|
Name |
Accession |
Description |
Interval |
E-value |
| UvrD |
COG0210 |
Superfamily I DNA or RNA helicase [Replication, recombination and repair]; |
11-446 |
1.47e-31 |
|
Superfamily I DNA or RNA helicase [Replication, recombination and repair];
Pssm-ID: 439980 [Multi-domain] Cd Length: 721 Bit Score: 129.28 E-value: 1.47e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 11 IFAGAGSGKSTTLVLRVVFMLCHLGVEPQRLTVISFTNAsctqlreqllrllahwqypfdAAQ-------------ARQC 77
Cdd:COG0210 24 VLAGAGSGKTRVLTHRIAYLIAEGGVDPEQILAVTFTNK---------------------AARemrerieallgrlARGL 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 78 -VRTFHSALGSLAR---EVLGNPRWFEQLDDRDpaaepdnplaagrlrpaQQRLLKQAYQQcyaespafrakthkllelp 153
Cdd:COG0210 83 wVGTFHSLALRILRrhaELLGLPPNFTILDGDD-----------------QLRLIKELLKE------------------- 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 154 ppaePEEGARRQPKaplepfklagefqalplyEAFHAQAGFAESLGLRVERLDSgKLECGLREKIFVEamalFWARFQAL 233
Cdd:COG0210 127 ----LGLDEKRFPP------------------RELLSLISRAKNEGLTPEELAE-LLAADPEWRAAAE----LYEAYQER 179
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 234 LREEGLMTFD--------------AAFQQLGERmaggalaetalapFTHLLIDEFQDVSPQIVLWLQALHrrlatqGTAP 299
Cdd:COG0210 180 LRANNALDFDdllllavrlleenpEVLEKYQNR-------------FRYILVDEYQDTNPAQYELLRLLA------GDGR 240
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 300 SLMAIGDDWQSIYGWRGSSPELFIDFDRHFPsrgrgrKSALLVLETNYRSVEPIIRDGEKVLAGVRFKQDKTCRAFRPiq 379
Cdd:COG0210 241 NLCVVGDDDQSIYGFRGADPENILRFEKDFP------DAKVIKLEQNYRSTQNILDAANAVIANNPGRLGKNLWTDNG-- 312
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1544625912 380 PGDhGVKLVQRFDLRAQLPKLLAEIRAQCEHAAARESserTAVllLSRRNEPLQAIQAELDRA-LPVK 446
Cdd:COG0210 313 EGE-KVRLYVAPDEEEEARFVADEIRELHEEGVPLSD---IAV--LYRTNAQSRALEEALRRAgIPYR 374
|
|
| DEXQc_UvrD |
cd17932 |
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch ... |
264-347 |
8.49e-21 |
|
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. UvrD 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: 350690 [Multi-domain] Cd Length: 189 Bit Score: 89.88 E-value: 8.49e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 264 APFTHLLIDEFQDVSPQIVLWLqalhRRLATQGTapSLMAIGDDWQSIYGWRGSSPELFIDFDRHFPSrgrgrkSALLVL 343
Cdd:cd17932 118 SRFRYILVDEYQDTNPLQYELL----KLLAGDGK--NLFVVGDDDQSIYGFRGADPENILDFEKDFPD------AKVIKL 185
|
....
gi 1544625912 344 ETNY 347
Cdd:cd17932 186 EENY 189
|
|
| UvrD-helicase |
pfam00580 |
UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural ... |
11-330 |
1.32e-18 |
|
UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyze ATP dependent unwinding of double stranded DNA to single stranded DNA. Swiss:P23478, Swiss:P08394 have large insertions near to the carboxy-terminus relative to other members of the family.
