|
Name |
Accession |
Description |
Interval |
E-value |
| Sig70-cyanoRpoD |
TIGR02997 |
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ... |
247-531 |
2.35e-100 |
|
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: 305.32 E-value: 2.35e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 247 LLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRGRSSREKLITANLRLVVHIAKQY 326
Cdd:TIGR02997 15 LLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIKANLRLVVSVAKKY 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 327 QNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEG 406
Cdd:TIGR02997 95 QNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKL 174
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 407 NYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGiETPTMSVGKQLMRNHVRNLLNVLSPK 486
Cdd:TIGR02997 175 GRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDG-ESPEEQVERESLRQDLESLLAELTPR 253
|
250 260 270 280
....*....|....*....|....*....|....*....|....*
gi 16604647 487 ERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLK 531
Cdd:TIGR02997 254 ERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
|
|
| RpoD |
COG0568 |
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ... |
302-544 |
6.06e-96 |
|
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: 292.73 E-value: 6.06e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 302 HRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRT 381
Cdd:COG0568 26 AGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRT 105
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 382 IRLPENVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGIE 461
Cdd:COG0568 106 IRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDEEAP 185
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 462 TPTMSVGKQLMRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMNSHGLHA 541
Cdd:COG0568 186 SPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRKLRD 265
|
...
gi 16604647 542 YAD 544
Cdd:COG0568 266 YLD 268
|
|
| PRK07406 |
PRK07406 |
RNA polymerase sigma factor RpoD; Validated |
203-536 |
3.98e-89 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236012 [Multi-domain] Cd Length: 373 Bit Score: 278.98 E-value: 3.98e-89
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 203 APKSNDVDDEGYVPQKTSAKKKY-KQGADNDDALQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEP 281
Cdd:PRK07406 32 SSENADELSEKEAKAKALARIKIgPKKVYTEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREP 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 282 TIGEWAEAMGISSPVLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFAT 361
Cdd:PRK07406 112 SDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFST 191
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 362 YAYWWIRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQ 441
Cdd:PRK07406 192 YATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLET 271
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 442 PIWSDQDTTFQEITpDSGIETPTMSVGKQLMRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQ 521
Cdd:PRK07406 272 PIGKEEDSRLGDFI-EADGETPEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQ 350
|
330
....*....|....*.
gi 16604647 522 LESRALYRLKQ-NMNS 536
Cdd:PRK07406 351 IEAKALRKLRHpNRNS 366
|
|
| PRK05949 |
PRK05949 |
RNA polymerase sigma factor; Validated |
247-532 |
5.44e-73 |
|
RNA polymerase sigma factor; Validated
Pssm-ID: 180321 [Multi-domain] Cd Length: 327 Bit Score: 235.51 E-value: 5.44e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 247 LLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRGRSSREKLITANLRLVVHIAKQY 326
Cdd:PRK05949 32 LLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKMIEANLRLVVAIAKKY 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 327 QNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEG 406
Cdd:PRK05949 112 QKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKL 191
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 407 NYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGIeTPTMSVGKQLMRNHVRNLLNVLSPK 486
Cdd:PRK05949 192 GRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEGP-SPDQYITQELLRQDLNNLLAELTPQ 270
|
250 260 270 280
....*....|....*....|....*....|....*....|....*.
gi 16604647 487 ERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQ 532
Cdd:PRK05949 271 QREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR 316
|
|
| PRK07405 |
PRK07405 |
RNA polymerase sigma factor SigD; Validated |
247-537 |
1.61e-68 |
|
RNA polymerase sigma factor SigD; Validated
Pssm-ID: 180963 [Multi-domain] Cd Length: 317 Bit Score: 223.48 E-value: 1.61e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 247 LLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRGRSSREKLITANLRLVVHIAKQY 326
Cdd:PRK07405 22 LLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKMVEANLRLVVSVAKKY 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 327 QNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEG 406
Cdd:PRK07405 102 LKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQL 181
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 407 NYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGiETPTMSVGKQLMRNHVRNLLNVLSPK 486
Cdd:PRK07405 182 GRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG-ASPEDFATQSSLQLDLERLMEDLTPQ 260
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....
