|
Name |
Accession |
Description |
Interval |
E-value |
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
1-645 |
0e+00 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 629.77 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 1 MNKDLKDIHGVGPKILRSFRYKGIWNTYDLISYVPKSYEDF-VVQNLKDLKHGDEVTLQGYIADAPKRF----KKQVVVL 75
Cdd:COG1200 4 LDTPLTYLKGVGPKRAKLLAKLGIRTVGDLLFHLPRRYEDRtRLTPIAELRPGETVTVEGTVVSVEVVRrrrrRRILEVT 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 76 kypLKVENSIVELTIFGRPYLEKELQVNQMVLVKGKYNFFKNEL-LVS--FITKD----IKTPILKPIYQIDE-LHDKVV 147
Cdd:COG1200 84 ---LSDGTGSLTLVFFNQPYLKKQLKPGTRVLVSGKVERFRGGLqMVHpeYELLDeeeaELAGRLTPVYPLTEgLSQKTL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 148 SNIIQTIFDEQVVDIFETLPDEIIQKYQLIQRKEAYYHLHFPSSMEMLKKAQYRFKVEEAFFH--SLKYLHQLTPKHPRK 225
Cdd:COG1200 161 RKLIRQALDLLAPDLPEPLPEELRARYGLPSLAEALRNIHFPPSDEDLHPARRRLAFEELLALqlALLLRRARRRKRKGP 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 226 SIEYQIQWIKEMIGRIPYQLTLDQQEAVNDIFRDFKQEVSMYRLIQGDVGTGKTNVAFIGMLGMINAGYQSALMAPTEIL 305
Cdd:COG1200 241 ALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVEAGYQAALMAPTEIL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 306 AKQHYENFTKLYPDI-LSV-FIT-SQS-KQKDQILKDIQTGVYKVIFGTH-ILGLSVEFSNLGLVIIDEQHKFGVEIRDQ 380
Cdd:COG1200 321 AEQHYRSLSKLLEPLgIRVaLLTgSTKaKERREILAALASGEADIVVGTHaLIQDDVEFKNLGLVVIDEQHRFGVEQRLA 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 381 LIKKSVTKDTLYLTATPIPRSLSLSYFGDLEISNIKQKPKHKLPIQTMIFYDEPIDEIIKLIKESQSINEQTFIVTPLIE 460
Cdd:COG1200 401 LREKGEAPHVLVMTATPIPRTLAMTLYGDLDVSVIDELPPGRKPIKTRVVPEERRDEVYERIREEIAKGRQAYVVCPLIE 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 461 QG----LKgpSIESMLDILRNELEHEHLYVIHGRLDSSEVDTILAEFILNPKGVLLATTMIEVGIDVPNATKIFIMGANN 536
Cdd:COG1200 481 ESekldLQ--AAEETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVDVPNATVMVIENAER 558
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 537 FGLSQLHQLRGRVGRGKKLGKCYLVTDKSDHD----RLEFLVSTEDGFLLSEYDLKLRGPGIFSSFIQSGQTKYQFIDMI 612
Cdd:COG1200 559 FGLSQLHQLRGRVGRGSAQSYCLLLYDAPLSEtareRLEVMRETNDGFEIAEEDLELRGPGEFLGTRQSGLPDLRIADLV 638
|
650 660 670
....*....|....*....|....*....|....*.
