|
Name |
Accession |
Description |
Interval |
E-value |
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
1-796 |
0e+00 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 941.85 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 1 MDYAKVAVNLPLknlFRQFTYKVPPSLDFIGEGWRVVVPFGRQLLEGFIVEADEAPDASLA-IKSIVDVVGTEPWFDEEM 79
Cdd:COG1198 1 MKIAEVALPVPL---DRPFDYLVPEGLELVQPGSRVLVPFGRRQVVGIVVGLKEESDVDPAkLKPILAVLDDEPLLPEEL 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 80 LGTAHWIAQYYLCPLAEALRLFIPGkksiaavgryyaepgaeGLLSErerslytylaqegamtrreiarleggegalkgl 159
Cdd:COG1198 78 LELLRWVADYYLCPLGEVLRLALPA-----------------GLRQG--------------------------------- 107
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 160 itkkavsltyevtYKLKEKFERTVALSTDGLAQKeagilRGKGQLLVLSLL-QGTNPLPVRVLEDR-GVSAGVIRNLVSK 237
Cdd:COG1198 108 -------------YPARIKTERYVRLTLGEELPK-----RAPKQRRVLEALrEHGGPLTLSELAKEaGVSRSVLKALVKK 169
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 238 GILTEGKQRVLRDSYHADAAPRDEMILTDEQQAAINAveICRKRGTFHTFLLRGVTGSGKTEVYLRLTDKALRDGKQVMV 317
Cdd:COG1198 170 GLLEIEEREVDRDPFAPDVPAEPPPTLNEEQQAAVEA--IRAAAGGFSVFLLHGVTGSGKTEVYLQAIAEVLAQGKQALV 247
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 318 LVPEIALTDQIVKRFKSWFGNAVAVAHSKLSASERADVWDRMRNGKARVLIGVRSAVFCPFKDLGLVVIDEEHESTYKQE 397
Cdd:COG1198 248 LVPEIALTPQTVERFRARFGARVAVLHSGLSDGERLDEWRRARRGEARIVIGTRSALFAPFPNLGLIIVDEEHDSSYKQE 327
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 398 ERPGYNARLVAQVRANAHGAPVVLGSATPDLETYYWAQKGRYTELIMNERAhKGAHLPAVSIVDMREELQKGNKsVFSDT 477
Cdd:COG1198 328 DGPRYHARDVAVVRAKLEGAPVVLGSATPSLESLYNAQKGRYRLLELPERA-GGAPLPEVELVDMREEPLEGGR-ILSPP 405
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 478 LRDAIEETVKSGEQAIILLNRRGFSTFVMCRDCGESIQCPNCAVALVYHAKQAQLVCHYCGHTEPVPKVCPKCGSKRIRF 557
Cdd:COG1198 406 LLEAIEETLERGEQVLLFLNRRGYAPFLLCRDCGWVAKCPNCDVSLTYHRSRRRLRCHYCGYEEPVPKQCPECGSDSLRP 485
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 558 FGTGTEKAEESLRTLCEGIRPLRMDQDTTARKFSHEKIMRAFRSGEYNVLLGTQMVAKGHDVPNVTLVGILSADSTLNLP 637
Cdd:COG1198 486 FGPGTERVEEELAELFPDARVLRMDRDTTRRKGALEKLLEAFARGEADILVGTQMLAKGHDFPNVTLVGVLDADLGLNSP 565
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 638 DFRSGERCFALLTQAAGRAGRGDKPGRVIFQAYDAENPILRMAAEQDYVSFARDELKQRQDLQYPPFVTMLKMTVHHESE 717
Cdd:COG1198 566 DFRAAERTFQLLTQVAGRAGRAEKPGEVLIQTYNPEHPVIQALLNHDYEAFYEEELAERKAAGYPPFGRLALLRASGKDE 645
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 718 TKALELAQRFVNALEAFQLESKVpyQILGPFPALVPVVNRVWRVNVLIKSQHMKPIKDWIRA-----SGFLENG-NLYFD 791
Cdd:COG1198 646 EAAEEFAQALARALRALLSADGV--EVLGPAPAPIARLRGRYRWQLLLKAPSRAALQQLLRAllallEKPLPRKvRWSID 723
|
....*
gi 496306713 792 VDPIS 796
Cdd:COG1198 724 VDPQS 728
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
1-796 |
0e+00 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 805.92 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 1 MDYAKVAVNLPLknlFRQFTYKVPPSLDfIGEGWRVVVPFGRQLLEGFIVEADEAPDASLA-IKSIVDVVGTEPWFDEEM 79
Cdd:PRK05580 2 MKIARVLLPVPL---PRPFDYLIPEGLE-VQPGDRVRVPFGNRKLIGVVVGVEEGSEVPADkLKPILEVLDLEPLLPPEL 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 80 LGTAHWIAQYYLCPLAEALRLFIPGKKSIAAvgryyaepgaegllsererslytylaqegamtrreiarleggegalkgl 159
Cdd:PRK05580 78 LRLLDWAADYYLSPLGEVLRLALLAELALAA------------------------------------------------- 108
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 160 itkkavsltyevtyklkekfertvalstdglaqkeagilrgkgqllvlsllqgtnplpvrvledrgvSAGVIRNLVSKGI 239
Cdd:PRK05580 109 -------------------------------------------------------------------SSAVLKGLVKKGL 121
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 240 LTEGKQRVLRDSYHADAaPRDEMILTDEQQAAINAVeicRKRGTFHTFLLRGVTGSGKTEVYLRLTDKALRDGKQVMVLV 319
Cdd:PRK05580 122 IELEEVEVLRLRPPPDP-AFEPPTLNPEQAAAVEAI---RAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQGKQALVLV 197
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 320 PEIALTDQIVKRFKSWFGNAVAVAHSKLSASERADVWDRMRNGKARVLIGVRSAVFCPFKDLGLVVIDEEHESTYKQEER 399
Cdd:PRK05580 198 PEIALTPQMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALFLPFKNLGLIIVDEEHDSSYKQQEG 277
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 400 PGYNARLVAQVRANAHGAPVVLGSATPDLETYYWAQKGRYTELIMNERAHkGAHLPAVSIVDMREELQKGNKSVFSDTLR 479
Cdd:PRK05580 278 PRYHARDLAVVRAKLENIPVVLGSATPSLESLANAQQGRYRLLRLTKRAG-GARLPEVEIIDMRELLRGENGSFLSPPLL 356
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 480 DAIEETVKSGEQAIILLNRRGFSTFVMCRDCGESIQCPNCAVALVYHAKQAQLVCHYCGHTEPVPKVCPKCGSKRIRFFG 559
Cdd:PRK05580 357 EAIKQRLERGEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGSTDLVPVG 436
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 560 TGTEKAEESLRTLCEGIRPLRMDQDTTARKFSHEKIMRAFRSGEYNVLLGTQMVAKGHDVPNVTLVGILSADSTLNLPDF 639
Cdd:PRK05580 437 PGTERLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNVTLVGVLDADLGLFSPDF 516
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 640 RSGERCFALLTQAAGRAGRGDKPGRVIFQAYDAENPILRMAAEQDYVSFARDELKQRQDLQYPPFVTMLKMTVHHESETK 719
Cdd:PRK05580 517 RASERTFQLLTQVAGRAGRAEKPGEVLIQTYHPEHPVIQALLAQDYDAFAEQELEERRAAGYPPFGRLALLRASAKDEEK 596
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 720 ALELAQRFVNALEAFQLESKVpyQILGPFPALVPVVNRVWRVNVLIKSQHMKP----IKDWIRASGFLENG---NLYFDV 792
Cdd:PRK05580 597 AEKFAQQLAALLPNLLPLLDV--EVLGPAPAPIAKIAGRYRYQLLLKSPSRADlqklLRAWLALLQKLPQArkvRWSIDV 674
|
....
