|
Name |
Accession |
Description |
Interval |
E-value |
| RpoD |
COG0568 |
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ... |
333-570 |
8.64e-68 |
|
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: 220.31 E-value: 8.64e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 333 RDELVKS-TRsLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPS 411
Cdd:COG0568 32 KRKLVEAnLR-LVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRTIRLPV 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 412 SIIRTINHIQKARKTLKTSHGIKyAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVGDCFTTKFLEFTPDTTMESPEE 491
Cdd:COG0568 111 HMAETLNKLRRAKRQLLQELGRE-PTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDEEAPSPEE 189
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15232364 492 AVMRQSARRDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRDQPNAEDLRYYLN 570
Cdd:COG0568 190 ALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRKLRDYLD 268
|
|
| Sig70-cyanoRpoD |
TIGR02997 |
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ... |
278-557 |
5.46e-62 |
|
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Pssm-ID: 274382 [Multi-domain] Cd Length: 298 Bit Score: 206.33 E-value: 5.46e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 278 ETEMSTGVKIVADMERIRTQLEEESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRDELVKSTRSLVLFLARNYRGLGIA 357
Cdd:TIGR02997 21 EIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIKANLRLVVSVAKKYQNRGLE 100
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 358 HEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPSSIIRTINHIQKARKTLktSHGIKYAA 437
Cdd:TIGR02997 101 LLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQREL--SQKLGRTP 178
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 438 DE-EIAKLTGHSVKKIR----AANQCLkvvgSIDKKVGDCFTTKFLEFTPDTTmESPEEAVMRQSARRDIHDLLEGLEPR 512
Cdd:TIGR02997 179 SEaEIAEALELEPEQVRellqRARQPV----SLDAPVGDEEDTELGDLLEDDG-ESPEEQVERESLRQDLESLLAELTPR 253
|
250 260 270 280
....*....|....*....|....*....|....*....|....*
gi 15232364 513 EKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:TIGR02997 254 ERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
|
|
| PRK07406 |
PRK07406 |
RNA polymerase sigma factor RpoD; Validated |
271-561 |
1.71e-58 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236012 [Multi-domain] Cd Length: 373 Bit Score: 199.62 E-value: 1.71e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 271 RERISRNETEMSTGVKIvAD---MERIRTQLEEESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRDELVKSTRSLVLFL 347
Cdd:PRK07406 74 RIRLLRPDEEIELARKI-ADlleLEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSI 152
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 348 ARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPSSIIRTINHIQKARKTL 427
Cdd:PRK07406 153 AKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVL 232
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 428 KTSHGIKyAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVG---DCFTTKFLEftpdTTMESPEEAVMRQSARRDIHD 504
Cdd:PRK07406 233 SQEFGRK-PTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGkeeDSRLGDFIE----ADGETPEDDVAKNLLREDLEG 307
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*..
gi 15232364 505 LLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRdQPN 561
Cdd:PRK07406 308 VLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR-HPN 363
|
|
| PRK07405 |
PRK07405 |
RNA polymerase sigma factor SigD; Validated |
285-557 |
9.46e-48 |
|
RNA polymerase sigma factor SigD; Validated
Pssm-ID: 180963 [Multi-domain] Cd Length: 317 Bit Score: 169.17 E-value: 9.46e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 285 VKIVADMERIRTQLEEESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRDELVKSTRSLVLFLARNYRGLGIAHEDLIQA 364
Cdd:PRK07405 35 VQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQE 114
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 365 GYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPSSIIRTINHIQKARKTLKTSHGiKYAADEEIAKL 444
Cdd:PRK07405 115 GTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLG-RAATIGELAEE 193
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 445 TGHSVKKIRA----ANQCLkvvgSIDKKVGDCFTTKFLEFTPDTTmESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLR 520
Cdd:PRK07405 194 LELTPKQVREylerARQPL----SLDLRVGDNQDTELGELLEDTG-ASPEDFATQSSLQLDLERLMEDLTPQQKEVIALR 268
|
250 260 270
....*....|....*....|....*....|....*..
gi 15232364 521 YGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:PRK07405 269 FGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLR 305
|
|
| PRK05949 |
PRK05949 |
RNA polymerase sigma factor; Validated |
278-557 |
2.05e-47 |
|
RNA polymerase sigma factor; Validated
Pssm-ID: 180321 [Multi-domain] Cd Length: 327 Bit Score: 168.48 E-value: 2.05e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 278 ETEMSTGVKIVADME--RIRTQLEEESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRDELVKSTRSLVLFLARNYRGLG 355
Cdd:PRK05949 36 EQEIVYGKQVQQMMSllEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKMIEANLRLVVAIAKKYQKRN 115
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 356 IAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPSSIIRTINHIQKARKTLKTSHGiKY 435
Cdd:PRK05949 116 MEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLG-RS 194
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 436 AADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVGDCFTTKFLEFTPDTTMeSPEEAVMRQSARRDIHDLLEGLEPREKQ 515
Cdd:PRK05949 195 ATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEGP-SPDQYITQELLRQDLNNLLAELTPQQRE 273
|
250 260 270 280
....*....|....*....|....*....|....*....|..