Pssm-ID: 395462 [Multi-domain] Cd Length: 267 Bit Score: 85.76 E-value: 1.32e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 11 IFAGAGSGKSTTLVLRVVFMLCHLGVEPQRLTVISFTNASctqlreqllrllahwqypfdAAQARQCVR----------- 79
Cdd:pfam00580 18 VLAGAGSGKTRVLTERIAYLILEGGIDPEEILAVTFTNKA--------------------AREMKERILkllgkaelsel 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 80 ---TFHSalgsLAREVL-------GNPRWFEQLDDRDpaaepdnplaagrlrpaQQRLLKQAYQQCYAESPAfrakthkl 149
Cdd:pfam00580 78 nisTFHS----FCLRILrkyanriGLLPNFSILDELD-----------------QLALLKELLEKDRLNLDP-------- 128
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 150 lelpppaepeegarrqpkAPLEPFKLAGEFQALPlyeafhaqagfaeSLGLRVERLDSGKLEcgLREKIFVEamalFWAR 229
Cdd:pfam00580 129 ------------------KLLRKLELKELISKAK-------------NRLLSPEELQQGAAD--PRDKLAAE----FYQE 171
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 230 FQALLREEGLMTFD-------AAFQQlgermaGGALAETALAPFTHLLIDEFQDVSPQIVLWLqalhRRLATQGtaPSLM 302
Cdd:pfam00580 172 YQERLKENNALDFDdlllltlELLRS------DPELLEAYRERFKYILVDEFQDTNPIQYRLL----KLLAGGH--ENLF 239
|
330 340
....*....|....*....|....*...
gi 1544625912 303 AIGDDWQSIYGWRGSSPELFIDFDRHFP 330
Cdd:pfam00580 240 LVGDPDQSIYGFRGADIENILKFEKDFP 267
|
|
| helD |
PRK11054 |
DNA helicase IV; Provisional |
223-515 |
4.81e-16 |
|
DNA helicase IV; Provisional
Pssm-ID: 182930 [Multi-domain] Cd Length: 684 Bit Score: 81.15 E-value: 4.81e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 223 MALFWARFQALLREEGLMTFDAAFQQLGERMAGGALAetalAPFTHLLIDEFQDVSPQIVLWLQALHRrlatQGTAPSLM 302
Cdd:PRK11054 392 MAPLLKAWKKALKAENAVDFSGLIHQAVNYLEKGRFI----SPWKHILVDEFQDISPQRAALLAALRK----QNSQTTLF 463
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 303 AIGDDWQSIYGWRGSSPELFIDFDRHFPSrgrgrkSALLVLETNYRSVEPIirdGEkvLAGvRFKQD------KTCRAFR 376
Cdd:PRK11054 464 AVGDDWQAIYRFSGADLSLTTAFHERFGE------GDRCHLDTTYRFNSRI---GE--VAN-RFIQQnphqlkKPLNSLT 531
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 377 piqPGDH-GVKLVQRFDLRAQLPKLLAEIRAQcehaaaressERtaVLLLSRRN--EPlqaiqAELDRA------LPVKG 447
Cdd:PRK11054 532 ---KGDKkAVTLLPEDQLEALLDKLSGYAKPD----------ER--ILLLARYHhlRP-----ALLDKAatrwpkLQIDF 591
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 448 MTIHRAKGLQAEVAIVVD-----DCLPGEKHPLrnalyaasgffrnSYDQAM----ED----ESLRLAYVAITRGVSRVl 514
Cdd:PRK11054 592 MTIHASKGQQADYVIILGlqegqDGFPAPARES-------------IMEEALlpppEDfpdaEERRLLYVALTRAKHRV- 657
|
.
gi 1544625912 515 W 515
Cdd:PRK11054 658 W 658
|
|
| recB |
TIGR00609 |
exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with ... |
270-349 |
1.32e-07 |
|
exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with potent ATP-dependent exodeoxyribonuclease activity. Ejection of RecD, as occurs at chi recombinational hotspots, cripples exonuclease activity in favor of recombinagenic helicase activity. All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. 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: 273172 [Multi-domain] Cd Length: 1087 Bit Score: 54.74 E-value: 1.32e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 270 LIDEFQDVSPQivlwlQ-ALHRRLATQGTAPSLMAIGDDWQSIYGWRGSspelfidfDRHFPSRGRGRKSALLVLETNYR 348
Cdd:TIGR00609 301 LIDEFQDTDPQ-----QyRIFSKLFIAQKETSLFLIGDPKQAIYSFRGA--------DIFTYLQAKSKADARYTLGTNWR 367
|
.
gi 1544625912 349 S 349
Cdd:TIGR00609 368 S 368
|
|
| UvrD_C_2 |
pfam13538 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
448-482 |
1.09e-04 |
|
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.