gi 919114479 613 QDLDILKRVRKDAARYAKQ---LEKYPYLKNRINKL 645
Cdd:COG1200 639 RDADLLEAAREDAEELLEEdpeLASHPALRRWLGLR 674
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
4-645 |
0e+00 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 608.69 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 4 DLKDIHGVGPKILRSFRYKGIWNTYDLISYVPKSYEDF-VVQNLKDLKHGDEVTLQGYIADAPKRFKKQVVvLKYPLKVE 82
Cdd:PRK10917 10 PLTSLKGVGPKTAEKLAKLGIHTVQDLLLHLPRRYEDRtRLKPIAELRPGEKVTVEGEVLSAEVVFGKRRR-LTVTVSDG 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 83 NSIVELTIF--GRPYLEKELQVNQMVLVKGKYNFFKN-------ELLVSFITKDIKTPILKPIYQIDE-LHDKVVSNIIQ 152
Cdd:PRK10917 89 TGNLTLRFFnfNQPYLKKQLKVGKRVAVYGKVKRGKYglemvhpEYEVLEEESPELEGRLTPVYPLTEgLKQKTLRKLIK 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 153 TIFdEQVVDIFETLPDEIIQKYQLIQRKEAYYHLHFPSSMEMLKKAQYRFKVEEAFFH--SLKYLHQLTPKHPRKSIEYQ 230
Cdd:PRK10917 169 QAL-ELLDALPELLPEELLEKYGLLSLAEALRAIHFPPSDEDLHPARRRLKFEELFALqlSLLLLRAGRRSKKAGPLPYD 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 231 IQWIKEMIGRIPYQLTLDQQEAVNDIFRDFKQEVSMYRLIQGDVGTGKTNVAFIGMLGMINAGYQSALMAPTEILAKQHY 310
Cdd:PRK10917 248 GELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEAGYQAALMAPTEILAEQHY 327
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 311 ENFTKLYPDI-LSV-FIT-SQS-KQKDQILKDIQTGVYKVIFGTH-ILGLSVEFSNLGLVIIDEQHKFGVEIRDQLIKKS 385
Cdd:PRK10917 328 ENLKKLLEPLgIRVaLLTgSLKgKERREILEAIASGEADIVIGTHaLIQDDVEFHNLGLVIIDEQHRFGVEQRLALREKG 407
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 386 VTKDTLYLTATPIPRSLSLSYFGDLEISNIKQKPKHKLPIQTMIFYDEPIDEIIKLIKESQSINEQTFIVTPLIEQG--- 462
Cdd:PRK10917 408 ENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPPGRKPITTVVIPDSRRDEVYERIREEIAKGRQAYVVCPLIEESekl 487
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 463 -LKgpSIESMLDILRNELEHEHLYVIHGRLDSSEVDTILAEFILNPKGVLLATTMIEVGIDVPNATKIFIMGANNFGLSQ 541
Cdd:PRK10917 488 dLQ--SAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVPNATVMVIENAERFGLAQ 565
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 542 LHQLRGRVGRGKKLGKCYLVTD--KSD--HDRLEFLVSTEDGFLLSEYDLKLRGPGIFSSFIQSGQTKYQFIDMIQDLDI 617
Cdd:PRK10917 566 LHQLRGRVGRGAAQSYCVLLYKdpLSEtaRERLKIMRETNDGFVIAEKDLELRGPGELLGTRQSGLPEFKVADLVRDEEL 645
|
650 660
....*....|....*....|....*...
gi 919114479 618 LKRVRKDAaryAKQLEKYPYLKNRINKL 645
Cdd:PRK10917 646 LEEARKDA---RELLERDPELAEALLER 670
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
23-625 |
8.43e-163 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 480.69 E-value: 8.43e-163
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 23 GIWNTYDLISYVPKSYEDFV-VQNLKDLKHGDEVTLQGYIADAPKRFKKQVVVLKYPLKVENSIV-ELTIFGRPYLEKEL 100
Cdd:TIGR00643 2 GIHTVQDLLFYFPRRYEDRTlLQTIGELLPGERATIVGEVLSHCIFGFKRRKVLKLRLKDGGYKKlELRFFNRAFLKKKF 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 101 QVNQMVLVKGKYNFFKNELLVS----FITKDIKTPILK--PIYQIDE-LHDKVVSNIIQTIFDEQVVDIFETLPDEIIQK 173
Cdd:TIGR00643 82 KVGSKVVVYGKVKSSKFKAYLIhpefISEKDGVEFELKilPVYPLTEgLTQKKLRKLIQQALDQLDKSLEDPLPEELREK 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 174 YQLIQRKEAYYHLHFPSSMEMLKKAQYRFKVEEAFFHSLKYL---HQLTPKHPRKSIEYQIQWIKEMIGRIPYQLTLDQQ 250
Cdd:TIGR00643 162 YGLLSLEDALRAIHFPKTLSLLELARRRLIFDEFFYLQLAMLarrLGEKQQFSAPPANPSEELLTKFLASLPFKLTRAQK 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 251 EAVNDIFRDFKQEVSMYRLIQGDVGTGKTNVAFIGMLGMINAGYQSALMAPTEILAKQHYENFTKLYPDI-LSV-FIT-- 326
Cdd:TIGR00643 242 RVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAPTEILAEQHYNSLRNLLAPLgIEVaLLTgs 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 327 SQSKQKDQILKDIQTGVYKVIFGTH-ILGLSVEFSNLGLVIIDEQHKFGVEIRDQLIKK---SVTKDTLYLTATPIPRSL 402