gi 15232364 516 VMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:PRK05949 274 VLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLR 315
|
|
| PRK07921 |
PRK07921 |
RNA polymerase sigma factor SigB; Reviewed |
333-568 |
5.12e-47 |
|
RNA polymerase sigma factor SigB; Reviewed
Pssm-ID: 181169 [Multi-domain] Cd Length: 324 Bit Score: 167.22 E-value: 5.12e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 333 RDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPSS 412
Cdd:PRK07921 88 RRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVH 167
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 413 IIRTINHIQKARKTLKTSHGiKYAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVGDCFTTKFLEFTPDTTMESPEEA 492
Cdd:PRK07921 168 LVEQVNKLARIKRELHQQLG-REATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENA 246
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15232364 493 VMRQSARRDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRDQPNAEDLRYY 568
Cdd:PRK07921 247 VIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSY 322
|
|
| PRK05901 |
PRK05901 |
RNA polymerase sigma factor; Provisional |
319-569 |
6.76e-44 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 235640 [Multi-domain] Cd Length: 509 Bit Score: 163.24 E-value: 6.76e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 319 EKLLMRNLHYGWYCRDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMST 398
Cdd:PRK05901 259 RRDLQWIGRDGKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITR 338
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 399 MVSRHARGVHIPSSIIRTINHIQKARKTLKTSHGiKYAADEEIAKLTGHSVKKIRAANQclkvVG----SIDKKVGDCFT 474
Cdd:PRK05901 339 AMADQARTIRIPVHMVETINKLGRIERELLQELG-REPTPEELAKEMGFTPEKVREIQK----YNrepiSLDKTIGKEGD 413
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 475 TKFLEFTPDTTMESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMA 554
Cdd:PRK05901 414 SQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLR 493
|
250
....*....|....*
gi 15232364 555 KLRDQPNAEDLRYYL 569
Cdd:PRK05901 494 KLRHPSRSQVLRDFL 508
|
|
| PRK07598 |
PRK07598 |
RNA polymerase sigma factor SigC; Validated |
260-569 |
3.94e-43 |
|
RNA polymerase sigma factor SigC; Validated
Pssm-ID: 236067 [Multi-domain] Cd Length: 415 Bit Score: 159.26 E-value: 3.94e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 260 RVRRPPKYRKKRERISRNETEMSTGVKIVADMERIRTQLeeesGKVASLSCWAAAAGMNEKLLMRNLHYG---WY----- 331
Cdd:PRK07598 86 KVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSEL----GHRPSLERWAKTADISLADLKPTLAEGkrrWAeiakl 161
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 332 --------------CRDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMS 397
Cdd:PRK07598 162 tveeleqiqkqglrAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGIT 241
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 398 TMVSRHARGVHIPSSIIRTINHIQKARKTLKTSHGiKYAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVGDCFTTKF 477
Cdd:PRK07598 242 RAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKG-RTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTEL 320
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 478 LEFTpDTTMESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:PRK07598 321 GDLL-ETDDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLR 399
|
330
....*....|...
