|
Name |
Accession |
Description |
Interval |
E-value |
| Mfd |
COG1197 |
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and ... |
27-1163 |
0e+00 |
|
Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription];
Pssm-ID: 440810 [Multi-domain] Cd Length: 1130 Bit Score: 1431.78 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 27 KQRQLLLGLSGSAKSLAIASSLKSQDK-VLVMTSTYGEAERLINDLISILGSDLVYPFLVDDSPMVEFLVSSQEKIFSRV 105
Cdd:COG1197 2 GGRLTLSGLPGSARALLLAALARALGRpLLVVTADEREAERLAEDLRFFLPDLPVLLFPAWETLPYDRFSPSPDIVSERL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 106 EALRFLRdESQRGILVCNVAASRVFLPNPQVFDDSILELQVGQECEQRELKNHLISLGYKKVTQVQSQGEFSLRGDILDI 185
Cdd:COG1197 82 ATLRRLA-SGKPGIVVTPVRALLQRLPPPELLAAASLSLKVGDELDLEELRERLVAAGYERVDQVEEPGEFAVRGGILDI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 186 FETSQICPYRIEFFGDEIDGIREFDTETQLSKDSKTQVLIYPASDILLTNEDYHRGQKFLEHEIDkaLSPTLKSYLEEVf 265
Cdd:COG1197 161 FPPGSEHPVRIEFFGDEIESIRTFDPETQRSLEKVDEVELLPAREFPLDEEAIERFRERLRELFG--LDPKLDELYEAL- 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 266 sctKEQVLHADIRKFLSVFYKKQWTLIDYLNQ-VPVIFDDFQKIMNQYDAFDKETASYFTEDLHNS-KAVSSLQY----F 339
Cdd:COG1197 238 ---SEGIAFAGIEYYLPLFYEELATLFDYLPEdALVVLDEPERIEEAAEEFWEEIEERYEARRHDRgRPLLPPEElfldP 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 340 ADVESQFKKYvPASFFSNFQkglGNLKFNNLYQFNQYPMQEFFNQFSFLKEEIERYKKLKYTIVLQSSSKTELKKLSTIL 419
Cdd:COG1197 315 EELFAALKRR-PRVTLSPFA---ALPEGAGVVNLGARPLPSFAGQLEALLEELKRLLKDGGRVLLAAESEGRRERLLELL 390
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 420 DEYDIKIDN-SNESEICKGTVNLIEGNLRHGFHFVDENLVFITEYEIFKKKIKRKYRRQNISNAERLKDYNELQKGDYVV 498
Cdd:COG1197 391 RDHGIPARLvESLAELSPGGVAITVGPLEHGFELPDAKLAVITESELFGERVKRRRRKKKRSADAFIRDLSELKPGDYVV 470
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 499 HQIHGIGQYLGIETIEIKGIHRDYVSVLYQNGDRISIPVEQIQTLSKYVSSDGKAPKLNKLNDGRFKKAKQKVKSQVEDI 578
Cdd:COG1197 471 HVDHGIGRYLGLETLEVGGAERDYLVLEYAGGDKLYVPVDQLDLISRYVGSEGEAPKLDKLGGSDWQKAKAKAKKAVRDI 550
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 579 ADDLIKLYAERSQLKGFAFSKDDEDQNAFDEAFPYVETEDQLRSIEEIKKDMQASQPMDRLLVGDVGFGKTEVAMRAAFK 658
Cdd:COG1197 551 AAELLKLYAERAARKGFAFSPDTPWQREFEAAFPYEETPDQLRAIEEVKADMESPRPMDRLVCGDVGFGKTEVALRAAFK 630
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 659 AVNDHKQvvvlvpttvlAQQHYSNFKERFEQFAVNVDVLSRFRSKKEQTETLEKLKKGQVDILIGTHRVLSKDVEFADLG 738
Cdd:COG1197 631 AVMDGKQvavlvpttllAQQHYETFKERFAGFPVRVEVLSRFRTAKEQKETLEGLADGKVDIVIGTHRLLSKDVKFKDLG 710
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 739 LMIIDEEQRFGVKHKEALKELKKKVDVLTLTATPIPRTLHMSMLGIRDLSVIETPPTNRYPVQTYVLEQNDRVIRDAVLR 818
Cdd:COG1197 711 LLIIDEEQRFGVRHKEKLKALRANVDVLTLTATPIPRTLQMSLSGIRDLSIIATPPEDRLPVKTFVGEYDDALIREAILR 790
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 819 EMDRGGQVYYLYNKVDTIEKKVSELQELIPEASIGFVHGQMSEIRLENTLLDFIEGQYDILVTTTIIETGVDIPNANTLF 898
Cdd:COG1197 791 ELLRGGQVFYVHNRVEDIEKVAARLQELVPEARIAVAHGQMSERELERVMLDFYEGEFDVLVCTTIIETGIDIPNANTII 870
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 899 IENADHMGLSTLYQLRGRVGRSNRIAYAYLMYRPDKTLTEVSEKRLEAIKGFTELGSGFKIAMRDLSIRGAGNLLGSSQS 978
Cdd:COG1197 871 IERADRFGLAQLYQLRGRVGRSHRRAYAYLLYPPDKVLTEDAEKRLEAIQEFTELGAGFKLAMHDLEIRGAGNLLGEEQS 950
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 979 GFIDSVGFELYSQLLEEAIAKKNGTDKKREKGNAELILQIDAYLPDEYISDERHKIEIYKRIRQIDDRVNYEELQDELID 1058
Cdd:COG1197 951 GHIAEVGFDLYLQMLEEAVAALKGGKEPEEEWEPEINLGVPALIPEDYIPDVRQRLELYKRIASAESEEELDELQEELID 1030
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 1059 RFGEYPDVVAYLLEIGLAKAYLDKVFVNRVERKNNKLVIQFEKISqqlFLTQDYFQALSQT-SLKANISENQGLievVFD 1137
Cdd:COG1197 1031 RFGPLPEEVENLLAVARLKLLARRLGIEKIDAGGKGIRIEFSPNT---PLDPEKLIRLIQKqPGRYKLDGDDKL---VIT 1104
|
1130 1140
....*....|....*....|....*.