gi 496306713 793 DPIS 796
Cdd:PRK05580 675 DPQS 678
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
288-795 |
0e+00 |
|
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: 614.78 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 288 LLRGVTGSGKTEVYLRLTDKALRDGKQVMVLVPEIALTDQIVKRFKSWFGNAVAVAHSKLSASERADVWDRMRNGKARVL 367
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGSQVAVLHSGLSDSEKLQAWRKVKNGEILVV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 368 IGVRSAVFCPFKDLGLVVIDEEHESTYKQEERPGYNARLVAQVRANAHGAPVVLGSATPDLETYYWAQKGRYTELIMNER 447
Cdd:TIGR00595 81 IGTRSALFLPFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAKKFNCPVVLGSATPSLESYHNAKQKAYRLLVLTRR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 448 aHKGAHLPAVSIVDMREELQKgnkSVFSDTLRDAIEETVKSGEQAIILLNRRGFSTFVMCRDCGESIQCPNCAVALVYHA 527
Cdd:TIGR00595 161 -VSGRKPPEVKLIDMRKEPRQ---SFLSPELITAIEQTLAAGEQSILFLNRRGYSKNLLCRSCGYILCCPNCDVSLTYHK 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 528 KQAQLVCHYCGHTEPVPKVCPKCGSKRIRFFGTGTEKAEESLRTLCEGIRPLRMDQDTTARKFSHEKIMRAFRSGEYNVL 607
Cdd:TIGR00595 237 KEGKLRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQFANGKADIL 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 608 LGTQMVAKGHDVPNVTLVGILSADSTLNLPDFRSGERCFALLTQAAGRAGRGDKPGRVIFQAYDAENPILRMAAEQDYVS 687
Cdd:TIGR00595 317 IGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAGRAGRAEDPGQVIIQTYNPNHPAIQAALTGDYEA 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 688 FARDELKQRQDLQYPPFVTMLKMTVHHESETKALELAQRFVNALEAFQLESKVpyqILGPFPALVPVVNRVWRVNVLIKS 767
Cdd:TIGR00595 397 FYEQELAQRRALNYPPFTRLIRLIFRGKNEEKAQQTAQAAHELLKQNLDEKLE---VLGPSPAPIAKIAGRYRYQILLKS 473
|
490 500 510
....*....|....*....|....*....|....
gi 496306713 768 ----QHMKPIKDWIRAsgFLENGNLY--FDVDPI 795
Cdd:TIGR00595 474 ksflVLQKLVNKTLLK--EIPSSSVYceVDVDPI 505
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
457-697 |
4.30e-123 |
|
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: 369.27 E-value: 4.30e-123
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 457 VSIVDMREELqkgNKSVFSDTLRDAIEETVKSGEQAIILLNRRGFSTFVMCRDCGESIQCPNCAVALVYHAKQAQLVCHY 536
Cdd:cd18804 1 IEIVDMKEEE---LKSGFSPKLLDAIKETLEKGEQVILFLNRRGYSPSVLCRDCGYVPECPNCDVSMTYHKSTNKLKCHY 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 537 CGHTEPVPKVCPKCGSKRIRFFGTGTEKAEESLRTLCEGIRPLRMDQDTTARKFSHEKIMRAFRSGEYNVLLGTQMVAKG 616
Cdd:cd18804 78 CGYQEPIPKQCPECGSEDLVFKGIGTERVEEELKTLFPEARIARIDRDTTRKKGALEKLLDQFERGEIDILIGTQMIAKG 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 617 HDVPNVTLVGILSADSTLNLPDFRSGERCFALLTQAAGRAGRGDKPGRVIFQAYDAENPILRMAAEQDYVSFARDELKQR 696
Cdd:cd18804 158 LDFPNVTLVGILNADSGLNSPDFRASERAFQLLTQVSGRAGRGDKPGKVIIQTYNPEHPLIQAAKEEDYEAFYEEELAER 237
|
.
gi 496306713 697 Q 697
Cdd:cd18804 238 K 238
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
268-447 |
8.12e-91 |
|
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: 282.94 E-value: 8.12e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 268 QQAAINAVEicRKRGTFHTFLLRGVTGSGKTEVYLRLTDKALRDGKQVMVLVPEIALTDQIVKRFKSWFGNAVAVAHSKL 347
Cdd:cd17929 1 QRKAYEAIV--SSLGGFKTFLLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKRFGDKVAVLHSKL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 348 SASERADVWDRMRNGKARVLIGVRSAVFCPFKDLGLVVIDEEHESTYKQEERPGYNARLVAQVRANAHGAPVVLGSATPD 427
Cdd:cd17929 79 SDKERADEWRKIKRGEAKVVIGARSALFAPFKNLGLIIVDEEHDSSYKQDSGPRYHARDVAIYRAKLENAPVVLGSATPS 158
|
170 180
....*....|....*....|
gi 496306713 428 LETYYWAQKGRYTELIMNER 447
Cdd:cd17929 159 LESYYNAQQGKYRLLQLTER 178
|
|
| PriA_3primeBD |
pfam17764 |
3'DNA-binding domain (3'BD); This domain represents the N-terminal DNA-binding domain found in ... |
5-103 |
1.53e-31 |
|
3'DNA-binding domain (3'BD); This domain represents the N-terminal DNA-binding domain found in the PriA protein. The 3'BD, which has been shown to bind the 3' end of the leading-strand arm of replication fork structures.
Pssm-ID: 465491 [Multi-domain] Cd Length: 96 Bit Score: 118.33 E-value: 1.53e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 5 KVAVNLPLknlFRQFTYKVPPSLDfIGEGWRVVVPFGRQLLEGFIVEADEAPDASLA-IKSIVDVVGTEPWFDEEMLGTA 83
Cdd:pfam17764 1 EVAVPLPL---DRPFDYRVPEELA-VKIGMRVLVPFGKRKVTGIVVGLSEESEVDPEkLKPILEVLDEEPLLTPELLELA 76
|
90 100
....*....|....*....|
gi 496306713 84 HWIAQYYLCPLAEALRLFIP 103
Cdd:pfam17764 77 RWMAEYYLCPLGEVLRAALP 96
|
|
| PRK14873 |
PRK14873 |
primosomal protein N'; |
4-707 |
6.03e-29 |
|
primosomal protein N';
Pssm-ID: 237844 [Multi-domain] Cd Length: 665 Bit Score: 123.12 E-value: 6.03e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 4 AKVAVNLPLKNLFRQFTYKVPPSLDF-IGEGWRVVVPFGRQLLEGFIVEADEAPDASLAIKSIVDVVGTEPWFDEEMLGT 82
Cdd:PRK14873 14 ARVLPDLGLPHLDRLFDYLVPEELSDdAQPGVRVRVRFGGRLVDGFVLERRSDSDHEGKLRWLERVVSPEPVLTPEIRRL 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 83 AHWIAQYYLCPLAEALRLFIPGKksiaaVGRYYAEPGAEGLLSERERslytylaqegAMTRREIARLEGGegalkglitk 162
Cdd:PRK14873 94 ARAVADRYAGTRADVLRLAVPPR-----HARVEKEPVATPPPPLTAP----------PPDPSGWAAYGRG---------- 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 163 kavsltyevtyklkekfertvalstdglaqkeagilrgkgQLLVLSLLQGtnplpvrvledRGVSAgvirnlvskgilte 242
Cdd:PRK14873 149 ----------------------------------------PRFLAALAAG-----------RAARA-------------- 163
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 243 gkqrvlrdsyHADAAPRDEMILTDEQQAAinaveicrkrgtfhtfllrgvtgsgktevylrltdKALRDGKQVMVLVPEI 322
Cdd:PRK14873 164 ----------VWQALPGEDWARRLAAAAA-----------------------------------ATLRAGRGALVVVPDQ 198
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 323 ALTDQIVKRFKSWFGN-AVAVAHSKLSASERADVWDRMRNGKARVLIGVRSAVFCPFKDLGLVVIDEEHESTYKQEERPG 401
Cdd:PRK14873 199 RDVDRLEAALRALLGAgDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSAVFAPVEDLGLVAIWDDGDDLLAEPRAPY 278
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 402 YNARLVAQVRANAHGAPVVLGSATPDLETYYWAQKGrYTELIMNERAHKGAHLPAVSIVD------MREELQKGNK--SV 473
Cdd:PRK14873 279 PHAREVALLRAHQHGCALLIGGHARTAEAQALVESG-WAHDLVAPRPVVRARAPRVRALGdsglalERDPAARAARlpSL 357
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 474 FSDTLRDAIEEtvksgEQAIILLNRRGFSTFVMCRDCGESIQCPNCAVALVYHAKQAQLVCHYCGHTEPVPKvCPKCGSK 553
Cdd:PRK14873 358 AFRAARDALEH-----GPVLVQVPRRGYVPSLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWR-CPRCGSD 431
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 554 RIRFFGTGTekaeeslrtlcegirplrmdqDTTArkfshEKIMRAFRsgeynvllGTQMVAKGHD--VPNV----TLV-- 625
Cdd:PRK14873 432 RLRAVVVGA---------------------RRTA-----EELGRAFP--------GVPVVTSGGDqvVDTVdagpALVva 477
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 626 --G-------------ILSADSTLNLPDFRSGERCFALLTQAAGRAGRGDKPGRVIFQAyDAENPILRMAAEQDYVSFAR 690
Cdd:PRK14873 478 tpGaeprveggygaalLLDAWALLGRQDLRAAEDTLRRWMAAAALVRPRADGGQVVVVA-ESSLPTVQALIRWDPVGHAE 556
|
730
....*....|....*..