gi 15232364 558 dQPNAEDL-RYYL 569
Cdd:PRK07598 400 -QPKRRNRiRDYL 411
|
|
| PRK09210 |
PRK09210 |
RNA polymerase sigma factor RpoD; Validated |
343-569 |
1.27e-37 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236413 [Multi-domain] Cd Length: 367 Bit Score: 142.82 E-value: 1.27e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 343 LVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPSSIIRTINHIQK 422
Cdd:PRK09210 141 LVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR 220
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 423 ARKTLKTSHGiKYAADEEIAKLTGHSVKKIRaanQCLKVVG---SIDKKVGDCFTTKFLEFTPDTTMESPEEAVMRQSAR 499
Cdd:PRK09210 221 VQRQLLQELG-REPTPEEIAEEMDMPPEKVR---EILKIAQepvSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLK 296
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 500 RDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRDQPNAEDLRYYL 569
Cdd:PRK09210 297 EQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFL 366
|
|
| FliA |
COG1191 |
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ... |
333-558 |
1.92e-34 |
|
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: 130.33 E-value: 1.92e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 333 RDELVKSTRSLVLFLARNYRGLGIA-HEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSM------STMVSRHAR 405
Cdd:COG1191 17 REELIEEYLPLVKKIASRLAGRLPAeLDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAIldylrdEDWVPRSVR 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 406 gvhipssiiRTINHIQKARKTLKTSHGIKYaADEEIAKLTGHSVKKIRAANQCLKV--VGSIDKKVGDcfttkFLEFTPD 483
Cdd:COG1191 97 ---------ELARKIEEAIEELEQELGREP-TDEEIAEELGISLEEVQEALEAANAyqLLSLDEPLED-----GDDLLDL 161
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15232364 484 TTMESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRD 558
Cdd:COG1191 162 LESGDPEEELEHEELREALAEAIEQLPERERLVLSLYY----FEELTLKEIAEVLGVSESRVSRLHKKALARLRE 232
|
|
| PRK05658 |
PRK05658 |
RNA polymerase sigma factor RpoD; Validated |
334-569 |
2.33e-30 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 235549 [Multi-domain] Cd Length: 619 Bit Score: 125.68 E-value: 2.33e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 334 DELVKSTRSLVLFLARNY--RGLGIAheDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPS 411
Cdd:PRK05658 383 KEMVEANLRLVISIAKKYtnRGLQFL--DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 460
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 412 SIIRTINHIQK-ARKTLktsHGI-KYAADEEIAKLTGHSVKKIRaanQCLKVVG---SIDKKVGDCFTTKFLEFTPDTTM 486
Cdd:PRK05658 461 HMIETINKLNRiSRQML---QEIgREPTPEELAERLGMPEDKVR---KVLKIAKepiSLETPIGDDEDSHLGDFIEDKNA 534
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 487 ESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRDQPNAEDLR 566
Cdd:PRK05658 535 ELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLR 614
|
...
gi 15232364 567 YYL 569
Cdd:PRK05658 615 SFL 617
|
|
| PRK05657 |
PRK05657 |
RNA polymerase sigma factor RpoS; Validated |
343-558 |
2.60e-26 |
|
RNA polymerase sigma factor RpoS; Validated
Pssm-ID: 235548 [Multi-domain] Cd Length: 325 Bit Score: 109.66 E-value: 2.60e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 343 LVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPSSIIRTINHIQK 422
Cdd:PRK05657 98 LVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKELNVYLR 177
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 423 ARKTLkTSHGIKYAADEEIAKLTGHS---VKKIRAANQclkVVGSIDKKVGDCFTTKFLEFTPDTTMESPEEAVMRQSAR 499
Cdd:PRK05657 178 AAREL-EHKLDHEPSAEEIAELLDKPvddVSRMLALNE---RITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMK 253
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*....
gi 15232364 500 RDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRD 558
Cdd:PRK05657 254 QSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLRE 312
|
|
| SigBFG |
TIGR02980 |
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ... |
333-559 |
1.80e-23 |
|
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: 98.84 E-value: 1.80e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 333 RDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYvqywirkSMSTMVS---RHAR---- 405
Cdd:TIGR02980 5 REKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTF-------AVPTIMGeikRFFRddtw 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 406 GVHIPSSIIRTINHIQKARKTLKTSHGIKYAAdEEIAKLTGHSVKKIRAANQCLK--VVGSIDKKVGDCfttkflEFTPD 483