Cdd:TIGR00643 322 LKGKRRKELLETIASGQIHLVVGTHaLIQEKVEFKRLALVIIDEQHRFGVEQRKKLREKgqgGFTPHVLVMSATPIPRTL 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 403 SLSYFGDLEISNIKQKPKHKLPIQTMIFYDEPIDEIIKLIKESQSINEQTFIVTPLIEQG--LKGPSIESMLDILRNELE 480
Cdd:TIGR00643 402 ALTVYGDLDTSIIDELPPGRKPITTVLIKHDEKDIVYEFIEEEIAKGRQAYVVYPLIEESekLDLKAAEALYERLKKAFP 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 481 HEHLYVIHGRLDSSEVDTILAEFILNPKGVLLATTMIEVGIDVPNATKIFIMGANNFGLSQLHQLRGRVGRGKKLGKCYL 560
Cdd:TIGR00643 482 KYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLL 561
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 919114479 561 VT----DKSDHDRLEFLVSTEDGFLLSEYDLKLRGPGIFSSFIQSGQTKYQFIDMIQDLDILKRVRKDA 625
Cdd:TIGR00643 562 VYknpkSESAKKRLRVMADTLDGFVIAEEDLELRGPGDLLGTKQSGYPEFRVADLVRDREILVEAREDA 630
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
242-605 |
9.58e-80 |
|
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: 271.54 E-value: 9.58e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 242 PYQLTLDQQEAVNDIFRDFKQEVSMYRLIQGDVGTGKTNVAFIGMLGMINAGYQSALMAPTEILAKQHYENFTKLYPD-- 319
Cdd:TIGR00580 449 PFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANfp 528
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 320 ----ILSVFITSqsKQKDQILKDIQTGVYKVIFGTH-ILGLSVEFSNLGLVIIDEQHKFGVEIRDQL--IKKSVtkDTLY 392
Cdd:TIGR00580 529 vtieLLSRFRSA--KEQNEILKELASGKIDILIGTHkLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLkeLRTSV--DVLT 604
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 393 LTATPIPRSLSLSYFGDLEISNIKQKPKHKLPIQT--MIFYDEPIDEIIK--LIKESQSineqtFIVTPLIEqglkgpSI 468
Cdd:TIGR00580 605 LSATPIPRTLHMSMSGIRDLSIIATPPEDRLPVRTfvMEYDPELVREAIRreLLRGGQV-----FYVHNRIE------SI 673
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 469 ESMLDILRNELEHEHLYVIHGRLDSSEVDTILAEFILNPKGVLLATTMIEVGIDVPNATKIFIMGANNFGLSQLHQLRGR 548
Cdd:TIGR00580 674 EKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGR 753
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 919114479 549 VGRGKKLGKCYL-------VTDKSdHDRLEFLVSTED---GFLLSEYDLKLRGPGIFSSFIQSGQTK 605
Cdd:TIGR00580 754 VGRSKKKAYAYLlyphqkaLTEDA-QKRLEAIQEFSElgaGFKIALHDLEIRGAGNLLGEEQSGHIE 819
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
202-419 |
4.79e-76 |
|
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: 242.44 E-value: 4.79e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 202 FKVEEAFFHSLK--YLHQLTPKHPRKSIEYQIQWIKEMIGRIPYQLTLDQQEAVNDIFRDFKQEVSMYRLIQGDVGTGKT 279
Cdd:cd17992 1 LAFEELFALQLAllLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 280 NVAFIGMLGMINAGYQSALMAPTEILAKQHYENFTKLYP--DILSVFIT-SQS-KQKDQILKDIQTGVYKVIFGTH-ILG 354
Cdd:cd17992 81 VVAALAMLAAVENGYQVALMAPTEILAEQHYDSLKKLLEplGIRVALLTgSTKaKEKREILEKIASGEIDIVIGTHaLIQ 160
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 919114479 355 LSVEFSNLGLVIIDEQHKFGVEIRDQLIKKSVTKDTLYLTATPIPRSLSLSYFGDLEISNIKQKP 419
Cdd:cd17992 161 EDVEFHNLGLVIIDEQHRFGVEQRLKLREKGETPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
|
|
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
232-593 |
2.17e-73 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 256.15 E-value: 2.17e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 232 QWIKEMIGRIPYQLTLDQQEAVNDIFRDFKQEVSMYRLIQGDVGTGKTNVA----FIgmlgMINAGYQSALMAPTEILAK 307
Cdd:COG1197 574 PWQREFEAAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTEVAlraaFK----AVMDGKQVAVLVPTTLLAQ 649
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 308 QHYENFTKL---YP---DILSVFITSqsKQKDQILKDIQTGVYKVIFGTH-ILGLSVEFSNLGLVIIDEQHKFGVEIRDQ 380
