|
Name |
Accession |
Description |
Interval |
E-value |
| RpoD |
COG0568 |
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ... |
498-792 |
5.51e-79 |
|
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: 255.36 E-value: 5.51e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 498 LRVIGRYGLLTAEEEVVLGTRRRAGaeaaaalergefttrrertrlerrvrdGRRAWEAFICANLRLVVSISTHYSaHRG 577
Cdd:COG0568 3 LREIGRVPLLTAEEEVELARRIQAG---------------------------DEEAKRKLVEANLRLVVSIAKKYQ-GRG 54
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 578 iagLDPIDLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSRTIRVPVHADEQIKKIRRSAEQVVAAHp 657
Cdd:COG0568 55 ---LPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQEL- 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 658 elvtaedgGRRAVVSRVAELLDESIERVEWLLARDAPIQSLGEPrwIVEDDRVTLGtlaELLPDERT---EQEFEELERT 734
Cdd:COG0568 131 --------GREPTPEEIAEELGVPEEKVREMLRLAREPVSLDAP--VGDDEDSELG---DLLEDEEApspEEALEEELLR 197
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*...
gi 1788635277 735 EIVESLLLSLDQRERLVLEARFGLLTGEEETLDQVGARLGVTRERARQIQKKALEALR 792
Cdd:COG0568 198 EELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLR 255
|
|
| Sig70-cyanoRpoD |
TIGR02997 |
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ... |
492-792 |
2.13e-66 |
|
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: 222.89 E-value: 2.13e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 492 DAFHDWLRVIGRYGLLTAEEEVVLG-------------TRRRAGAEAAAALERGEFTTRRERTRLERRVRDGRRAWEAFI 558
Cdd:TIGR02997 1 DLVRLYLQEIGRVPLLTPEEEIELArqvqqmmvleelrEELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 559 CANLRLVVSISTHYSAHrgiaGLDPIDLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSRTIRVPVHA 638
Cdd:TIGR02997 81 KANLRLVVSVAKKYQNR----GLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHI 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 639 DEQIKKIRRsaeqvvaAHPELVTAEdgGRRAVVSRVAELLDESIERVEWLLARDAPIQSLGEPrwIVEDDRVTLGtlaEL 718
Cdd:TIGR02997 157 TEKLNKIKK-------VQRELSQKL--GRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAP--VGDEEDTELG---DL 222
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1788635277 719 LPDErTEQEFEELERT---EIVESLLLSLDQRERLVLEARFGLLTGEEETLDQVGARLGVTRERARQIQKKALEALR 792
Cdd:TIGR02997 223 LEDD-GESPEEQVEREslrQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
|
|
| RpoD_Cterm |
TIGR02393 |
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ... |
558-792 |
1.34e-63 |
|
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc. [Transcription, Transcription factors]
Pssm-ID: 274108 [Multi-domain] Cd Length: 238 Bit Score: 212.93 E-value: 1.34e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 558 ICANLRLVVSISTHYsAHRGiagLDPIDLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSRTIRVPVH 637
Cdd:TIGR02393 6 VESNLRLVVSIAKKY-TNRG---LSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 638 ADEQIKKIRRSAEQVVAahpELvtaedgGRRAVVSRVAELLDESIERVEWL--LARDaPIqSLGEPrwIVEDDRVTLGTL 715
Cdd:TIGR02393 82 MVETINKLIKAERQLTQ---EL------GREPTDEELAERMGMPAEKVREIkkIAQE-PI-SLETP--IGEEEDSFLGDF 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 716 AE----LLPDERTEQefeELERTEIvESLLLSLDQRERLVLEARFGLLTGEEETLDQVGARLGVTRERARQIQKKALEAL 791
Cdd:TIGR02393 149 IEdesiESPDDAAAK---ELLREQL-DEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKL 224
|
.
gi 1788635277 792 R 792
Cdd:TIGR02393 225 R 225
|
|
| PRK05901 |
PRK05901 |
RNA polymerase sigma factor; Provisional |
453-792 |
5.05e-62 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 235640 [Multi-domain] Cd Length: 509 Bit Score: 217.56 E-value: 5.05e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 453 DDREPDLVAEPELFGLDLDGDDAAAAGPVEQAAGIHVCADAFHDWLRVIGRYGLLTAEEEVVLGTRRRAGAEAAAALERG 532
Cdd:PRK05901 172 KKEAKELEKLSDDDDFVWDEDDSEALRQARKDAKLTATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEELLAEG 251
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 533 EFTTRRERTRLERRVRDGRRAWEAFICANLRLVVSISTHYSAhRGiagLDPIDLVQESHPGLMRAVQKFDERRGLKFSTY 612
Cdd:PRK05901 252 EKLDPELRRDLQWIGRDGKRAKNHLLEANLRLVVSLAKRYTN-RG---LSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTY 327
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 613 ATWWIRQSITRALAEKSRTIRVPVHADEQIKKIRRSAEQVvaaHPELvtaedgGRRAVVSRVAELLDESIERVEWL--LA 690
Cdd:PRK05901 328 ATWWIRQAITRAMADQARTIRIPVHMVETINKLGRIEREL---LQEL------GREPTPEELAKEMGFTPEKVREIqkYN 398
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 691 RDaPIqSLGEPrwIVEDDRVTLGTLAE----LLPDERTeqEFEELerTEIVESLLLSLDQRERLVLEARFGLLTGEEETL 766
Cdd:PRK05901 399 RE-PI-SLDKT--IGKEGDSQFGDFIEdseaVSPVDAV--SFTLL--QDQLQEVLETLSEREAGVIRMRFGLTDGQPKTL 470
|
330 340
....*....|....*....|....*.
gi 1788635277 767 DQVGARLGVTRERARQIQKKALEALR 792
Cdd:PRK05901 471 DEIGQVYGVTRERIRQIESKTLRKLR 496
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
1-485 |
8.84e-58 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 207.18 E-value: 8.84e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 1 MARMLYQWQQEAFEAWAAH----EHRGVIEAITGSGKTRLGVLAArAALMAGYKVVVMVPTIELLDQWMRTLHDELPevt 76
Cdd:COG1061 77 TSFELRPYQQEALEALLAAlergGGRGLVVAPTGTGKTVLALALA-AELLRGKRVLVLVPRRELLEQWAEELRRFLG--- 152
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 77 vGRLGGGRHDDLHRhDLVIGTVHSIAPtfdHDAVPLLSRHRqGLVIADECHRYAADRFAGALsEHFD--WRLGLTATYER 154
Cdd:COG1061 153 -DPLAGGGKKDSDA-PITVATYQSLAR---RAHLDELGDRF-GLVIIDEAHHAGAPSYRRIL-EAFPaaYRLGLTATPFR 225
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 155 ADGLHEEVLdpFFGGAVHRLWYDRALAEGVIAPFDIALVGVELDaGPRARYDALSKQIRETrqallgylpadvrdrhagg 234
Cdd:COG1061 226 SDGREILLF--LFDGIVYEYSLKEAIEDGYLAPPEYYGIRVDLT-DERAEYDALSERLREA------------------- 283
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 235 agegvpfpvllrfvtawaaspeesprrtlasrllgsiaerrgLLADAPAKIDAVGALAPAVRRAHGSLVFAETKDAARAA 314
Cdd:COG1061 284 ------------------------------------------LAADAERKDKILRELLREHPDDRKTLVFCSSVDHAEAL 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 315 SARLADAGLRTAAVYSGLGREERHDRLGRLRDGEIDVLAAPRVLDEGIDVPDADLGIVVAASRSRRQMVQRLGRVIrrkR 394
Cdd:COG1061 322 AELLNEAGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILLRPTGSPREFIQRLGRGL---R 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 395 PPRAGRLVHLYALRTVEDPEVsgDEHLAAVLEHARRHRVFTGVDDPGLLPFLVEPVPVDDREPDLVAEPELFGLDLDGDD 474
Cdd:COG1061 399 PAPGKEDALVYDFVGNDVPVL--EELAKDLRDLAGYRVEFLDEEESEELALLIAVKPALEVKGELEEELLEELELLEDAL 476
|
490
....*....|.