Cdd:TIGR02980 78 AVRVPRRLKELGVKINKATEELTQRLGRSPTI-AEIAERLGVSEEEVVEALEAGNayQALSLDASIEDD------DGDPI 150
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15232364 484 TTMES---PEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRDQ 559
Cdd:TIGR02980 151 ALLDTlgdEDDALETVEDRLALKPLLAALPERERRILLLRF----FEDKTQSEIAERLGISQMHVSRLLRRALKKLREQ 225
|
|
| FliA_WhiG |
TIGR02479 |
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ... |
336-557 |
8.45e-22 |
|
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: 94.26 E-value: 8.45e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 336 LVKSTRSLVLFLARNYRGLGIAH---EDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHArgvHIPSS 412
Cdd:TIGR02479 1 LIRRYLPLVKRIAGRLSVGLPSSvelDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLD---WVPRS 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 413 IIRTINHIQKARKTLKTSHGiKYAADEEIAKLTGHSVKKIRAANQ---CLKVVgSIDKKVGDCF-TTKFLEFTPDTTMES 488
Cdd:TIGR02479 78 LRQKARKLERAIRELEARLG-REPTEEEIAEELGMDLKEYRQALNeinALSLV-SLDELLESGDdGGSLIDRIEDDKSED 155
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15232364 489 PEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:TIGR02479 156 PEEELEREELREALAEAIESLSEREQLVLSLYY----YEELNLKEIGEVLGLTESRVSQIHSQALKKLR 220
|
|
| rpoH2 |
PRK07500 |
RNA polymerase factor sigma-32; Reviewed |
343-557 |
5.19e-19 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 236033 [Multi-domain] Cd Length: 289 Bit Score: 87.40 E-value: 5.19e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 343 LVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHArgvhipsSIIRT-INHIQ 421
Cdd:PRK07500 52 LVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNW-------SIVRGgTSSAQ 124
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 422 KA--------RKTLK------TSHGIKyaadEEIAKLTGHSVK-------KIRAANQCLKVVGSIDKKvGDCFTTKFLEF 480
Cdd:PRK07500 125 KAlffnlrrlRARLAqadeelTKQEIH----REIATALGVSLSdvemmdaRLSGPDASLNAPQSEEDE-GRSERMDFLVD 199
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15232364 481 TPDTTMESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYGLQDyrPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:PRK07500 200 DSPLPDEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLRED--GATLEALGEELGISKERVRQIEARALEKLR 274
|
|
| sigma70-ECF |
TIGR02937 |
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ... |
333-559 |
7.23e-18 |
|
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: 80.85 E-value: 7.23e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 333 RDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHtrGYKFSTYVQYWIRKSMstmvsrhargvhipss 412
Cdd:TIGR02937 3 FEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDP--EGSFKAWLFRIARNLI---------------- 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 413 iirtINHIQKARKTLKTSHGIKYAADEEiakltghsvkkiraanqclkvvgsidkkvgdcfttkfleftpdttmESPEEA 492
Cdd:TIGR02937 65 ----LDYLRRKRRLRRELDLLEELLDSD----------------------------------------------PSPEEE 94
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15232364 493 VMRQSARRDIHDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRDQ 559
Cdd:TIGR02937 95 LEQEEEREALREALEKLPEREREVLVLRY----LEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
|
|
| PRK06596 |
PRK06596 |
RNA polymerase factor sigma-32; Reviewed |
319-558 |
3.22e-16 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 235838 [Multi-domain] Cd Length: 284 Bit Score: 79.06 E-value: 3.22e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 319 EKLLMRNLHYGwycRD-----ELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIR 393
Cdd:PRK06596 34 EYMLAKRLREH---GDleaakQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIK 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 394 KSMSTMVSRHARGVHIPSSiirtinhiqKARKTL-----KTSHGIKYAADEE---IAKLTGHSVKKIRAANQCLKVV--- 462
Cdd:PRK06596 111 AEIHEYILRNWRIVKVATT---------KAQRKLffnlrKAKKRLGWLNPEEvemVAEELGVSEEEVREMESRLSGQdas 181
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 463 --GSIDKKVGDCFTTK-FLE---FTPDTTMESPEEAVMRQSArrdIHDLLEGLEPREKQVMVLRYgLQDyRPKSLEEIGK 536
Cdd:PRK06596 182 ldAPIDDDDEESGAPQdYLEdksSDPADVLEEDNWEDQRRAL---LADALEGLDERSRDIIEARW-LDD-DKSTLQELAA 256
|
250 260
....*....|....*....|..