Cdd:COG1197 650 QHYETFKERfagFPvrvEVLSRFRTA--KEQKETLEGLADGKVDIVIGTHrLLSKDVKFKDLGLLIIDEEQRFGVRHKEK 727
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 381 L--IKKSVtkDTLYLTATPIPRSLSLSYFGDLEISNIKQKPKHKLPIQTmiF---YDEpideiiKLIKESqsIN-E---- 450
Cdd:COG1197 728 LkaLRANV--DVLTLTATPIPRTLQMSLSGIRDLSIIATPPEDRLPVKT--FvgeYDD------ALIREA--ILrEllrg 795
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 451 -QTFIVTPLIEqglkgpSIESMLDILRNELEHEHLYVIHGRLDSSEVDTILAEFI---LNpkgVLLATTMIEVGIDVPNA 526
Cdd:COG1197 796 gQVFYVHNRVE------DIEKVAARLQELVPEARIAVAHGQMSERELERVMLDFYegeFD---VLVCTTIIETGIDIPNA 866
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 919114479 527 TKIFIMGANNFGLSQLHQLRGRVGRGKKLGKCYLVTDKSD------HDRLEFLVSTED---GFLLSEYDLKLRGPG 593
Cdd:COG1197 867 NTIIIERADRFGLAQLYQLRGRVGRSHRRAYAYLLYPPDKvltedaEKRLEAIQEFTElgaGFKLAMHDLEIRGAG 942
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
242-603 |
6.19e-59 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 214.61 E-value: 6.19e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 242 PYQLTLDQQEAVNDIFRDFKQEVSMYRLIQGDVGTGKTNVAFIGMLGMINAGYQSALMAPTEILAKQHYENFTKLYP--- 318
Cdd:PRK10689 598 PFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFAnwp 677
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 319 ---DILSVFITsqSKQKDQILKDIQTGVYKVIFGTHILGLS-VEFSNLGLVIIDEQHKFGVEIRDQLIKKSVTKDTLYLT 394
Cdd:PRK10689 678 vriEMLSRFRS--AKEQTQILAEAAEGKIDILIGTHKLLQSdVKWKDLGLLIVDEEHRFGVRHKERIKAMRADVDILTLT 755
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 395 ATPIPRSLSLSYFGDLEISNIKQKPKHKLPIQTMIF-YDEPIdeiiklIKESqsineqtfivtpLIEQGLKG-------- 465
Cdd:PRK10689 756 ATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVReYDSLV------VREA------------ILREILRGgqvyylyn 817
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 466 --PSIESMLDILRNELEHEHLYVIHGRLDSSEVDTILAEFILNPKGVLLATTMIEVGIDVPNATKIFIMGANNFGLSQLH 543
Cdd:PRK10689 818 dvENIQKAAERLAELVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLH 897
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 919114479 544 QLRGRVGRGKKLGKCYLVT------DKSDHDRLEFLVSTED---GFLLSEYDLKLRGPGIFSSFIQSGQ 603
Cdd:PRK10689 898 QLRGRVGRSHHQAYAWLLTphpkamTTDAQKRLEAIASLEDlgaGFALATHDLEIRGAGELLGEEQSGQ 966
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
233-416 |
1.67e-55 |
|
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: 187.01 E-value: 1.67e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 233 WIKEMIGRIPYQLTLDQQEAVNDIFRDFKQEVSMYRLIQGDVGTGKTNVAFIGMLGMINAGYQSALMAPTEILAKQHYEN 312
Cdd:cd17991 4 EQEEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQHYET 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 313 FTK---LYP---DILSVFITsqSKQKDQILKDIQTGVYKVIFGTH-ILGLSVEFSNLGLVIIDEQHKFGVEIRDQL--IK 383
Cdd:cd17991 84 FKErfaNFPvnvELLSRFTT--AAEQREILEGLKEGKVDIVIGTHrLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLkeLR 161
|
170 180 190
....*....|....*....|....*....|...
gi 919114479 384 KSVtkDTLYLTATPIPRSLSLSYFGDLEISNIK 416
Cdd:cd17991 162 PNV--DVLTLSATPIPRTLHMALSGIRDLSVIA 192
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
234-416 |
6.20e-52 |
|
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: 176.84 E-value: 6.20e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 234 IKEMIGRIPYQLTLDQQEAVNDIFRDFKQEVSMYRLIQGDVGTGKTNVAFIGMLGMINAGYQSALMAPTEILAKQHYENF 313
Cdd:cd17918 5 IQELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEA 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 314 TKLYPDILSVFITSQSKQkdQILKDIQtgvykVIFGTH-ILGLSVEFSNLGLVIIDEQHKFGVEIRDQLIKKSVTkDTLY 392
Cdd:cd17918 85 RKFLPFINVELVTGGTKA--QILSGIS-----LLVGTHaLLHLDVKFKNLDLVIVDEQHRFGVAQREALYNLGAT-HFLE 156
|
170 180
....*....|....*....|....