gi 2546864662 1138 IRNKKDYEILEGLLTFGESLANIKDS 1163
Cdd:COG1197 1105 LDLEDPEERLEALEELLEALAKLAKE 1130
|
|
| mfd |
TIGR00580 |
transcription-repair coupling factor (mfd); All proteins in this family for which functions ... |
159-1077 |
0e+00 |
|
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: 1018.05 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 159 LISLGYKKVTQVQSQGEFSLRGDILDIFETSQICPYRIEFFGDEIDGIREFDTETQLSKDSKTQVLIYPAS-DILLTNED 237
Cdd:TIGR00580 1 LVELGYERVDLVEEEGEFSVRGEILDIFPPGSELPVRIEFFGDEIESIREFDVDSQRSLEELLEITILPAKeFILLEEET 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 238 YHRGQKFLEHEIDKALSPTLKSyleevfscTKEQVLHADIRKFLSVFYKKQWTLIDYLNQ-VPVIFDDFQKIMNQYDAFD 316
Cdd:TIGR00580 81 IARLKDNAARVEDAKHLETIEA--------LSEGTLPAGEEMFLPLFFEDLSSLFDYLPDnTPILLDDPERFHSAARFLQ 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 317 KETASYFTEDLHNSKAVSSLQYFADVESQFKKYVPASFFS-NFQKGLGNLKFNNLYQFNQYPMQEFFNQFSFLKEEIERY 395
Cdd:TIGR00580 153 RELEEFYNALEEAKKLINPPRLDLDPSELAFEASAISLSRvQLENEHLSLKASEAIEGAQKHSRLEFGEILAFKEELFRW 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 396 KKLKYTIVLQSSSKTELKKLSTILDEYDIKIDNSNESEICK-GTVNLIEGNLRHGFHFVDENLVFITEYEIFKKKIKRKY 474
Cdd:TIGR00580 233 LKAGFKITVAAESESQAERLKSLLAEHDIAAQVIDESCIIIpAVRYVMIGALSSGFILPTAGLAVITESELFGSRVLRRP 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 475 RRQNISNAeRLKDYNELQKGDYVVHQIHGIGQYLGIETIEIKGIHRDYVSVLYQNGDRISIPVEQIQTLSKYVSSDGKAP 554
Cdd:TIGR00580 313 KKSRLKSK-PIESLNELNPGDYVVHLDHGIGRFLGLETLEVGGIERDYLVLEYAGEDKLYVPVEQLHLISRYVGGSGKNP 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 555 KLNKLNDGRFKKAKQKVKSQVEDIADDLIKLYAERSQLKGFAFSKDDEDQNAFDEAFPYVETEDQLRSIEEIKKDMQASQ 634
Cdd:TIGR00580 392 ALDKLGGKSWEKTKAKVKKSVREIAAKLIELYAKRKAIKGHAFPPDLEWQQEFEDSFPFEETPDQLKAIEEIKADMESPR 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 635 PMDRLLVGDVGFGKTEVAMRAAFKAVNDHKQVVVLVPTTVLAQQHYSNFKERFEQFAVNVDVLSRFRSKKEQTETLEKLK 714
Cdd:TIGR00580 472 PMDRLVCGDVGFGKTEVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEILKELA 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 715 KGQVDILIGTHRVLSKDVEFADLGLMIIDEEQRFGVKHKEALKELKKKVDVLTLTATPIPRTLHMSMLGIRDLSVIETPP 794
Cdd:TIGR00580 552 SGKIDILIGTHKLLQKDVKFKDLGLLIIDEEQRFGVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPP 631
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 795 TNRYPVQTYVLEQNDRVIRDAVLREMDRGGQVYYLYNKVDTIEKKVSELQELIPEASIGFVHGQMSEIRLENTLLDFIEG 874
Cdd:TIGR00580 632 EDRLPVRTFVMEYDPELVREAIRRELLRGGQVFYVHNRIESIEKLATQLRELVPEARIAIAHGQMTENELEEVMLEFYKG 711
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 875 QYDILVTTTIIETGVDIPNANTLFIENADHMGLSTLYQLRGRVGRSNRIAYAYLMYRPDKTLTEVSEKRLEAIKGFTELG 954
Cdd:TIGR00580 712 EFQVLVCTTIIETGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKKKAYAYLLYPHQKALTEDAQKRLEAIQEFSELG 791
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 955 SGFKIAMRDLSIRGAGNLLGSSQSGFIDSVGFELYSQLLEEAIAKKNGTDKKREKGNAELILQIDAYLPDEYISDERHKI 1034
Cdd:TIGR00580 792 AGFKIALHDLEIRGAGNLLGEEQSGHIESIGFDLYMELLEEAIEELKGGKPPKLEEETDIELPYSAFIPDDYIADDSLRL 871
|
890 900 910 920
....*....|....*....|....*....|....*....|...
gi 2546864662 1035 EIYKRIRQIDDRVNYEELQDELIDRFGEYPDVVAYLLEIGLAK 1077
Cdd:TIGR00580 872 EFYKRIASAETEEELEKIRDELIDRFGPLPEEARTLLDVARLK 914
|
|
| PRK10689 |
PRK10689 |
transcription-repair coupling factor; Provisional |
98-1099 |
0e+00 |
|
transcription-repair coupling factor; Provisional
Pssm-ID: 182649 [Multi-domain] Cd Length: 1147 Bit Score: 681.47 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 98 QEKIFSRVEALRFLrDESQRGILV--CNVAASRVFlpnPQVF-DDSILELQVGQECEQRELKNHLISLGYKKVTQVQSQG 174
Cdd:PRK10689 85 QDIISSRLSTLYQL-PTMQRGVLIlpVNTLMQRVC---PHSFlHGHALVMKKGQRLSRDALRAQLEQAGYRHVDQVMEHG 160
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 175 EFSLRGDILDIFETSQICPYRIEFFGDEIDGIREFDTETQLSKDSKTQVLIYPAsdilltnedyhrgqkfleHEIdkals 254
Cdd:PRK10689 161 EYATRGALLDLFPMGSEEPYRIDFFDDEIDSLRVFDVDSQRTLEEVEAINLLPA------------------HEF----- 217
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 255 PTLKSYLEEVFSCTKEQVlhaDIRKFLSVFY----KKQWTL-IDYLNqvPVIFDdfQKIMNQYDAFDKETASYFTEDLHN 329
Cdd:PRK10689 218 PTDKAAIELFRSQWRDTF---EVKRDAEHIYqqvsKGTLPAgIEYWQ--PLFFS--EPLPPLFSYFPANTLLVNTGDLET 290
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 330 SKAvsslQYFADVESQFKK---------YVPASFFSNFQKGLGNLKfnnlyqfnQYPMQEFFNQFsfLKEEIER----YK 396
Cdd:PRK10689 291 SAE----RFWADTLARFENrgvdpmrplLPPESLWLRVDELFSELK--------NWPRVQLKTEH--LPTKAANtnlgYQ 356
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 397 KLKyTIVLQSSSKTELKKLSTILDEYDIKIDNSNESEICKGTVN-------------------------LIEGNLRHGFH 451
Cdd:PRK10689 357 KLP-DLAVQAQQKAPLDALRRFLESFDGPVVFSVESEGRREALGellarikiapkrimrldeasdrgryLMIGAAEHGFI 435
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 452 FVDENLVFITEYEIF--KKKIKRKYRRQNISNAERLKDYNELQKGDYVVHQIHGIGQYLGIETIEIKGIHRDYVSVLYQN 529
Cdd:PRK10689 436 DTVRNLALICESDLLgeRVARRRQDSRRTINPDTLIRNLAELHPGQPVVHLEHGVGRYAGMTTLEAGGIKGEYLMLTYAN 515
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 530 GDRISIPVEQIQTLSKYVS-SDGKAPkLNKLNDGRFKKAKQKVKSQVEDIADDLIKLYAERSQLKGFAFSKDDEDQNAFD 608
Cdd:PRK10689 516 DAKLYVPVSSLHLISRYAGgAEENAP-LHKLGGDAWSRARQKAAEKVRDVAAELLDIYAQRAAKEGFAFKHDREQYQLFC 594
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 609 EAFPYVETEDQLRSIEEIKKDMQASQPMDRLLVGDVGFGKTEVAMRAAFKAVNDHKQVVVLVPTTVLAQQHYSNFKERFE 688
Cdd:PRK10689 595 DSFPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVENHKQVAVLVPTTLLAQQHYDNFRDRFA 674