gi 1788635277 475 AAAAGPVEQAA 485
Cdd:COG1061 477 LLVLAELLLLE 487
|
|
| rpoS_proteo |
TIGR02394 |
RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds ... |
484-792 |
1.88e-57 |
|
RNA polymerase sigma factor RpoS; 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 RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393). [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]
Pssm-ID: 131447 [Multi-domain] Cd Length: 285 Bit Score: 198.03 E-value: 1.88e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 484 AAGIHVCADAFHDWLRVIGRYGLLTAEEEVVLGTRRRAGAEAaaalergefttrrertrlerrvrdgrrAWEAFICANLR 563
Cdd:TIGR02394 5 AETETRVADVTQLYLREIGFKPLLTAEEEIAYARRALAGDFE---------------------------ARKVMIESNLR 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 564 LVVSISTHYsAHRGIAGLDpidLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSRTIRVPVHADEQIK 643
Cdd:TIGR02394 58 LVVSIAKHY-VNRGLPLLD---LIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKELN 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 644 KIRRSAEQVvaahpelvtAEDGGRRAVVSRVAELLDESIERVEWLLARDAPIQSLGEPrwiVEDDRVTlgTLAELLPDER 723
Cdd:TIGR02394 134 VYLRAARQL---------EKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAP---LDDDSSK--SLLDTIADEQ 199
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1788635277 724 TEQEFEELERTEI---VESLLLSLDQRERLVLEARFGLLTGEEETLDQVGARLGVTRERARQIQKKALEALR 792
Cdd:TIGR02394 200 SIDPESLVQNDDLkqlIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLR 271
|
|
| PRK07921 |
PRK07921 |
RNA polymerase sigma factor SigB; Reviewed |
491-792 |
1.05e-54 |
|
RNA polymerase sigma factor SigB; Reviewed
Pssm-ID: 181169 [Multi-domain] Cd Length: 324 Bit Score: 191.87 E-value: 1.05e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 491 ADAFHDWLRVIGRYGLLTAEEEVVLGTRRRAGAEAAAALERGEFTTRRERTRLERRVRDGRRAWEAFICANLRLVVSIST 570
Cdd:PRK07921 25 ADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHLLETRKRLSEARKRDLAAVVRDGEAARRHLLEANLRLVVSLAK 104
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 571 HYSAhRGIAGLDpidLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSRTIRVPVHADEQIKKIRRSAE 650
Cdd:PRK07921 105 RYTG-RGMPLLD---LIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKR 180
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 651 QVvaaHPELvtaedgGRRAVVSRVAELLDESIERVEWLLARDAPIQSLGEPrwIVEDDRVTLGTLAELLPDERTEQEFEE 730
Cdd:PRK07921 181 EL---HQQL------GREATDEELAEESGIPEEKIADLLEHSRDPVSLDMP--VGSDEEAPLGDFIEDSEATSAENAVIA 249
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1788635277 731 LERTEIVESLLLSLDQRERLVLEARFGLLTGEEETLDQVGARLGVTRERARQIQKKALEALR 792
Cdd:PRK07921 250 GLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLR 311
|
|
| PRK05657 |
PRK05657 |
RNA polymerase sigma factor RpoS; Validated |
437-792 |
2.20e-52 |
|
RNA polymerase sigma factor RpoS; Validated
Pssm-ID: 235548 [Multi-domain] Cd Length: 325 Bit Score: 185.16 E-value: 2.20e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 437 VDDPGLLPFLVEPVPVDDREPDLVAEPELFGLDLDGDDaaaagpveqaagihvcADAFHDWLRVIGRYGLLTAEEEVVLG 516
Cdd:PRK05657 14 FDENGVEVFDEKALVEEEPSDNDLAEEELLSQGATQRV----------------LDATQLYLNEIGYSPLLTAEEEVYFA 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 517 TRRRAGAEaaaalergefttrrertrlerrvrDGRRAweaFICANLRLVVSISTHYSaHRGIAGLDpidLVQESHPGLMR 596
Cdd:PRK05657 78 RRALRGDF------------------------AARQR---MIESNLRLVVKIAKRYL-NRGLALLD---LIEEGNLGLIR 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 597 AVQKFDERRGLKFSTYATWWIRQSITRALAEKSRTIRVPVHadeqikkIRRSAEQVVAAHPELVTAEDggRRAVVSRVAE 676
Cdd:PRK05657 127 AVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVH-------VVKELNVYLRAARELEHKLD--HEPSAEEIAE 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 677 LLDESIERVEWLLARDAPIQSLGEPRwivedDRVTLGTLAELLPDERTEQEFEELERTEIVESL---LLSLDQRERLVLE 753
Cdd:PRK05657 198 LLDKPVDDVSRMLALNERITSLDTPL-----GGDPEKSLLDILADEQENGPEDTTQDDDMKQSIvkwLFELNDKQREVLA 272
|
330 340 350
....*....|....*....|....*....|....*....
gi 1788635277 754 ARFGLLTGEEETLDQVGARLGVTRERARQIQKKALEALR 792
Cdd:PRK05657 273 RRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLR 311
|
|
| PRK09210 |
PRK09210 |
RNA polymerase sigma factor RpoD; Validated |
497-792 |
2.43e-52 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236413 [Multi-domain] Cd Length: 367 Bit Score: 186.34 E-value: 2.43e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 497 WLRVIGRYGLLTAEEEVVLGTRRRAGAEAAAalergefttrrertrlerrvrdgRRAWEAficaNLRLVVSISTHYSAhR 576
Cdd:PRK09210 101 YLKEIGRVPLLTAEEEIELAKRIEEGDEEAK-----------------------QRLAEA----NLRLVVSIAKRYVG-R 152
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 577 GIAGLDpidLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSRTIRVPVHADEQIKKIRRSAEQVVaah 656
Cdd:PRK09210 153 GMLFLD---LIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLL--- 226
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 657 pelvtaEDGGRRAVVSRVAELLDESIERV-EWLLARDAPIqSLGEPrwIVEDDRVTLGtlaELLPDERTEQEFEELERT- 734
Cdd:PRK09210 227 ------QELGREPTPEEIAEEMDMPPEKVrEILKIAQEPV-SLETP--IGEEDDSHLG---DFIEDQDATSPADHAAYEl 294
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 735 --EIVESLLLSLDQRERLVLEARFGLLTGEEETLDQVGARLGVTRERARQIQKKALEALR 792
Cdd:PRK09210 295 lkEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 354
|
|
| PRK07406 |
PRK07406 |
RNA polymerase sigma factor RpoD; Validated |
550-792 |
1.27e-51 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236012 [Multi-domain] Cd Length: 373 Bit Score: 184.60 E-value: 1.27e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 550 GRRAWEAFICANLRLVVSISTHYSAHrgiaGLDPIDLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKS 629
Cdd:PRK07406 134 GRRAKEKMVQSNLRLVVSIAKKYMNR----GLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQS 209
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 630 RTIRVPVHADEQIKKIRRSAEQVvaahpelvtAEDGGRRAVVSRVAELLDESIERVEWlLARDA--PIqSLGEPRWIVED 707
Cdd:PRK07406 210 RTIRLPVHLYETISRIKKTTKVL---------SQEFGRKPTEEEIAESMEMTIEKLRF-IAKSAqlPI-SLETPIGKEED 278
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 708 DRvtLGTLAElLPDERTEQEFEELERTEIVESLLLSLDQRERLVLEARFGLLTGEEETLDQVGARLGVTRERARQIQKKA 787
Cdd:PRK07406 279 SR--LGDFIE-ADGETPEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKA 355
|
....*
gi 1788635277 788 LEALR 792
Cdd:PRK07406 356 LRKLR 360
|
|
| PRK05949 |
PRK05949 |
RNA polymerase sigma factor; Validated |
491-794 |
1.66e-46 |
|
RNA polymerase sigma factor; Validated
Pssm-ID: 180321 [Multi-domain] Cd Length: 327 Bit Score: 168.87 E-value: 1.66e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 491 ADAFHDWLRVIGRYGLLTAEEEVVLGTRRRAGAEAAAALERGEF-------------TTRRERTRLERRVRDGRRAWEAF 557
Cdd:PRK05949 17 ADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKklgrepslpewaeAVNLSETELKQTLKQGKRAKQKM 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 558 ICANLRLVVSISTHYSAHRgiagLDPIDLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSRTIRVPVH 637
Cdd:PRK05949 97 IEANLRLVVAIAKKYQKRN----MEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIH 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 638 ADEQIKKIRRSAEQVvaahpelvtAEDGGRRAVVSRVAELLD-ESIERVEWLLARDAPIqSLgEPRwiVEDDRVTlgTLA 716
Cdd:PRK05949 173 ITEKLNKIKKTQREL---------SQKLGRSATPAEIAKELElEPSQIREYLSMARQPI-SL-DVR--VGDNQDT--ELS 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 717 ELLPDERTEQEF---EELERTEiVESLLLSLDQRERLVLEARFGLLTGEEETLDQVGARLGVTRERARQIQKKALEALRV 793
Cdd:PRK05949 238 ELLEDEGPSPDQyitQELLRQD-LNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR 316
|
.
gi 1788635277 794 R 794
Cdd:PRK05949 317 R 317
|
|
| PRK05658 |
PRK05658 |
RNA polymerase sigma factor RpoD; Validated |
551-792 |
4.82e-45 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 235549 [Multi-domain] Cd Length: 619 Bit Score: 171.90 E-value: 4.82e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 551 RRAWEAFICANLRLVVSISTHYsAHRGIAGLDpidLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSR 630
Cdd:PRK05658 379 RRAKKEMVEANLRLVISIAKKY-TNRGLQFLD---LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 454
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 631 TIRVPVHADEQIKKIRRSAEQVVAahpELvtaedgGRRAVVSRVAELLDESIERVEWLL--ARDaPIqSLGEPrwIVEDD 708
Cdd:PRK05658 455 TIRIPVHMIETINKLNRISRQMLQ---EI------GREPTPEELAERLGMPEDKVRKVLkiAKE-PI-SLETP--IGDDE 521
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 709 RVTLGTLAE----LLPDERTEQefEELErtEIVESLLLSLDQRERLVLEARFGLLTGEEETLDQVGARLGVTRERARQIQ 784
Cdd:PRK05658 522 DSHLGDFIEdknaELPIDAAIQ--ESLR--EATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 597
|
....*...
gi 1788635277 785 KKALEALR 792
Cdd:PRK05658 598 AKALRKLR 605
|
|
| PRK07598 |
PRK07598 |
RNA polymerase sigma factor SigC; Validated |
550-792 |
4.88e-45 |
|
RNA polymerase sigma factor SigC; Validated
Pssm-ID: 236067 [Multi-domain] Cd Length: 415 Bit Score: 167.35 E-value: 4.88e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 550 GRRAWEAFICANLRLVVSISTHYSAHrgiaGLDPIDLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKS 629
Cdd:PRK07598 173 GLRAKEHMIKANLRLVVSVAKKYQNR----GLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQS 248
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 630 RTIRVPVHADEQIKKIRRSAEQVvaahpelvtAEDGGRRAVVSRVAELLDESIERVEWLLARDAPIQSLgEPRwIVEDDR 709
Cdd:PRK07598 249 RTIRLPVHITEKLNKIKKAQRKI---------SQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSL-ETK-VGKDKD 317
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 710 VTLGTLAE---LLPDERTEQefEELERTeiVESLLLSLDQRERLVLEARFGLLTGEEETLDQVGARLGVTRERARQIQKK 786
Cdd:PRK07598 318 TELGDLLEtddISPEEMLMR--ESLQRD--LQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESK 393
|
....*.