gi 496306713 691 DELKQRQDLQYPPFVTM 707
Cdd:PRK14873 557 RELAERAEVGFPPAVRM 573
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
254-426 |
1.34e-22 |
|
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: 96.10 E-value: 1.34e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 254 ADAAPRDEmilTDEQQAAINAVEICRKRGTFHTFLLRGVTGSGKTEVYLRLTDKALRDGKQVMVLVPEIALTDQ----IV 329
Cdd:cd17991 9 EASFPYEE---TPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQhyetFK 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 330 KRFKSwFGNAVAVAHSKLSASERADVWDRMRNGKARVLIGVRSAVF--CPFKDLGLVVIDEEHESTYKQEERpgynarlV 407
Cdd:cd17991 86 ERFAN-FPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSkdVEFKNLGLLIIDEEQRFGVKQKEK-------L 157
|
170 180
....*....|....*....|
gi 496306713 408 AQVRANAHgapvVLG-SATP 426
Cdd:cd17991 158 KELRPNVD----VLTlSATP 173
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
264-426 |
6.54e-21 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 91.40 E-value: 6.54e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 264 LTDEQQAAINAVEICRKRGtfhtfLLRGVTGSGKTEVYLR--LTDKALRDGKQVMVLVPEIALTDQIVKRFKSWFGNAVA 341
Cdd:smart00487 9 LRPYQKEAIEALLSGLRDV-----ILAAPTGSGKTLAALLpaLEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGL 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 342 VAHSKLSASERADVWDRMRNGKARVLIG-------VRSAVFCPFKDLGLVVIDEEHESTYKqeerpGYNARLVAQVRANA 414
Cdd:smart00487 84 KVVGLYGGDSKREQLRKLESGKTDILVTtpgrlldLLENDKLSLSNVDLVILDEAHRLLDG-----GFGDQLEKLLKLLP 158
|
170
....*....|..
gi 496306713 415 HGAPVVLGSATP 426
Cdd:smart00487 159 KNVQLLLLSATP 170
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
254-663 |
1.85e-20 |
|
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: 97.04 E-value: 1.85e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 254 ADAAPRDEmilTDEQQAAINAVEICRKRGTFHTFLLRGVTGSGKTEVYLRLTDKALRDGKQVMVLVPEIALTDQ----IV 329
Cdd:TIGR00580 445 EDSFPFEE---TPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQhfetFK 521
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 330 KRFKSwFGNAVAVAHSKLSASERADVWDRMRNGKARVLIG----VRSAVfcPFKDLGLVVIDEEHESTYKQEERpgynar 405
Cdd:TIGR00580 522 ERFAN-FPVTIELLSRFRSAKEQNEILKELASGKIDILIGthklLQKDV--KFKDLGLLIIDEEQRFGVKQKEK------ 592
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 406 lVAQVRANAHgapVVLGSATPDLETYYWAQKG-RYTELIMnerahkgahLPAVSIVDMREELQKgnksvFSDTL-RDAIE 483
Cdd:TIGR00580 593 -LKELRTSVD---VLTLSATPIPRTLHMSMSGiRDLSIIA---------TPPEDRLPVRTFVME-----YDPELvREAIR 654
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 484 ETVKSGEQAIILLNRRgfstfvmcrdcgESIQcpncavalvyhAKQAQLvchycghTEPVPKVcpkcgskRIRfFGTGTE 563
Cdd:TIGR00580 655 RELLRGGQVFYVHNRI------------ESIE-----------KLATQL-------RELVPEA-------RIA-IAHGQM 696
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 564 KAEESlrtlcegirplrmdqdttarkfshEKIMRAFRSGEYNVLLGTQMVAKGHDVPNVTLVGILSADsTLNLPDfrsge 643
Cdd:TIGR00580 697 TENEL------------------------EEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERAD-KFGLAQ----- 746
|
410 420
....*....|....*....|
gi 496306713 644 rcfalLTQAAGRAGRGDKPG 663
Cdd:TIGR00580 747 -----LYQLRGRVGRSKKKA 761
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
265-427 |
2.81e-20 |
|
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: 88.45 E-value: 2.81e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 265 TDEQQAAINAVEicrkrgTFHTFLLRGVTGSGKTEVYLRLTDKALR---DGKQVMVLVPEIALTDQIVKRFKSWFGNAVA 341
Cdd:pfam00270 1 TPIQAEAIPAIL------EGRDVLVQAPTGSGKTLAFLLPALEALDkldNGPQALVLAPTRELAEQIYEELKKLGKGLGL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 342 VAHSKLSASERADVWDRMRngKARVLIGVRSAVF------CPFKDLGLVVIDEEHESTYKqEERPGYnARLVAQVRANAH 415
Cdd:pfam00270 75 KVASLLGGDSRKEQLEKLK--GPDILVGTPGRLLdllqerKLLKNLKLLVLDEAHRLLDM-GFGPDL-EEILRRLPKKRQ 150
|
170
....*....|..