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 689 QFAVNVDVLSRFRSKKEQTETLEKLKKGQVDILIGTHRVLSKDVEFADLGLMIIDEEQRFGVKHKEALKELKKKVDVLTL 768
Cdd:PRK10689 675 NWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQSDVKWKDLGLLIVDEEHRFGVRHKERIKAMRADVDILTL 754
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 769 TATPIPRTLHMSMLGIRDLSVIETPPTNRYPVQTYVLEQNDRVIRDAVLREMDRGGQVYYLYNKVDTIEKKVSELQELIP 848
Cdd:PRK10689 755 TATPIPRTLNMAMSGMRDLSIIATPPARRLAVKTFVREYDSLVVREAILREILRGGQVYYLYNDVENIQKAAERLAELVP 834
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 849 EASIGFVHGQMSEIRLENTLLDFIEGQYDILVTTTIIETGVDIPNANTLFIENADHMGLSTLYQLRGRVGRSNRIAYAYL 928
Cdd:PRK10689 835 EARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDIPTANTIIIERADHFGLAQLHQLRGRVGRSHHQAYAWL 914
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 929 MYRPDKTLTEVSEKRLEAIKGFTELGSGFKIAMRDLSIRGAGNLLGSSQSGFIDSVGFELYSQLLEEAI-AKKNGTDKKR 1007
Cdd:PRK10689 915 LTPHPKAMTTDAQKRLEAIASLEDLGAGFALATHDLEIRGAGELLGEEQSGQMETIGFSLYMELLENAVdALKAGREPSL 994
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 1008 E---KGNAELILQIDAYLPDEYISDERHKIEIYKRIRQIDDRVNYEELQDELIDRFGEYPDVVAYLLEIGLAKAYLDKVF 1084
Cdd:PRK10689 995 EdltSQQTEVELRMPSLLPDDFIPDVNTRLSFYKRIASAKNENELEEIKVELIDRFGLLPDPARNLLDIARLRQQAQKLG 1074
|
1050
....*....|....*
gi 2546864662 1085 VNRVERKNNKLVIQF 1099
Cdd:PRK10689 1075 IRKLEGNEKGGFIEF 1089
|
|
| RecG |
COG1200 |
RecG-like helicase [Replication, recombination and repair]; |
582-982 |
2.44e-117 |
|
RecG-like helicase [Replication, recombination and repair];
Pssm-ID: 440813 [Multi-domain] Cd Length: 684 Bit Score: 379.39 E-value: 2.44e-117
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 582 LIKLYAERSQLKGFAFSKDDEDQNAFDEAFPYVETEDQLRSIEEIKKDMQASQPMDRLLVGDVGFGKTEVAMRAAFKAVN 661
Cdd:COG1200 227 LLLRRARRRKRKGPALPGDGELLEAFLAALPFELTGAQKRVIAEIAADLASPHPMNRLLQGDVGSGKTVVALLAMLAAVE 306
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 662 DHKQvvvlvpttvlAQQHYSNFKERFEQFAVNVDVLSRFRSKKEQTETLEKLKKGQVDILIGTHRVLSKDVEFADLGLMI 741
Cdd:COG1200 307 AGYQaalmapteilAEQHYRSLSKLLEPLGIRVALLTGSTKAKERREILAALASGEADIVVGTHALIQDDVEFKNLGLVV 386
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 742 IDEEQRFGVKHKEALKELKKKVDVLTLTATPIPRTLHMSMLGIRDLSVI-ETPPtNRYPVQTYVL--EQNDRVIrDAVLR 818
Cdd:COG1200 387 IDEQHRFGVEQRLALREKGEAPHVLVMTATPIPRTLAMTLYGDLDVSVIdELPP-GRKPIKTRVVpeERRDEVY-ERIRE 464
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 819 EMDRGGQVYYLY------NKVD--TIEKKVSELQELIPEASIGFVHGQMSEIRLENTLLDFIEGQYDILVTTTIIETGVD 890
Cdd:COG1200 465 EIAKGRQAYVVCplieesEKLDlqAAEETYEELREAFPGLRVGLLHGRMKPAEKDAVMAAFKAGEIDVLVATTVIEVGVD 544
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 891 IPNANTLFIENADHMGLSTLYQLRGRVGRSNRIAYAYLMYRPDktLTEVSEKRLEAIkgfTELGSGFKIAMRDLSIRGAG 970
Cdd:COG1200 545 VPNATVMVIENAERFGLSQLHQLRGRVGRGSAQSYCLLLYDAP--LSETARERLEVM---RETNDGFEIAEEDLELRGPG 619
|
410
....*....|..
gi 2546864662 971 NLLGSSQSGFID 982
Cdd:COG1200 620 EFLGTRQSGLPD 631
|
|
| PRK10917 |
PRK10917 |
ATP-dependent DNA helicase RecG; Provisional |
582-1039 |
4.65e-112 |
|
ATP-dependent DNA helicase RecG; Provisional
Pssm-ID: 236794 [Multi-domain] Cd Length: 681 Bit Score: 364.86 E-value: 4.65e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 582 LIKLYAERSQLKGFAFSKDDEDQNAFDEAFPYVETEDQLRSIEEIKKDMQASQPMDRLLVGDVGFGKTEVAMRAAFKAVN 661
Cdd:PRK10917 229 LLLLRAGRRSKKAGPLPYDGELLKKFLASLPFELTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIE 308
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 662 DHKQvvvlvpttvlAQQHYSNFKERFEQFAVNVDVLSRFRSKKEQTETLEKLKKGQVDILIGTHRVLSKDVEFADLGLMI 741
Cdd:PRK10917 309 AGYQaalmapteilAEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQDDVEFHNLGLVI 388
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 742 IDEEQRFGVKHKEALKELKKKVDVLTLTATPIPRTLHMSMLGIRDLSVI-ETPPtNRYPVQTYVL--EQNDRVIrDAVLR 818
Cdd:PRK10917 389 IDEQHRFGVEQRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIdELPP-GRKPITTVVIpdSRRDEVY-ERIRE 466
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 819 EMDRGGQVYYLY------NKVD--TIEKKVSELQELIPEASIGFVHGQMSEIRLENTLLDFIEGQYDILVTTTIIETGVD 890
Cdd:PRK10917 467 EIAKGRQAYVVCplieesEKLDlqSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVD 546
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 891 IPNANTLFIENADHMGLSTLYQLRGRVGRSNRIAYAYLMYRPDktLTEVSEKRLEAIKGFTelgSGFKIAMRDLSIRGAG 970
Cdd:PRK10917 547 VPNATVMVIENAERFGLAQLHQLRGRVGRGAAQSYCVLLYKDP--LSETARERLKIMRETN---DGFVIAEKDLELRGPG 621
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2546864662 971 NLLGSSQSGFIDsvgFELYS-----QLLEEAiakkngtdkKREkgnAELILQIDAYLPDEYISDERHKIEIYKR 1039
Cdd:PRK10917 622 ELLGTRQSGLPE---FKVADlvrdeELLEEA---------RKD---ARELLERDPELAEALLERWLGERERYDK 680
|
|
| DEXHc_TRCF |
cd17991 |
DEXH/Q-box helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
600-792 |
2.29e-103 |
|
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: 323.75 E-value: 2.29e-103
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 600 DDEDQNAFDEAFPYVETEDQLRSIEEIKKDMQASQPMDRLLVGDVGFGKTEVAMRAAFKAVNDHKQVVVLVPTTVLAQQH 679
Cdd:cd17991 1 DGEEQEEFEASFPYEETPDQLKAIEEILKDMESGKPMDRLICGDVGFGKTEVAMRAAFKAVLSGKQVAVLVPTTLLAQQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 680 YSNFKERFEQFAVNVDVLSRFRSKKEQTETLEKLKKGQVDILIGTHRVLSKDVEFADLGLMIIDEEQRFGVKHKEALKEL 759
Cdd:cd17991 81 YETFKERFANFPVNVELLSRFTTAAEQREILEGLKEGKVDIVIGTHRLLSKDVEFKNLGLLIIDEEQRFGVKQKEKLKEL 160
|
170 180 190
....*....|....*....|....*....|...