gi 1788635277 787 ALEALR 792
Cdd:PRK07598 394 ALQKLR 399
|
|
| PRK07405 |
PRK07405 |
RNA polymerase sigma factor SigD; Validated |
492-794 |
1.21e-43 |
|
RNA polymerase sigma factor SigD; Validated
Pssm-ID: 180963 [Multi-domain] Cd Length: 317 Bit Score: 160.70 E-value: 1.21e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 492 DAFHDWLRVIGRYGLLTAEEEVVLGT-------------RRRAGAEAAAALERGEFTTRRERTRLERRVRDGRRAWEAFI 558
Cdd:PRK07405 8 DLVRTYLREIGRVPLLTHEEEILYGKqvqrlvalqeireELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKMV 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 559 CANLRLVVSISTHYSAHrgiaGLDPIDLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSRTIRVPVHA 638
Cdd:PRK07405 88 EANLRLVVSVAKKYLKR----NVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHI 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 639 DEQIKKIRRSAEQVvaahpelvtAEDGGRRAVVSRVAELLDESIERVEWLLARDAPIQSLgEPRwiVEDDRVTlgTLAEL 718
Cdd:PRK07405 164 TEKLNKIKKAQRQL---------SQQLGRAATIGELAEELELTPKQVREYLERARQPLSL-DLR--VGDNQDT--ELGEL 229
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1788635277 719 LPDERTEQE---FEELERTEIvESLLLSLDQRERLVLEARFGLLTGEEETLDQVGARLGVTRERARQIQKKALEALRVR 794
Cdd:PRK07405 230 LEDTGASPEdfaTQSSLQLDL-ERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR 307
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
5-151 |
3.97e-31 |
|
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350684 [Multi-domain] Cd Length: 146 Bit Score: 118.95 E-value: 3.97e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 5 LYQWQQEAFEAWAAHEH--RGVIEAITGSGKTRLGVLAARAALMAgyKVVVMVPTIELLDQWMRTLHDELPEVTVGRLGG 82
Cdd:cd17926 1 LRPYQEEALEAWLAHKNnrRGILVLPTGSGKTLTALALIAYLKEL--RTLIVVPTDALLDQWKERFEDFLGDSSIGLIGG 78
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 83 GRHDDLHRHDLVIGTVHSIAPtfdHDAVPLLSRHRQGLVIADECHRYAADRFAGALSEH-FDWRLGLTAT 151
Cdd:cd17926 79 GKKKDFDDANVVVATYQSLSN---LAEEEKDLFDQFGLLIVDEAHHLPAKTFSEILKELnAKYRLGLTAT 145
|
|
| FliA |
COG1191 |
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ... |
555-794 |
1.06e-28 |
|
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: 114.92 E-value: 1.06e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 555 EAFICANLRLVVSISTHYsAHRGIAGLDpiDLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEK---SRT 631
Cdd:COG1191 18 EELIEEYLPLVKKIASRL-AGRLPAELD--DLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDYLRDEdwvPRS 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 632 IRvpvhadEQIKKIRRSAEQVVAAHpelvtaedgGRRAVVSRVAELLDESIERV-EWLLA-RDAPIQSLGEPrwiVEDDr 709
Cdd:COG1191 95 VR------ELARKIEEAIEELEQEL---------GREPTDEEIAEELGISLEEVqEALEAaNAYQLLSLDEP---LEDG- 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 710 vtlGTLAELLPDERTEQEFEELERTEIVESLLLSLDQRERLVLEARFglltGEEETLDQVGARLGVTRERARQIQKKALE 789
Cdd:COG1191 156 ---DDLLDLLESGDPEEELEHEELREALAEAIEQLPERERLVLSLYY----FEELTLKEIAEVLGVSESRVSRLHKKALA 228
|
....*
gi 1788635277 790 ALRVR 794
Cdd:COG1191 229 RLREY 233
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
5-154 |
8.76e-26 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 104.29 E-value: 8.76e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 5 LYQWQQEAFEAWAAH----EHRGVIEAITGSGKTRLGVLAARAALMAGY--KVVVMVPTIELLDQWMRTLHDELPE-VTV 77
Cdd:pfam04851 4 LRPYQIEAIENLLESikngQKRGLIVMATGSGKTLTAAKLIARLFKKGPikKVLFLVPRKDLLEQALEEFKKFLPNyVEI 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 78 GRLGGGRHDDLHRHD--LVIGTVHSIApTFDHDAVPLLSRHRQGLVIADECHRYAADRFAGALsEHFD--WRLGLTATYE 153
Cdd:pfam04851 84 GEIISGDKKDESVDDnkIVVTTIQSLY-KALELASLELLPDFFDVIIIDEAHRSGASSYRNIL-EYFKpaFLLGLTATPE 161
|
.
gi 1788635277 154 R 154
Cdd:pfam04851 162 R 162
|
|
| rpoH_proteo |
TIGR02392 |
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ... |
558-792 |
8.88e-25 |
|
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: 104.67 E-value: 8.88e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 558 ICANLRLVVSISTHYSAHrgiaGLDPIDLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSRTIRVPVH 637
Cdd:TIGR02392 41 VLSHLRFVVKIARGYRGY----GLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATT 116
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 638 AdEQIK---KIRRSAEQVVAA-HPELVTAedggrravvsrVAELLDESIERV----EWLLARDApiqSLGEPrwiVEDDR 709
Cdd:TIGR02392 117 K-AQRKlffNLRKMKKRLQGWlNPEEVEA-----------IAEELGVSEREVremeSRLSGQDM---SLNAS---IDDDE 178
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 710 VTLGTLAELLPDERTEQE--FEELE----RTEIVESLLLSLDQRERLVLEARFglLTGEEETLDQVGARLGVTRERARQI 783
Cdd:TIGR02392 179 DDGGAPIAYLVDKRSDPEdtLEEEQweelQRQALANALGSLDARSRRIIEARW--LDDDKLTLQELAAEYGVSAERIRQI 256
|
....*....
gi 1788635277 784 QKKALEALR 792
Cdd:TIGR02392 257 EKNAMKKLK 265
|
|
| SF2_C_XPB |
cd18789 |
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
257-407 |
9.61e-25 |
|
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350176 [Multi-domain] Cd Length: 153 Bit Score: 100.79 E-value: 9.61e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 257 ESPRRTLASRLLGSIAERRGLLADAPAKIDAVGALAPAVRRAHGSLVFAETKDAARAASARladagLRTAAVYSGLGREE 336
Cdd:cd18789 8 MTPEFYREYLGLGAHRKRRLLAAMNPNKLRALEELLKRHEQGDKIIVFTDNVEALYRYAKR-----LLKPFITGETPQSE 82
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1788635277 337 RHDRLGRLRDGEIDVLAAPRVLDEGIDVPDADLGIVVAASR-SRRQMVQRLGRVIRRKrpPRAGRLVHLYAL 407
Cdd:cd18789 83 REEILQNFREGEYNTLVVSKVGDEGIDLPEANVAIQISGHGgSRRQEAQRLGRILRPK--KGGGKNAFFYSL 152
|
|
| SigBFG |
TIGR02980 |
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ... |
551-792 |
3.63e-24 |
|
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: 101.53 E-value: 3.63e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 551 RRAWEAFICANLRLVVSISTHYSaHRGiAGLDpiDLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSR 630
Cdd:TIGR02980 2 KEAREKLVELNLPLVRSIARRFR-NRG-EPHE--DLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTW 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 631 TIRVPVHADEQIKKIRRSAEQVVAAHpelvtaedgGRRAVVSRVAELLDESIERV-EWLLARDA-PIQSLGEPrwiVEDD 708
Cdd:TIGR02980 78 AVRVPRRLKELGVKINKATEELTQRL---------GRSPTIAEIAERLGVSEEEVvEALEAGNAyQALSLDAS---IEDD 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 709 RVTLGTLAELLPDErtEQEFEELERTEIVESLLLSLDQRERLVLEARFglltGEEETLDQVGARLGVTRERARQIQKKAL 788
Cdd:TIGR02980 146 DGDPIALLDTLGDE--DDALETVEDRLALKPLLAALPERERRILLLRF----FEDKTQSEIAERLGISQMHVSRLLRRAL 219
|
....
gi 1788635277 789 EALR 792
Cdd:TIGR02980 220 KKLR 223
|
|
| rpoH2 |
PRK07500 |
RNA polymerase factor sigma-32; Reviewed |
551-793 |
5.90e-23 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 236033 [Multi-domain] Cd Length: 289 Bit Score: 99.72 E-value: 5.90e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 551 RRAWEAFICANLRLVVSISTHYSAHrgiaGLDPIDLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSR 630
Cdd:PRK07500 39 EDALHRIISAHMRLVISMAGKFRRF----GLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWS 114
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 631 TIRVPVHADEQ--IKKIRRSAEQVVAAHPELVtaedggRRAVVSRVAELLDESIERVEWLLAR--------DAPIQSLGE 700
Cdd:PRK07500 115 IVRGGTSSAQKalFFNLRRLRARLAQADEELT------KQEIHREIATALGVSLSDVEMMDARlsgpdaslNAPQSEEDE 188
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 701 PR--WI--VEDDrvtlgtlaELLPDERTEQEFEELERTEIVESLLLSLDQRERLVLEARfgLLTGEEETLDQVGARLGVT 776
Cdd:PRK07500 189 GRseRMdfLVDD--------SPLPDEQVESSIDGERRRRWLTQALQTLNERELRIIRER--RLREDGATLEALGEELGIS 258
|
250
....*....|....*..