Pssm-ID: 463913 [Multi-domain] Cd Length: 52 Bit Score: 39.86 E-value: 1.09e-04
10 20 30
....*....|....*....|....*....|....*..
gi 1544625912 448 MTIHRAKGLQAEVAIVVDDCLPGEKHPL--RNALYAA 482
Cdd:pfam13538 5 LTVHKAQGSEFPAVFLVDPDLTAHYHSMlrRRLLYTA 41
|
|
| SF1_C_RecD |
cd18809 |
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ... |
448-513 |
7.71e-03 |
|
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350196 [Multi-domain] Cd Length: 80 Bit Score: 35.62 E-value: 7.71e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1544625912 448 MTIHRAKGLQAEVAIVVddcLPGEKHPLrnalyaasgffrnsydqamedeSLRLAYVAITRGVSRV 513
Cdd:cd18809 36 MTIHKSQGSEFDRVIVV---LPTSHPML----------------------SRGLLYTALTRARKLL 76
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| UvrD |
COG0210 |
Superfamily I DNA or RNA helicase [Replication, recombination and repair]; |
11-446 |
1.47e-31 |
|
Superfamily I DNA or RNA helicase [Replication, recombination and repair];
Pssm-ID: 439980 [Multi-domain] Cd Length: 721 Bit Score: 129.28 E-value: 1.47e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 11 IFAGAGSGKSTTLVLRVVFMLCHLGVEPQRLTVISFTNAsctqlreqllrllahwqypfdAAQ-------------ARQC 77
Cdd:COG0210 24 VLAGAGSGKTRVLTHRIAYLIAEGGVDPEQILAVTFTNK---------------------AARemrerieallgrlARGL 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 78 -VRTFHSALGSLAR---EVLGNPRWFEQLDDRDpaaepdnplaagrlrpaQQRLLKQAYQQcyaespafrakthkllelp 153
Cdd:COG0210 83 wVGTFHSLALRILRrhaELLGLPPNFTILDGDD-----------------QLRLIKELLKE------------------- 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 154 ppaePEEGARRQPKaplepfklagefqalplyEAFHAQAGFAESLGLRVERLDSgKLECGLREKIFVEamalFWARFQAL 233
Cdd:COG0210 127 ----LGLDEKRFPP------------------RELLSLISRAKNEGLTPEELAE-LLAADPEWRAAAE----LYEAYQER 179
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 234 LREEGLMTFD--------------AAFQQLGERmaggalaetalapFTHLLIDEFQDVSPQIVLWLQALHrrlatqGTAP 299
Cdd:COG0210 180 LRANNALDFDdllllavrlleenpEVLEKYQNR-------------FRYILVDEYQDTNPAQYELLRLLA------GDGR 240
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 300 SLMAIGDDWQSIYGWRGSSPELFIDFDRHFPsrgrgrKSALLVLETNYRSVEPIIRDGEKVLAGVRFKQDKTCRAFRPiq 379
Cdd:COG0210 241 NLCVVGDDDQSIYGFRGADPENILRFEKDFP------DAKVIKLEQNYRSTQNILDAANAVIANNPGRLGKNLWTDNG-- 312
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1544625912 380 PGDhGVKLVQRFDLRAQLPKLLAEIRAQCEHAAARESserTAVllLSRRNEPLQAIQAELDRA-LPVK 446
Cdd:COG0210 313 EGE-KVRLYVAPDEEEEARFVADEIRELHEEGVPLSD---IAV--LYRTNAQSRALEEALRRAgIPYR 374
|
|
| RecB |
COG1074 |
3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, ... |
13-445 |
1.38e-26 |
|
3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];
Pssm-ID: 440692 [Multi-domain] Cd Length: 866 Bit Score: 114.29 E-value: 1.38e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 13 AGAGSGKSTTLVLRVVFMLCHLGVEPQRLTVISFTNA--------------SCTQLREQLLRLLAHWQYPFDAA-----Q 73
Cdd:COG1074 25 ASAGSGKTYTLVARYLRLLLERGLDPEEILVVTFTRAaaaemrerirerlaEAADLEDPDLEELARARRRLARAlenldR 104
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 74 ARqcVRTFHS----ALGSLAREvLGNPRWFEQLDDRDpaaepdnplaagrlrpaqQRLLKQAYQQCYAEspaFRAKTHKL 149