gi 2546864662 760 KKKVDVLTLTATPIPRTLHMSMLGIRDLSVIET 792
Cdd:cd17991 161 RPNVDVLTLSATPIPRTLHMALSGIRDLSVIAT 193
|
|
| recG |
TIGR00643 |
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair] |
586-982 |
3.65e-100 |
|
ATP-dependent DNA helicase RecG; [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273192 [Multi-domain] Cd Length: 630 Bit Score: 331.23 E-value: 3.65e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 586 YAERSQLKGFAFSKDDEDQNAFDEAFPYVETEDQLRSIEEIKKDMQASQPMDRLLVGDVGFGKTEVAMRAAFKAVNDHKQ 665
Cdd:TIGR00643 207 LGEKQQFSAPPANPSEELLTKFLASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQ 286
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 666 VVVLVPTTVLAQQHYSNFKERFEQFAVNVDVLSRFRSKKEQTETLEKLKKGQVDILIGTHRVLSKDVEFADLGLMIIDEE 745
Cdd:TIGR00643 287 VALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQEKVEFKRLALVIIDEQ 366
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 746 QRFGVKHKEALK---ELKKKVDVLTLTATPIPRTLHMSMLGIRDLSVIETPPTNRYPVQTYVLEQNDRVIRDAVLR-EMD 821
Cdd:TIGR00643 367 HRFGVEQRKKLRekgQGGFTPHVLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEKDIVYEFIEeEIA 446
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 822 RGGQVYYLYNKVDTIEK--------KVSELQELIPEASIGFVHGQMSEIRLENTLLDFIEGQYDILVTTTIIETGVDIPN 893
Cdd:TIGR00643 447 KGRQAYVVYPLIEESEKldlkaaeaLYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPN 526
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 894 ANTLFIENADHMGLSTLYQLRGRVGRSNRIAYAYLMYRPDKtlTEVSEKRLEAIKGFTElgsGFKIAMRDLSIRGAGNLL 973
Cdd:TIGR00643 527 ATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKNPK--SESAKKRLRVMADTLD---GFVIAEEDLELRGPGDLL 601
|
....*....
gi 2546864662 974 GSSQSGFID 982
Cdd:TIGR00643 602 GTKQSGYPE 610
|
|
| SF2_C_TRCF |
cd18810 |
C-terminal helicase domain of the transcription-repair coupling factor; Transcription-repair ... |
799-948 |
1.29e-68 |
|
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: 226.46 E-value: 1.29e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 799 PVQTYVLEQNDRVIRDAVLREMDRGGQVYYLYNKVDTIEKKVSELQELIPEASIGFVHGQMSEIRLENTLLDFIEGQYDI 878
Cdd:cd18810 1 PVRTYVMPYDDELIREAIERELLRGGQVFYVHNRIESIEKLATQLRQLVPEARIAIAHGQMTENELEEVMLEFAKGEYDI 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 879 LVTTTIIETGVDIPNANTLFIENADHMGLSTLYQLRGRVGRSNRIAYAYLMYRPDKTLTEVSEKRLEAIK 948
Cdd:cd18810 81 LVCTTIIESGIDIPNANTIIIERADKFGLAQLYQLRGRVGRSKERAYAYFLYPDQKKLTEDALKRLEAIQ 150
|
|
| DEXHc_RecG |
cd17992 |
DEXH/Q-box helicase domain of RecG; ATP-dependent DNA helicase RecG plays a critical role in ... |
582-794 |
3.07e-60 |
|
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: 205.84 E-value: 3.07e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 582 LIKLYAERSQLKGFAFSKDDEDQNAFDEAFPYVETEDQLRSIEEIKKDMQASQPMDRLLVGDVGFGKTEVAMRAAFKAVN 661
Cdd:cd17992 13 LLLRRRKIEELKGIILEISGELLKKFLEALPFELTGAQKRVIDEILRDLASEKPMNRLLQGDVGSGKTVVAALAMLAAVE 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 662 DHKQVVVLVPTTVLAQQHYSNFKERFEQFAVNVDVLSRFRSKKEQTETLEKLKKGQVDILIGTHRVLSKDVEFADLGLMI 741
Cdd:cd17992 93 NGYQVALMAPTEILAEQHYDSLKKLLEPLGIRVALLTGSTKAKEKREILEKIASGEIDIVIGTHALIQEDVEFHNLGLVI 172
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 2546864662 742 IDEEQRFGVKHKEALKELKKKVDVLTLTATPIPRTLHMSMLGIRDLSVIETPP 794
Cdd:cd17992 173 IDEQHRFGVEQRLKLREKGETPHVLVMTATPIPRTLALTLYGDLDVSIIDELP 225
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
799-949 |
5.66e-60 |
|
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: 202.50 E-value: 5.66e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 799 PVQTYVLEQNDR-VIRDAVLREMDRGGQVYYLYNKVDTIEKKVSE--------LQELIPEASIGFVHGQMSEIRLENTLL 869
Cdd:cd18792 1 PIRTYVIPHDDLdLVYEAIERELARGGQVYYVYPRIEESEKLDLKsiealaeeLKELVPEARVALLHGKMTEDEKEAVML 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 870 DFIEGQYDILVTTTIIETGVDIPNANTLFIENADHMGLSTLYQLRGRVGRSNRIAYAYLMYRPDKTLTEVSEKRLEAIKG 949
Cdd:cd18792 81 EFREGEYDILVSTTVIEVGIDVPNANTMIIEDADRFGLSQLHQLRGRVGRGKHQSYCYLLYPDPKKLTETAKKRLRAIAE 160
|
|
| DEXHc_RecG |
cd17918 |
DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins; The DEAD-like helicase ... |
600-790 |
6.70e-49 |
|
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: 171.83 E-value: 6.70e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 600 DDEDQNAFDEAFPYVETEDQLRSIEEIKKDMQASQPMDRLLVGDVGFGKTEVAMRAAFKAVNDHKQVVVLVPTTVLAQQH 679
Cdd:cd17918 1 DRALIQELCKSLPFSLTKDQAQAIKDIEKDLHSPEPMDRLLSGDVGSGKTLVALGAALLAYKNGKQVAILVPTEILAHQH 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 680 YSNFKERFEQFavNVDVLSRFRskKEQTETleklkkgQVDILIGTHRVLSKDVEFADLGLMIIDEEQRFGVKHkEALKEL 759
Cdd:cd17918 81 YEEARKFLPFI--NVELVTGGT--KAQILS-------GISLLVGTHALLHLDVKFKNLDLVIVDEQHRFGVAQ-REALYN 148
|
170 180 190
....*....|....*....|....*....|.
gi 2546864662 760 KKKVDVLTLTATPIPRTLHMSMLGIRDLSVI 790
Cdd:cd17918 149 LGATHFLEATATPIPRTLALALSGLLDLSVI 179
|
|
| CarD_TRCF |
smart01058 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
490-587 |
1.95e-38 |
|
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes. This family includes the presumed N-terminal domain. CarD interacts with the zinc-binding protein CarG, to form a complex that regulates multiple processes in Myxococcus xanthus. This family also includes a domain to the N-terminal side of the DEAD helicase of TRCF proteins. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription. This domain is involved in binding to the stalled RNA polymerase.