gi 496306713 416 gapVVLGSATPD 427
Cdd:pfam00270 151 ---ILLLSATLP 159
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
287-425 |
8.10e-19 |
|
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: 83.61 E-value: 8.10e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 287 FLLRGVTGSGKTEVYLR-LTDKALRDGKQVMVLVPEIALTDQIVKRFKSWF--GNAVAVAHSKLSASERAdvwdRMRNGK 363
Cdd:cd00046 4 VLITAPTGSGKTLAALLaALLLLLKKGKKVLVLVPTKALALQTAERLRELFgpGIRVAVLVGGSSAEERE----KNKLGD 79
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 364 ARVLIGVRSAVFCP--------FKDLGLVVIDEEHESTYKQEERPGYNARLvaqVRANAHGAPVVLGSAT 425
Cdd:cd00046 80 ADIIIATPDMLLNLllredrlfLKDLKLIIVDEAHALLIDSRGALILDLAV---RKAGLKNAQVILLSAT 146
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
253-698 |
2.57e-15 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 79.68 E-value: 2.57e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 253 HADAAPRDEMILTDEQQAAINAVEICRKRGTFHtFLLRGVTGSGKTEVYLRLTdKALRDGKQVMVLVPEIALTDQIVKRF 332
Cdd:COG1061 70 AGDEASGTSFELRPYQQEALEALLAALERGGGR-GLVVAPTGTGKTVLALALA-AELLRGKRVLVLVPRRELLEQWAEEL 147
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 333 KSWFGNAVAVAHSKlsaseradvwdrmrNGKARVLIG-----VRSAVFCPFKDL-GLVVIDEEHE---STYKQeerpgyn 403
Cdd:COG1061 148 RRFLGDPLAGGGKK--------------DSDAPITVAtyqslARRAHLDELGDRfGLVIIDEAHHagaPSYRR------- 206
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 404 arlvaqvRANAHGAPVVLG-SATPDLETYYWAQKGRYTELIMN---ERAHKGAHLPAVSIVDMREELQKGNK--SVFSDT 477
Cdd:COG1061 207 -------ILEAFPAAYRLGlTATPFRSDGREILLFLFDGIVYEyslKEAIEDGYLAPPEYYGIRVDLTDERAeyDALSER 279
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 478 LRDAIeetVKSGEQAIILLNRrgfstfvmcrdcgesiqcpncavALVYHAKQAQLVchycghtepvpkvcpkcgskrirF 557
Cdd:COG1061 280 LREAL---AADAERKDKILRE-----------------------LLREHPDDRKTL-----------------------V 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 558 FGTGTEKAEESLRTLCE-GIRPLRMDQDTTARKfsHEKIMRAFRSGEYNVLLGTQMVAKGHDVPNVTLVGILSADSTLnl 636
Cdd:COG1061 311 FCSSVDHAEALAELLNEaGIRAAVVTGDTPKKE--REEILEAFRDGELRILVTVDVLNEGVDVPRLDVAILLRPTGSP-- 386
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 496306713 637 pdfrsgercfALLTQAAGRAGRGDKPGR--VIFQAYDAENPILR-MAAEQDYVSFARDELKQRQD 698
Cdd:COG1061 387 ----------REFIQRLGRGLRPAPGKEdaLVYDFVGNDVPVLEeLAKDLRDLAGYRVEFLDEEE 441
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
261-426 |
7.66e-15 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 72.70 E-value: 7.66e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 261 EMILTDEQQAAINAVEICRKRGtFHTFLLRGVTGSGKTEVYLRLTDKALRDG--KQVMVLVPEIALTDQIVKRFKSWFGN 338
Cdd:pfam04851 1 KLELRPYQIEAIENLLESIKNG-QKRGLIVMATGSGKTLTAAKLIARLFKKGpiKKVLFLVPRKDLLEQALEEFKKFLPN 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 339 avAVAHSKLSASERADVWdrmrNGKARVLIGVRSAVFCPFKDL---------GLVVIDEEHESTYKqeerpgyNARLVaq 409
Cdd:pfam04851 80 --YVEIGEIISGDKKDES----VDDNKIVVTTIQSLYKALELAslellpdffDVIIIDEAHRSGAS-------SYRNI-- 144
|
170
....*....|....*...
gi 496306713 410 vrANAHGAPVVLG-SATP 426
Cdd:pfam04851 145 --LEYFKPAFLLGlTATP 160
|
|
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
265-390 |
8.43e-14 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 75.49 E-value: 8.43e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 265 TDEQQAAINAVE------------ICrkrgtfhtfllrGVTGSGKTEVYLRLTDKALRDGKQVMVLVPEIALTDQ----I 328
Cdd:COG1197 588 TPDQLRAIEEVKadmesprpmdrlVC------------GDVGFGKTEVALRAAFKAVMDGKQVAVLVPTTLLAQQhyetF 655
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 496306713 329 VKRFKSWfgnAVAVAH-SKL-SASERADVWDRMRNGKARVLIG--------VRsavfcpFKDLGLVVIDEEH 390
Cdd:COG1197 656 KERFAGF---PVRVEVlSRFrTAKEQKETLEGLADGKVDIVIGthrllskdVK------FKDLGLLIIDEEQ 718
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
264-663 |
1.01e-13 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 74.80 E-value: 1.01e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 264 LTDEQQAAINavEICR--------KRgtfhtfLLRGVTGSGKTEVYLRLTDKALRDGKQVMVLVP-EIaLTDQIVKRFKS 334
Cdd:PRK10917 262 LTGAQKRVVA--EILAdlaspkpmNR------LLQGDVGSGKTVVAALAALAAIEAGYQAALMAPtEI-LAEQHYENLKK 332
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 335 WFGNA---VAVAHSKLSASERADVWDRMRNGKARVLIG--------VRsavfcpFKDLGLVVIDEEHestykqeeRPGYN 403
Cdd:PRK10917 333 LLEPLgirVALLTGSLKGKERREILEAIASGEADIVIGthaliqddVE------FHNLGLVIIDEQH--------RFGVE 398
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 404 ARLvaQVRANAHGAPVVLGSATP-----------DLEtyywaqkgrytelimnerahkgahlpaVSIVDmreELQKGNK- 471
Cdd:PRK10917 399 QRL--ALREKGENPHVLVMTATPiprtlamtaygDLD---------------------------VSVID---ELPPGRKp 446
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 472 ---SVFSDTLRDA----IEETVKSGEQAIIllnrrgfstfvmcrdcgesiqcpncavalvyhakqaqlvchycghtepvp 544
Cdd:PRK10917 447 ittVVIPDSRRDEvyerIREEIAKGRQAYV-------------------------------------------------- 476
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 545 kVCPkcgskRIrffgTGTEK-----AEESLRTLCEGIRPL-------RMDQDttarkfshEK--IMRAFRSGEYNVLLGT 610
Cdd:PRK10917 477 -VCP-----LI----EESEKldlqsAEETYEELQEAFPELrvgllhgRMKPA--------EKdaVMAAFKAGEIDILVAT 538
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*
gi 496306713 611 QMVAKGHDVPNVTLVGILSAdstlnlpdfrsgERcFAL--LTQAAGRAGRGDKPG 663
Cdd:PRK10917 539 TVIEVGVDVPNATVMVIENA------------ER-FGLaqLHQLRGRVGRGAAQS 580
|
|
| PriA_CRR |
pfam18319 |
PriA DNA helicase Cys-rich region (CRR) domain; This is a cys-rich region (CRR) domain found ... |
516-542 |
1.03e-12 |
|
PriA DNA helicase Cys-rich region (CRR) domain; This is a cys-rich region (CRR) domain found in PriA DNA helicases. In bacteria, the replication restart process is orchestrated by the PriA DNA helicase, which identifies replication forks via structure-specific DNA binding and interactions with fork-associated ssDNA-binding proteins (SSBs). The CRR region which is embedded within the C-terminal helicase lobe has been identified to bind two Zn2+ ions. This 50-residue insertion forms a structure on the surface of the helicase core in which two Zn2+ ions are coordinated by invariant Cys residues. Biochemical experiments have shown that sequence changes to Zn2+-binding Cys residues in the PriA CRR can eliminate helicase, but not ATPase, activity and can block assembly of PriB onto DNA-bound PriA, implicating the CRR in multiple functions in PriA.