gi 1788635277 777 RERARQIQKKALEALRV 793
Cdd:PRK07500 259 KERVRQIEARALEKLRR 275
|
|
| PRK06596 |
PRK06596 |
RNA polymerase factor sigma-32; Reviewed |
558-792 |
2.25e-22 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 235838 [Multi-domain] Cd Length: 284 Bit Score: 97.94 E-value: 2.25e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 558 ICANLRLVVSISTHYSAHrgiaGLdPI-DLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITralaE---KSRTIr 633
Cdd:PRK06596 54 VLSHLRFVVHIARGYRGY----GL-PQaDLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIH----EyilRNWRI- 123
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 634 VPVHADEQIKK----IRRSAEQVVAAHPELVT--AEDGGrravVSRvaellDESIERVEWLLARDApiqSLGEPrwiVED 707
Cdd:PRK06596 124 VKVATTKAQRKlffnLRKAKKRLGWLNPEEVEmvAEELG----VSE-----EEVREMESRLSGQDA---SLDAP---IDD 188
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 708 DRVTLGTLAELLPDERTEQEfEELE-------RTEIVESLLLSLDQRERLVLEARFglLTGEEETLDQVGARLGVTRERA 780
Cdd:PRK06596 189 DDEESGAPQDYLEDKSSDPA-DVLEednwedqRRALLADALEGLDERSRDIIEARW--LDDDKSTLQELAAEYGVSAERV 265
|
250
....*....|..
gi 1788635277 781 RQIQKKALEALR 792
Cdd:PRK06596 266 RQIEKNAMKKLK 277
|
|
| PRK05572 |
PRK05572 |
RNA polymerase sporulation sigma factor, SigF/SigG family; |
561-792 |
3.08e-19 |
|
RNA polymerase sporulation sigma factor, SigF/SigG family;
Pssm-ID: 180137 [Multi-domain] Cd Length: 252 Bit Score: 88.10 E-value: 3.08e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 561 NLRLVVSISTHYSAHrgiaGLDPIDLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSrTIRVPVHADE 640
Cdd:PRK05572 41 NLRLVWSVVQRFLNR----GYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKE 115
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 641 QIKKIRRSAEQVVAAHpelvtaedgGRRAVVSRVAELLDESIERVewLLARDA--PIQSLGEPrwIVEDDrvtlG---TL 715
Cdd:PRK05572 116 TANKIRKDKDELSKEL---------GREPTIEELAEYLGVTPEEV--VLAQEAsrSPQSIHET--VHEND----GdpiTL 178
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1788635277 716 AELLPDERTEQEFEELERTEIVEslllSLDQRERLVLEARFglltGEEETLDQVGARLGVTRERARQIQKKALEALR 792
Cdd:PRK05572 179 LDQIADQSEEDWFDKIALKEAIR----ELDERERLIVYLRY----FKDKTQSEVAKRLGISQVQVSRLEKKILKQMK 247
|
|
| spore_sigF |
TIGR02885 |
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma ... |
553-792 |
8.04e-19 |
|
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: 86.31 E-value: 8.04e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 553 AWEAFICANLRLVVSISTHYSaHRGiagLDPIDLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSrTI 632
Cdd:TIGR02885 12 ARDKLIECNLRLVWSIVKRFL-NRG---YEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-II 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 633 RVPVHADEQIKKIRRSAEQVVAahpELvtaedgGRRAVVSRVAELLDESIERVEWLLARDAPIQSLGEPRWIVEDDRVtl 712
Cdd:TIGR02885 87 KVSRSLKELARKIRYMKEELSK---EL------GREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPI-- 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 713 gTLAELLPDERTEQE--FEELERTEIVEslllSLDQRERLVLEARFglltGEEETLDQVGARLGVTRERARQIQKKALEA 790
Cdd:TIGR02885 156 -YLLDQIADKGSEDSdwLEKIALKEAIS----KLDERERQIIMLRY----FKDKTQTEVANMLGISQVQVSRLEKKVLKK 226
|
..
gi 1788635277 791 LR 792
Cdd:TIGR02885 227 MK 228
|
|
| FliA_WhiG |
TIGR02479 |
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ... |
585-792 |
5.96e-18 |
|
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: 83.48 E-value: 5.96e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 585 DLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSI---TRALAEKSRTIRvpvhadEQIKKIRRSAEQVVAAHpelvt 661
Cdd:TIGR02479 28 DLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMldeLRRLDWVPRSLR------QKARKLERAIRELEARL----- 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 662 aedgGRRAVVSRVAELLDESIERVEWLL--ARDAPIQSLGEprwiVEDDRVTLGTLAELLPDERTEQEFEELERTEIVES 739
Cdd:TIGR02479 97 ----GREPTEEEIAEELGMDLKEYRQALneINALSLVSLDE----LLESGDDGGSLIDRIEDDKSEDPEEELEREELREA 168
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*.
gi 1788635277 740 L---LLSLDQRERLVLEarfgLLTGEEETLDQVGARLGVTRERARQIQKKALEALR 792
Cdd:TIGR02479 169 LaeaIESLSEREQLVLS----LYYYEELNLKEIGEVLGLTESRVSQIHSQALKKLR 220
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
5-159 |
6.64e-18 |
|
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350790 [Multi-domain] Cd Length: 163 Bit Score: 81.45 E-value: 6.64e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 5 LYQWQQEA----FEAWAAHEHRGVIEAITGSGKTRLGVLAARAALMAGY--KVVVMVPTIELLDQWMRTLHDELPEVTVG 78
Cdd:cd18032 1 PRYYQQEAiealEEAREKGQRRALLVMATGTGKTYTAAFLIKRLLEANRkkRILFLAHREELLEQAERSFKEVLPDGSFG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 79 RLGGGRHDDLhRHDLVIGTVHSIAPTFDHDAvplLSRHRQGLVIADECHRYAADRFAGALsEHFD--WRLGLTATYERAD 156
Cdd:cd18032 81 NLKGGKKKPD-DARVVFATVQTLNKRKRLEK---FPPDYFDLIIIDEAHHAIASSYRKIL-EYFEpaFLLGLTATPERTD 155
|
...
gi 1788635277 157 GLH 159
Cdd:cd18032 156 GLD 158
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
5-151 |
1.08e-17 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 82.15 E-value: 1.08e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 5 LYQWQQEAFEAWAAHEHRGVIEAITGSGKTRLGVLAARAALMAGY--KVVVMVPTIELLDQWMRTLHDELPE---VTVGR 79
Cdd:smart00487 9 LRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKggRVLVLVPTRELAEQWAEELKKLGPSlglKVVGL 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 80 LGGGRHDDLHRH------DLVIGTVHSIaptFDHDAVPLLSRHRQGLVIADECHRYAADRFAGALSEHFDW------RLG 147
Cdd:smart00487 89 YGGDSKREQLRKlesgktDILVTTPGRL---LDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLlpknvqLLL 165
|
....
gi 1788635277 148 LTAT 151
Cdd:smart00487 166 LSAT 169
|
|
| PRK07670 |
PRK07670 |
FliA/WhiG family RNA polymerase sigma factor; |
571-792 |
6.02e-17 |
|
FliA/WhiG family RNA polymerase sigma factor;
Pssm-ID: 181075 [Multi-domain] Cd Length: 251 Bit Score: 81.24 E-value: 6.02e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 571 HYSAHRGIAGL----DPIDLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKS---RTIRvpvhadEQIK 643
Cdd:PRK07670 36 HYHVQRISVGLpksvSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKEDwlpRSMR------EKTK 109
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 644 KIRRSAEQVVAAHpelvtaedgGRRAVVSRVAELLDESIERVEWLLARD--APIQSLGEPrwIVEDDRVTLGTLAelLPD 721
Cdd:PRK07670 110 KVEAAIEKLEQRY---------MRNVTPKEVAAELGMTEEEVEATMNEGffANLLSIDEK--THDQDDGENVSVT--IRD 176
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1788635277 722 ERTEQEFEELERTEIVESL---LLSLDQRERLVLearfGLLTGEEETLDQVGARLGVTRERARQIQKKALEALR 792
Cdd:PRK07670 177 DKTPTPEEKLLKEELIEELaekIKQLSEKEQLVI----SLFYKEELTLTEIGQVLNLSTSRISQIHSKALFKLK 246
|
|
| PRK05911 |
PRK05911 |
RNA polymerase sigma factor sigma-28; Reviewed |
574-792 |
8.89e-16 |
|
RNA polymerase sigma factor sigma-28; Reviewed
Pssm-ID: 235644 [Multi-domain] Cd Length: 257 Bit Score: 78.12 E-value: 8.89e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 574 AHRGIAGL----DPIDLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSRTIRvPVHadeqiKKIRRSA 649
Cdd:PRK05911 40 AHRLISGMpshvKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQDWVPR-SVH-----QKANKLA 113
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 650 EQVVAAHPELvtaedgGRRAVVSRVAELLDESIERVE-WLL-ARDAPIQSLGEPRWIVEDDRVTLGtLAELLPDERTEQE 727
Cdd:PRK05911 114 DAMDSLRQSL------GKEPTDGELCEYLNISQQELSgWFSsARPALILSLNEEFPCQSDDEAGLA-LEERIADERAETG 186
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1788635277 728 FEELERTE---IVESLLLSLDQRERLVLearfGLLTGEEETLDQVGARLGVTRERARQIQKKALEALR 792
Cdd:PRK05911 187 YDVVDKKEfssILAEAILALEEKERKVM----ALYYYEELVLKEIGKILGVSESRVSQIHSKALLKLR 250
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
20-151 |
1.69e-13 |
|
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region.