gi 15232364 537 LLKVSKEWIRKIERRAMAKLRD 558
Cdd:PRK06596 257 EYGVSAERVRQIEKNAMKKLKA 278
|
|
| fliA |
PRK06986 |
flagellar biosynthesis sigma factor; Validated |
359-557 |
4.80e-16 |
|
flagellar biosynthesis sigma factor; Validated
Pssm-ID: 235901 [Multi-domain] Cd Length: 236 Bit Score: 77.58 E-value: 4.80e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 359 EDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRH---ARGVHipsSIIRTINH-IQKarktLKTSHGiK 434
Cdd:PRK06986 39 DDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLdwvPRSVR---RNAREVAQaIRQ----LEQELG-R 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 435 YAADEEIAKLTGHSVKKIRA---ANQCLKVVgSIDKKVGDCftTKFLEFTPDTTMESPEEAVMRQSARRDIHDLLEGLEP 511
Cdd:PRK06986 111 EPTDTEVAEKLGLSLEEYREmllDTNISQLF-SIDELRGEH--GDSILVTEDHQDEDPLQQLEDEELREALVEAIESLPE 187
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 15232364 512 REKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:PRK06986 188 REQLVLSLYY----QEELNLKEIGAVLGVSESRVSQIHSQAIKRLR 229
|
|
| PRK06288 |
PRK06288 |
RNA polymerase sigma factor WhiG; Reviewed |
356-557 |
7.07e-15 |
|
RNA polymerase sigma factor WhiG; Reviewed
Pssm-ID: 235770 [Multi-domain] Cd Length: 268 Bit Score: 75.11 E-value: 7.07e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 356 IAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVsrhaRGVH-IPSSIIRTINHIQKARKTLKTSHGiK 434
Cdd:PRK06288 59 VEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDEL----RSIDwIPRSVRQKARQIERAIAMLEARLG-R 133
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 435 YAADEEIAKLTGHSVKKIRAAnqCLKVVG----SID--KKVGD-CFTTKFLEFTPDTTMESPEEAVMRQSARRDIHDLLE 507
Cdd:PRK06288 134 TPSDEEIADELGISLEEYNSL--LSKLSGtsvvSLNdlWFGGDeGDEVSLMDTLESPAALNPDEIAEREEIKRVIVEAIK 211
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 15232364 508 GLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:PRK06288 212 TLPEREKKVLILYY----YEDLTLKEIGKVLGVTESRISQLHTKAVLQLR 257
|
|
| Sigma70_r2 |
pfam04542 |
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ... |
336-405 |
5.80e-14 |
|
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: 66.84 E-value: 5.80e-14
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 336 LVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHAR 405
Cdd:pfam04542 1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
|
|
| Sigma70_r4 |
pfam04545 |
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
505-558 |
9.77e-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: 62.83 E-value: 9.77e-13
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 15232364 505 LLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRD 558
Cdd:pfam04545 1 ALASLPPRERQVLVLRY----GEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
|
|
| PRK05572 |
PRK05572 |
RNA polymerase sporulation sigma factor, SigF/SigG family; |
333-559 |
2.33e-12 |
|
RNA polymerase sporulation sigma factor, SigF/SigG family;
Pssm-ID: 180137 [Multi-domain] Cd Length: 252 Bit Score: 67.30 E-value: 2.33e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 333 RDELVKSTRSLVL-----FLARNYRglgiaHEDLIQAGYVGVLQGAERFDHTRGYKFSTY--------VQYWIRKSMSTM 399
Cdd:PRK05572 34 RDTLVEKNLRLVWsvvqrFLNRGYE-----PDDLFQIGCIGLLKAVDKFDLSYDVKFSTYavpmiigeIQRFLRDDGTVK 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 400 VSRhargvhipsSIIRTINHIQKARKTLKTSHGiKYAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKV----GDCFTT 475
Cdd:PRK05572 109 VSR---------SLKETANKIRKDKDELSKELG-REPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVhendGDPITL 178
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 476 KfleftpDTTMESPEEAVMRQSARRDIhdlLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAK 555
Cdd:PRK05572 179 L------DQIADQSEEDWFDKIALKEA---IRELDERERLIVYLRY----FKDKTQSEVAKRLGISQVQVSRLEKKILKQ 245
|
....
gi 15232364 556 LRDQ 559
Cdd:PRK05572 246 MKEK 249
|
|
| PRK08583 |
PRK08583 |
RNA polymerase sigma factor SigB; Validated |
334-558 |
4.56e-12 |
|
RNA polymerase sigma factor SigB; Validated
Pssm-ID: 236306 [Multi-domain] Cd Length: 257 Bit Score: 66.26 E-value: 4.56e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 334 DELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYvqywirkSMSTMV---SRHAR----G 406
Cdd:PRK08583 32 EKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAF-------AVPTIIgeiKRYLRdktwS 104
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 407 VHIPSSIIRTINHIQKARKTLkTSHGIKYAADEEIAKLTGHSVKKIRAA------NQCLKVVGSI--DKkvgDCFTTKFL 478
Cdd:PRK08583 105 VHVPRRIKELGPKIKKAVDEL-TTELQRSPKISEIADRLGVSEEEVLEAmemgksYQALSVDHSIeaDS---DGSTVTLL 180
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 479 EFtpdttMESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRD 558
Cdd:PRK08583 181 DI-----VGQQEDGYELTEQRMILEKILPVLSDREKSIIQCTF----IENLSQKETGERLGISQMHVSRLQRQAIKKLRE 251