Pssm-ID: 465708 [Multi-domain] Cd Length: 27 Bit Score: 62.54 E-value: 1.03e-12
10 20
....*....|....*....|....*..
gi 496306713 516 CPNCAVALVYHAKQAQLVCHYCGHTEP 542
Cdd:pfam18319 1 CPNCDVSLTYHKSRNRLRCHYCGYTEP 27
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
264-663 |
1.90e-12 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 70.85 E-value: 1.90e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 264 LTDEQQAAINavEICR--KRGTFHTFLLRGVTGSGKTEVYLRLTDKALRDGKQVMVLVP-EIaLTDQIVKRFKSWFGNA- 339
Cdd:COG1200 260 LTGAQKRVIA--EIAAdlASPHPMNRLLQGDVGSGKTVVALLAMLAAVEAGYQAALMAPtEI-LAEQHYRSLSKLLEPLg 336
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 340 --VAVAHSKLSASERADVWDRMRNGKARVLIG--------VRsavfcpFKDLGLVVIDEEHestykqeeRPGynarlVAQ 409
Cdd:COG1200 337 irVALLTGSTKAKERREILAALASGEADIVVGthaliqddVE------FKNLGLVVIDEQH--------RFG-----VEQ 397
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 410 vRA-------NAHgapvVLG-SATP-----------DLEtyywaqkgrytelimnerahkgahlpaVSIVDmreELQKGN 470
Cdd:COG1200 398 -RLalrekgeAPH----VLVmTATPiprtlamtlygDLD---------------------------VSVID---ELPPGR 442
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 471 K----SVFSDTLRD----AIEETVKSGEQAiillnrrgfstFVmcrdcgesiqcpncavalvyhakqaqlvchycghtep 542
Cdd:COG1200 443 KpiktRVVPEERRDevyeRIREEIAKGRQA-----------YV------------------------------------- 474
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 543 vpkVCPkcgskRIrffgTGTEK-----AEESLRTLCEGIRPL-------RMDQDttarkfshEK--IMRAFRSGEYNVLL 608
Cdd:COG1200 475 ---VCP-----LI----EESEKldlqaAEETYEELREAFPGLrvgllhgRMKPA--------EKdaVMAAFKAGEIDVLV 534
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*..
gi 496306713 609 GTQMVAKGHDVPNVTLVGILSAdstlnlpdfrsgERcFAL--LTQAAGRAGRGDKPG 663
Cdd:COG1200 535 ATTVIEVGVDVPNATVMVIENA------------ER-FGLsqLHQLRGRVGRGSAQS 578
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
265-399 |
2.05e-12 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 70.93 E-value: 2.05e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 265 TDEQQAAINAV--EICRKRGTFHtfLLRGVTGSGKTEVYLRLTDKALRDGKQVMVLVPEIALTDQIVKRFKSWFGN---A 339
Cdd:PRK10689 602 TPDQAQAINAVlsDMCQPLAMDR--LVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFANwpvR 679
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 496306713 340 VAVAHSKLSASERADVWDRMRNGKARVLIG----VRSAVfcPFKDLGLVVIDEEHESTYKQEER 399
Cdd:PRK10689 680 IEMLSRFRSAKEQTQILAEAAEGKIDILIGthklLQSDV--KWKDLGLLIVDEEHRFGVRHKER 741
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
264-414 |
2.08e-12 |
|
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: 66.29 E-value: 2.08e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 264 LTDEQQAAINAVEICRKRGTFHTFLLRGVTGSGKTEVYLRLTDKALRDGKQVMVLVPEIALTDQIVKRFKSWFGN---AV 340
Cdd:cd17918 16 LTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQHYEEARKFLPFinvEL 95
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 496306713 341 AVAHSKLSASERADvwdrmrngkarVLIGVRSAVF--CPFKDLGLVVIDEEHESTYKQEERPgYNARLVAQVRANA 414
Cdd:cd17918 96 VTGGTKAQILSGIS-----------LLVGTHALLHldVKFKNLDLVIVDEQHRFGVAQREAL-YNLGATHFLEATA 159
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
264-390 |
2.77e-11 |
|
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: 64.09 E-value: 2.77e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 264 LTDEQQAAINavEICR--KRGTFHTFLLRGVTGSGKTEVYLRLTDKALRDGKQVMVLVP-EIaLTDQIVKRFKSWFGNA- 339
Cdd:cd17992 46 LTGAQKRVID--EILRdlASEKPMNRLLQGDVGSGKTVVAALAMLAAVENGYQVALMAPtEI-LAEQHYDSLKKLLEPLg 122
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*.
gi 496306713 340 --VAVAHSKLSASERADVWDRMRNGKARVLIGVRsAVF---CPFKDLGLVVIDEEH 390
Cdd:cd17992 123 irVALLTGSTKAKEKREILEKIASGEIDIVIGTH-ALIqedVEFHNLGLVIIDEQH 177
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
563-658 |
2.86e-10 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 57.22 E-value: 2.86e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 563 EKAEESLRTLceGIRPLRMDQDTTARKfsHEKIMRAFRSGEYNVLLGTQMVAKGHDVPNVTLVGILSADSTlnlpdfrsg 642
Cdd:smart00490 1 EELAELLKEL--GIKVARLHGGLSQEE--REEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWS--------- 67
|
90
....*....|....*.
gi 496306713 643 ercFALLTQAAGRAGR 658
Cdd:smart00490 68 ---PASYIQRIGRAGR 80
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
558-658 |
3.41e-10 |
|
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: 57.99 E-value: 3.41e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 558 FGTGTEKAEESLRTLCEGIRPLRMDQDTTARKfsHEKIMRAFRSGEYNVLLGTQMVAKGHDVPNVTLVGILSADSTLnlp 637
Cdd:pfam00271 21 FSQTKKTLEAELLLEKEGIKVARLHGDLSQEE--REEILEDFRKGKIDVLVATDVAERGLDLPDVDLVINYDLPWNP--- 95
|
90 100
....*....|....*....|.
gi 496306713 638 dfrsgercfALLTQAAGRAGR 658
Cdd:pfam00271 96 ---------ASYIQRIGRAGR 107
|
|
| SF2_C_UvrB |
cd18790 |
C-terminal helicase domain of the UvrB family helicases; Excinuclease ABC subunit B (or UvrB) ... |
560-669 |
4.16e-08 |
|
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: 53.40 E-value: 4.16e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 560 TGTEK-AEESLRTLCE-GIRPLRM--DQDTTARKfsheKIMRAFRSGEYNVLLGTQMVAKGHDVPNVTLVGILSADSTLN 635
Cdd:cd18790 34 TLTKRmAEDLTEYLQElGVKVRYLhsEIDTLERV----EIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDADKEGF 109
|
90 100 110
....*....|....*....|....*....|....
gi 496306713 636 LPDFRSgercfalLTQAAGRAGRgDKPGRVIFQA 669
Cdd:cd18790 110 LRSETS-------LIQTIGRAAR-NVNGKVILYA 135
|
|
| DEXHc_RecQ |
cd17920 |
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ... |
268-425 |
5.58e-08 |
|
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box helicase superfamily is a family of highly conserved DNA repair helicases. This domain contains the ATP-binding region.