Cdd:COG1074 105 AA--ISTIHSfcqrLLREFAFE-AGLDPNFELLDDAE------------------ALLLEEAVDDLLRE---AYAPLDAL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 150 LELPPPAEPEEGARRQPKAPLEPFKLAGEFQALPLYEAFHAQAG-FAESLGLRVERL----DSGKLECGLREKIFVEAMA 224
Cdd:COG1074 161 ALARLLDAFGRDDDSLEELLLALYKLRSRPDWLEELAELDEALEaLREALLKAKEALaalrEALAAAAAPLLAALLRLLA 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 225 LFWARFQALLREEGLMTFD----AAFQQLGERmAGGALAETALAPFTHLLIDEFQDVSP---QIvlwLQALHRrlATQGT 297
Cdd:COG1074 241 AVLARYERRKRERGLLDFDdllhRALRLLRDE-DAPWVAERLRERYRHILVDEFQDTSPlqwEI---LRRLAG--EALAD 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 298 APSLMAIGDDWQSIYGWRGSSPELFIDFDRHFPSRGRGRKsalLVLETNYRSVEPII--------RDGEKVLAGVRFKQD 369
Cdd:COG1074 315 GRTLFLVGDPKQSIYRFRGADPELFLEARRALEGRVDGER---LTLTTNFRSTPEVVdavnalfaQLMGAGFGEIPYEPV 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 370 KTCRA-------FRPIQPGDhgvklVQRFDLRAQLPKLLA-EIRAQCEHAAARESSERTA----VLLLSRRNEPLQAIQA 437
Cdd:COG1074 392 EALRPgaypaveLWPLEPDD-----VSEEDAREREARAVAaRIRRLLAEGTTVEGGGRPVrpgdIAVLVRTRSEAAAIAR 466
|
....*....
gi 1544625912 438 ELDRA-LPV 445
Cdd:COG1074 467 ALKAAgIPV 475
|
|
| DEXQc_UvrD |
cd17932 |
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch ... |
264-347 |
8.49e-21 |
|
DEXQD-box helicase domain of UvrD; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. UvrD 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: 350690 [Multi-domain] Cd Length: 189 Bit Score: 89.88 E-value: 8.49e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 264 APFTHLLIDEFQDVSPQIVLWLqalhRRLATQGTapSLMAIGDDWQSIYGWRGSSPELFIDFDRHFPSrgrgrkSALLVL 343
Cdd:cd17932 118 SRFRYILVDEYQDTNPLQYELL----KLLAGDGK--NLFVVGDDDQSIYGFRGADPENILDFEKDFPD------AKVIKL 185
|
....
gi 1544625912 344 ETNY 347
Cdd:cd17932 186 EENY 189
|
|
| UvrD-helicase |
pfam00580 |
UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural ... |
11-330 |
1.32e-18 |
|
UvrD/REP helicase N-terminal domain; The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyze ATP dependent unwinding of double stranded DNA to single stranded DNA. Swiss:P23478, Swiss:P08394 have large insertions near to the carboxy-terminus relative to other members of the family.
Pssm-ID: 395462 [Multi-domain] Cd Length: 267 Bit Score: 85.76 E-value: 1.32e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 11 IFAGAGSGKSTTLVLRVVFMLCHLGVEPQRLTVISFTNASctqlreqllrllahwqypfdAAQARQCVR----------- 79
Cdd:pfam00580 18 VLAGAGSGKTRVLTERIAYLILEGGIDPEEILAVTFTNKA--------------------AREMKERILkllgkaelsel 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 80 ---TFHSalgsLAREVL-------GNPRWFEQLDDRDpaaepdnplaagrlrpaQQRLLKQAYQQCYAESPAfrakthkl 149
Cdd:pfam00580 78 nisTFHS----FCLRILrkyanriGLLPNFSILDELD-----------------QLALLKELLEKDRLNLDP-------- 128
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 150 lelpppaepeegarrqpkAPLEPFKLAGEFQALPlyeafhaqagfaeSLGLRVERLDSGKLEcgLREKIFVEamalFWAR 229
Cdd:pfam00580 129 ------------------KLLRKLELKELISKAK-------------NRLLSPEELQQGAAD--PRDKLAAE----FYQE 171
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 230 FQALLREEGLMTFD-------AAFQQlgermaGGALAETALAPFTHLLIDEFQDVSPQIVLWLqalhRRLATQGtaPSLM 302
Cdd:pfam00580 172 YQERLKENNALDFDdlllltlELLRS------DPELLEAYRERFKYILVDEFQDTNPIQYRLL----KLLAGGH--ENLF 239
|
330 340
....*....|....*....|....*...