gi 16604647 487 ERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRL---KQNMNSH 537
Cdd:PRK07405 261 QKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLrkrKANIQEY 314
|
|
| PRK07921 |
PRK07921 |
RNA polymerase sigma factor SigB; Reviewed |
233-543 |
1.43e-66 |
|
RNA polymerase sigma factor SigB; Reviewed
Pssm-ID: 181169 [Multi-domain] Cd Length: 324 Bit Score: 218.83 E-value: 1.43e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 233 DALQLFLWGPETKQLLTAKEEAELISHIQHLLKLEkvkTKLESqngCEPTigewaeamgisSPVLKSDI----HRGRSSR 308
Cdd:PRK07921 26 DLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAE---HLLET---RKRL-----------SEARKRDLaavvRDGEAAR 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 309 EKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENV 388
Cdd:PRK07921 89 RHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHL 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 389 YMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGIETPTMSVG 468
Cdd:PRK07921 169 VEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVI 248
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16604647 469 KQLMRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMNSHGLHAYA 543
Cdd:PRK07921 249 AGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYA 323
|
|
| PRK07598 |
PRK07598 |
RNA polymerase sigma factor SigC; Validated |
245-532 |
1.70e-63 |
|
RNA polymerase sigma factor SigC; Validated
Pssm-ID: 236067 [Multi-domain] Cd Length: 415 Bit Score: 213.58 E-value: 1.70e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 245 KQLLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGIS----SPVLKSDIHR----------------- 303
Cdd:PRK07598 92 KLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTADISladlKPTLAEGKRRwaeiakltveeleqiqk 171
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 304 -GRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTI 382
Cdd:PRK07598 172 qGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTI 251
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 383 RLPENVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGIeT 462
Cdd:PRK07598 252 RLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDLLETDDI-S 330
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 463 PTMSVGKQLMRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQ 532
Cdd:PRK07598 331 PEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQ 400
|
|
| PRK05901 |
PRK05901 |
RNA polymerase sigma factor; Provisional |
247-531 |
2.30e-59 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 235640 [Multi-domain] Cd Length: 509 Bit Score: 204.84 E-value: 2.30e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 247 LLTAKEEAELISHIQHLLKLEKvktKLESQNGCEPTIGEwaEAMGISspvlksdiHRGRSSREKLITANLRLVVHIAKQY 326
Cdd:PRK05901 225 LLNAEEEVELAKRIEAGLYAEE---LLAEGEKLDPELRR--DLQWIG--------RDGKRAKNHLLEANLRLVVSLAKRY 291
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 327 QNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPenVYML-----LGKVseARKT 401
Cdd:PRK05901 292 TNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIP--VHMVetinkLGRI--EREL 367
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 402 cVQEGNYRPSKEELAGHVGVSTEK---LDKllYNtRTPLSMQQPIWSDQDTTFQEITPDSGIETPTMSVGKQLMRNHVRN 478
Cdd:PRK05901 368 -LQELGREPTPEELAKEMGFTPEKvreIQK--YN-REPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQE 443
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|...