|
|
| PRK07670 |
PRK07670 |
FliA/WhiG family RNA polymerase sigma factor; |
334-557 |
7.99e-12 |
|
FliA/WhiG family RNA polymerase sigma factor;
Pssm-ID: 181075 [Multi-domain] Cd Length: 251 Bit Score: 65.45 E-value: 7.99e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 334 DELVKSTRSLVLF-LARNYRGL--GIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARgvhIP 410
Cdd:PRK07670 25 DELIRRYMPLVHYhVQRISVGLpkSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKEDW---LP 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 411 SSIIRTINHIQKARKTLKTSHGiKYAADEEIAKLTGHSVKKIRAA--NQCLKVVGSIDKKVGDCFTTKFLEFT-PDTTME 487
Cdd:PRK07670 102 RSMREKTKKVEAAIEKLEQRYM-RNVTPKEVAAELGMTEEEVEATmnEGFFANLLSIDEKTHDQDDGENVSVTiRDDKTP 180
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 488 SPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:PRK07670 181 TPEEKLLKEELIEELAEKIKQLSEKEQLVISLFY----KEELTLTEIGQVLNLSTSRISQIHSKALFKLK 246
|
|
| PRK05911 |
PRK05911 |
RNA polymerase sigma factor sigma-28; Reviewed |
333-557 |
2.16e-11 |
|
RNA polymerase sigma factor sigma-28; Reviewed
Pssm-ID: 235644 [Multi-domain] Cd Length: 257 Bit Score: 64.25 E-value: 2.16e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 333 RDELVKSTRSLVLFLA-RNYRGL--GIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHArgvHI 409
Cdd:PRK05911 25 RDVLIEFYLPLVKNVAhRLISGMpsHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQD---WV 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 410 PSSIIRTINHIQKARKTLKTSHGiKYAADEEIAKLTGHSVKKIR----AANQCLKVVGSIDKKV--GDCFTTKFLEFTPD 483
Cdd:PRK05911 102 PRSVHQKANKLADAMDSLRQSLG-KEPTDGELCEYLNISQQELSgwfsSARPALILSLNEEFPCqsDDEAGLALEERIAD 180
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15232364 484 TTMESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:PRK05911 181 ERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYY----YEELVLKEIGKILGVSESRVSQIHSKALLKLR 250
|
|
| Sigma70_r4 |
cd06171 |
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
499-557 |
6.10e-11 |
|
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: 57.88 E-value: 6.10e-11
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 15232364 499 RRDIHDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:cd06171 1 RERLEEALDKLPEREREVILLRF----GEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
|
|
| PRK05803 |
PRK05803 |
RNA polymerase sporulation sigma factor SigK; |
333-556 |
6.77e-11 |
|
RNA polymerase sporulation sigma factor SigK;
Pssm-ID: 180266 [Multi-domain] Cd Length: 233 Bit Score: 62.66 E-value: 6.77e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 333 RDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVqywirksmstmvsrhARGvhIPSS 412
Cdd:PRK05803 51 RNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA---------------ARC--IENE 113
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 413 IIRTINHIQKARKTLKTSHGIKYAAD-EEIakltghSVKKIRAANQclkvvGSIDKKVgdcfttkfleftpDTTMEspee 491
Cdd:PRK05803 114 ILMHLRNLKKTKKEVSLQDPIGVDKEgNEI------SLIDILGSEE-----DDVIEQV-------------ELKME---- 165
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15232364 492 avmrqsaRRDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKL 556
Cdd:PRK05803 166 -------VEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKL 223
|
|
| RpoE |
COG1595 |
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ... |
487-559 |
1.12e-09 |
|
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: 57.70 E-value: 1.12e-09
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15232364 487 ESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYgLQDYrpkSLEEIGKLLKVSKEWIRKIERRAMAKLRDQ 559
Cdd:COG1595 106 ADPEEALEAEELLEALLAALERLPPRQREVLVLRY-LEGL---SYAEIAEILGISEGTVKSRLSRARKKLREA 174
|
|
| PLN02541 |
PLN02541 |
uracil phosphoribosyltransferase |
46-72 |
1.85e-08 |
|
uracil phosphoribosyltransferase
Pssm-ID: 215297 Cd Length: 244 Bit Score: 55.56 E-value: 1.85e-08
10 20
....*....|....*....|....*..
gi 15232364 46 LVFVHPHPLIKHWLSLLRSDQTSFPIF 72
Cdd:PLN02541 33 LVFVPPHPLIKHWLSVLRNEQTPPPIF 59
|
|
| PRK07408 |
PRK07408 |
RNA polymerase sigma factor SigF; Reviewed |
359-516 |
1.10e-07 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 180965 [Multi-domain] Cd Length: 256 Bit Score: 53.39 E-value: 1.10e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 359 EDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPSSIIRTINHIQKARKTLKTSHGiKYAAD 438
Cdd:PRK07408 54 EDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRWQELQRQAKKVRQELRQELG-RQPTD 132
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 439 EEIAKLTGHSVK---KIRAANQCLKVVgSIDKKVG---DCFTTkFLEFTPDTTMESpeeavmRQSARRDIHDL---LEGL 509
Cdd:PRK07408 133 QEIAQALDISLEewqEIKLALQNRTPL-SLDAPVNqdeDGSTS-LGDLLPDPRYRS------FQLAQEDRIRLqqaLAQL 204
|
....*..