gi 919114479 393 LTATPIPRSLSLSYFGDLEISNIK 416
Cdd:cd17918 157 ATATPIPRTLALALSGLLDLSVID 180
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
424-575 |
4.29e-36 |
|
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. They 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: 350179 [Multi-domain] Cd Length: 160 Bit Score: 132.78 E-value: 4.29e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 424 PIQTMIFYDEPIDEIIKLIKESQSINEQTFIVTPLIEQG--LKGPSIESMLDILRNELEHEHLYVIHGRLDSSEVDTILA 501
Cdd:cd18792 1 PIRTYVIPHDDLDLVYEAIERELARGGQVYYVYPRIEESekLDLKSIEALAEELKELVPEARVALLHGKMTEDEKEAVML 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 502 EFILNPKGVLLATTMIEVGIDVPNATKIFIMGANNFGLSQLHQLRGRVGRGKKLGKCYLVT------DKSDHDRLEFLVS 575
Cdd:cd18792 81 EFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYpdpkklTETAKKRLRAIAE 160
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
424-575 |
1.95e-34 |
|
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It 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: 350198 [Multi-domain] Cd Length: 159 Bit Score: 128.23 E-value: 1.95e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 424 PIQTMIFYDEPIDEIIKLIKESQSINEQTFIVTPLIE----QGLKGPSIESML--DILRNELEhehLYVIHGRLDSSEVD 497
Cdd:cd18811 1 PITTYLIFHTRLDKVYEFVREEIAKGRQAYVIYPLIEesekLDLKAAVAMYEYlkERFRPELN---VGLLHGRLKSDEKD 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 498 TILAEFILNPKGVLLATTMIEVGIDVPNATKIFIMGANNFGLSQLHQLRGRVGRGKKLGKCYLVT----DKSDHDRLEFL 573
Cdd:cd18811 78 AVMAEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYkdplTETAKQRLRVM 157
|
..
gi 919114479 574 VS 575
Cdd:cd18811 158 TE 159
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
424-562 |
9.66e-26 |
|
C-terminal 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 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: 350197 [Multi-domain] Cd Length: 151 Bit Score: 103.58 E-value: 9.66e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 424 PIQTMIF-YDepiDEIIKLIKESQ-SINEQTFIVTPLIEqglkgpSIESMLDILRNELEHEHLYVIHGRLDSSEVDTILA 501
Cdd:cd18810 1 PVRTYVMpYD---DELIREAIERElLRGGQVFYVHNRIE------SIEKLATQLRQLVPEARIAIAHGQMTENELEEVML 71
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 919114479 502 EFILNPKGVLLATTMIEVGIDVPNATKIFIMGANNFGLSQLHQLRGRVGRGKKLGKCYLVT 562
Cdd:cd18810 72 EFAKGEYDILVCTTIIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLY 132
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
246-398 |
3.87e-21 |
|
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: 90.76 E-value: 3.87e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 246 TLDQQEAVNDIF--RDFkqevsmyrLIQGDVGTGKTNVAFIGMLGMIN---AGYQSALMAPTEILAKQHYENFTKL--YP 318
Cdd:pfam00270 1 TPIQAEAIPAILegRDV--------LVQAPTGSGKTLAFLLPALEALDkldNGPQALVLAPTRELAEQIYEELKKLgkGL 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 319 DILSVFITSQSKQKDQiLKDIQTgvYKVIFGTH-----ILGLSVEFSNLGLVIIDEQHK-----FGVEIRDQLIKKSVTK 388
Cdd:pfam00270 73 GLKVASLLGGDSRKEQ-LEKLKG--PDILVGTPgrlldLLQERKLLKNLKLLVLDEAHRlldmgFGPDLEEILRRLPKKR 149
|
170
....*....|
gi 919114479 389 DTLYLTATPI 398
Cdd:pfam00270 150 QILLLSATLP 159
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
242-421 |
2.01e-17 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 81.00 E-value: 2.01e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 242 PYQLTLDQQEAVNDIFRDFKqevsmYRLIQGDVGTGKTNVAFIGML--GMINAGYQSALMAPTEILAKQHYENFTKLYPD 319
Cdd:smart00487 6 FEPLRPYQKEAIEALLSGLR-----DVILAAPTGSGKTLAALLPALeaLKRGKGGRVLVLVPTRELAEQWAEELKKLGPS 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 320 ---ILSVFITSQSKQKDqiLKDIQTGVYKVIFGT------HILGLSVEFSNLGLVIIDEQHKFGVEIRDQLIKKSV---- 386
Cdd:smart00487 81 lglKVVGLYGGDSKREQ--LRKLESGKTDILVTTpgrlldLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLkllp 158
|
170 180 190
....*....|....*....|....*....|....*....