gi 16604647 479 LLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLK 531
Cdd:PRK05901 444 VLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLR 496
|
|
| PRK09210 |
PRK09210 |
RNA polymerase sigma factor RpoD; Validated |
307-544 |
3.70e-57 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236413 [Multi-domain] Cd Length: 367 Bit Score: 195.20 E-value: 3.70e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 307 SREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPe 386
Cdd:PRK09210 130 AKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIP- 208
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 387 nVYML--LGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGIETPT 464
Cdd:PRK09210 209 -VHMVetINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPA 287
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 465 MSVGKQLMRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMNSHGLHAYAD 544
Cdd:PRK09210 288 DHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE 367
|
|
| PRK05658 |
PRK05658 |
RNA polymerase sigma factor RpoD; Validated |
301-531 |
5.04e-52 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 235549 [Multi-domain] Cd Length: 619 Bit Score: 187.31 E-value: 5.04e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 301 IHRG-RSSRE---KLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIF 376
Cdd:PRK05658 371 ISKGeAKARRakkEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 450
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 377 QNSRTIRLPenVYML-----LGKVSeaRKtCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTF 451
Cdd:PRK05658 451 DQARTIRIP--VHMIetinkLNRIS--RQ-MLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHL 525
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 452 QEITPDSGIETPTMSVGKQLMRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLK 531
Cdd:PRK05658 526 GDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605
|
|
| PRK05657 |
PRK05657 |
RNA polymerase sigma factor RpoS; Validated |
306-539 |
6.22e-52 |
|
RNA polymerase sigma factor RpoS; Validated
Pssm-ID: 235548 [Multi-domain] Cd Length: 325 Bit Score: 180.15 E-value: 6.22e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 306 SSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLP 385
Cdd:PRK05657 86 AARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLP 165
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 386 ENVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLL-YNTRTpLSMQQPIWSDQDTTFQEITPDSGIETPT 464
Cdd:PRK05657 166 VHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLaLNERI-TSLDTPLGGDPEKSLLDILADEQENGPE 244
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16604647 465 MSVGKQLMRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMNSHGL 539
Cdd:PRK05657 245 DTTQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGL 319
|
|
| FliA |
COG1191 |
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ... |
308-536 |
1.87e-39 |
|
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: 143.81 E-value: 1.87e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 308 REKLITANLRLVVHIAKQYQNRGL-NFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSrtiRLPE 386
Cdd:COG1191 17 REELIEEYLPLVKKIASRLAGRLPaELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDYLRDED---WVPR 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 387 NVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLL--YNTRTPLSMQQPIWSDQDT--TFQEITPDSGIEt 462
Cdd:COG1191 94 SVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALeaANAYQLLSLDEPLEDGDDLldLLESGDPEEELE- 172
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16604647 463 ptmsvgKQLMRNHVRNLLNVLSPKERRIIKLRFgidgGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMNS 536
Cdd:COG1191 173 ------HEELREALAEAIEQLPERERLVLSLYY----FEELTLKEIAEVLGVSESRVSRLHKKALARLREYLKE 236
|
|
| rpoH2 |
PRK07500 |
RNA polymerase factor sigma-32; Reviewed |
302-545 |
6.62e-34 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 236033 [Multi-domain] Cd Length: 289 Bit Score: 130.16 E-value: 6.62e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 302 HRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRT 381
Cdd:PRK07500 36 HRDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSI 115
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 382 IR---------LPENVYMLLGKVSEARKTCVQEGNYRpskeELAGHVGVST---EKLDKLLynTRTPLSMQQPIWSDQDT 449
Cdd:PRK07500 116 VRggtssaqkaLFFNLRRLRARLAQADEELTKQEIHR----EIATALGVSLsdvEMMDARL--SGPDASLNAPQSEEDEG 189
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 450 TFQEI--------TPDsgiETPTMSVGKQLMRNHVRNLLNVLSPKERRIIKLRFGIDGGkqRSLSEIGEIYGLSKERVRQ 521
Cdd:PRK07500 190 RSERMdflvddspLPD---EQVESSIDGERRRRWLTQALQTLNERELRIIRERRLREDG--ATLEALGEELGISKERVRQ 264
|
250 260
....*....|....*....|....
gi 16604647 522 LESRALYRLKQNMNSHGLHAYADL 545
Cdd:PRK07500 265 IEARALEKLRRALLSQSPEVAYFA 288
|
|
| rpoH_proteo |
TIGR02392 |
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ... |
310-536 |
1.94e-31 |
|
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: 122.77 E-value: 1.94e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 310 KLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSR-----TIRL 384
Cdd:TIGR02392 39 KLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRlvkvaTTKA 118
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 385 PENVYMLLGKVSEARKtcvqeGNYRPSK-EELAGHVGVSTEklDKLLYNTR---TPLSMQQPIWSDQDTTFQEIT--PDS 458
Cdd:TIGR02392 119 QRKLFFNLRKMKKRLQ-----GWLNPEEvEAIAEELGVSER--EVREMESRlsgQDMSLNASIDDDEDDGGAPIAylVDK 191
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 459 GIETPTMSVGKQ---LMRNHVRNLLNVLSPKERRIIKLRFGIDGGKqrSLSEIGEIYGLSKERVRQLESRALYRLKQNMN 535
Cdd:TIGR02392 192 RSDPEDTLEEEQweeLQRQALANALGSLDARSRRIIEARWLDDDKL--TLQELAAEYGVSAERIRQIEKNAMKKLKAALA 269
|
.