Pssm-ID: 350668 [Multi-domain] Cd Length: 146 Bit Score: 68.58 E-value: 1.69e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 20 EHRGVIEAITGSGKTRLGVLAA-RAALMAGYKVVVMVPTIELLDQWMRTLHDELPE-VTVGRLGGGRhDDLHRH------ 91
Cdd:cd00046 1 GENVLITAPTGSGKTLAALLAAlLLLLKKGKKVLVLVPTKALALQTAERLRELFGPgIRVAVLVGGS-SAEEREknklgd 79
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1788635277 92 -DLVIGTVHSIapTFDHDAVPLLSRHRQGLVIADECHRYA-ADRFAGALSEHFDW-------RLGLTAT 151
Cdd:cd00046 80 aDIIIATPDML--LNLLLREDRLFLKDLKLIIVDEAHALLiDSRGALILDLAVRKaglknaqVILLSAT 146
|
|
| PRK07408 |
PRK07408 |
RNA polymerase sigma factor SigF; Reviewed |
585-792 |
7.15e-13 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 180965 [Multi-domain] Cd Length: 256 Bit Score: 69.18 E-value: 7.15e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 585 DLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSRTIRVP---VHADEQIKKIRRSAEQVVaahpelvt 661
Cdd:PRK07408 55 DLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPrrwQELQRQAKKVRQELRQEL-------- 126
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 662 aedgGRRAVVSRVAELLDESIErvEW-----------LLARDAPIQSlgeprwiVEDDRVTLGtlaELLPDERT-EQEFE 729
Cdd:PRK07408 127 ----GRQPTDQEIAQALDISLE--EWqeiklalqnrtPLSLDAPVNQ-------DEDGSTSLG---DLLPDPRYrSFQLA 190
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1788635277 730 ELERTEIVESLLLsLDQRERLVLEARFglltGEEETLDQVGARLG-----VTreraRQIqKKALEALR 792
Cdd:PRK07408 191 QEDRIRLQQALAQ-LEERTREVLEFVF----LHDLTQKEAAERLGispvtVS----RRV-KKGLDQLK 248
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
322-393 |
3.71e-12 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 62.61 E-value: 3.71e-12
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1788635277 322 GLRTAAVYSGLGREERHDRLGRLRDGEIDVLAAPRVLDEGIDVPDADLGIVVAASRSRRQMVQRLGRVIRRK 393
Cdd:smart00490 11 GIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82
|
|
| PRK08215 |
PRK08215 |
RNA polymerase sporulation sigma factor SigG; |
553-792 |
1.93e-11 |
|
RNA polymerase sporulation sigma factor SigG;
Pssm-ID: 181296 [Multi-domain] Cd Length: 258 Bit Score: 64.97 E-value: 1.93e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 553 AWEAFICANLRLVVSISTHYSaHRGiAGLDpiDLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSrTI 632
Cdd:PRK08215 38 AREKLINGNLRLVLSVIQRFN-NRG-ENVD--DLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PI 112
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 633 RVPvhadeqiKKIRRSAEQVVAAHPELVTAEDggRRAVVSRVAELLDesIERVEWLLARDApIQ---SLGEPrwIVEDDR 709
Cdd:PRK08215 113 RVS-------RSLRDIAYKALQVREKLINENS--KEPTVEEIAKELE--VPREEVVFALDA-IQdpvSLFEP--IYHDGG 178
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 710 VTLgTLAELLPDERTEQEfEELERTEIVESLLLsLDQRERLVLEARFglltGEEETLDQVGARLGVTRERARQIQKKALE 789
Cdd:PRK08215 179 DPI-YVMDQISDEKNKDE-NWLEEIALKEAMKK-LNDREKLILNLRF----FQGKTQMEVAEEIGISQAQVSRLEKAALK 251
|
...
gi 1788635277 790 ALR 792
Cdd:PRK08215 252 HMR 254
|
|
| PRK08583 |
PRK08583 |
RNA polymerase sigma factor SigB; Validated |
564-792 |
2.06e-11 |
|
RNA polymerase sigma factor SigB; Validated
Pssm-ID: 236306 [Multi-domain] Cd Length: 257 Bit Score: 65.10 E-value: 2.06e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 564 LVVSISTHYSAHRGIAGldpiDLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSRTIRVPVHADEQIK 643
Cdd:PRK08583 41 LVESLAYKYSKGQSHHE----DLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGP 116
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 644 KIRRSAEqvvaahpELVTaeDGGRRAVVSRVAELLDESIERVEWLLARDAPIQSLGEPRWIVEDDRVTLGTLAELLPDEr 723
Cdd:PRK08583 117 KIKKAVD-------ELTT--ELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGSTVTLLDIVGQQ- 186
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1788635277 724 tEQEFEELERTEIVESLLLSLDQRERLVLEARFglltgeEETLDQ--VGARLGVTRERARQIQKKALEALR 792
Cdd:PRK08583 187 -EDGYELTEQRMILEKILPVLSDREKSIIQCTF------IENLSQkeTGERLGISQMHVSRLQRQAIKKLR 250
|
|
| Sigma70_r4 |
pfam04545 |
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
740-792 |
2.88e-11 |
|
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: 58.98 E-value: 2.88e-11
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 1788635277 740 LLLSLDQRERLVLEARFGlltgEEETLDQVGARLGVTRERARQIQKKALEALR 792
Cdd:pfam04545 1 ALASLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKLR 49
|
|
| PRK06288 |
PRK06288 |
RNA polymerase sigma factor WhiG; Reviewed |
585-792 |
3.03e-11 |
|
RNA polymerase sigma factor WhiG; Reviewed
Pssm-ID: 235770 [Multi-domain] Cd Length: 268 Bit Score: 64.71 E-value: 3.03e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 585 DLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALaeksRTIrvpvhaDEQIKKIRRSAEQVVAAHPELVTAEd 664
Cdd:PRK06288 63 DLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDEL----RSI------DWIPRSVRQKARQIERAIAMLEARL- 131
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 665 gGRRAVVSRVAELLDESIERVEWLLAR--DAPIQSLGEPRWIVED-DRVTLG-TL---AELLPDERTEQefEELERTeIV 737
Cdd:PRK06288 132 -GRTPSDEEIADELGISLEEYNSLLSKlsGTSVVSLNDLWFGGDEgDEVSLMdTLespAALNPDEIAER--EEIKRV-IV 207
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 1788635277 738 ESlLLSLDQRERLVLEarfgLLTGEEETLDQVGARLGVTRERARQIQKKALEALR 792
Cdd:PRK06288 208 EA-IKTLPEREKKVLI----LYYYEDLTLKEIGKVLGVTESRISQLHTKAVLQLR 257
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
302-393 |
3.82e-11 |
|
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 60.69 E-value: 3.82e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 302 LVFAETKDAARAASARLADaGLRTAAVYSGLGREERHDRLGRLRDGEIDVLAAPRVLDEGIDVPDADLGIVVAASRSRRQ 381
Cdd:pfam00271 19 LIFSQTKKTLEAELLLEKE-GIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNPAS 97
|
90
....*....|..
gi 1788635277 382 MVQRLGRVIRRK 393
Cdd:pfam00271 98 YIQRIGRAGRAG 109
|
|
| PRK07122 |
PRK07122 |
RNA polymerase sigma factor SigF; Reviewed |
585-792 |
1.53e-10 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 168831 [Multi-domain] Cd Length: 264 Bit Score: 62.49 E-value: 1.53e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 585 DLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSRTIRVPvhadeqiKKIRRSAEQVVAAHPELvtAED 664
Cdd:PRK07122 69 DLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP-------RRLKELHLRLGRATAEL--SQR 139
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 665 GGRRAVVSRVAELLD-ESIERVEWLLARDA-PIQSLGEPrwiVEDDRVTLGTLAELLPDErtEQEFEELERTEIVESLLL 742
Cdd:PRK07122 140 LGRAPTASELAAELGmDREEVVEGLVAGSAyNTLSIDSG---GGSGDDDARAIADTLGDV--DAGLDQIENREALRPLLA 214
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 1788635277 743 SLDQRERLVLEARFglltGEEETLDQVGARLGVTRERARQIQKKALEALR 792
Cdd:PRK07122 215 ALPERERTVLVLRF----FESMTQTQIAERVGISQMHVSRLLAKTLARLR 260
|
|
| Sigma70_r2 |
pfam04542 |
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ... |
560-631 |
4.59e-10 |
|
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: 56.06 E-value: 4.59e-10
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1788635277 560 ANLRLVVSISTHYSAHrgiaGLDPIDLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSRT 631
Cdd:pfam04542 4 RYLPLVYSLARRYLGD----GADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
9-154 |
6.66e-10 |
|
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 58.79 E-value: 6.66e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 9 QQEAFEAwaAHEHRGVI-EAITGSGKTRLGVLAARAAL---MAGYKVVVMVPTIELLDQWMRTLHD--ELPEVTVGRLGG 82
Cdd:pfam00270 4 QAEAIPA--ILEGRDVLvQAPTGSGKTLAFLLPALEALdklDNGPQALVLAPTRELAEQIYEELKKlgKGLGLKVASLLG 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 83 G-----RHDDLHRHDLVIGTvhsiaPTFDHDAVPLLSRHRQ-GLVIADECHRYAADRFAGALSEHFD------WRLGLTA 150
Cdd:pfam00270 82 GdsrkeQLEKLKGPDILVGT-----PGRLLDLLQERKLLKNlKLLVLDEAHRLLDMGFGPDLEEILRrlpkkrQILLLSA 156
|
....
gi 1788635277 151 TYER 154
Cdd:pfam00270 157 TLPR 160
|
|
| sigma70-ECF |
TIGR02937 |
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ... |
552-792 |
4.91e-09 |
|
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: 55.82 E-value: 4.91e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 552 RAWEAFICANLRLVVSISTHYSAHRgiagLDPIDLVQESHPGLMRAVQKFDERRglKFSTYATWWIRQSITRALAEKSRt 631
Cdd:TIGR02937 1 EAFEELYERYLPLVYRYARRYLGDD----ADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFRIARNLILDYLRRKRR- 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 632 irvpvhadeqikkirrsaeqvvaahpelvtaedggRRAVVSRVAELLDEsiervewllardapiqslgeprwiveddrvt 711
Cdd:TIGR02937 74 -----------------------------------LRRELDLLEELLDS------------------------------- 87
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 712 lgtlaellpDERTEQEFEELERTEIVESLLLSLDQRERLVLEARFGlltgEEETLDQVGARLGVTRERARQIQKKALEAL 791
Cdd:TIGR02937 88 ---------DPSPEEELEQEEEREALREALEKLPEREREVLVLRYL----EGLSYKEIAEILGISVGTVKRRLKRARKKL 154
|
.