gi 1544625912 303 AIGDDWQSIYGWRGSSPELFIDFDRHFP 330
Cdd:pfam00580 240 LVGDPDQSIYGFRGADIENILKFEKDFP 267
|
|
| helD |
PRK11054 |
DNA helicase IV; Provisional |
223-515 |
4.81e-16 |
|
DNA helicase IV; Provisional
Pssm-ID: 182930 [Multi-domain] Cd Length: 684 Bit Score: 81.15 E-value: 4.81e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 223 MALFWARFQALLREEGLMTFDAAFQQLGERMAGGALAetalAPFTHLLIDEFQDVSPQIVLWLQALHRrlatQGTAPSLM 302
Cdd:PRK11054 392 MAPLLKAWKKALKAENAVDFSGLIHQAVNYLEKGRFI----SPWKHILVDEFQDISPQRAALLAALRK----QNSQTTLF 463
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 303 AIGDDWQSIYGWRGSSPELFIDFDRHFPSrgrgrkSALLVLETNYRSVEPIirdGEkvLAGvRFKQD------KTCRAFR 376
Cdd:PRK11054 464 AVGDDWQAIYRFSGADLSLTTAFHERFGE------GDRCHLDTTYRFNSRI---GE--VAN-RFIQQnphqlkKPLNSLT 531
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 377 piqPGDH-GVKLVQRFDLRAQLPKLLAEIRAQcehaaaressERtaVLLLSRRN--EPlqaiqAELDRA------LPVKG 447
Cdd:PRK11054 532 ---KGDKkAVTLLPEDQLEALLDKLSGYAKPD----------ER--ILLLARYHhlRP-----ALLDKAatrwpkLQIDF 591
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 448 MTIHRAKGLQAEVAIVVD-----DCLPGEKHPLrnalyaasgffrnSYDQAM----ED----ESLRLAYVAITRGVSRVl 514
Cdd:PRK11054 592 MTIHASKGQQADYVIILGlqegqDGFPAPARES-------------IMEEALlpppEDfpdaEERRLLYVALTRAKHRV- 657
|
.
gi 1544625912 515 W 515
Cdd:PRK11054 658 W 658
|
|
| uvrD |
PRK11773 |
DNA-dependent helicase II; Provisional |
266-349 |
1.28e-11 |
|
DNA-dependent helicase II; Provisional
Pssm-ID: 236976 [Multi-domain] Cd Length: 721 Bit Score: 67.20 E-value: 1.28e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 266 FTHLLIDEFQDVSPQIVLWLqalhRRLAtqGTAPSLMAIGDDWQSIYGWRGSSPELFIDFDRHFPsrgrgrKSALLVLET 345
Cdd:PRK11773 214 FTHILVDEFQDTNAIQYAWI----RLLA--GDTGKVMIVGDDDQSIYGWRGAQVENIQRFLNDFP------GAETIRLEQ 281
|
....
gi 1544625912 346 NYRS 349
Cdd:PRK11773 282 NYRS 285
|
|
| PRK13909 |
PRK13909 |
RecB-like helicase; |
266-354 |
1.84e-09 |
|
RecB-like helicase;
Pssm-ID: 237554 [Multi-domain] Cd Length: 910 Bit Score: 60.37 E-value: 1.84e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 266 FTHLLIDEFQDVSP---QIVLWL---------QALHRrlatqgtapSLMAIGDDWQSIYGWRGSSPELFIDFDRHFpsrg 333
Cdd:PRK13909 329 ISHILIDEFQDTSVlqyKILLPLideiksgegQKKFR---------SFFYVGDVKQSIYRFRGGKKELFDKVSKDF---- 395
|
90 100
....*....|....*....|.