gi 16604647 536 S 536
Cdd:TIGR02392 270 A 270
|
|
| PRK06596 |
PRK06596 |
RNA polymerase factor sigma-32; Reviewed |
310-534 |
2.64e-29 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 235838 [Multi-domain] Cd Length: 284 Bit Score: 117.20 E-value: 2.64e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 310 KLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRlpenvy 389
Cdd:PRK06596 52 QLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVK------ 125
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 390 mlLGKVSEARKTCVqegNYRPSK-----------EELAGHVGVSTEklDKLLYNTR---TPLSMQQPIWSDQDTTFQEIT 455
Cdd:PRK06596 126 --VATTKAQRKLFF---NLRKAKkrlgwlnpeevEMVAEELGVSEE--EVREMESRlsgQDASLDAPIDDDDEESGAPQD 198
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 456 --PDSGIETPTMSVGKQLMRNHVRNL---LNVLSPKERRIIKLRFGIDGGKqrSLSEIGEIYGLSKERVRQLESRALYRL 530
Cdd:PRK06596 199 ylEDKSSDPADVLEEDNWEDQRRALLadaLEGLDERSRDIIEARWLDDDKS--TLQELAAEYGVSAERVRQIEKNAMKKL 276
|
....
gi 16604647 531 KQNM 534
Cdd:PRK06596 277 KAAI 280
|
|
| PRK08215 |
PRK08215 |
RNA polymerase sporulation sigma factor SigG; |
295-534 |
1.89e-26 |
|
RNA polymerase sporulation sigma factor SigG;
Pssm-ID: 181296 [Multi-domain] Cd Length: 258 Bit Score: 108.11 E-value: 1.89e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 295 PVLKSD--------IHRG-RSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYW 365
Cdd:PRK08215 17 PVLKNEemrelferMQNGdKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVP 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 366 WIRQSIRKSIFQNSrTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWS 445
Cdd:PRK08215 97 MIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYH 175
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 446 DQ-DTTF--QEITPDsgietptmsvgKQLMRNHVRNL-----LNVLSPKERRIIKLRFgIDGGKQrslSEIGEIYGLSKE 517
Cdd:PRK08215 176 DGgDPIYvmDQISDE-----------KNKDENWLEEIalkeaMKKLNDREKLILNLRF-FQGKTQ---MEVAEEIGISQA 240
|
250
....*....|....*..
gi 16604647 518 RVRQLESRALYRLKQNM 534
Cdd:PRK08215 241 QVSRLEKAALKHMRKYI 257
|
|
| spore_sigF |
TIGR02885 |
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma ... |
305-534 |
2.57e-25 |
|
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore. [Transcription, Transcription factors, Cellular processes, Sporulation and germination]
Pssm-ID: 131931 [Multi-domain] Cd Length: 231 Bit Score: 104.41 E-value: 2.57e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 305 RSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIfQNSRTIRL 384
Cdd:TIGR02885 10 KEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFL-RDDGIIKV 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 385 PENVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEItpdSGIETPT 464
Cdd:TIGR02885 89 SRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLL---DQIADKG 165
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 465 MSVGKQLMRNHVRNLLNVLSPKERRIIKLRFgidgGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNM 534
Cdd:TIGR02885 166 SEDSDWLEKIALKEAISKLDERERQIIMLRY----FKDKTQTEVANMLGISQVQVSRLEKKVLKKMKEKL 231
|
|
| PRK05803 |
PRK05803 |
RNA polymerase sporulation sigma factor SigK; |
305-538 |
9.36e-25 |
|
RNA polymerase sporulation sigma factor SigK;
Pssm-ID: 180266 [Multi-domain] Cd Length: 233 Bit Score: 102.72 E-value: 9.36e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 305 RSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAywwirqsirksifqnSRTIrl 384
Cdd:PRK05803 48 EEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA---------------ARCI-- 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 385 pEN-VYMLLgkvsearktcvqegnyRPSKEelaghvgvstekldkllynTRTPLSMQQPIWSDQDTTfqEIT-------- 455
Cdd:PRK05803 111 -ENeILMHL----------------RNLKK-------------------TKKEVSLQDPIGVDKEGN--EISlidilgse 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 456 PDSGIETptmsVGKQLMRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMN 535
Cdd:PRK05803 153 EDDVIEQ----VELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELY 228
|
...
