELAEVLDMSEEDI 169
Cdd:PRK05572  96 EIQRFLRDDGTVkVSRSLKETA--NKIRKDKDELSKELGREPTIEELAEYLGVTPEEV 151
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
32-275 6.14e-17

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 78.06  E-value: 6.14e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  32 TADEEVELAQKIRAGDKVALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIR 111
Cdd:PRK05803  32 SEEEERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIE 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 112 QSILQALaeqsrivrlplnkigsinkinkayahleqenerppspeelaevldmseedikESMKNSGRHLSMDAPL---VE 188
Cdd:PRK05803 112 NEILMHL----------------------------------------------------RNLKKTKKEVSLQDPIgvdKE 139

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 189 GEDSNLYDVLRSGESPSPDK-ELMLEslQIEIERALQTLTPREADLVRLYFGLNGKHPMTLEEIGETFDLTRERVRQIKE 267
Cdd:PRK05803 140 GNEISLIDILGSEEDDVIEQvELKME--VEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEK 217


                 ....*...
gi 312445485 268 KAIKRLKH 275
Cdd:PRK05803 218 RALKKLFK 225
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 135-207 1.40e-16

Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.


Pssm-ID: 427997 [Multi-domain]  Cd Length: 78  Bit Score: 72.64  E-value: 1.40e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 312445485  135 INKINKAYAHLEQENERPPSPEELAEVLDMSEEDIKESMKNSGRHLSMDAPLVEGEDSNLYDVLRSGESPSPD 207
Cdd:pfam04539   3 LNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPE 75
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 53-282 2.09e-16

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 76.88  E-value: 2.09e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  53 KLIKANLRFVVSVSKQYQNQ-GLSLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNK 131
Cdd:PRK07408  29 QLVELNLGLVRKEAHRWSNQcSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRW 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 132 IGSINKINKAYAHLEQENERPPSPEELAEVLDMSEEDIKEsMKNSGRH---LSMDAPLVEGEDSN--LYDVLRSGESPSp 206
Cdd:PRK07408 109 QELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQE-IKLALQNrtpLSLDAPVNQDEDGStsLGDLLPDPRYRS- 186

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 312445485 207 dKELMLESlQIEIERALQTLTPREADLVRLYFglngKHPMTLEEIGETFDLTRERV-RQIKeKAIKRLKHNSRSKIL 282
Cdd:PRK07408 187 -FQLAQED-RIRLQQALAQLEERTREVLEFVF----LHDLTQKEAAERLGISPVTVsRRVK-KGLDQLKKLLQPEDD 256
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 50-274 1.07e-15

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 72.77  E-value: 1.07e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485   50 ALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGFKfiSYAVWWIRqsilqalaeqsrivrlpl 129
Cdd:TIGR02937   2 AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFK--AWLFRIAR------------------ 61

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  130 nkigsinkiNKAYAHLEQENERPPSPEELAEVLDmseedikesmknsgrhlsmdaplvegedsnlydvlrsgESPSPDKE 209
Cdd:TIGR02937  62 ---------NLILDYLRRKRRLRRELDLLEELLD--------------------------------------SDPSPEEE 94

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 312445485  210 LMLESLQIEIERALQTLTPREADLVRLYFGlngkHPMTLEEIGETFDLTRERVRQIKEKAIKRLK 274
Cdd:TIGR02937  95 LEQEEEREALREALEKLPEREREVLVLRYL----EGLSYKEIAEILGISVGTVKRRLKRARKKLR 155
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 52-274 3.66e-15

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 73.66  E-value: 3.66e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  52 EKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPlNK 131
Cdd:PRK07122  43 DRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP-RR 121

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 132 IGSIN-KINKAYAHLEQENERPPSPEELAEVLDMSEEDIKESM--KNSGRHLSMDAPLVEGEDSNLYDVLRSGespspDK 208
Cdd:PRK07122 122 LKELHlRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLvaGSAYNTLSIDSGGGSGDDDARAIADTLG-----DV 196

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 209 ELMLEslQIEIERAL----QTLTPREADLVRLYFGLNgkhpMTLEEIGETFDLTRERVRQIKEKAIKRLK 274
Cdd:PRK07122 197 DAGLD--QIENREALrpllAALPERERTVLVLRFFES----MTQTQIAERVGISQMHVSRLLAKTLARLR 260
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 222-275 6.61e-13

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 62.06  E-value: 6.61e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 312445485  222 ALQTLTPREADLVRLYFGlngkHPMTLEEIGETFDLTRERVRQIKEKAIKRLKH 275
Cdd:pfam04545   1 ALASLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
32-274 2.51e-12

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 64.88  E-value: 2.51e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  32 TADEEVELAQKIRAGDKVALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIR 111
Cdd:PRK08301  35 SKEEEEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIE 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 112 QSILQALAEQSRIvrlplnkigsinkinkayahleqenerppspeeLAEVldmseedikesmknsgrhlSMDAPLVEGED 191
Cdd:PRK08301 115 NEILMYLRRNNKV---------------------------------KAEV-------------------SFDEPLNIDWD 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 192 SN---LYDVLRSgespspDKELMLESLQIEIER-----ALQTLTPREADLVRLYFGLNGKHPMTLEEIGETFDLTRERVR 263
Cdd:PRK08301 143 GNellLSDVLGT------DNDIIYKDIEDEVDRkllkkALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYIS 216

                        250
                 ....*....|.
gi 312445485 264 QIKEKAIKRLK 274
Cdd:PRK08301 217 RLEKRIIKRLK 227
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 78-274 1.22e-10