Pssm-ID: 350678 [Multi-domain] Cd Length: 200 Bit Score: 53.69 E-value: 5.58e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 268 QQAAINAVeiCRKRgtfHTFLLRGvTGSGKTEVY-LrltdKALRDGKQVMVLVPEIAL-TDQiVKRFKSWFGNAVAVaHS 345
Cdd:cd17920 17 QLEAINAV--LAGR---DVLVVMP-TGGGKSLCYqL----PALLLDGVTLVVSPLISLmQDQ-VDRLQQLGIRAAAL-NS 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 346 KLSASERADVWDRMRNGKARVL-----IGVRSAVF------CPFKDLGLVVIDEEH-ESTYKQEERPGYnaRLVAQVRAN 413
Cdd:cd17920 85 TLSPEEKREVLLRIKNGQYKLLyvtpeRLLSPDFLellqrlPERKRLALIVVDEAHcVSQWGHDFRPDY--LRLGRLRRA 162
|
170
....*....|..
gi 496306713 414 AHGAPVVLGSAT 425
Cdd:cd17920 163 LPGVPILALTAT 174
|
|
| Cas3 |
COG1203 |
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; ... |
268-499 |
7.45e-08 |
|
CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]; CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system
Pssm-ID: 440816 [Multi-domain] Cd Length: 535 Bit Score: 55.86 E-value: 7.45e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 268 QQAAINAVEICRKRGTfHTFLLRGVTGSGKTEVYLRLTDKALRDGKQ--VMVLVPEIALTDQIVKRFKSWFGNAVAVAHS 345
Cdd:COG1203 132 QNEALELALEAAEEEP-GLFILTAPTGGGKTEAALLFALRLAAKHGGrrIIYALPFTSIINQTYDRLRDLFGEDVLLHHS 210
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 346 K--LSASERADVWD--------RMRNGKARVLIG--VR--SAVFCPFKD-----LGL----VVIDEEHesTYKQEerpgY 402
Cdd:COG1203 211 LadLDLLEEEEEYEsearwlklLKELWDAPVVVTtiDQlfESLFSNRKGqerrlHNLansvIILDEVQ--AYPPY----M 284
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 403 NARLVAQVR-ANAHGAPVVLGSAT-PDLETyywAQKGRYTELIMNERAHKGAHlpAVSIVDMREELQKGNKSvfSDTLRD 480
Cdd:COG1203 285 LALLLRLLEwLKNLGGSVILMTATlPPLLR---EELLEAYELIPDEPEELPEY--FRAFVRKRVELKEGPLS--DEELAE 357
|
250
....*....|....*....
gi 496306713 481 AIEETVKSGEQAIILLNRR 499
Cdd:COG1203 358 LILEALHKGKSVLVIVNTV 376
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
264-679 |
6.55e-07 |
|
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, recombination and repair];
Pssm-ID: 443274 [Multi-domain] Cd Length: 451 Bit Score: 52.57 E-value: 6.55e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 264 LTDEQQAAINAVE--ICRKRgtfhTFLLRGVTGSGKTEVYLRLTDKALRDGKQVMVLVPEIALTDQIVKRFKSWFGN-AV 340
Cdd:COG4098 111 LTPAQQKASDELLeaIKKKE----EHLVWAVCGAGKTEMLFPAIAEALKQGGRVCIATPRVDVVLELAPRLQQAFPGvDI 186
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 341 AVAHSKlsaSEraDVWDRmrngkARVLIG-----VRsavfcpFKD-LGLVVIDEEHESTYKqeerpgYNARLVAQV-RAN 413
Cdd:COG4098 187 AALYGG---SE--EKYRY-----AQLVIAtthqlLR------FYQaFDLLIIDEVDAFPYS------GDPMLQYAVkRAR 244
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 414 AHGAPVVLGSATPDLETYYWAQKGRYTELIMNERAHkGAHLPA---VSIVDMREELQKGNKSvfsDTLRDAIEETVKSGE 490
Cdd:COG4098 245 KPDGKLIYLTATPSKALQRQVKRGKLKVVKLPARYH-GHPLPVpkfKWLGNWKKRLRRGKLP---RKLLKWLKKRLKEGR 320
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 491 QAIIllnrrgfstFVmcrdcgesiqcPNcaVALVyhakqaqlvchycghtepvpkvcpkcgskrirffgtgtEKAEESLR 570
Cdd:COG4098 321 QLLI---------FV-----------PT--IELL--------------------------------------EQLVALLQ 340
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 571 TLCEGIR--------PLRmdqdttarkfsHEKIMrAFRSGEYNVLLGTQMVAKGHDVPNVTlVGILSADSTLnlpdFRSg 642
Cdd:COG4098 341 KLFPEERiagvhaedPER-----------KEKVQ-AFRDGEIPILVTTTILERGVTFPNVD-VAVLGADHPV----FTE- 402
|
410 420 430
....*....|....*....|....*....|....*....
gi 496306713 643 ercfALLTQAAGRAGR-GDKP-GRVIFQAYDAENPILRM 679
Cdd:COG4098 403 ----AALVQIAGRVGRsADYPtGEVIFFHHGKTRAMKRA 437
|
|
| DEXHc_cas3 |
cd17930 |
DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase ... |
287-425 |
8.72e-07 |
|
DEXH/Q-box helicase domain of Cas3; CRISPR-associated (Cas) 3 is a nuclease-helicase responsible for degradation of dsDNA. The two enzymatic units of Cas3, a histidine-aspartate (HD) nuclease and a Superfamily 2 (SF2) helicase, may be expressed from separate genes as Cas3' (SF2 helicase) and Cas3'' (HD nuclease) or may be fused as a single HD-SF2 polypeptide. The nucleolytic activity of most Cas3 enzymes is transition metal ion-dependent. Cas3 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: 350688 [Multi-domain] Cd Length: 186 Bit Score: 49.98 E-value: 8.72e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 287 FLLRGVTGSGKTEVYLRLTDKALRDGKQ--VMVLVPEIALTDQIVKRFKSWFGNA-----VAVAHSK-----------LS 348
Cdd:cd17930 4 VILEAPTGSGKTEAALLWALKLAARGGKrrIIYALPTRATINQMYERIREILGRLddedkVLLLHSKaalellesdeePD 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 349 ASERADVWDRMRNGKA-----------RVLIGV--RSAVFCPFKDLG--LVVIDEEHesTYKQEerpgYNARLVAQVR-- 411
Cdd:cd17930 84 DDPVEAVDWALLLKRSwlapivvttidQLLESLlkYKHFERRLHGLAnsVVVLDEVQ--AYDPE----YMALLLKALLel 157
|
170
....*....|....
gi 496306713 412 ANAHGAPVVLGSAT 425
Cdd:cd17930 158 LGELGGPVVLMTAT 171
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
593-662 |
8.86e-07 |
|
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: 49.26 E-value: 8.86e-07
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 593 EKIMRAFRSGEYNVLLGTQMVAKGHDVPNVTLVGILSADstlnlpdfRSGercFALLTQAAGRAGRGDKP 662
Cdd:cd18811 77 DAVMAEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAE--------RFG---LSQLHQLRGRVGRGDHQ 135
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
293-425 |
9.22e-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: 49.95 E-value: 9.22e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 293 TGSGKTEVYLRLTDKALRDGKQVMV-LVPEIALTDQIVKRFKSWFGNAVavahSKLSASERADVWDRMRNGKARVLIGV- 370
Cdd:cd17921 26 TSSGKTLIAELAILRALATSGGKAVyIAPTRALVNQKEADLRERFGPLG----KNVGLLTGDPSVNKLLLAEADILVATp 101
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 496306713 371 -------RSAVFCPFKDLGLVVIDEEHEstYKQEERpGYNA-RLVAQVRANAHGAPVVLGSAT 425
Cdd:cd17921 102 ekldlllRNGGERLIQDVRLVVVDEAHL--IGDGER-GVVLeLLLSRLLRINKNARFVGLSAT 161
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
593-663 |
1.29e-06 |
|
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: 48.80 E-value: 1.29e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 496306713 593 EKIMRAFRSGEYNVLLGTQMVAKGHDVPNVTLVGILSADstlnlpdfRSGercFALLTQAAGRAGRGDKPG 663
Cdd:cd18792 76 EAVMLEFREGEYDILVSTTVIEVGIDVPNANTMIIEDAD--------RFG---LSQLHQLRGRVGRGKHQS 135
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
264-426 |
4.07e-06 |
|
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: 47.30 E-value: 4.07e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 264 LTDEQQAAINAVeicRKRGTFHTFLLRGVTGSGKTEVYLRLTDKALRDGkqVMVLVPEIALTDQIVKRFKSWFGNavavA 343
Cdd:cd17926 1 LRPYQEEALEAW---LAHKNNRRGILVLPTGSGKTLTALALIAYLKELR--TLIVVPTDALLDQWKERFEDFLGD----S 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 344 HSKLSASERADVWDrmrNGKARV-----LIGVRSAVFCPFKDLGLVVIDEEHEstykqeerpgYNARLVAQVRANAhGAP 418
Cdd:cd17926 72 SIGLIGGGKKKDFD---DANVVVatyqsLSNLAEEEKDLFDQFGLLIVDEAHH----------LPAKTFSEILKEL-NAK 137
|
....*....