gi 16604647 536 SHG 538
Cdd:PRK05803 229 RAE 231
|
|
| PRK05572 |
PRK05572 |
RNA polymerase sporulation sigma factor, SigF/SigG family; |
308-535 |
8.85e-21 |
|
RNA polymerase sporulation sigma factor, SigF/SigG family;
Pssm-ID: 180137 [Multi-domain] Cd Length: 252 Bit Score: 91.96 E-value: 8.85e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 308 REKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIfQNSRTIRLPEN 387
Cdd:PRK05572 34 RDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFL-RDDGTVKVSRS 112
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 388 VYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQD---TTFQEITPDSGietpt 464
Cdd:PRK05572 113 LKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGdpiTLLDQIADQSE----- 187
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 16604647 465 msvGKQLMRNHVRNLLNVLSPKERRIIKLRFgidgGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMN 535
Cdd:PRK05572 188 ---EDWFDKIALKEAIRELDERERLIVYLRY----FKDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKLD 251
|
|
| FliA_WhiG |
TIGR02479 |
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ... |
311-534 |
7.64e-20 |
|
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: 88.48 E-value: 7.64e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 311 LITANLRLVVHIAKQYQNR---GLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAywwiRQSIRKSIFQNSRTIR-LPE 386
Cdd:TIGR02479 1 LIRRYLPLVKRIAGRLSVGlpsSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYA----VQRIRGAMLDELRRLDwVPR 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 387 NVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLY--NTRTPLSMQQPIWSDQD-TTFQEITPDSGIETP 463
Cdd:TIGR02479 77 SLRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNeiNALSLVSLDELLESGDDgGSLIDRIEDDKSEDP 156
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 16604647 464 TMSVGKQLMRNHVRNLLNVLSPKERRIIKLRFgidgGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNM 534
Cdd:TIGR02479 157 EEELEREELREALAEAIESLSEREQLVLSLYY----YEELNLKEIGEVLGLTESRVSQIHSQALKKLRAKL 223
|
|
| Sigma70_r2 |
pfam04542 |
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ... |
311-381 |
1.47e-19 |
|
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: 82.64 E-value: 1.47e-19
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 16604647 311 LITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRT 381
Cdd:pfam04542 1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
|
|
| sigma70-ECF |
TIGR02937 |
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ... |
306-534 |
2.00e-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: 82.40 E-value: 2.00e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 306 SSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSgcRFATYAYWWIRQSIRKSIFQNSRtirlp 385
Cdd:TIGR02937 1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFRIARNLILDYLRRKRR----- 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 386 envymllgkvsearktcvqegnyrpskeelaghvgvstekldkllyntrtplsmqqpiwsDQDTTFQEITPDSGIETPTM 465
Cdd:TIGR02937 74 ------------------------------------------------------------LRRELDLLEELLDSDPSPEE 93
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16604647 466 SVGKQLMRNHVRNLLNVLSPKERRIIKLRFgidgGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNM 534
Cdd:TIGR02937 94 ELEQEEEREALREALEKLPEREREVLVLRY----LEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
|
|
| PRK08301 |
PRK08301 |
RNA polymerase sporulation sigma factor SigE; |
306-535 |
1.90e-17 |
|
RNA polymerase sporulation sigma factor SigE;
Pssm-ID: 236228 [Multi-domain] Cd Length: 234 Bit Score: 81.83 E-value: 1.90e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 306 SSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAywwirqsirksifqnSRTIrlp 385
Cdd:PRK08301 52 AVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA---------------SRCI--- 113
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 386 EN-VYMLLgkvseaRktcvqegnyRPSKeelaghvgvstekldkllynTRTPLSMQQPIWSDQD-----------TTFQE 453
Cdd:PRK08301 114 ENeILMYL------R---------RNNK--------------------VKAEVSFDEPLNIDWDgnelllsdvlgTDNDI 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 454 ITPDsgIETptmSVGKQLMrnhvRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQN 533
Cdd:PRK08301 159 IYKD--IED---EVDRKLL----KKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229
|
..