Pssm-ID: 215001 [Multi-domain] Cd Length: 99 Bit Score: 138.36 E-value: 1.95e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 490 ELQKGDYVVHQIHGIGQYLGIETIEIKGIHRDYVSVLYQNGDRISIPVEQIQTLSKYVSSDGKA-PKLNKLNDGRFKKAK 568
Cdd:smart01058 1 ELKIGDYVVHPDHGVGRYEGIETIEVGGEKREYLVLEYAGGDKLYVPVDNLDLGSRYVGSEGEVePVLDKLGGGSWSKRK 80
|
90
....*....|....*....
gi 2546864662 569 QKVKSQVEDIADDLIKLYA 587
Cdd:smart01058 81 RKAKSGIRDIAAELLRLYA 99
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
799-949 |
9.34e-37 |
|
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: 135.93 E-value: 9.34e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 799 PVQTYVL--EQNDRVIRdAVLREMDRGGQVYYLYNKVDTIE----KKVSELQE-----LIPEASIGFVHGQMSEIRLENT 867
Cdd:cd18811 1 PITTYLIfhTRLDKVYE-FVREEIAKGRQAYVIYPLIEESEkldlKAAVAMYEylkerFRPELNVGLLHGRLKSDEKDAV 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 868 LLDFIEGQYDILVTTTIIETGVDIPNANTLFIENADHMGLSTLYQLRGRVGRSNRIAYAYLMYRPDktLTEVSEKRLEAI 947
Cdd:cd18811 80 MAEFREGEVDILVSTTVIEVGVDVPNATVMVIEDAERFGLSQLHQLRGRVGRGDHQSYCLLVYKDP--LTETAKQRLRVM 157
|
..
gi 2546864662 948 KG 949
Cdd:cd18811 158 TE 159
|
|
| TRCF |
smart00982 |
This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in ... |
1016-1101 |
1.10e-28 |
|
This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognised by the transcription-repair-coupling factor (TRCF) which releases RNAP and the truncated transcript.
Pssm-ID: 198050 [Multi-domain] Cd Length: 100 Bit Score: 110.63 E-value: 1.10e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 1016 LQIDAYLPDEYISDERHKIEIYKRIRQIDDRVNYEELQDELIDRFGEYPDVVAYLLEIGLAKAYLDKVFVNRVERKNNKL 1095
Cdd:smart00982 2 LPVPALIPEDYIPDVRQRLELYKRIASAETEEELDEIQEELIDRFGPLPEEVKNLLEVARLKLLAKKLGIEKIDAGGKGI 81
|
....*.
gi 2546864662 1096 VIQFEK 1101
Cdd:smart00982 82 VIEFSP 87
|
|
| CarD_CdnL_TRCF |
pfam02559 |
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of ... |
491-586 |
3.15e-27 |
|
CarD-like/TRCF domain; CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes. This family includes the presumed N-terminal domain, CdnL. CarD interacts with the zinc-binding protein CarG to form a complex that regulates multiple processes in Myxococcus xanthus. This family also includes a domain to the N-terminal side of the DEAD helicase of TRCF (transcription-repair-coupling factor) proteins. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription. This domain is involved in binding to the stalled RNA polymerase. The family includes members otherwise referred to as CdnL, for CarD N-terminal like, which differ functionally from CarD. The TRCF domain mentioned above is the RNA polymerase-interacting domain or RID.
Pssm-ID: 460590 [Multi-domain] Cd Length: 89 Bit Score: 105.99 E-value: 3.15e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 491 LQKGDYVVHQIHGIGQYLGIETIEikgiHRDYVSVLYQNGDRISIPVEQIQTLSKYVSSDgkapKLNKLNDG-RFKKAKQ 569
Cdd:pfam02559 1 LKVGDYVVHPDHGIGRIEGIEKLE----TKDYYVLEYAGGDKLYVPVDNLDLIRKYISKG----ELDKLGDGrRWRKYKE 72
|
90
....*....|....*..
gi 2546864662 570 KVKSQVEDIADDLIKLY 586
Cdd:pfam02559 73 KLKSGDIEEAAELIKLY 89
|
|
| UvrB_inter |
pfam17757 |
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the ... |
142-230 |
7.04e-27 |
|
UvrB interaction domain; This domain is found in the UvrB protein where it interacts with the UvrA protein.
Pssm-ID: 465486 [Multi-domain] Cd Length: 91 Bit Score: 105.17 E-value: 7.04e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 142 LELQVGQECEQRELKNHLISLGYKKVTQVQSQGEFSLRGDILDIF-ETSQICPYRIEFFGDEIDGIREFDTETQLSKDSK 220
Cdd:pfam17757 1 LSLKVGQEIDRDELLRKLVELGYERNDIVFERGTFRVRGDIVDIFpAYSEDEAIRIEFFGDEIESIREFDPLTGRSLEKL 80
|
90
....*....|
gi 2546864662 221 TQVLIYPASD 230
Cdd:pfam17757 81 DEVTIYPASH 90
|
|
| TRCF |
pfam03461 |
TRCF domain; |
1016-1101 |
8.23e-27 |
|
TRCF domain;
Pssm-ID: 460928 [Multi-domain] Cd Length: 95 Bit Score: 105.20 E-value: 8.23e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 1016 LQIDAYLPDEYISDERHKIEIYKRIRQIDDRVNYEELQDELIDRFGEYPDVVAYLLEIGLAKAYLDKVFVNRVERKNNKL 1095
Cdd:pfam03461 1 LDVDAYIPDDYIPDESQRLELYKRLASIETEEELDDLQEELIDRFGPLPEEVENLLEIARLKLLAKKLGIEKIDLKGGGI 80
|
....*.
gi 2546864662 1096 VIQFEK 1101
Cdd:pfam03461 81 RITFSE 86
|
|
| PRK05298 |
PRK05298 |
excinuclease ABC subunit UvrB; |
133-229 |
6.22e-19 |
|
excinuclease ABC subunit UvrB;
Pssm-ID: 235395 [Multi-domain] Cd Length: 652 Bit Score: 92.42 E-value: 6.22e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 133 NPQVFDDSILELQVGQECEQRELKNHLISLGYKKVTQVQSQGEFSLRGDILDIF--ETSQICpYRIEFFGDEIDGIREFD 210
Cdd:PRK05298 150 SPEEYLKMVLSLRVGQEIDRRELLRRLVDLQYERNDIDFQRGTFRVRGDVIEIFpaYYEERA-IRIEFFGDEIERISEFD 228
|
90
....*....|....*....
gi 2546864662 211 TETQLSKDSKTQVLIYPAS 229
Cdd:PRK05298 229 PLTGEVLGELDRVTIYPAS 247
|
|
| UvrB |
COG0556 |
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]; |
133-229 |
2.42e-18 |
|
Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair];
Pssm-ID: 440322 [Multi-domain] Cd Length: 657 Bit Score: 90.45 E-value: 2.42e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 133 NPQVFDDSILELQVGQECEQRELKNHLISLGYKKVTQVQSQGEFSLRGDILDIF--ETSQICpYRIEFFGDEIDGIREFD 210
Cdd:COG0556 147 SPEEYLKMVLSLRVGEEIDRDELLRRLVELQYERNDIDFTRGTFRVRGDVIEIFpaYSEERA-IRIEFFGDEIERISEFD 225
|
90
....*....|....*....