gi 1788635277 792 R 792
Cdd:TIGR02937 155 R 155
|
|
| PRK05803 |
PRK05803 |
RNA polymerase sporulation sigma factor SigK; |
561-791 |
1.01e-08 |
|
RNA polymerase sporulation sigma factor SigK;
Pssm-ID: 180266 [Multi-domain] Cd Length: 233 Bit Score: 56.49 E-value: 1.01e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 561 NLRLVVSISTHYSAhrgiAGLDPIDLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALaeksrtirvpvhadE 640
Cdd:PRK05803 58 NLRLVAHIVKKFEN----TGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHL--------------R 119
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 641 QIKKIRrsaeQVVAAHPELVTAEDGGRravvsrvAELLDesiervewllardapiqslgeprwiveddrvTLGTLAELLp 720
Cdd:PRK05803 120 NLKKTK----KEVSLQDPIGVDKEGNE-------ISLID-------------------------------ILGSEEDDV- 156
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1788635277 721 DERTEQEFEElertEIVESLLLSLDQRERLVLEARFGLLTGEEETLDQVGARLGVTRERARQIQKKALEAL 791
Cdd:PRK05803 157 IEQVELKMEV----EKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKL 223
|
|
| fliA |
PRK06986 |
flagellar biosynthesis sigma factor; Validated |
585-799 |
2.41e-08 |
|
flagellar biosynthesis sigma factor; Validated
Pssm-ID: 235901 [Multi-domain] Cd Length: 236 Bit Score: 55.62 E-value: 2.41e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 585 DLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSI---TRALAEKSRTIRvpvhadeqiKKIRRSAEQVVAAHPELvt 661
Cdd:PRK06986 40 DLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMldeLRSLDWVPRSVR---------RNAREVAQAIRQLEQEL-- 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 662 aedgGRRAVVSRVAELLDESIERV-EWLLARDA----PIQSLGEprwiVEDDRVTLGTLAEllpDERTEQEFEELERTEI 736
Cdd:PRK06986 109 ----GREPTDTEVAEKLGLSLEEYrEMLLDTNIsqlfSIDELRG----EHGDSILVTEDHQ---DEDPLQQLEDEELREA 177
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1788635277 737 VESLLLSLDQRERLVLearfGLLTGEEETLDQVGARLGVTRERARQIQKKALEALRVRCVEWE 799
Cdd:PRK06986 178 LVEAIESLPEREQLVL----SLYYQEELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLGEWT 236
|
|
| SF2_C_FANCM_Hef |
cd18801 |
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M ... |
330-404 |
2.95e-08 |
|
C-terminal helicase domain of Fanconi anemia group M family helicases; Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350188 [Multi-domain] Cd Length: 143 Bit Score: 53.13 E-value: 2.95e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1788635277 330 SGLGREERHDRLGRLRDGEIDVLAAPRVLDEGIDVPDADLGIVVAASRSRRQMVQRLGRVIRRkrppRAGRLVHL 404
Cdd:cd18801 72 KGMSQKEQKEVIEQFRKGGYNVLVATSIGEEGLDIGEVDLIICYDASPSPIRMIQRMGRTGRK----RQGRVVVL 142
|
|
| Sigma70_r4 |
cd06171 |
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
735-792 |
3.06e-08 |
|
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: 50.57 E-value: 3.06e-08
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 1788635277 735 EIVESLLLSLDQRERLVLEARFGlltgEEETLDQVGARLGVTRERARQIQKKALEALR 792
Cdd:cd06171 2 ERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
22-129 |
7.80e-08 |
|
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase RecG family is part of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350676 [Multi-domain] Cd Length: 180 Bit Score: 52.80 E-value: 7.80e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 22 RGVIEAITGSGKTRLGVLAARAALMAGYKVVVMVPTIELLDQWMRTLHDELPEVTVGRL-GGGRHDDLHRHDLVIGTvHS 100
Cdd:cd17918 38 DRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEARKFLPFINVELVtGGTKAQILSGISLLVGT-HA 116
|
90 100
....*....|....*....|....*....
gi 1788635277 101 IAptfdHDAVpllSRHRQGLVIADECHRY 129
Cdd:cd17918 117 LL----HLDV---KFKNLDLVIVDEQHRF 138
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
30-129 |
9.33e-08 |
|
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. It is a member of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350750 [Multi-domain] Cd Length: 225 Bit Score: 53.69 E-value: 9.33e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 30 GSGKTRLGVLAARAALMAGYKVVVMVPTiELL-DQWMRTLHDELPE--VTVGRLGG--------GRHDDLH--RHDLVIG 96
Cdd:cd17992 76 GSGKTVVAALAMLAAVENGYQVALMAPT-EILaEQHYDSLKKLLEPlgIRVALLTGstkakekrEILEKIAsgEIDIVIG 154
|
90 100 110
....*....|....*....|....*....|...
gi 1788635277 97 TvHSIAptfdHDAVPLlsrHRQGLVIADECHRY 129
Cdd:cd17992 155 T-HALI----QEDVEF---HNLGLVIIDEQHRF 179
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
5-127 |
1.47e-07 |
|
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350679 [Multi-domain] Cd Length: 181 Bit Score: 52.26 E-value: 1.47e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 5 LYQWQQEAFEAWAAHEHRGVIEAITGSGKTRLGVLAARAALMA-GYKVVVMVPTIELLDQWMRTLHDEL--PEVTVGRL- 80
Cdd:cd17921 2 LNPIQREALRALYLSGDSVLVSAPTSSGKTLIAELAILRALATsGGKAVYIAPTRALVNQKEADLRERFgpLGKNVGLLt 81
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 1788635277 81 GGGRHDDLH--RHDLVIGTVHSIAPTFDHDAVPLLSRHRqgLVIADECH 127
Cdd:cd17921 82 GDPSVNKLLlaEADILVATPEKLDLLLRNGGERLIQDVR--LVVVDEAH 128
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
8-128 |
2.57e-07 |
|
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350685 [Multi-domain] Cd Length: 201 Bit Score: 52.05 E-value: 2.57e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 8 WQQEAFEAwAAHEHRGVIEAITGSGKTRLGVLAARAAL---MAGY--KVVVMVPTIELLDQWMRTL--HDELPEVTVGRL 80
Cdd:cd17927 6 YQLELAQP-ALKGKNTIICLPTGSGKTFVAVLICEHHLkkfPAGRkgKVVFLANKVPLVEQQKEVFrkHFERPGYKVTGL 84
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....
gi 1788635277 81 GGGRHDD------LHRHDLVIGTVHSIAPTFDHDAVPLLSRHrqGLVIADECHR 128
Cdd:cd17927 85 SGDTSENvsveqiVESSDVIIVTPQILVNDLKSGTIVSLSDF--SLLVFDECHN 136
|
|
| COG0610 |
COG0610 |
Type I site-specific restriction-modification system, R (restriction) subunit and related ... |
21-188 |
4.64e-07 |
|
Type I site-specific restriction-modification system, R (restriction) subunit and related helicases ... [Defense mechanisms];
Pssm-ID: 440375 [Multi-domain] Cd Length: 936 Bit Score: 53.72 E-value: 4.64e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 21 HRGVIEAITGSGKTRLGVLAARAAL----MAGYKVVVMVPTIELLDQWMRTLHDELPEvTVGRLGGGRH--DDLHR--HD 92
Cdd:COG0610 279 KGGVIWHTQGSGKSLTMVFLAQKLArlpdLDNPTVVVVTDRKDLDDQLFDTFKAFGRE-SVVQAESRADlrELLESdsGG 357
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 93 LVIGTVHSIAPTFDHDAVPLLSRHRQGLVIADECHRYAADRFAGALSEHFD--WRLGLTAT-YERADGLHEEVldpfFGG 169
Cdd:COG0610 358 IIVTTIQKFPEALDEIKYPELSDRKNIIVIVDEAHRSQYGGLAKNMRDALPnaSFFGFTGTpIFKEDRTTLEV----FGD 433
|
170 180
....*....|....*....|.
gi 1788635277 170 AVHRlwYD--RALAEGVIAPF 188
Cdd:COG0610 434 YIHT--YTitQAIEDGATLPL 452
|
|
| DEXHc_XPB |
cd18029 |
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription ... |
23-157 |
4.71e-07 |
|
DEXH-box helicase domain of TFIIH XPB subunit and similar proteins; TFIIH basal transcription factor complex helicase XPB subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350787 [Multi-domain] Cd Length: 169 Bit Score: 50.38 E-value: 4.71e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 23 GVIEAITGSGKTRLGVLAaraalMAGYK--VVVMVPTIELLDQWMRTLHD--ELPEVTVGRLGGGRHDDLHRHDLVIGTV 98
Cdd:cd18029 29 GVIVLPCGAGKTLVGITA-----ACTIKksTLVLCTSAVSVEQWRRQFLDwtTIDDEQIGRFTSDKKEIFPEAGVTVSTY 103
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1788635277 99 HSIAPTFD--HDA---VPLLSRHRQGLVIADECHRYAADRF---AGALSEHFdwRLGLTATYERADG 157
Cdd:cd18029 104 SMLANTRKrsPESekfMEFITEREWGLIILDEVHVVPAPMFrrvLTLQKAHC--KLGLTATLVREDD 168
|
|
| SWI2_SNF2 |
pfam18766 |
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins. |
23-128 |
8.55e-07 |
|
SWI2/SNF2 ATPase; A SWi2/SNF2 ATPase found in polyvalent proteins.