gi 15232364 510 EPREKQV 516
Cdd:PRK07408 205 EERTREV 211
|
|
| PRK07122 |
PRK07122 |
RNA polymerase sigma factor SigF; Reviewed |
333-559 |
1.46e-07 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 168831 [Multi-domain] Cd Length: 264 Bit Score: 52.86 E-value: 1.46e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 333 RDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYvqywirkSMSTM---VSRHAR---- 405
Cdd:PRK07122 42 RDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSF-------AVPTImgeVRRHFRdnsw 114
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 406 GVHIPSSIIRTinHIQKARKTLKTSHGIKYA--ADEEIAKLTGHSVKKIraanQCLkVVG------SIDKKVGDCFT-TK 476
Cdd:PRK07122 115 SVKVPRRLKEL--HLRLGRATAELSQRLGRAptASELAAELGMDREEVV----EGL-VAGsayntlSIDSGGGSGDDdAR 187
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 477 FLEFT---PDTTMESPEEavmRQSARrdihDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAM 553
Cdd:PRK07122 188 AIADTlgdVDAGLDQIEN---REALR----PLLAALPERERTVLVLRF----FESMTQTQIAERVGISQMHVSRLLAKTL 256
|
....*.
gi 15232364 554 AKLRDQ 559
Cdd:PRK07122 257 ARLRDQ 262
|
|
| Sigma70_r3 |
pfam04539 |
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ... |
416-493 |
3.56e-07 |
|
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: 47.98 E-value: 3.56e-07
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15232364 416 TINHIQKARKTLKTSHGIKyAADEEIAKLTGHSVKKIRAANQCLKVVGSIDKKVGDCFTTKFLEFTPDTTMESPEEAV 493
Cdd:pfam04539 2 LLNKIKRAQRELEQELGRE-PTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEEAV 78
|
|
| PRK11924 |
PRK11924 |
RNA polymerase sigma factor; Provisional |
483-557 |
2.52e-06 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 183384 [Multi-domain] Cd Length: 179 Bit Score: 48.04 E-value: 2.52e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15232364 483 DTTMESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYglqdYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:PRK11924 100 AETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRY----VEGLSYREIAEILGVPVGTVKSRLRRARQLLR 170
|
|
| PRK09639 |
PRK09639 |
RNA polymerase sigma factor SigX; Provisional |
487-559 |
2.46e-05 |
|
RNA polymerase sigma factor SigX; Provisional
Pssm-ID: 236602 [Multi-domain] Cd Length: 166 Bit Score: 44.94 E-value: 2.46e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15232364 487 ESPEEAVMRQSARRDIHDLLEGLEPREKQVMVLRYglQDYrpkSLEEIGKLLKVSKEWIRKIERRAMAKLRDQ 559
Cdd:PRK09639 91 PSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF--SGY---SYKEIAEALGIKESSVGTTLARAKKKFRKI 158
|
|
| PRK08295 |
PRK08295 |
RNA polymerase sporulation sigma factor SigH; |
334-550 |
4.90e-05 |
|
RNA polymerase sporulation sigma factor SigH;
Pssm-ID: 181361 [Multi-domain] Cd Length: 208 Bit Score: 44.51 E-value: 4.90e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 334 DELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMSTMVSRHARGVHIPssi 413
Cdd:PRK08295 27 EYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIITAIKTANRQKHIP--- 103
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 414 irtinhiqkarktLKTSHgikyaadeeiakltghsvkkiraanqclkvvgSIDKKVGDCFTTKFLEFT-PDTTMESPEEA 492
Cdd:PRK08295 104 -------------LNSYV--------------------------------SLDKPIYDEESDRTLLDViSEAKVTDPEEL 138
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15232364 493 VMRQSARRDIHD-LLEGLEPREKQvmVLRYGLQDYrpkSLEEIGKLLKVSKEWI--------RKIER 550
Cdd:PRK08295 139 IISKEELEDIEEkIEELLSELEKE--VLELYLDGK---SYQEIAEELNRHVKSIdnalqrvkRKLEK 200
|
|
| PRK08301 |
PRK08301 |
RNA polymerase sporulation sigma factor SigE; |
499-557 |
5.51e-05 |
|
RNA polymerase sporulation sigma factor SigE;
Pssm-ID: 236228 [Multi-domain] Cd Length: 234 Bit Score: 44.85 E-value: 5.51e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 15232364 499 RRDIHDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLR 557
Cdd:PRK08301 169 RKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLK 227
|
|
| Upp |
COG0035 |
Uracil phosphoribosyltransferase [Nucleotide transport and metabolism]; Uracil ... |
47-74 |
5.75e-04 |
|
Uracil phosphoribosyltransferase [Nucleotide transport and metabolism]; Uracil phosphoribosyltransferase is part of the Pathway/BioSystem: Pyrimidine salvage
Pssm-ID: 439805 Cd Length: 209 Bit Score: 41.59 E-value: 5.75e-04
10 20
....*....|....*....|....*...