gi 1544625912 334 rgrKSALLVLETNYRSVEPII 354
Cdd:PRK13909 396 ---KQKVDNLDTNYRSAPLIV 413
|
|
| COG3972 |
COG3972 |
Superfamily I DNA and RNA helicases [Replication, recombination and repair]; |
242-482 |
1.05e-08 |
|
Superfamily I DNA and RNA helicases [Replication, recombination and repair];
Pssm-ID: 443172 [Multi-domain] Cd Length: 565 Bit Score: 57.92 E-value: 1.05e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 242 FDAAFQQLGErmagGALAETALAPFTHLLIDEFQDVSPqivLWLQALhRRLATQGTApSLMAIGDDWQSIYGwRGSSPEL 321
Cdd:COG3972 269 FDEACKALLE----AIQGEIIPPIYDAILIDEAQDFEP---EFLRLL-YQLLKPPKK-RLIWAYDEAQNIYG-RKIPSAG 338
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 322 FIDFDRhfpsrgrgRKSalLVLETNYRSVEPIIR----------------DGEKVLAGVRFKQDKTCRAFRPIQPGDHGV 385
Cdd:COG3972 339 GIPAGI--------GRD--TILKKNYRNTRPILTfahafgmgllrppgllQGDAEDYEVERPGDKVTLIRPPEPAGRKGP 408
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 386 KL-VQRFDLRAQLPKLLAEIRAQCEHAAARESSErTAVLLL--SRRNEPLQAIQAELDRA-----LP------------- 444
Cdd:COG3972 409 LPeFKKYDDRAEELEAIAEEIKKNLRDEGLRPSD-IAVIYLgnNEAKELGDRLAAALERQgidsyIAgarsdpnffwkdg 487
|
250 260 270 280
....*....|....*....|....*....|....*....|..
gi 1544625912 445 -VKGMTIHRAKGLQAEVAIVV--DDCLPGEK-HPLRNALYAA 482
Cdd:COG3972 488 gVTISTIHRAKGLEAPVVIIVglDQLAKGESlERLRNLLYVA 529
|
|
| recB |
PRK10876 |
exonuclease V subunit beta; Provisional |
239-355 |
1.42e-08 |
|
exonuclease V subunit beta; Provisional
Pssm-ID: 236784 [Multi-domain] Cd Length: 1181 Bit Score: 57.67 E-value: 1.42e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 239 LMTFDAAFQQLGermaGGALAETALAPFTHLLIDEFQDVSPQivlwlQ-ALHRRLATQGTAPSLMAIGDDWQSIYGWRGS 317
Cdd:PRK10876 355 LSRLDSALQSEG----GEALAAAIRTRYPVAMIDEFQDTDPQ-----QyRIFRRIYRHQPETALLLIGDPKQAIYAFRGA 425
|
90 100 110
....*....|....*....|....*....|....*...
gi 1544625912 318 SPELFIdfdrhfpsRGRGRKSALLVLETNYRSVEPIIR 355
Cdd:PRK10876 426 DIFTYM--------KARSEVSAHYTLDTNWRSAPGMVN 455
|
|
| SF1_C_UvrD |
cd18807 |
C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase ... |
366-512 |
2.66e-08 |
|
C-terminal helicase domain of UvrD family helicases; UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. This family also includes ATP-dependent helicase/nuclease AddA and helicase/nuclease RecBCD subunit RecB, among others. UvrD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350194 [Multi-domain] Cd Length: 150 Bit Score: 53.00 E-value: 2.66e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 366 FKQDKTcRAFRPIQPG---DHGVKLVQRFDLRAQLPKLLAEIRAqcEHAAARESSERTAVLLLSRRNepLQAIQAELDra 442
Cdd:cd18807 13 IKQNKN-RPKKPLKAGnksGGPVELLLAKDEADEAKAIADEIKR--LIESGPVQYSDIAILVRTNRQ--ARVIEEALR-- 85
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1544625912 443 lpVKGMTIHRAKGLQAEVAIVVDdclpGEKH--PLRNALYAASGffrnsyDQAMEDESLRLAYVAITRGVSR 512
Cdd:cd18807 86 --VTLMTIHASKGLEFPVVFIVG----LGEGfiPSDASYHAAKE------DEERLEEERRLLYVALTRAKKE 145
|
|
| recB |
TIGR00609 |
exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with ... |
270-349 |
1.32e-07 |
|
exodeoxyribonuclease V, beta subunit; The RecBCD holoenzyme is a multifunctional nuclease with potent ATP-dependent exodeoxyribonuclease activity. Ejection of RecD, as occurs at chi recombinational hotspots, cripples exonuclease activity in favor of recombinagenic helicase activity. All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. 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: 273172 [Multi-domain] Cd Length: 1087 Bit Score: 54.74 E-value: 1.32e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 270 LIDEFQDVSPQivlwlQ-ALHRRLATQGTAPSLMAIGDDWQSIYGWRGSspelfidfDRHFPSRGRGRKSALLVLETNYR 348
Cdd:TIGR00609 301 LIDEFQDTDPQ-----QyRIFSKLFIAQKETSLFLIGDPKQAIYSFRGA--------DIFTYLQAKSKADARYTLGTNWR 367
|
.