Pssm-ID: 465860 [Multi-domain] Cd Length: 222 Bit Score: 50.51 E-value: 8.55e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 23 GVIEAITGSGKTRLGVLAARAAL--MAGYKVVVMVPTIELLDQWMRTLHDELPEVTV---------GRLGGGRhddlhrh 91
Cdd:pfam18766 22 GVIWHTQGSGKSLTMVFLARKLRreLKNPTVVVVTDRNDLDDQLTKTFAACGREVPVqaesrkdlrELLRGSG------- 94
|
90 100 110
....*....|....*....|....*....|....*..
gi 1788635277 92 DLVIGTVHSIApTFDHDAVPLLSRHRQGLVIADECHR 128
Cdd:pfam18766 95 GIIFTTIQKFG-ETPDEGFPVLSDRRNIIVLVDEAHR 130
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
30-128 |
9.18e-07 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 52.46 E-value: 9.18e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 30 GSGKTrlgVLAARAALMA---GYKVVVMVPTiELL-DQWMRTLHDELPEVTV------GRLGGGRHDDLHRH------DL 93
Cdd:PRK10917 292 GSGKT---VVAALAALAAieaGYQAALMAPT-EILaEQHYENLKKLLEPLGIrvalltGSLKGKERREILEAiasgeaDI 367
|
90 100 110
....*....|....*....|....*....|....*
gi 1788635277 94 VIGTvHSIaptFdHDAVPLlsrHRQGLVIADECHR 128
Cdd:PRK10917 368 VIGT-HAL---I-QDDVEF---HNLGLVIIDEQHR 394
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
5-127 |
2.45e-06 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 51.05 E-value: 2.45e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 5 LYQWQQEAFEAWAAHEHRGVIEAITGSGKTRLGVLAARAALMAGYKVVVMVPTIELLDQWMRTLHDELPE--VTVGRLGG 82
Cdd:COG1204 23 LYPPQAEALEAGLLEGKNLVVSAPTASGKTLIAELAILKALLNGGKALYIVPLRALASEKYREFKRDFEElgIKVGVSTG 102
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 1788635277 83 GRHDD---LHRHDLVIGT---VHSIaptFDHDAVPLlsrHRQGLVIADECH 127
Cdd:COG1204 103 DYDSDdewLGRYDILVATpekLDSL---LRNGPSWL---RDVDLVVVDEAH 147
|
|
| DEXHc_RE_I_HsdR |
cd18030 |
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of ... |
20-142 |
2.89e-06 |
|
DEXH-box helicase domain of type I restriction enzyme HdsR subunit; The HdsR motor subunit of type I restriction-modification enzymes contains the DNA cleavage and ATP-dependent DNA translocation activities of the heteromeric complex. It is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350788 [Multi-domain] Cd Length: 208 Bit Score: 48.76 E-value: 2.89e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 20 EHRGVIEAITGSGKTRLGVLAAR-AALMAG-YKVVVMVPTIELLDQWMRTLHDELPEvTVGRLGGGRH-DDLHRHD---L 93
Cdd:cd18030 47 KKGGYIWHTQGSGKSLTMFKAAKlLIEDPKnPKVVFVVDRKDLDYQTSSTFSRFAAE-DVVRANSTKElKELLKNLsggI 125
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 1788635277 94 VIGTVHSIAPTFDHDAVPLLSRHRQGLVIADECHRYAADRFAGALSEHF 142
Cdd:cd18030 126 IVTTIQKFNNAVKEESKPVLIYRKNIVVIVDEAHRSQFGELAKALKKAL 174
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
5-160 |
5.81e-06 |
|
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play an important role in RNA degradation, processing and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350786 [Multi-domain] Cd Length: 177 Bit Score: 47.33 E-value: 5.81e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 5 LYQWQQEAFEAWAAHEHRGVIEAITGSGKTRLGVLAARAALMAGYKVVVMVPTIELLDQWMRTLHD-ELPEVTVG-RLGG 82
Cdd:cd18028 2 LYPPQAEAVRAGLLKGENLLISIPTASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFKKlEEIGLKVGiSTGD 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 83 GRHDD--LHRHDLVIGTVHSiaptFDHdavplLSRHRQ------GLVIADECHrYAADRFAGALSEHFDWRL-------- 146
Cdd:cd18028 82 YDEDDewLGDYDIIVATYEK----FDS-----LLRHSPswlrdvGVVVVDEIH-LISDEERGPTLESIVARLrrlnpntq 151
|
170
....*....|....*.
gi 1788635277 147 --GLTATYERADGLHE 160
Cdd:cd18028 152 iiGLSATIGNPDELAE 167
|
|
| SF2_C_LHR |
cd18796 |
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
286-402 |
6.13e-06 |
|
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases. LHR family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350183 [Multi-domain] Cd Length: 150 Bit Score: 46.87 E-value: 6.13e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 286 DAVGALAPAVRRAHGSLVFAETKD------AARAASARLADAGLRTAAVYSGLGREERHDRLGRLRDGEIDVLAAPRVLD 359
Cdd:cd18796 26 DAYAEVIFLLERHKSTLVFTNTRSqaerlaQRLRELCPDRVPPDFIALHHGSLSRELREEVEAALKRGDLKVVVATSSLE 105
|
90 100 110 120
....*....|....*....|....*....|....*....|...
gi 1788635277 360 EGIDVPDADLGIVVAASRSRRQMVQRLGRVIRRKRPPRAGRLV 402
Cdd:cd18796 106 LGIDIGDVDLVIQIGSPKSVARLLQRLGRSGHRPGAASKGRLV 148
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
348-391 |
9.53e-06 |
|
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350172 [Multi-domain] Cd Length: 77 Bit Score: 44.23 E-value: 9.53e-06
10 20 30 40
....*....|....*....|....*....|....*....|....
gi 1788635277 348 EIDVLAAPRVLDEGIDVPDADLGIVVAASRSRRQMVQRLGRVIR 391
Cdd:cd18785 22 SLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGR 65
|
|
| SF2_C_dicer |
cd18802 |
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave ... |
341-388 |
3.17e-05 |
|
C-terminal helicase domain of the endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350189 [Multi-domain] Cd Length: 142 Bit Score: 44.50 E-value: 3.17e-05
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 1788635277 341 LGRLRDGEIDVLAAPRVLDEGIDVPDADLGIVVAASRSRRQMVQRLGR 388
Cdd:cd18802 83 LDKFRDGELNLLIATSVLEEGIDVPACNLVIRFDLPKTLRSYIQSRGR 130
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
9-143 |
3.35e-05 |
|
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350687 [Multi-domain] Cd Length: 178 Bit Score: 45.28 E-value: 3.35e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 9 QQEAFEA-WAAHE--HRGVIEAITGSGKTRLGVLAARAALMAGYKVVVMVPTIELLDQWMR-----------TLHDELpe 74
Cdd:cd17929 1 QRKAYEAiVSSLGgfKTFLLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKrfkkrfgdkvaVLHSKL-- 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 75 vTVGRlgggRHDDLHR-----HDLVIGTVHSI-APtfdhdaVPLLsrhrqGLVIADECH----------RYAADRFAGAL 138
Cdd:cd17929 79 -SDKE----RADEWRKikrgeAKVVIGARSALfAP------FKNL-----GLIIVDEEHdssykqdsgpRYHARDVAIYR 142
|
....*
gi 1788635277 139 SEHFD 143
Cdd:cd17929 143 AKLEN 147
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
30-129 |
8.43e-05 |
|
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350749 [Multi-domain] Cd Length: 193 Bit Score: 44.10 E-value: 8.43e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 30 GSGKTRLGVLAARAALMAGYKVVVMVPTIELLDQWMRTLHDELPE--VTVGRLGGGRHDDLHRH----------DLVIGT 97
Cdd:cd17991 46 GFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYETFKERFANfpVNVELLSRFTTAAEQREileglkegkvDIVIGT 125
|
90 100 110
....*....|....*....|....*....|....*.
gi 1788635277 98 vHSiaptfdhdavpLLSRHRQ----GLVIADECHRY 129
Cdd:cd17991 126 -HR-----------LLSKDVEfknlGLLIIDEEQRF 149
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
331-411 |
9.63e-05 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 45.88 E-value: 9.63e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 331 GLGREERHDRLGRLRDGEIDVLAAPRVLDEGIDVPDADLGI----VVAASRSrrqmVQRLGRVIRRkrppRAGRLVHLYA 406
Cdd:COG1111 394 GLTQKEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLVIfyepVPSEIRS----IQRKGRTGRK----REGRVVVLIA 465
|
....*
gi 1788635277 407 LRTVE 411
Cdd:COG1111 466 KGTRD 470
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
30-128 |
9.76e-05 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 45.81 E-value: 9.76e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 30 GSGKTrlgVLAARAALMA---GYKVVVMVPTiELL-DQWMRTLHDELPE--VTV----GRLGGGRHDDLHRH------DL 93
Cdd:COG1200 290 GSGKT---VVALLAMLAAveaGYQAALMAPT-EILaEQHYRSLSKLLEPlgIRValltGSTKAKERREILAAlasgeaDI 365
|
90 100 110
....*....|....*....|....*....|....*....