gi 16604647 534 MN 535
Cdd:PRK08301 230 IN 231
|
|
| PRK05911 |
PRK05911 |
RNA polymerase sigma factor sigma-28; Reviewed |
308-536 |
2.25e-17 |
|
RNA polymerase sigma factor sigma-28; Reviewed
Pssm-ID: 235644 [Multi-domain] Cd Length: 257 Bit Score: 81.97 E-value: 2.25e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 308 REKLITANLRLVVHIAKQYQN---RGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSrtiRL 384
Cdd:PRK05911 25 RDVLIEFYLPLVKNVAHRLISgmpSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQD---WV 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 385 PENVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSM----QQPIWSDQDT--TFQEITPDS 458
Cdd:PRK05911 102 PRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILslneEFPCQSDDEAglALEERIADE 181
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16604647 459 GIETPTMSVGKQLMRNHVRNLLNVLSPKERRIIKLRFgidgGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQNMNS 536
Cdd:PRK05911 182 RAETGYDVVDKKEFSSILAEAILALEEKERKVMALYY----YEELVLKEIGKILGVSESRVSQIHSKALLKLRATLSA 255
|
|
| PRK07122 |
PRK07122 |
RNA polymerase sigma factor SigF; Reviewed |
296-534 |
4.00e-17 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 168831 [Multi-domain] Cd Length: 264 Bit Score: 81.36 E-value: 4.00e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 296 VLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSI 375
Cdd:PRK07122 30 GLPAGSPEFQRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHF 109
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 376 FQNSRTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLL-----YNTrtpLSMQQPIWSDQDTT 450
Cdd:PRK07122 110 RDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLvagsaYNT---LSIDSGGGSGDDDA 186
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 451 fQEITPDSGIETPTMSVGKQlmRNHVRNLLNVLSPKERRIIKLRFgIDGGKQrslSEIGEIYGLSKERVRQLESRALYRL 530
Cdd:PRK07122 187 -RAIADTLGDVDAGLDQIEN--REALRPLLAALPERERTVLVLRF-FESMTQ---TQIAERVGISQMHVSRLLAKTLARL 259
|
....
gi 16604647 531 KQNM 534
Cdd:PRK07122 260 RDQL 263
|
|
| Sigma70_r3 |
pfam04539 |
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ... |
390-467 |
1.29e-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: 74.56 E-value: 1.29e-16
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16604647 390 MLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGIETPTMSV 467
Cdd:pfam04539 1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEEAV 78
|
|
| PRK07408 |
PRK07408 |
RNA polymerase sigma factor SigF; Reviewed |
308-536 |
1.07e-15 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 180965 [Multi-domain] Cd Length: 256 Bit Score: 76.88 E-value: 1.07e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 308 REKLITANLRLVVHIAKQYQNR-GLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPE 386
Cdd:PRK07408 27 RNQLVELNLGLVRKEAHRWSNQcSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPR 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 387 NVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLD--KLLYNTRTPLSMQQPIWSDQD--TTFQEITPDSGIEt 462
Cdd:PRK07408 107 RWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQeiKLALQNRTPLSLDAPVNQDEDgsTSLGDLLPDPRYR- 185
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16604647 463 ptmsvGKQLM---RNHVRNLLNVLSPKERRIIKLRFgidgGKQRSLSEIGEIYGLSKERV-RQLEsRALYRLKQNMNS 536
Cdd:PRK07408 186 -----SFQLAqedRIRLQQALAQLEERTREVLEFVF----LHDLTQKEAAERLGISPVTVsRRVK-KGLDQLKKLLQP 253
|
|
| PRK06288 |
PRK06288 |
RNA polymerase sigma factor WhiG; Reviewed |
308-531 |
1.15e-14 |
|
RNA polymerase sigma factor WhiG; Reviewed
Pssm-ID: 235770 [Multi-domain] Cd Length: 268 Bit Score: 74.34 E-value: 1.15e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 308 REKLITANLRLVVHIAKQY-----QNrgLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYwwirQSIRKSIFQNSRTI 382