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 60.40  E-value: 1.22e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  78 DLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNKigsINKINKAYAHLEQENERPPSPEE 157
Cdd:PRK05911  55 DLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQDWVPRSVHQK---ANKLADAMDSLRQSLGKEPTDGE 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 158 LAEVLDMSEEDIKESMKNSGRHLSM----DAPLVEGEDSNL--------------YDVLRSGESPSPdkelmleslqieI 219
Cdd:PRK05911 132 LCEYLNISQQELSGWFSSARPALILslneEFPCQSDDEAGLaleeriaderaetgYDVVDKKEFSSI------------L 199

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 312445485 220 ERALQTLTPREADLVRLYFglngKHPMTLEEIGETFDLTRERVRQIKEKAIKRLK 274
Cdd:PRK05911 200 AEAILALEEKERKVMALYY----YEELVLKEIGKILGVSESRVSQIHSKALLKLR 250
Sigma70_r1_2 pfam00140
Sigma-70 factor, region 1.2;
17-48 2.52e-10

Sigma-70 factor, region 1.2;


Pssm-ID: 425482 [Multi-domain]  Cd Length: 34  Bit Score: 54.62  E-value: 2.52e-10
                          10        20        30
                  ....*....|....*....|....*....|..
gi 312445485   17 SLDKYLQEIGKVDLITADEEVELAQKIRAGDK 48
Cdd:pfam00140   2 SVRLYLKEIGRIPLLTAEEEVELAKRIEAGDE 33
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
27-181 3.03e-10

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 58.77  E-value: 3.03e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  27 KVDLITADEEVELAQkirAGDKVALEKLIKANLRFVVSVSKQYQNQGLSLPDLINEGNLGLMKAAKRYDETRGFKFISYA 106
Cdd:PRK08295   5 DYDELEDEELVELAR---SGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFA 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 107 VWWIRQSILQALAEQSRIVRLPLNKIGSINKINkayahLEQENER------PPSPEELAEVLDMSEEDIKESMKNSGRHL 180
Cdd:PRK08295  82 ELCITRQIITAIKTANRQKHIPLNSYVSLDKPI-----YDEESDRtlldviSEAKVTDPEELIISKEELEDIEEKIEELL 156


                 .
gi 312445485 181 S 181
Cdd:PRK08295 157 S 157
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 216-274 1.62e-09

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 52.88  E-value: 1.62e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 312445485 216 QIEIERALQTLTPREADLVRLYFGlngkHPMTLEEIGETFDLTRERVRQIKEKAIKRLK 274
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 35-274 5.38e-08

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 51.53  E-value: 5.38e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  35 EEVELAQKIRAGDKVALEKLIKANLRFVVSVSKQY-QNQGLSLpDLINEGNLGLMKAAKRYDETRGFKFisyavwWIRqs 113
Cdd:COG1595    3 SDEELLERLRAGDEAAFEELYERYRPRLYRYARRLlGDRADAE-DLVQETFLRLWRKLDSFRGRGSFRA------WLY-- 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 114 ilqalaeqsRIVRlplnkigsinkiNKAYAHLEQENERPPSPEELAEVLDmseedikesmknsgrhlsmdaplvegedsn 193
Cdd:COG1595   74 ---------RIAR------------NLAIDHLRKRRRRRELLDELAEELP------------------------------ 102

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 194 lydvlrsGESPSPDKELMLESLQIEIERALQTLTPREADLVRLYFgLNGkhpMTLEEIGETFDLTRERVRQIKEKAIKRL 273
Cdd:COG1595  103 -------DEAADPEEALEAEELLEALLAALERLPPRQREVLVLRY-LEG---LSYAEIAEILGISEGTVKSRLSRARKKL 171


                 .
gi 312445485 274 K 274
Cdd:COG1595  172 R 172
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
53-274 1.37e-06

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 48.32  E-value: 1.37e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485  53 KLIKANLRFVVSVSKQYQNQGLSL---PDLINEGNLGLMKAAKRYDETRGfKFISYAVWWIRQSILQALAEQSRIVRLPL 129
Cdd:PRK12427  19 KYLNAYLPLVKKVVRQLAFQADSVidrEDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDWRPRRLR 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 130 NKIgsiNKINKAYAHLEQENERPPSPEELAEVLDMSEEDIKE--SMKNSGRHLSMDApLVEGEDSNLYDVLRSGEspspD 207
Cdd:PRK12427  98 QKT---HKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEylLLENAGTLESLDE-LLALEAHNDILQSRDLE----E 169

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 312445485 208 KELMLESLQieieRALQTLTPREADLVRLYFglngKHPMTLEEIGETFDLTRERVRQIKEKAIKRLK 274
Cdd:PRK12427 170 NIIIEDNLK----QALSQLDEREQLILHLYY----QHEMSLKEIALVLDLTEARICQLNKKIAQKIK 228
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 21-46 1.01e-03

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 40.55  E-value: 1.01e-03
                         10        20
                 ....*....|....*....|....*.
gi 312445485  21 YLQEIGKVDLITADEEVELAQKIRAG 46
Cdd:PRK05658 109 YLREMGTVELLTREGEIEIAKRIEAG 134
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 204-272 3.73e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 37.23  E-value: 3.73e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 312445485 204 PSP-DKELMLESLQiEIERALQTLTPReADLVRLYFGLNGkhpMTLEEIGETFDLTRERVRQIKEKAIKR 272
Cdd:PRK12525  97 PSPeEQWMVIETLL-AIDRLLDGLSGK-ARAAFLMSQLEG---LTYVEIGERLGVSLSRIHQYMVEAFKC 161
 
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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