gi 15232364 47 VFVHPHPLIKHWLSLLRSDQTSFPIFVR 74
Cdd:COG0035 4 VHVVDHPLIQHKLTLLRDKNTDTKEFRR 31
|
|
| PRK09641 |
PRK09641 |
RNA polymerase sigma factor SigW; Provisional |
351-538 |
1.62e-03 |
|
RNA polymerase sigma factor SigW; Provisional
Pssm-ID: 182012 [Multi-domain] Cd Length: 187 Bit Score: 39.68 E-value: 1.62e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 351 YRGLGIAHE--DLIQAGYVGVLQGAERFDHTRgyKFSTyvqyWIRKsMSTMVsrhargvhipssiirTINHIQKaRKTlk 428
Cdd:PRK09641 36 YRMLGNRHEaeDAAQEAFIRAYVNIDSYDINR--KFST----WLYR-IATNL---------------TIDRLRK-RKP-- 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 429 tshgiKYAADEEIAK---LTGHSvkKIRAanqclkvvgsidkkvgdcfttkfleftpdtTMESPEEAVMRQSARRDIHDL 505
Cdd:PRK09641 91 -----DYYLDAEVAGtegLTMYS--QLAA------------------------------DDALPEEQVVSLELQETIQEA 133
|
170 180 190
....*....|....*....|....*....|...
gi 15232364 506 LEGLEPREKQVMVLRYgLQDyrpKSLEEIGKLL 538
Cdd:PRK09641 134 ILQLPEKYRTVIVLKY-IED---LSLKEISEIL 162
|
|
| upp |
PRK00129 |
uracil phosphoribosyltransferase; Reviewed |
47-72 |
1.91e-03 |
|
uracil phosphoribosyltransferase; Reviewed
Pssm-ID: 234653 Cd Length: 209 Bit Score: 39.69 E-value: 1.91e-03
10 20
....*....|....*....|....*.
gi 15232364 47 VFVHPHPLIKHWLSLLRSDQTSFPIF 72
Cdd:PRK00129 4 VHVVDHPLIQHKLTLLRDKNTSTKRF 29
|
|
| PRK09648 |
PRK09648 |
RNA polymerase sigma factor ShbA; |
488-559 |
2.20e-03 |
|
RNA polymerase sigma factor ShbA;
Pssm-ID: 236607 [Multi-domain] Cd Length: 189 Bit Score: 39.57 E-value: 2.20e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15232364 488 SPEEAVMRQSARRDIHDLLEGLEPREKQVMVLR--YGLqdyrpkSLEEIGKLLKVSKEWIRKIERRAMAKLRDQ 559
Cdd:PRK09648 119 GPEERALRSESSNRMRELLDTLPEKQREILILRvvVGL------SAEETAEAVGSTPGAVRVAQHRALARLRAE 186
|
|
| PRK08215 |
PRK08215 |
RNA polymerase sporulation sigma factor SigG; |
320-405 |
9.61e-03 |
|
RNA polymerase sporulation sigma factor SigG;
Pssm-ID: 181296 [Multi-domain] Cd Length: 258 Bit Score: 38.00 E-value: 9.61e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232364 320 KLLMRNLHYG-WYCRDELVKSTRSLVLFLAR--NYRGLGIahEDLIQAGYVGVLQGAERFDHTRGYKFSTY--------V 388
Cdd:PRK08215 25 RELFERMQNGdKEAREKLINGNLRLVLSVIQrfNNRGENV--DDLFQVGCIGLMKAIDNFDLSQNVKFSTYavpmiigeI 102
|
90
....*....|....*..
gi 15232364 389 QYWIRKSMSTMVSRHAR 405
Cdd:PRK08215 103 RRYLRDNNPIRVSRSLR 119
|
|
|