gi 496306713 419 VVLG-SATP 426
Cdd:cd17926 138 YRLGlTATP 146
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
593-666 |
4.67e-06 |
|
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, 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: 350174 [Multi-domain] Cd Length: 131 Bit Score: 46.73 E-value: 4.67e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 496306713 593 EKIMRAFRSGEYNVLLGTQMVAKGHDVPNVTLVgILsadstLNLPdfRSGE----RCfalltqaaGRAGRGDKPGRVI 666
Cdd:cd18787 67 ERALKKFRSGKVRVLVATDVAARGLDIPGVDHV-IN-----YDLP--RDAEdyvhRI--------GRTGRAGRKGTAI 128
|
|
| PriA_C |
pfam18074 |
Primosomal protein N C-terminal domain; This is the C-terminal domain found in PriA DNA ... |
703-794 |
5.13e-06 |
|
Primosomal protein N C-terminal domain; This is the C-terminal domain found in PriA DNA helicase, a multifunctional enzyme that mediates the process of restarting prematurely terminated DNA replication reactions in bacteria. The C-terminal domain (CTD) bears similarity to the S10 subunit which binds branched rRNA within the bacterial ribosome. The C-terminal domain is part of the helicase domain of PriA proteins. It acts together with the 3' DNA-binding domain to form a site for binding ssDNA-binding protein (SSB).
Pssm-ID: 465633 [Multi-domain] Cd Length: 96 Bit Score: 45.67 E-value: 5.13e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 703 PFVTMLKMTVHHESETKALELAQRFVNALEAFQLESKVpyQILGPFPALVPVVNRVWRVNVLIKSQHMKPIKDWIRA--- 779
Cdd:pfam18074 1 PFSRLALIRVSGKDEEKAEKFAEELAELLKELLKLQGV--EILGPAPAPIAKIKGRYRYQLLLKSKSRKALHQLLRElle 78
|
90
....*....|....*...
gi 496306713 780 ---SGFLENGNLYFDVDP 794
Cdd:pfam18074 79 elqKLPKRKVRISIDVDP 96
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
264-499 |
7.97e-06 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 49.12 E-value: 7.97e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 264 LTDEQQAAInaveicrKRGTF--HTFLLRGVTGSGKT---EVYLRltdKALRDGKQVMVLVPEIALTDQIVKRFKSWFGN 338
Cdd:COG1204 23 LYPPQAEAL-------EAGLLegKNLVVSAPTASGKTliaELAIL---KALLNGGKALYIVPLRALASEKYREFKRDFEE 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 339 A---VAVA----HSKLSASERAD--VwdrMRNGKARVLIGVRSAVfcpFKDLGLVVIDEEH--EStykqEER-PGYNArL 406
Cdd:COG1204 93 LgikVGVStgdyDSDDEWLGRYDilV---ATPEKLDSLLRNGPSW---LRDVDLVVVDEAHliDD----ESRgPTLEV-L 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 407 VAQVRANAHGAPVVLGSATpdletyywaqkgrytelIMNerAHKGAH-LPAVSI------VDMREELQKGNKSVFSDTLR 479
Cdd:COG1204 162 LARLRRLNPEAQIVALSAT-----------------IGN--AEEIAEwLDAELVksdwrpVPLNEGVLYDGVLRFDDGSR 222
|
250 260
....*....|....*....|....*..
gi 496306713 480 -------DAIEETVKSGEQAIILLNRR 499
Cdd:COG1204 223 rskdptlALALDLLEEGGQVLVFVSSR 249
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
274-390 |
2.03e-05 |
|
DEXH-box helicase domain of 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. Dicers exist throughout eukaryotes, and a subset have 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 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: 350792 [Multi-domain] Cd Length: 200 Bit Score: 46.11 E-value: 2.03e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 274 AVEICRKRGTfhtfLLRGVTGSGKTEV-------YLRLTDKALRDGKQVMVLVPEIALTDQIVKRFKSWFGNAVAVAHSK 346
Cdd:cd18034 10 LFEAALKRNT----IVVLPTGSGKTLIavmlikeMGELNRKEKNPKKRAVFLVPTVPLVAQQAEAIRSHTDLKVGEYSGE 85
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 496306713 347 L-SASERADVWDR-MRNGK-----ARVLIGVRSAVFCPFKDLGLVVIDEEH 390
Cdd:cd18034 86 MgVDKWTKERWKEeLEKYDvlvmtAQILLDALRHGFLSLSDINLLIFDECH 136
|
|
| PRK05298 |
PRK05298 |
excinuclease ABC subunit UvrB; |
594-669 |
6.26e-05 |
|
excinuclease ABC subunit UvrB;
Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 46.58 E-value: 6.26e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 594 KIMRAFRSGEYNVLLGTQMVAKGHDVPNVTLVGILSAD------STlnlpdfRSgercfalLTQAAGRAGRGDKpGRVIF 667
Cdd:PRK05298 487 EIIRDLRLGEFDVLVGINLLREGLDIPEVSLVAILDADkegflrSE------RS-------LIQTIGRAARNVN-GKVIL 552
|
..
gi 496306713 668 QA 669
Cdd:PRK05298 553 YA 554
|
|
| COG2888 |
COG2888 |
Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 ... |
507-553 |
7.05e-05 |
|
Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 family [General function prediction only];
Pssm-ID: 442134 [Multi-domain] Cd Length: 52 Bit Score: 40.87 E-value: 7.05e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 496306713 507 CRDCGESIQ--------CPNCAVALVYHakqaqlvCHYCGHTEPVPKVCPKCGSK 553
Cdd:COG2888 3 CPSCGREIApeggvafyCPNCGEALIIR-------CPKCRKQSNALYFCPKCGFE 50
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
603-667 |
2.01e-04 |
|
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: 40.38 E-value: 2.01e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 496306713 603 EYNVLLGTQMVAKGHDVPNVTLVGILSADSTlnlpdfrsgercFALLTQAAGRAGR-GDKPGRVIF 667
Cdd:cd18785 22 SLEILVATNVLGEGIDVPSLDTVIFFDPPSS------------AASYIQRVGRAGRgGKDEGEVIL 75
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
593-663 |
2.13e-04 |
|
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: 42.33 E-value: 2.13e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 496306713 593 EKIMRAFRSGEYNVLLGTQMVAKGHDVPNVTLVGILSADsTLNLpdfrsgercfALLTQAAGRAGRGDKPG 663
Cdd:cd18810 67 EEVMLEFAKGEYDILVCTTIIESGIDIPNANTIIIERAD-KFGL----------AQLYQLRGRVGRSKERA 126
|
|
| DDXDc_reverse_gyrase |
cd17924 |
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of ... |
293-387 |
5.65e-04 |
|
DDXD-box helicase domain of reverse gyrase; Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase 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: 350682 [Multi-domain] Cd Length: 189 Bit Score: 41.93 E-value: 5.65e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 293 TGSGKTEVYLRLTDKALRDGKQVMVLVPEIALTDQIVKRFKSWFGNA-----VAVAHSKLSASERADVWDRMRNGKARVL 367
Cdd:cd17924 41 TGVGKTTFGLATSLYLASKGKRSYLIFPTKSLVKQAYERLSKYAEKAgvevkILVYHSRLKKKEKEELLEKIEKGDFDIL 120
|
90 100
....*....|....*....|....*
gi 496306713 368 IGV-----RSAVFCPFKDLGLVVID 387
Cdd:cd17924 121 VTTnqflsKNFDLLSNKKFDFVFVD 145
|
|
| DZR |
pfam12773 |
Double zinc ribbon; This family consists of a pair of zinc ribbon domains. |
516-552 |
1.08e-03 |
|
Double zinc ribbon; This family consists of a pair of zinc ribbon domains.