gi 1788635277 94 VIGTvhsiaptfdH----DAVPLlsrHRQGLVIADECHR 128
Cdd:COG1200 366 VVGT---------HaliqDDVEF---KNLGLVVIDEQHR 392
|
|
| DEXDc_ComFA |
cd17925 |
DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon ... |
9-99 |
1.99e-04 |
|
DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon protein 1) is part of the complex mediating the binding and uptake of single-stranded DNA. ComFA is required for DNA uptake but not for binding. It belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350683 [Multi-domain] Cd Length: 143 Bit Score: 42.29 E-value: 1.99e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 9 QQEAFEA----WAAHEHRgVIEAITGSGKTRLGVLAARAALMAGYKVVVMVPTIELLDQWMRTLHDELPEVTVGRLGGGR 84
Cdd:cd17925 2 QQKASNAlvetIDAKEDL-LVWAVTGAGKTEMLFPAIAQALRQGGRVAIASPRIDVCLELAPRLKAAFPGAAIVLLHGGS 80
|
90
....*....|....*
gi 1788635277 85 HDDLHRHDLVIGTVH 99
Cdd:cd17925 81 EDQYQRSPLVIATTH 95
|
|
| SF2_C_UvrB |
cd18790 |
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ... |
322-391 |
2.25e-04 |
|
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) plays a central role in nucleotide excision repair (NER). Together with other components of the NER system, like UvrA, UvrC, UvrD (helicase II), and DNA polymerase I, it recognizes and cleaves damaged DNA in a multistep ATP-dependent reaction. UvrB is critical for the second phase of damage recognition by verifying the nature of the damage and forming the pre-incision complex. Its ATPase site becomes activated in the presence of UvrA and damaged DNA. Its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350177 [Multi-domain] Cd Length: 171 Bit Score: 42.62 E-value: 2.25e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1788635277 322 GLRTAAVYSGLGREERHDRLGRLRDGEIDVLAAPRVLDEGIDVPDADLGIVVAAS-----RSRRQMVQRLGRVIR 391
Cdd:cd18790 51 GVKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADkegflRSETSLIQTIGRAAR 125
|
|
| HsdR |
COG4096 |
Type I site-specific restriction endonuclease, part of a restriction-modification system ... |
22-226 |
3.13e-04 |
|
Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms];
Pssm-ID: 443272 [Multi-domain] Cd Length: 806 Bit Score: 44.45 E-value: 3.13e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 22 RGVIEAI------------TGSGKTRLGV-LAARaaLM-AGYK--VVVMVPTIELLDQWMRTLHDELP-EVTVGRL-GGG 83
Cdd:COG4096 168 RRVEEAIakgqrrallvmaTGTGKTRTAIaLIYR--LLkAGRAkrILFLADRNALVDQAKNAFKPFLPdLDAFTKLyNKS 245
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 84 RHDDLHRhDLVIGTVHS----IAPTFDHDAVPLLSRHRQGLVIADECHR--YAADRfagALSEHFD-WRLGLTAT----- 151
Cdd:COG4096 246 KDIDKSA-RVYFSTYQTmmnrIDGEEEEPGYRQFPPDFFDLIIIDECHRgiYSKWR---AILDYFDaLQIGLTATpkdti 321
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 152 ----YEradglheevldpFFGGA-VHRLWYDRALAEGVIAPFDIALVGVELDA-GprARYDALSKQI-RETRQALLGYLP 224
Cdd:COG4096 322 drntYE------------YFNGNpVYTYSLEQAVADGFLVPYKVIRIDTKFDReG--IRYDAGEDLSdEEGEEIELEELE 387
|
..
gi 1788635277 225 AD 226
Cdd:COG4096 388 ED 389
|
|
| YprA |
COG1205 |
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ... |
291-395 |
3.39e-04 |
|
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, recombination and repair];
Pssm-ID: 440818 [Multi-domain] Cd Length: 758 Bit Score: 44.06 E-value: 3.39e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 291 LAPAVRRAHGSLVF------AETKDAARAASARLADAGLRTAAVYSGLGREERHDRLGRLRDGEIDVLAAPRVLDEGIDV 364
Cdd:COG1205 281 LADLVREGLRTLVFtrsrrgAELLARYARRALREPDLADRVAAYRAGYLPEERREIERGLRSGELLGVVSTNALELGIDI 360
|
90 100 110
....*....|....*....|....*....|.
gi 1788635277 365 PDADLGIVVAASRSRRQMVQRLGRVIRRKRP 395
Cdd:COG1205 361 GGLDAVVLAGYPGTRASFWQQAGRAGRRGQD 391
|
|
| SF2_C_EcoAI-like |
cd18799 |
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family ... |
293-388 |
7.10e-04 |
|
C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases; This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoAI R protein (R.EcoAI). The EcoAI enzyme recognizes 5'-GAGN(7)GTCA-3'. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350186 [Multi-domain] Cd Length: 116 Bit Score: 39.85 E-value: 7.10e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 293 PAVRRAHGSLVFAETKDAARAASARLADAGLRTAAVYSGLGREER-HDRLGRLRDGEI--DVLAAPRVLDEGIDVPDADL 369
Cdd:cd18799 1 PYKYVEIKTLIFCVSIEHAEFMAEAFNEAGIDAVALNSDYSDRERgDEALILLFFGELkpPILVTVDLLTTGVDIPEVDN 80
|
90
....*....|....*....
gi 1788635277 370 GIVVAASRSRRQMVQRLGR 388
Cdd:cd18799 81 VVFLRPTESRTLFLQMLGR 99
|
|
| PRK13766 |
PRK13766 |
Hef nuclease; Provisional |
331-406 |
7.67e-04 |
|
Hef nuclease; Provisional
Pssm-ID: 237496 [Multi-domain] Cd Length: 773 Bit Score: 42.94 E-value: 7.67e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1788635277 331 GLGREERHDRLGRLRDGEIDVLAAPRVLDEGIDVPDADLGIVVAASRSRRQMVQRLGRVIRRkrppRAGRLVHLYA 406
Cdd:PRK13766 406 GMSQKEQIEILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVIFYEPVPSEIRSIQRKGRTGRQ----EEGRVVVLIA 477
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
25-142 |
7.88e-04 |
|
primosomal protein N'; All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273162 [Multi-domain] Cd Length: 505 Bit Score: 42.76 E-value: 7.88e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 25 IEAITGSGKTRLGVLAARAALMAGYKVVVMVPTIELLDQWMR-----------TLHDELPevTVGRLGGGRHDDLHRHDL 93
Cdd:TIGR00595 2 LFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQrfkyrfgsqvaVLHSGLS--DSEKLQAWRKVKNGEILV 79
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 1788635277 94 VIGTVHSIAPTFDhdavpllsrhRQGLVIADECH----------RYAADRFAGALSEHF 142
Cdd:TIGR00595 80 VIGTRSALFLPFK----------NLGLIIVDEEHdssykqeegpRYHARDVAVYRAKKF 128
|
|
| PRK08301 |
PRK08301 |
RNA polymerase sporulation sigma factor SigE; |
561-792 |
1.39e-03 |
|
RNA polymerase sporulation sigma factor SigE;
Pssm-ID: 236228 [Multi-domain] Cd Length: 234 Bit Score: 40.99 E-value: 1.39e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 561 NLRLVVSISTHYSAhrgiAGLDPIDLVQESHPGLMRAVQKFDERRGLKFSTYATWWIRQSITRALAEKSRTirvpvhade 640
Cdd:PRK08301 61 NLRLVVYIARKFEN----TGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKV--------- 127
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 641 qikkirrsaeqvvaahpelvtaedggrRAVVSrvaelLDESIErVEW----LLARDApiqsLGeprwiVEDDRVTlgtla 716
Cdd:PRK08301 128 ---------------------------KAEVS-----FDEPLN-IDWdgneLLLSDV----LG-----TDNDIIY----- 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1788635277 717 ellpdERTEqefEELERtEIVESLLLSLDQRERLVLEARFGLLTGEEETLDQVGARLGVTRERARQIQKKALEALR 792
Cdd:PRK08301 161 -----KDIE---DEVDR-KLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLK 227
|
|
| ERCC3_RAD25_C |
pfam16203 |
ERCC3/RAD25/XPB C-terminal helicase; This is the C-terminal helicase domain of ERCC3, RAD25 ... |
328-394 |
2.04e-03 |
|
ERCC3/RAD25/XPB C-terminal helicase; This is the C-terminal helicase domain of ERCC3, RAD25 and XPB helicases.
Pssm-ID: 406585 Cd Length: 248 Bit Score: 40.66 E-value: 2.04e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1788635277 328 VYSGLGREERHDRLGRLRDG-EIDVLAAPRVLDEGIDVPDADLGIVVAAS-RSRRQMVQRLGRVIRRKR 394
Cdd:pfam16203 85 IYGGTSQAERMRILQNFKHNpNVNTIFLSKVGDTSIDLPEANVLIQISSHfGSRRQEAQRLGRILRAKR 153
|
|
| rad25 |
TIGR00603 |
DNA repair helicase rad25; All proteins in this family for which functions are known are ... |
356-394 |
3.45e-03 |
|
DNA repair helicase rad25; All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273168 [Multi-domain] Cd Length: 732 Bit Score: 40.94 E-value: 3.45e-03
10 20 30 40
....*....|....*....|....*....|....*....|
gi 1788635277 356 RVLDEGIDVPDADLGIVVAASR-SRRQMVQRLGRVIRRKR 394
Cdd:TIGR00603 550 KVGDTSIDLPEANVLIQISSHYgSRRQEAQRLGRILRAKK 589
|
|
| COG4889 |
COG4889 |
Predicted helicase [General function prediction only]; |
336-392 |
4.72e-03 |
|
Predicted helicase [General function prediction only];
Pssm-ID: 443917 [Multi-domain] Cd Length: 1571 Bit Score: 40.71 E-value: 4.72e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1788635277 336 ERHDRLGRLR----DGEIDVLAAPRVLDEGIDVPDADLGIVVAASRSRRQMVQRLGRVIRR 392
Cdd:COG4889 527 ERNEKLDWLKaetpENTCRILSNARCLSEGVDVPALDAVLFLTPRKSQVDVVQSVGRVMRK 587
|
|
| RpoE |
COG1595 |
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ... |
709-792 |
4.75e-03 |
|
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: 38.82 E-value: 4.75e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 709 RVTLGTLAELLPDER--TEQEFEELERTEIVESLLLSLDQRERLVLEARFGlltgEEETLDQVGARLGVTRERARQIQKK 786
Cdd:COG1595 91 RELLDELAEELPDEAadPEEALEAEELLEALLAALERLPPRQREVLVLRYL----EGLSYAEIAEILGISEGTVKSRLSR 166
|
....*.
gi 1788635277 787 ALEALR 792
Cdd:COG1595 167 ARKKLR 172
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
30-129 |
7.30e-03 |
|
transcription-repair coupling factor (mfd); All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273152 [Multi-domain] Cd Length: 926 Bit Score: 40.03 E-value: 7.30e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1788635277 30 GSGKTRLGVLAARAALMAGYKVVVMVPTIELLDQWMRTLHDE---LPeVTVGRLGGGRH--------DDLH--RHDLVIG 96
Cdd:TIGR00580 482 GFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERfanFP-VTIELLSRFRSakeqneilKELAsgKIDILIG 560
|
90 100 110
....*....|....*....|....*....|...
gi 1788635277 97 TvHSIAptfdHDAVpllSRHRQGLVIADECHRY 129
Cdd:TIGR00580 561 T-HKLL----QKDV---KFKDLGLLIIDEEQRF 585
|
|
| |