gi 919114479 387 -TKDTLYLTATP---IPRSLSLSYFGDLEISNIKQKPKH 421
Cdd:smart00487 159 kNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEP 197
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
249-588 |
3.99e-15 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 78.53 E-value: 3.99e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 249 QQEAVNDIFRDFKQEvsMYR-LIQGDVGTGKTnvaFIGMLGMINAGYQSALM--APTEILAKQHYENFTKLYPDILSVfi 325
Cdd:COG1061 85 QQEALEALLAALERG--GGRgLVVAPTGTGKT---VLALALAAELLRGKRVLvlVPRRELLEQWAEELRRFLGDPLAG-- 157
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 326 tSQSKQKDqilkdiqtgvYKVIFGTH-ILGLSVEFSNL----GLVIIDEQHKFGVEIRDQLIKKSVTKDTLYLTATPI-- 398
Cdd:COG1061 158 -GGKKDSD----------APITVATYqSLARRAHLDELgdrfGLVIIDEAHHAGAPSYRRILEAFPAAYRLGLTATPFrs 226
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 399 -PRSLSLSYFGDL--EISnIKQ-------KPKHKLPI-------------------QTMIFYDEPIDEIIKLIKESQSIN 449
Cdd:COG1061 227 dGREILLFLFDGIvyEYS-LKEaiedgylAPPEYYGIrvdltderaeydalserlrEALAADAERKDKILRELLREHPDD 305
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 450 EQTFIVTPLIEQglkgpsIESMLDILRNelEHEHLYVIHGRLDSSEVDTILAEFILNPKGVLLATTMIEVGIDVPNATKI 529
Cdd:COG1061 306 RKTLVFCSSVDH------AEALAELLNE--AGIRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVA 377
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 919114479 530 FIMGANNFgLSQLHQLRGRVGRGKKLGKCYLVTDKSDHDR--LEFLVSTEDGFLLSEYDLK 588
Cdd:COG1061 378 ILLRPTGS-PREFIQRLGRGLRPAPGKEDALVYDFVGNDVpvLEELAKDLRDLAGYRVEFL 437
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
435-551 |
7.87e-14 |
|
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: 68.01 E-value: 7.87e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 435 IDEIIKLIKESQsiNEQTFIVTPLIEqglkgpsiESMLDILRNELEHEHLYvIHGRLDSSEVDTILAEFILNPKGVLLAT 514
Cdd:pfam00271 3 LEALLELLKKER--GGKVLIFSQTKK--------TLEAELLLEKEGIKVAR-LHGDLSQEEREEILEDFRKGKIDVLVAT 71
|
90 100 110
....*....|....*....|....*....|....*..
gi 919114479 515 TMIEVGIDVPNATKIFIMGAnNFGLSQLHQLRGRVGR 551
Cdd:pfam00271 72 DVAERGLDLPDVDLVINYDL-PWNPASYIQRIGRAGR 107
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
473-551 |
9.45e-13 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 63.77 E-value: 9.45e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 473 DILRNELEHEHL--YVIHGRLDSSEVDTILAEFILNPKGVLLATTMIEVGIDVPNATKIFIMGAnNFGLSQLHQLRGRVG 550
Cdd:smart00490 1 EELAELLKELGIkvARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL-PWSPASYIQRIGRAG 79
|
.
gi 919114479 551 R 551
Cdd:smart00490 80 R 80
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
269-396 |
9.13e-11 |
|
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: 60.49 E-value: 9.13e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 269 LIQGDVGTGKTNVAFIGML-GMINAGYQSALMAPTEILAKQHYENFTKLYPDILSVF-ITSQSKQKDQILKDIQTgvYKV 346
Cdd:cd00046 5 LITAPTGSGKTLAALLAALlLLLKKGKKVLVLVPTKALALQTAERLRELFGPGIRVAvLVGGSSAEEREKNKLGD--ADI 82
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 919114479 347 IFGTH--ILGLSVE-----FSNLGLVIIDEQH-----KFGVEIRDQLIKKSVTKD--TLYLTAT 396
Cdd:cd00046 83 IIATPdmLLNLLLRedrlfLKDLKLIIVDEAHallidSRGALILDLAVRKAGLKNaqVILLSAT 146
|
|
| RecG_wedge |
pfam17191 |
RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations. |
4-152 |
9.56e-09 |
|
RecG wedge domain; This DNA-binding domain has an OB-fold with large elaborations.