Cdd:PRK06288 33 REYLILKYSPLVKYVAGRIavgmpQN--VEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAV----TRIRGAIFDELRSI 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 383 -RLPENVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLL--YNTRTPLSMQQPIWSDQDT---TFQEITP 456
Cdd:PRK06288 107 dWIPRSVRQKARQIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLskLSGTSVVSLNDLWFGGDEGdevSLMDTLE 186
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 16604647 457 DSGIETPTMSVGKQLMRNHVRNLLNVLSPKERRIIKLRFGIDggkqRSLSEIGEIYGLSKERVRQLESRALYRLK 531
Cdd:PRK06288 187 SPAALNPDEIAEREEIKRVIVEAIKTLPEREKKVLILYYYED----LTLKEIGKVLGVTESRISQLHTKAVLQLR 257
|
|
| PRK07670 |
PRK07670 |
FliA/WhiG family RNA polymerase sigma factor; |
334-532 |
3.33e-14 |
|
FliA/WhiG family RNA polymerase sigma factor;
Pssm-ID: 181075 [Multi-domain] Cd Length: 251 Bit Score: 72.38 E-value: 3.33e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 334 QDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWwirqSIRKSIFQNSRTI-RLPENVYMLLGKVSEARKTCVQEGNYRPSK 412
Cdd:PRK07670 53 DDLKSLGMLGLYDALEKFDPSRDLKFDTYASF----RIRGAIIDGLRKEdWLPRSMREKTKKVEAAIEKLEQRYMRNVTP 128
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 413 EELAGHVGVSTEKL-----DKLLYNTrtpLSM-QQPIWSDQDTTFQEITPDSGIETPTMSVGKQLMRNHVRNLLNVLSPK 486
Cdd:PRK07670 129 KEVAAELGMTEEEVeatmnEGFFANL---LSIdEKTHDQDDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEK 205
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 16604647 487 ERRIIKLRFGidggKQRSLSEIGEIYGLSKERVRQLESRALYRLKQ 532
Cdd:PRK07670 206 EQLVISLFYK----EELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247
|
|
| Sigma70_r4 |
pfam04545 |
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
479-532 |
2.93e-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: 63.99 E-value: 2.93e-13
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 16604647 479 LLNVLSPKERRIIKLRFGidggKQRSLSEIGEIYGLSKERVRQLESRALYRLKQ 532
Cdd:pfam04545 1 ALASLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
|
|
| PRK08583 |
PRK08583 |
RNA polymerase sigma factor SigB; Validated |
309-532 |
5.94e-13 |
|
RNA polymerase sigma factor SigB; Validated
Pssm-ID: 236306 [Multi-domain] Cd Length: 257 Bit Score: 68.95 E-value: 5.94e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 309 EKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENV 388
Cdd:PRK08583 32 EKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRI 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 389 YMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLL-----YNTrtpLSMQQPIWSDQD---TTFQEI--TPDS 458
Cdd:PRK08583 112 KELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMemgksYQA---LSVDHSIEADSDgstVTLLDIvgQQED 188
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16604647 459 GIEtptmSVGKQLMrnhVRNLLNVLSPKERRIIKLRFgIDGGKQRslsEIGEIYGLSKERVRQLESRALYRLKQ 532
Cdd:PRK08583 189 GYE----LTEQRMI---LEKILPVLSDREKSIIQCTF-IENLSQK---ETGERLGISQMHVSRLQRQAIKKLRE 251
|
|
| fliA |
PRK06986 |
flagellar biosynthesis sigma factor; Validated |
304-535 |
2.20e-12 |
|
flagellar biosynthesis sigma factor; Validated
Pssm-ID: 235901 [Multi-domain] Cd Length: 236 Bit Score: 66.79 E-value: 2.20e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 304 GRSSREKLITANLRLVVHIAKQYQNR---GLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAywwiRQSIRKSIFQNSR 380
Cdd:PRK06986 6 GKMDQDELVEQYAPLVKRIALRLKARlpaSVDLDDLIQAGMIGLLEAARRYDGEQGASFETYA----GQRIRGAMLDELR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 381 tiRL---PENVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMqqPI--WSDQDTTFQEIT 455
Cdd:PRK06986 82 --SLdwvPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLF--SIdeLRGEHGDSILVT 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 456 PDSGIETPTMSVGKQLMRNHVRNLLNVLSPKERRIIKLRFgidggkQR--SLSEIGEIYGLSKERVRQLESRALYRLKQN 533
Cdd:PRK06986 158 EDHQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYY------QEelNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231
|
..