gi 2546864662 211 TETQLSKDSKTQVLIYPAS 229
Cdd:COG0556 226 PLTGEVLGELDRVTIYPAS 244
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
817-921 |
1.84e-16 |
|
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: 76.10 E-value: 1.84e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 817 LREMDRGGQVYYLYNKVDTIEKKVSELQELIpeaSIGFVHGQMSEIRLENTLLDFIEGQYDILVTTTIIETGVDIPNANT 896
Cdd:pfam00271 9 LLKKERGGKVLIFSQTKKTLEAELLLEKEGI---KVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDL 85
|
90 100
....*....|....*....|....*
gi 2546864662 897 LFIENADHmGLSTLYQLRGRVGRSN 921
Cdd:pfam00271 86 VINYDLPW-NPASYIQRIGRAGRAG 109
|
|
| uvrb |
TIGR00631 |
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA ... |
131-250 |
4.28e-16 |
|
excinuclease ABC, B subunit; All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. 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: 273185 [Multi-domain] Cd Length: 655 Bit Score: 83.50 E-value: 4.28e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 131 LPNPQVFDDSILELQVGQECEQRELKNHLISLGYKKVTQVQSQGEFSLRGDILDIFET-SQICPYRIEFFGDEIDGIREF 209
Cdd:TIGR00631 145 LGSPEEYLKMVLHLEVGKEIDRRELLRRLVELQYERNDVDFQRGTFRVRGDVVEIFPAyEDEFAVRIEFFGDEIERISRV 224
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 2546864662 210 DTETQLSKDSKTQVLIYPASDILLTNEDYHRGQKFLEHEID 250
Cdd:TIGR00631 225 DPLTGEVLRELDSFTIFPASHYVTPEERLERAIKNIEKELE 265
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
607-797 |
5.64e-15 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 74.84 E-value: 5.64e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 607 FDEAFPYVETEDQLRSIEEIKKDMQasqpmDRLLVGDVGFGKTEVAMRAAFKAVNDHKQVVVL--VPTTVLAQQHYSNFK 684
Cdd:smart00487 1 IEKFGFEPLRPYQKEAIEALLSGLR-----DVILAAPTGSGKTLAALLPALEALKRGKGGRVLvlVPTRELAEQWAEELK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 685 ERFEQFAVNVDVLSRFRSKKEQtetLEKLKKGQVDILIGT-----HRVLSKDVEFADLGLMIIDEEQR-----FGVKHKE 754
Cdd:smart00487 76 KLGPSLGLKVVGLYGGDSKREQ---LRKLESGKTDILVTTpgrllDLLENDKLSLSNVDLVILDEAHRlldggFGDQLEK 152
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 2546864662 755 ALKELKKKVDVLTLTATP---IPRTLHMSMLGIRDLSVIETPPTNR 797
Cdd:smart00487 153 LLKLLPKNVQLLLLSATPpeeIENLLELFLNDPVFIDVGFTPLEPI 198
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
616-779 |
5.99e-14 |
|
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: 70.73 E-value: 5.99e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 616 TEDQLRSIEEI--KKDMqasqpmdrLLVGDVGFGKTEVAMRAAFKAVN---DHKQVVVLVPTTVLAQQHYSNFKERFEQF 690
Cdd:pfam00270 1 TPIQAEAIPAIleGRDV--------LVQAPTGSGKTLAFLLPALEALDkldNGPQALVLAPTRELAEQIYEELKKLGKGL 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 691 AVNVdvlSRFRSKKEQTETLEKLKKgqVDILIGTH----RVLSKDVEFADLGLMIIDEEQR-----FGVKHKEALKELKK 761
Cdd:pfam00270 73 GLKV---ASLLGGDSRKEQLEKLKG--PDILVGTPgrllDLLQERKLLKNLKLLVLDEAHRlldmgFGPDLEEILRRLPK 147
|
170
....*....|....*...
gi 2546864662 762 KVDVLTLTATPiPRTLHM 779
Cdd:pfam00270 148 KRQILLLSATL-PRNLED 164
|
|
| ComFA |
COG4098 |
Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, ... |
768-920 |
2.01e-13 |
|
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: 74.14 E-value: 2.01e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 768 LTATPiPRTLHMSM-LGIRDLSVIetpPtNRY-----PVQTYVLEQN-DRVIR-----DAVLREMD----RGGQVYYLYN 831
Cdd:COG4098 253 LTATP-SKALQRQVkRGKLKVVKL---P-ARYhghplPVPKFKWLGNwKKRLRrgklpRKLLKWLKkrlkEGRQLLIFVP 327
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 832 KVDTIEKKVSELQELIPEASIGFVHGQmSEIRLEnTLLDFIEGQYDILVTTTIIETGVDIPNANTlFIENADH--MGLST 909
Cdd:COG4098 328 TIELLEQLVALLQKLFPEERIAGVHAE-DPERKE-KVQAFRDGEIPILVTTTILERGVTFPNVDV-AVLGADHpvFTEAA 404
|
170
....*....|.
gi 2546864662 910 LYQLRGRVGRS 920
Cdd:COG4098 405 LVQIAGRVGRS 415
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
851-919 |
5.96e-13 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 65.31 E-value: 5.96e-13
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2546864662 851 SIGFVHGQMSEIRLENTLLDFIEGQYDILVTTTIIETGVDIPNANTLFIENADhMGLSTLYQLRGRVGR 919
Cdd:smart00490 13 KVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLP-WSPASYIQRIGRAGR 80
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
636-771 |
1.18e-12 |
|
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: 66.66 E-value: 1.18e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 636 MDRLLVGDVGFGKTEVAMRAAFKAVND-HKQVVVLVPTTVLAQQHYSNFKERFeQFAVNVDVLSRFRSKKEQtetlEKLK 714
Cdd:cd00046 2 ENVLITAPTGSGKTLAALLAALLLLLKkGKKVLVLVPTKALALQTAERLRELF-GPGIRVAVLVGGSSAEER----EKNK 76
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 715 KGQVDILIGTHRVLSKDVE------FADLGLMIIDEEQRFGVKHKEALKELKK-------KVDVLTLTAT 771
Cdd:cd00046 77 LGDADIIIATPDMLLNLLLredrlfLKDLKLIIVDEAHALLIDSRGALILDLAvrkaglkNAQVILLSAT 146
|
|
| priA |
TIGR00595 |
primosomal protein N'; All proteins in this family for which functions are known are ... |
639-922 |
1.50e-11 |
|
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: 68.18 E-value: 1.50e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 639 LLVGDVGFGKTEVAMRAAFKAVNDHKQVVVLVPTTVLAQQHYSNFKERFEQfavNVDVLSRFRSKKEQTETLEKLKKGQV 718
Cdd:TIGR00595 1 LLFGVTGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFGS---QVAVLHSGLSDSEKLQAWRKVKNGEI 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 719 DILIGTHRVLSkdVEFADLGLMIIDEEQ----------RFGVKHKEALKELKKKVDVLTLTATPIPRTLHMSMLGIRDLS 788