gi 1544625912 349 S 349
Cdd:TIGR00609 368 S 368
|
|
| PRK10919 |
PRK10919 |
ATP-dependent DNA helicase Rep; Provisional |
268-355 |
3.19e-07 |
|
ATP-dependent DNA helicase Rep; Provisional
Pssm-ID: 182838 [Multi-domain] Cd Length: 672 Bit Score: 53.31 E-value: 3.19e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 268 HLLIDEFQDVSP---QIVLWLQalhrrlatqGTAPSLMAIGDDWQSIYGWRGSSPELFIDFDRHFPsrgrgrksALLV-- 342
Cdd:PRK10919 210 YLLVDEYQDTNTsqyELVKLLV---------GSRARFTVVGDDDQSIYSWRGARPQNLVLLSQDFP--------ALQVik 272
|
90
....*....|...
gi 1544625912 343 LETNYRSVEPIIR 355
Cdd:PRK10919 273 LEQNYRSSGRILK 285
|
|
| DExxQc_SF1-N |
cd17914 |
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ... |
262-329 |
5.84e-06 |
|
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. 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. SF1 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: 438706 [Multi-domain] Cd Length: 121 Bit Score: 45.55 E-value: 5.84e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1544625912 262 ALAPFTHLLIDEFQDVSPQIVLWLQALHRRLAtqgtapSLMAIGDDWQSIYGWRGSSPE-------LFIDFDRHF 329
Cdd:cd17914 43 AAAQLDNILVDEAAQILEPETSRLIDLALDQG------RVILVGDHDQLGPVWRGAVLAkicneqsLFTRLVRLG 111
|
|
| UvrD_C_2 |
pfam13538 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
448-482 |
1.09e-04 |
|
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.
Pssm-ID: 463913 [Multi-domain] Cd Length: 52 Bit Score: 39.86 E-value: 1.09e-04
10 20 30
....*....|....*....|....*....|....*..
gi 1544625912 448 MTIHRAKGLQAEVAIVVDDCLPGEKHPL--RNALYAA 482
Cdd:pfam13538 5 LTVHKAQGSEFPAVFLVDPDLTAHYHSMlrRRLLYTA 41
|
|
| UvrD_C |
pfam13361 |
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety ... |
434-513 |
1.05e-03 |
|
UvrD-like helicase C-terminal domain; This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.
Pssm-ID: 433145 [Multi-domain] Cd Length: 377 Bit Score: 41.62 E-value: 1.05e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1544625912 434 AIQAELDRALPVKG----MTIHRAKGLQAEVAIVVDdclpgekhpLRNALYAAsgfFRNSYDQAMEDESLRLAYVAITRG 509
Cdd:pfam13361 299 TLSNSELEGSDIKEripiMTIHQAKGLEFDTVFLAG---------LEEGIFPS---YRSIKDEGNLEEERRLFYVAITRA 366
|
....
gi 1544625912 510 VSRV 513
Cdd:pfam13361 367 KKRL 370
|
|
| DExxQc_SF1-N |
cd17914 |
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members ... |
8-50 |
1.38e-03 |
|
DEXQ-box helicase domain of superfamily 1 helicase; The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. 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. SF1 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: 438706 [Multi-domain] Cd Length: 121 Bit Score: 38.62 E-value: 1.38e-03
10 20 30 40
....*....|....*....|....*....|....*....|...
gi 1544625912 8 LARIFAGAGSGKSTTLVLRVVFMLCHLGVEPQRLTVISFTNAS 50
Cdd:cd17914 1 LSLIQGPPGTGKTRVLVKIVAALMQNKNGEPGRILLVTPTNKA 43
|
|
| SF1_C_RecD |
cd18809 |
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11. ... |
448-513 |
7.71e-03 |
|
C-terminal helicase domain of RecD family helicases; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 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: 350196 [Multi-domain] Cd Length: 80 Bit Score: 35.62 E-value: 7.71e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1544625912 448 MTIHRAKGLQAEVAIVVddcLPGEKHPLrnalyaasgffrnsydqamedeSLRLAYVAITRGVSRV 513
Cdd:cd18809 36 MTIHKSQGSEFDRVIVV---LPTSHPML----------------------SRGLLYTALTRARKLL 76
|
|
| |