Pssm-ID: 432773 [Multi-domain] Cd Length: 45 Bit Score: 37.35 E-value: 1.08e-03
10 20 30
....*....|....*....|....*....|....*..
gi 496306713 516 CPNCAVALVYHAKQaqlvCHYCGhTEPVPKVCPKCGS 552
Cdd:pfam12773 1 CPNCGHPNPPGAKF----CPACG-TPLKPDRCPNCGA 32
|
|
| DEXDc_RapA |
cd18011 |
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ... |
294-426 |
1.15e-03 |
|
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA 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: 350769 [Multi-domain] Cd Length: 207 Bit Score: 41.12 E-value: 1.15e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 294 GSGKT-EV-----YLRLtdkaLRDGKQVMVLVPEiALTDQIVKRFKSWFGNAVAVAHSKLSASER---ADVWDRMRngka 364
Cdd:cd18011 27 GLGKTiEAgliikELLL----RGDAKRVLILCPA-SLVEQWQDELQDKFGLPFLILDRETAAQLRrliGNPFEEFP---- 97
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 365 RVLIGV--------RSAVFCPFkDLGLVVIDEEHESTYKQEERPGYNARLVAQVRANAHGapVVLGSATP 426
Cdd:cd18011 98 IVIVSLdllkrseeRRGLLLSE-EWDLVVVDEAHKLRNSGGGKETKRYKLGRLLAKRARH--VLLLTATP 164
|
|
| DEXHc_RecQ4-like |
cd18018 |
DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) ... |
293-425 |
1.84e-03 |
|
DEAH-box helicase domain of RecQ4 and similar proteins; ATP-dependent DNA helicase Q4 (RecQ4) is part of the RecQ family of highly conserved DNA repair helicases that is part of 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. Mutations cause Rothmund-Thomson/RAPADILINO/Baller-Gerold syndrome.
Pssm-ID: 350776 [Multi-domain] Cd Length: 201 Bit Score: 40.32 E-value: 1.84e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 293 TGSGKTEVYlRLTDKALRDGKQVMVLV--PEIALT-DQI--VKRFKSwfgnaVAVAHSKLSASERADVWDRMRNGKARVL 367
Cdd:cd18018 36 TGAGKSLCY-QLPALLLRRRGPGLTLVvsPLIALMkDQVdaLPRAIK-----AAALNSSLTREERRRILEKLRAGEVKIL 109
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 496306713 368 I---------GVRSAVFCPfKDLGLVVIDEEH-ESTYKQEERPGYnaRLVAQVRANAHGAPVVLG-SAT 425
Cdd:cd18018 110 YvsperlvneSFRELLRQT-PPISLLVVDEAHcISEWSHNFRPDY--LRLCRVLRELLGAPPVLAlTAT 175
|
|
| DEADc_DDX56 |
cd17961 |
DEAD-box helicase domain of DEAD box protein 56; DDX56 is a helicase required for assembly of ... |
288-388 |
2.26e-03 |
|
DEAD-box helicase domain of DEAD box protein 56; DDX56 is a helicase required for assembly of infectious West Nile virus particles. New research suggests that DDX56 relocalizes to the site of virus assembly during WNV infection and that its interaction with WNV capsid in the cytoplasm may occur transiently during virion morphogenesis. DDX56 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350719 [Multi-domain] Cd Length: 206 Bit Score: 40.26 E-value: 2.26e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 288 LLRGVTGSGKTEVYL---------RLTDKALRDGKQVMVLVPEIALTDQIVKRFKS---WFGNAVAVAhsKLSASERADV 355
Cdd:cd17961 35 LARARTGSGKTAAYAlpiiqkilkAKAESGEEQGTRALILVPTRELAQQVSKVLEQltaYCRKDVRVV--NLSASSSDSV 112
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 496306713 356 WDRMRNGKARVLIG--------VRSAVFCPFKDLGLVVIDE 388
Cdd:cd17961 113 QRALLAEKPDIVVStparllshLESGSLLLLSTLKYLVIDE 153
|
|
| PTZ00424 |
PTZ00424 |
helicase 45; Provisional |
555-625 |
2.87e-03 |
|
helicase 45; Provisional
Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 40.97 E-value: 2.87e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 555 IRFFGTGTEKAEESLRTLCEGIRPLRMDQD----TTARKFS------HEK------------------IMRAFRSGEYNV 606
Cdd:PTZ00424 241 IRQFYVAVEKEEWKFDTLCDLYETLTITQAiiycNTRRKVDyltkkmHERdftvscmhgdmdqkdrdlIMREFRSGSTRV 320
|
90
....*....|....*....
gi 496306713 607 LLGTQMVAKGHDVPNVTLV 625
Cdd:PTZ00424 321 LITTDLLARGIDVQQVSLV 339
|
|
| SrmB |
COG0513 |
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
593-666 |
5.59e-03 |
|
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 40.13 E-value: 5.59e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 593 EKIMRAFRSGEYNVLLGTQMVAKGHDVPNVTLVgilsadstLN--LPDF------RSgercfalltqaaGRAGRGDKPGR 664
Cdd:COG0513 281 ERALDAFRNGKIRVLVATDVAARGIDIDDVSHV--------INydLPEDpedyvhRI------------GRTGRAGAEGT 340
|
..
gi 496306713 665 VI 666
Cdd:COG0513 341 AI 342
|
|
| SF2_C_DEAD |
cd18787 |
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ... |
292-368 |
6.13e-03 |
|
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, 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: 350174 [Multi-domain] Cd Length: 131 Bit Score: 37.49 E-value: 6.13e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 496306713 292 VTGSGKTEVYLRLTDKALRDGKqVMVLVPEIALTDQIVKRFKSwFGNAVAVAHSKLSASERADVWDRMRNGKARVLI 368
Cdd:cd18787 8 VEEEEKKLLLLLLLLEKLKPGK-AIIFVNTKKRVDRLAELLEE-LGIKVAALHGDLSQEERERALKKFRSGKVRVLV 82
|
|
| DEXDc_ComFA |
cd17925 |
DEXD-box helicase domain of ComFA; ATP-dependent helicase ComFA (also called ComF operon ... |
268-339 |
7.81e-03 |
|
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: 37.66 E-value: 7.81e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 496306713 268 QQAAINAVEICRKRGTFHtfLLRGVTGSGKTEVYLRLTDKALRDGKQVMVLVPEIALTDQIVKRFKSWFGNA 339
Cdd:cd17925 2 QQKASNALVETIDAKEDL--LVWAVTGAGKTEMLFPAIAQALRQGGRVAIASPRIDVCLELAPRLKAAFPGA 71
|
|
| DEXHc_RE_I_III_res |
cd18032 |
DEXH-box helicase domain of type III restriction enzyme res subunit; Members of this model ... |
268-395 |
8.95e-03 |
|
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: 37.93 E-value: 8.95e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 496306713 268 QQAAINAVEICRKRGtFHTFLLRGVTGSGKTEVYLRLTDKALRDG--KQVMVLVPEIALTDQIVKRFK-----SWFGNAV 340
Cdd:cd18032 5 QQEAIEALEEAREKG-QRRALLVMATGTGKTYTAAFLIKRLLEANrkKRILFLAHREELLEQAERSFKevlpdGSFGNLK 83
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 496306713 341 AvahsklsaseradvwDRMRNGKARVLIG--------VRSAVFCP--FKdlgLVVIDEEHESTYK 395
Cdd:cd18032 84 G---------------GKKKPDDARVVFAtvqtlnkrKRLEKFPPdyFD---LIIIDEAHHAIAS 130
|
|
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