Cdd:TIGR00595 78 LVVIGTRSALF--LPFKNLGLIIVDEEHdssykqeegpRYHARDVAVYRAKKFNCPVVLGSATPSLESYHNAKQKAYRLL 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 789 VIETPPTNRYPVQTYVL----EQNDRVIRDAVLREM----DRGGQ-----------------------------VYYLYN 831
Cdd:TIGR00595 156 VLTRRVSGRKPPEVKLIdmrkEPRQSFLSPELITAIeqtlAAGEQsilflnrrgysknllcrscgyilccpncdVSLTYH 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 832 KVDT-------------------------------IEKKVSELQELIPEASIGFVHGQMSEIR--LENTLLDFIEGQYDI 878
Cdd:TIGR00595 236 KKEGklrchycgyqepipktcpqcgsedlvykgygTEQVEEELAKLFPGARIARIDSDTTSRKgaHEALLNQFANGKADI 315
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*
gi 2546864662 879 LVTTTIIETGVDIPNANTLFIENAD-----------HMGLSTLYQLRGRVGRSNR 922
Cdd:TIGR00595 316 LIGTQMIAKGHHFPNVTLVGVLDADsglhspdfraaERGFQLLTQVAGRAGRAED 370
|
|
| DEXHc_priA |
cd17929 |
DEXH-box helicase domain of PriA; PriA, also known as replication factor Y or primosomal ... |
619-745 |
2.07e-10 |
|
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: 61.07 E-value: 2.07e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 619 QLRSIEEIKKDMQASQPMdrLLVGDVGFGKTEVAMRAAFKAVNDHKQVVVLVPTTVLAQQHYSNFKERfeqFAVNVDVLS 698
Cdd:cd17929 1 QRKAYEAIVSSLGGFKTF--LLHGVTGSGKTEVYIELIEKVLAKGKQVLVLVPEISLTPQLIKRFKKR---FGDKVAVLH 75
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 2546864662 699 RFRSKKEQTETLEKLKKGQVDILIGTHRVLSkdVEFADLGLMIIDEE 745
Cdd:cd17929 76 SKLSDKERADEWRKIKRGEAKVVIGARSALF--APFKNLGLIIVDEE 120
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
531-1101 |
6.80e-10 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 63.12 E-value: 6.80e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 531 DRISIPVEQIQTLSKYVSSDGKAPKLNKLNDGRFKKAKQKVKSQVEDIADDLIKLYAERSQlkgfAFSKDDEDQNAFDEA 610
Cdd:COG1061 6 IAERGADKLRSSLLLLDLERLELSLLRNLVEARRLAIKEGTREDGRRLPEEDTERELAEAE----ALEAGDEASGTSFEL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 611 FPYvetedQLRSIEEIKKDMQASQpmDR-LLVGDVGFGKTEVAMRAAFKAVND-------HKqvvvlvpttvlaqqhysn 682
Cdd:COG1061 82 RPY-----QQEALEALLAALERGG--GRgLVVAPTGTGKTVLALALAAELLRGkrvlvlvPR------------------ 136
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 683 fKERFEQFAvnvdvlSRFRSKKEQTETLEKLKKGQVDILIGTHRVLSKDVEFADL----GLMIIDEEQRFGVKHKEALKE 758
Cdd:COG1061 137 -RELLEQWA------EELRRFLGDPLAGGGKKDSDAPITVATYQSLARRAHLDELgdrfGLVIIDEAHHAGAPSYRRILE 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 759 LKKKVDVLTLTATPI---PRTLHMSMLG----------------IRDLSVIE-----TPPTNRYPVQTYVLEQ------- 807
Cdd:COG1061 210 AFPAAYRLGLTATPFrsdGREILLFLFDgivyeyslkeaiedgyLAPPEYYGirvdlTDERAEYDALSERLREalaadae 289
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 808 -NDRVIRDaVLREMDRGGQVYYLYNKVDTIEkkvsELQELIPEA--SIGFVHGQMSEIRLENTLLDFIEGQYDILVTTTI 884
Cdd:COG1061 290 rKDKILRE-LLREHPDDRKTLVFCSSVDHAE----ALAELLNEAgiRAAVVTGDTPKKEREEILEAFRDGELRILVTVDV 364
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 885 IETGVDIPNANTLFIenadHMGLSTLYQLRGRVGRSNRIAyaylmyrPDK---TLTEVSEKRLEAIKGFTElgsgfkiAM 961
Cdd:COG1061 365 LNEGVDVPRLDVAIL----LRPTGSPREFIQRLGRGLRPA-------PGKedaLVYDFVGNDVPVLEELAK-------DL 426
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 962 RDLSIrgagnllgsSQSGFIDSVGFELYSQLLEEAIAKKNGTDKKREKGNAELILQIDAYLPDEYISDERHKIEIYKRIR 1041
Cdd:COG1061 427 RDLAG---------YRVEFLDEEESEELALLIAVKPALEVKGELEEELLEELELLEDALLLVLAELLLLELLALALELLE 497
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 1042 QIDDRVNYEELQDELIDRFGEYPDVVAYLLEIGLAKAYLDKVFVNRVERKNNKLVIQFEK 1101
Cdd:COG1061 498 LAKAEGKAEEEEEEKELLLLLALAKLLKLLLLLLLLLLLELLELLAALLRLEELAALLLK 557
|
|
| PriA |
COG1198 |
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, ... |
616-745 |
1.43e-07 |
|
Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440811 [Multi-domain] Cd Length: 728 Bit Score: 55.89 E-value: 1.43e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 616 TEDQLRSIEEIKKDMQASQPMdrLLVGDVGFGKTEVAMRAAFKAVNDHKQvvvlvpttvlA----------QQhysnFKE 685
Cdd:COG1198 197 NEEQQAAVEAIRAAAGGFSVF--LLHGVTGSGKTEVYLQAIAEVLAQGKQ----------AlvlvpeialtPQ----TVE 260
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2546864662 686 RFEQ-FAVNVDVL-SRFrSKKEQTETLEKLKKGQVDILIGThR--VLSkdvEFADLGLMIIDEE 745
Cdd:COG1198 261 RFRArFGARVAVLhSGL-SDGERLDEWRRARRGEARIVIGT-RsaLFA---PFPNLGLIIVDEE 319
|
|
| PRK05580 |
PRK05580 |
primosome assembly protein PriA; Validated |
616-745 |
1.92e-07 |
|
primosome assembly protein PriA; Validated
Pssm-ID: 235514 [Multi-domain] Cd Length: 679 Bit Score: 55.55 E-value: 1.92e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 616 TEDQLRSIEEIKKDMQASQPmdrLLVGDVGFGKTEVAMRAAFKAVNDHKQvvvlvpttvlA----------QQhysnFKE 685
Cdd:PRK05580 146 NPEQAAAVEAIRAAAGFSPF---LLDGVTGSGKTEVYLQAIAEVLAQGKQ----------AlvlvpeialtPQ----MLA 208
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2546864662 686 RFEQ-FAVNVDVL-SRFrSKKEQTETLEKLKKGQVDILIGThR---VLSkdveFADLGLMIIDEE 745
Cdd:PRK05580 209 RFRArFGAPVAVLhSGL-SDGERLDEWRKAKRGEAKVVIGA-RsalFLP----FKNLGLIIVDEE 267
|
|
| CdnL |
COG1329 |
RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription]; |
492-598 |
1.65e-06 |
|
RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription];
Pssm-ID: 440940 [Multi-domain] Cd Length: 155 Bit Score: 48.97 E-value: 1.65e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 492 QKGDYVVHQIHGIGQYLGIETIEIKGIHRDY--VSVLYQNGdRISIPVEQIQTLS-KYVSSDGKAPK-LNKLNDG----- 562
Cdd:COG1329 2 KVGDKVVYPMHGVGVIEAIEEKEIAGEKKEYyvLRFPYDDM-TIMVPVDKAESVGlRPVISKEEVEKvLDVLKGRetvkp 80
|
90 100 110 120
....*....|....*....|....*....|....*....|...