gi 16604647 534 MN 535
Cdd:PRK06986 232 LG 233
|
|
| Sigma70_r4 |
cd06171 |
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
473-531 |
4.85e-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: 4.85e-11
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 16604647 473 RNHVRNLLNVLSPKERRIIKLRFGidggKQRSLSEIGEIYGLSKERVRQLESRALYRLK 531
Cdd:cd06171 1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
|
|
| RpoE |
COG1595 |
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ... |
461-539 |
3.50e-06 |
|
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: 47.68 E-value: 3.50e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16604647 461 ETPTMSVGKQLMRNHVRNLLNVLSPKERRIIKLRFgIDGgkqRSLSEIGEIYGLSKERVRQLESRALYRLKQNMNSHGL 539
Cdd:COG1595 106 ADPEEALEAEELLEALLAALERLPPRQREVLVLRY-LEG---LSYAEIAEILGISEGTVKSRLSRARKKLREALEEEGA 180
|
|
| PRK08295 |
PRK08295 |
RNA polymerase sporulation sigma factor SigH; |
309-510 |
1.72e-04 |
|
RNA polymerase sporulation sigma factor SigH;
Pssm-ID: 181361 [Multi-domain] Cd Length: 208 Bit Score: 42.97 E-value: 1.72e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 309 EKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENV 388
Cdd:PRK08295 27 EYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIITAIKTANRQKHIPLNS 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16604647 389 YmllgkVSearktcvqegnyrpskeelaghvgvstekLDKLLYNtrtplsmqqpiwSDQDTTFQEITPDSGIETP-TMSV 467
Cdd:PRK08295 107 Y-----VS-----------------------------LDKPIYD------------EESDRTLLDVISEAKVTDPeELII 140
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 16604647 468 GKQLMRNHVRNLLNVLSPKERRIIKLRfgIDGgkqRSLSEIGE 510
Cdd:PRK08295 141 SKEELEDIEEKIEELLSELEKEVLELY--LDG---KSYQEIAE 178
|
|
| PRK09648 |
PRK09648 |
RNA polymerase sigma factor ShbA; |
473-532 |
7.20e-03 |
|
RNA polymerase sigma factor ShbA;
Pssm-ID: 236607 [Multi-domain] Cd Length: 189 Bit Score: 38.03 E-value: 7.20e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 16604647 473 RNHVRNLLNVLSPKERRIIKLRF--GIdggkqrSLSEIGEIYGLSKERVRQLESRALYRLKQ 532
Cdd:PRK09648 130 SNRMRELLDTLPEKQREILILRVvvGL------SAEETAEAVGSTPGAVRVAQHRALARLRA 185
|
|
| Sigma70_r4_2 |
pfam08281 |
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
476-530 |
9.79e-03 |
|
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.
Pssm-ID: 400535 [Multi-domain] Cd Length: 54 Bit Score: 34.35 E-value: 9.79e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 16604647 476 VRNLLNVLSPKERRIIKLRFgIDGgkqRSLSEIGEIYGLSKERVRQLESRALYRL 530
Cdd:pfam08281 4 LLRALEELPPRQREVFLLRY-LEG---LSYAEIAELLGISEGTVKSRLSRARKKL 54
|
|
| |