Pssm-ID: 407316 [Multi-domain] Cd Length: 162 Bit Score: 54.75 E-value: 9.56e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 4 DLKDIHGVGP---KILRSFrykGIWNTYDLISYVPKSYED-FVVQNLKDLKHGDEVTLQGYIADAPKRFKKQVVVLKYPL 79
Cdd:pfam17191 1 PIKYAKGVGPkreKILKKL---GIETIGDLIWYFPRDYEDrRKIIPISDIRHDEKVTTKGKIVNFETKKIGSLVIISAVL 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 80 KVENSIVELTIFGRPYLEKELQVNQMVLVKG--KYNFFK----NELLVSFITKDIKTPILkPIYQIDE-LHDKVVSNIIQ 152
Cdd:pfam17191 78 SDGIGQVLLKWFNQEYIKKFLQKGKEVYITGtvKEGPFGpiemNNPEIEEITGEQEREIL-PVYPLTEgISQKNMRKIVK 156
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
249-398 |
3.78e-08 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 53.06 E-value: 3.78e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 249 QQEAVNDI--FRDFKQEVSmyrLIQGDVGTGKTNVAFIGMLG-MINAGYQSALM-APTEILAKQHYENFTKLYPDILSVf 324
Cdd:pfam04851 8 QIEAIENLleSIKNGQKRG---LIVMATGSGKTLTAAKLIARlFKKGPIKKVLFlVPRKDLLEQALEEFKKFLPNYVEI- 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 325 itsqSKQKDQILKDIQTGVYKVIFGT------HILGLSVEFS--NLGLVIIDEQHKFGVEIRDQLIKKSVTKDTLYLTAT 396
Cdd:pfam04851 84 ----GEIISGDKKDESVDDNKIVVTTiqslykALELASLELLpdFFDVIIIDEAHRSGASSYRNILEYFKPAFLLGLTAT 159
|
..
gi 919114479 397 PI 398
Cdd:pfam04851 160 PE 161
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
249-371 |
1.35e-07 |
|
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: 51.83 E-value: 1.35e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 249 QQEAVNDIFRDFKQevSMYRLIQGDVGTGKTNVAFIGMLGMINAGYQSALMAPtEI-LAKQHYENFTKLYPDILSVFITS 327
Cdd:cd17929 1 QRKAYEAIVSSLGG--FKTFLLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVP-EIsLTPQLIKRFKKRFGDKVAVLHSK 77
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 919114479 328 QS-KQKDQILKDIQTGVYKVIFGTHiLGLSVEFSNLGLVIIDEQH 371
Cdd:cd17929 78 LSdKERADEWRKIKRGEAKVVIGAR-SALFAPFKNLGLIIVDEEH 121
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
510-562 |
7.32e-07 |
|
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: 46.93 E-value: 7.32e-07
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 919114479 510 VLLATTMIEVGIDVPNATKIFIMGANNFgLSQLHQLRGRVGRGKKL-GKCYLVT 562
Cdd:cd18785 25 ILVATNVLGEGIDVPSLDTVIFFDPPSS-AASYIQRVGRAGRGGKDeGEVILFV 77
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
275-378 |
2.65e-06 |
|
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: 48.03 E-value: 2.65e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 275 GTGKTNVAFIGMLGMINAGYQSAL-MAPTEILAKQHYENFTKLY-PDILSV--FITSQSKQKDQILKdiqtgvYKVIFGT 350
Cdd:cd17921 27 SSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFgPLGKNVglLTGDPSVNKLLLAE------ADILVAT 100
|
90 100 110
....*....|....*....|....*....|....*
gi 919114479 351 --HILGL-----SVEFSNLGLVIIDEQHKFGVEIR 378
Cdd:cd17921 101 peKLDLLlrnggERLIQDVRLVVVDEAHLIGDGER 135
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
275-405 |
2.24e-04 |
|
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: 42.32 E-value: 2.24e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 275 GTGKTNVAFIGMLGMINAGYQSALMAPTEILAKQHYENFTKLYPDILSVFITSQS-KQKDQILKDiqtgvYKVIFGTH-- 351
Cdd:cd18028 27 ASGKTLIAEMAMVNTLLEGGKALYLVPLRALASEKYEEFKKLEEIGLKVGISTGDyDEDDEWLGD-----YDIIVATYek 101
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 919114479 352 ---ILGLSVEF-SNLGLVIIDEQHKFGVEIRDQLIKKSVTKDtlyLTATPIPRSLSLS 405
Cdd:cd18028 102 fdsLLRHSPSWlRDVGVVVVDEIHLISDEERGPTLESIVARL---RRLNPNTQIIGLS 156
|
|
| RecG_dom3_C |
pfam19833 |
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent ... |
576-627 |
2.39e-04 |
|
ATP-dependent DNA helicase RecG, domain 3, C-terminal; This domain is found in ATP-dependent DNA helicase RecG from bacteria the homolog from Arabidopsis, which has a critical role in recombination and DNA repair. This protein comprises three structural domains, the largest N-terminal Domain 1 which interacts with DNA junctions, and Domains 2 and 3 at the C-terminal which contain the characteriztic motifs that identify RecG as an SF2 helicase. This domain represents the C-terminal of Domain 3. Around 50 residues that extend from its end cross back to Domain 1 forming a hook that wraps around the extended alpha-helix. This interaction provides a link between Domain 1 and 3 and it is likely that these residues are involved in conformational changes associated with domain movements arising from ATP binding and hydrolysis.