gi 2546864662 563 -----RFKKAKQKVKS-QVEDIAdDLIK-LYAeRSQLKGFAFS 598
Cdd:COG1329 81 tnwsrRYREYEEKIKSgDIFEIA-EVVRdLYR-RDKEKKLSAG 121
|
|
| SF2_C_priA |
cd18804 |
C-terminal helicase domain of ATP-dependent helicase PriA; PriA, also known as replication ... |
836-921 |
3.94e-06 |
|
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: 49.55 E-value: 3.94e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 836 IEKKVSELQELIPEASIGFVHGQMSEIR--LENTLLDFIEGQYDILVTTTIIETGVDIPNANTLFIENADHM-------- 905
Cdd:cd18804 103 TERVEEELKTLFPEARIARIDRDTTRKKgaLEKLLDQFERGEIDILIGTQMIAKGLDFPNVTLVGILNADSGlnspdfra 182
|
90
....*....|....*....
gi 2546864662 906 ---GLSTLYQLRGRVGRSN 921
Cdd:cd18804 183 serAFQLLTQVSGRAGRGD 201
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
878-930 |
8.32e-06 |
|
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350172 [Multi-domain] Cd Length: 77 Bit Score: 45.00 E-value: 8.32e-06
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 2546864662 878 ILVTTTIIETGVDIPNANTLFIENAdHMGLSTLYQLRGRVGRSNRIAYAYLMY 930
Cdd:cd18785 25 ILVATNVLGEGIDVPSLDTVIFFDP-PSSAASYIQRVGRAGRGGKDEGEVILF 76
|
|
| Cas3_I |
cd09639 |
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short ... |
763-922 |
2.20e-05 |
|
CRISPR/Cas system-associated protein Cas3; CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I
Pssm-ID: 187770 [Multi-domain] Cd Length: 353 Bit Score: 48.19 E-value: 2.20e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 763 VDVLTLTATpIPRTLHMSMLGIRDLSVIETPPTNRYPVQTYVLEQNDRV----IRDAVLREMDRGGQVYYLYNKVDTIEK 838
Cdd:cd09639 155 VPILLMSAT-LPKFLKEYAEKIGYVEENEPLDLKPNERAPFIKIESDKVgeisSLERLLEFIKKGGSVAIIVNTVDRAQE 233
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 839 KVSELQELIPEASIGFVHGQMSE---IRLENTLL-DFIEGQYDILVTTTIIETGVDIpNANTLFienADHMGLSTLYQLR 914
Cdd:cd09639 234 FYQQLKEKGPEEEIMLIHSRFTEkdrAKKEAELLlEFKKSEKFVIVATQVIEASLDI-SVDVMI---TELAPIDSLIQRL 309
|
....*...
gi 2546864662 915 GRVGRSNR 922
Cdd:cd09639 310 GRLHRYGE 317
|
|
| cas3_core |
TIGR01587 |
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ... |
763-922 |
9.39e-05 |
|
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.
Pssm-ID: 273707 [Multi-domain] Cd Length: 359 Bit Score: 45.91 E-value: 9.39e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 763 VDVLTLTATpIP---RTLHMSMLGIRDLSVIETPPTNRYPVQTYVLEQNDRV----IRDAVLREMDRGGQVYYLYNKVDT 835
Cdd:TIGR01587 156 VPILLMSAT-LPkflKEYAEKIGYVEFNEPLDLKEERRFENHRFILIESDKVgeisSLERLLEFIKKGGSIAIIVNTVDR 234
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 836 IEKKVSELQELIPEASIGFVHGQMSE---IRLENTLLD--FIEGQYDILVTTTIIETGVDIpNANTLFienADHMGLSTL 910
Cdd:TIGR01587 235 AQEFYQQLKEKAPEEEIILYHSRFTEkdrAKKEAELLRemKKSNEKFVIVATQVIEASLDI-SADVMI---TELAPIDSL 310
|
170
....*....|..
gi 2546864662 911 YQLRGRVGRSNR 922
Cdd:TIGR01587 311 IQRLGRLHRYGR 322
|
|
| UB2H |
pfam14814 |
Bifunctional transglycosylase second domain; UB2H is the second domain of the ... |
144-215 |
2.44e-04 |
|
Bifunctional transglycosylase second domain; UB2H is the second domain of the transglycosylases, or penicillin-binding proteins PBP1bs)), the multi-domain membrane proteins essential for cell wall synthesis that are targeted by penicillin antibiotics. The exact function of the UB2H domain is uncertain, but it may act as the binding component of PBP1b with different binding partners, or it may participate in the regulation between DNA repair and/or synthesis and cell wall formation during the bacterial cell cycle.
Pssm-ID: 434234 [Multi-domain] Cd Length: 85 Bit Score: 41.00 E-value: 2.44e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 144 LQVGQECEQRELKNHLISLGYKKVTQVQSQGEFSLRGDILDIF----------ETSQicPYRIEFFGDEIDGIREFDTET 213
Cdd:pfam14814 1 LYPGQALSAAQLEQELKLLGYRKVSNPTRPGEYSVSGNRIELYrrgfdfpdgaEPAR--RVRLRFAGGRVARLQDLDTGR 78
|
..
gi 2546864662 214 QL 215
Cdd:pfam14814 79 DL 80
|
|
| SF2_C_XPB |
cd18789 |
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
854-899 |
3.88e-03 |
|
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350176 [Multi-domain] Cd Length: 153 Bit Score: 39.15 E-value: 3.88e-03
10 20 30 40
....*....|....*....|....*....|....*....|....*.
gi 2546864662 854 FVHGQMSEIRLENTLLDFIEGQYDILVTTTIIETGVDIPNANTLFI 899
Cdd:cd18789 73 FITGETPQSEREEILQNFREGEYNTLVVSKVGDEGIDLPEANVAIQ 118
|
|
| MPH1 |
COG1111 |
ERCC4-related helicase [Replication, recombination and repair]; |
834-1084 |
4.84e-03 |
|
ERCC4-related helicase [Replication, recombination and repair];
Pssm-ID: 440728 [Multi-domain] Cd Length: 718 Bit Score: 41.25 E-value: 4.84e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 834 DTIEKKVSELQEliPEASIGFVHGQ--------MSEIRLENTLLDFIEGQYDILVTTTIIETGVDIPNANT-LFIENadh 904
Cdd:COG1111 364 DTAEMIVEFLSE--PGIKAGRFVGQaskegdkgLTQKEQIEILERFRAGEFNVLVATSVAEEGLDIPEVDLvIFYEP--- 438
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 905 mGLSTL--YQLRGRVGRSNRIAYAYLMYRpdKTLTE----VSEKRLEAIKgfTELGSGFKIamrdLSIRGAGNLLGSSQS 978
Cdd:COG1111 439 -VPSEIrsIQRKGRTGRKREGRVVVLIAK--GTRDEayywSSRRKEKKMK--SILKKLKKL----LDKQEKEKLKESAQA 509
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2546864662 979 GfIDSvgfelYSQLLEEAIAKKNGTDKKREKGNAELILQIDAYLPDEYISDERHKIEIYKRIrqIDDRVNYEELQDELID 1058
Cdd:COG1111 510 T-LDE-----FESIKELAEDEINEKDLDEIESSENGAHVDWREPVLLQVIVSTLAESLELRE--LGEKVDDEVNLILEID 581
|
250 260
....*....|....*....|....*.
gi 2546864662 1059 RFGEYPDVVAYLLEIGLAKAYLDKVF 1084
Cdd:COG1111 582 RVDVVDDGSVLRVSRLLVEIGELDGK 607
|
|
| |