Pssm-ID: 437665 [Multi-domain] Cd Length: 87 Bit Score: 40.15 E-value: 2.39e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 919114479 576 TEDGFLLSEYDLKLRGPGIFSSFIQSGQT-KYQFIDMIQDLDILKRVRKDAAR 627
Cdd:pfam19833 1 TNDGFEIAEADLKLRGPGDLEGTQQSGIAfDLKIADIARDGQLLQLARTEAEE 53
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| RecG_wedge_OBF |
cd04488 |
RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal ... |
56-119 |
4.79e-04 |
|
RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched chain substrates.
Pssm-ID: 239934 [Multi-domain] Cd Length: 75 Bit Score: 39.10 E-value: 4.79e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 919114479 56 TLQGYIADAPKRFKKQVVVLKYPLKVENSIVELTIFG-RPYLEKELQVNQMVLVKGKYNFFKNEL 119
Cdd:cd04488 1 TVEGTVVSVEVVPRRGRRRLKVTLSDGTGTLTLVFFNfQPYLKKQLPPGTRVRVSGKVKRFRGGL 65
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| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
473-590 |
9.49e-04 |
|
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' 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 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: 350191 [Multi-domain] Cd Length: 238 Bit Score: 41.46 E-value: 9.49e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 473 DILRNELEHEHLYVihgRLDSSEVDtilaefilnpkgVLLATTMIEVGIDVPNATKIFIMGANNfGL------------S 540
Cdd:cd18804 125 DTTRKKGALEKLLD---QFERGEID------------ILIGTQMIAKGLDFPNVTLVGILNADS-GLnspdfraserafQ 188
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90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 919114479 541 QLHQLRGRVGRGKKLGKCYLVTDKSDHDRLEFLVST-EDGFLlsEYDLKLR 590
Cdd:cd18804 189 LLTQVSGRAGRGDKPGKVIIQTYNPEHPLIQAAKEEdYEAFY--EEELAER 237
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| SF2_C_XPB |
cd18789 |
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
484-558 |
1.06e-03 |
|
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: 39.93 E-value: 1.06e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 919114479 484 LYVIHGRLDSSEVDTILAEFILNPKGVLLATTMIEVGIDVPNATKIFIMGANNFGLSQLHQLRGRVGRGKKLGKC 558
Cdd:cd18789 71 KPFITGETPQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEANVAIQISGHGGSRRQEAQRLGRILRPKKGGGK 145
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| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
233-374 |
3.28e-03 |
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Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 40.65 E-value: 3.28e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 233 WIKEMIGRIPY-QLTLDQQEAVNDIFRDFKqevSMyrLIQGDVGTGKTNVAFIGMLGMINAGYQSALMAPTEILAKQHYE 311
Cdd:COG1204 10 KVIEFLKERGIeELYPPQAEALEAGLLEGK---NL--VVSAPTASGKTLIAELAILKALLNGGKALYIVPLRALASEKYR 84
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90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 312 NFTKLYPDI-LSVFITSqskqKDQILKDIQTGVYKVIFGTH-----ILGLSVEF-SNLGLVIIDEQHKFG 374
Cdd:COG1204 85 EFKRDFEELgIKVGVST----GDYDSDDEWLGRYDILVATPekldsLLRNGPSWlRDVDLVVVDEAHLID 150
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| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
249-397 |
4.46e-03 |
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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: 38.31 E-value: 4.46e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 249 QQEAVNDIFRDFKQEVsmYR-LIQGDVGTGKTNVAFIGMLGMINAGYQSALM--APTEILAKQHYENFTKLYPDILSVFI 325
Cdd:cd18032 5 QQEAIEALEEAREKGQ--RRaLLVMATGTGKTYTAAFLIKRLLEANRKKRILflAHREELLEQAERSFKEVLPDGSFGNL 82
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90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 919114479 326 TSQSKQKDQilkdiqtgvYKVIFGT--------HILGLSVEFsnLGLVIIDEQHKFGVEIRDQLIK--KSVTKdtLYLTA 395
Cdd:cd18032 83 KGGKKKPDD---------ARVVFATvqtlnkrkRLEKFPPDY--FDLIIIDEAHHAIASSYRKILEyfEPAFL--LGLTA 149
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..
gi 919114479 396 TP 397
Cdd:cd18032 150 TP 151
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