|
Name |
Accession |
Description |
Interval |
E-value |
| DNA_pol_A_theta |
cd08638 |
DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis and ... |
2091-2585 |
9.41e-174 |
|
DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis and in somatic hypermutation; DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis (TLS) and in somatic hypermutation (SHM). DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Pol theta is an exception among family A polymerases and generates processive single base substitutions. Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and DNA polymerase activity to fill in the resulting gap. Polymerase theta mostly has amino-terminal helicase domain, a carboxy-terminal polymerase domain and an intervening space region.
Pssm-ID: 176475 Cd Length: 373 Bit Score: 538.35 E-value: 9.41e-174
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2091 GIGFSTAECESQKHIMQAKLDAIETQAYQlaghsfsftssddiaevlflelklppnremknqgskktlgstrrgidngrk 2170
Cdd:cd08638 1 GIGFDPEELERQRALLQAKLKELEEEAYR--------------------------------------------------- 29
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2171 lrlgrqfSTSKDVLNKLKALHPLPGLILEWRRITNAITKVVFPLQREKCLNPFLGMERIYPV-SQSHTATGRITFTEPNI 2249
Cdd:cd08638 30 -------STSKEVLEQLKRLHPLPKLILEYRKLSKLLTTYVEPLLLLCKLSSSLQMYRIHPTwNQTGTATGRLSSSEPNL 102
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2250 QNVPRDFEIKMPTLvgesppsqavgkgllpmgrgkykkgfsvnprcqaqmeERAADRGMPFSISMRHAFVPFPGGSILAA 2329
Cdd:cd08638 103 QNVPKDFEIKDAPS-------------------------------------PPAGSEGDIPTISLRHAFIPPPGRVLLSA 145
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2330 DYSQLELRILAHLSHDRRLIQVLNTGADVFRSIAAEWKMIEPESVGDDLRQQAKQICYGIIYGMGAKSLGEQMGIKENDA 2409
Cdd:cd08638 146 DYSQLELRILAHLSGDPALIELLNSGGDVFKMIAAQWLGKPVEEVTDEERQQAKQLVYGILYGMGAKSLAEQLGVSEEEA 225
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2410 ACYIDSFKSRYTGINQFMTETVKNCKRDGFVQTILGRRRYLPGIKDNNPYRKAHAERQAINTIVQGSAADIVKIATVNIQ 2489
Cdd:cd08638 226 KQFIESFKNAYPGVRRFIRETIERARRNGFVETLTGRRRYLPEINSGNSSERAQAERQAVNTVIQGSAADIMKIAMINIH 305
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2490 KQLETFHSTfkshghregmlqsdqtglsrkrklqgmfCPIRGGFFILQLHDELLYEVAEEDVVQVAQIVKNEMESAVKLS 2569
Cdd:cd08638 306 EKLHSLLPN----------------------------LPAGRARLVLQIHDELLFEVPESDVDEVARIIKRSMENAAKLS 357
|
490
....*....|....*.
gi 139394648 2570 VKLKVKVKIGASWGEL 2585
Cdd:cd08638 358 VPLPVKVSIGKSWGSL 373
|
|
| DNA_pol_A |
pfam00476 |
DNA polymerase family A; |
2108-2584 |
7.55e-135 |
|
DNA polymerase family A;
Pssm-ID: 459825 Cd Length: 368 Bit Score: 427.24 E-value: 7.55e-135
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2108 AKLDAIETQAYQLAGHSFSFTSSDDIAEVLFLELKLPPNremknqgsKKTlgstrrgidngrklrlGRQFSTSKDVLNKL 2187
Cdd:pfam00476 1 ERLKELEQEIYELAGEEFNINSPKQLGEILFEKLGLPPG--------KKT----------------KTGYSTDAEVLEKL 56
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2188 KA-LHPLPGLILEWRRITNAITKVVFPLQreKCLNPFLGmeRIYP-VSQSHTATGRITFTEPNIQNVPrdfeIKMPtlvg 2265
Cdd:pfam00476 57 AAdEHPIPKLILEYRQLAKLKSTYVDALP--KLINPDTG--RIHTsFNQTVTATGRLSSSDPNLQNIP----IRTE---- 124
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2266 esppsqavgkgllpMGRgkykkgfsvnprcqaqmeeraadrgmpfsiSMRHAFVPFPGGSILAADYSQLELRILAHLSHD 2345
Cdd:pfam00476 125 --------------EGR------------------------------RIRKAFVAEPGWVLLSADYSQIELRILAHLSGD 160
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2346 RRLIQVLNTGADVFRSIAAEWKMIEPESVGDDLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYTGINQ 2425
Cdd:pfam00476 161 ENLIEAFRNGEDIHTATASEVFGVPLEEVTPEQRRRAKAINFGIIYGMSAFGLAQQLGISRKEAKEYIDRYFERYPGVKE 240
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2426 FMTETVKNCKRDGFVQTILGRRRYLPGIKDNNPYRKAHAERQAINTIVQGSAADIVKIATVNIQKQLEtfhstfkshghR 2505
Cdd:pfam00476 241 YMEETVEEAREKGYVETLLGRRRYLPDINSSNRNLRSFAERAAINAPIQGSAADIIKLAMIRVDEALK-----------E 309
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2506 EGMlqsdqtglsrKRKLqgmfcpirggffILQLHDELLYEVAEEDVVQVAQIVKNEMES--AVKLSVKLKVKVKIGASWG 2583
Cdd:pfam00476 310 EGL----------KARL------------LLQVHDELVFEVPEEEVEEVAALVKEEMENenAVKLSVPLKVDVGIGKNWG 367
|
.
gi 139394648 2584 E 2584
Cdd:pfam00476 368 E 368
|
|
| PolA |
COG0749 |
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ... |
1900-2586 |
1.54e-125 |
|
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and repair];
Pssm-ID: 440512 [Multi-domain] Cd Length: 575 Bit Score: 409.06 E-value: 1.54e-125
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 1900 VVGLAVCWGGRDAYYFSLqkeqkhseisASLVPPSLDPSLTLKdrmwYLQSCLrkeSDKECSVVIYDFIQSYKILLlSCG 1979
Cdd:COG0749 20 LVGISFAVEPGEAAYIPL----------AHGAPEQLDLDEVLA----ALKPLL---EDPAIPKIGQNLKYDLHVLA-RYG 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 1980 ISLEQSYEDPKVACWLLDPDSQEPTLHSIVTSFLPHELPLLE---GMETSQ-GIQSLGLNAGSEHSGRyRASVesilIFN 2055
Cdd:COG0749 82 IELAGVAFDTMLASYLLNPGRRRHGLDDLAERYLGHETISYEelaGKGKKQlTFDQVPLEEAAEYAAE-DADI----TLR 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2056 SMNQLNSLLQKENLQDVFRKVEMPSQYCLALLELNGIGFSTAECESQKHIMQAKLDAIETQAYQLAGHSFSFTSSDDIAE 2135
Cdd:COG0749 157 LHEVLKPELEEEGLLKLYEEIELPLVPVLARMERNGILVDRELLAELSAELAKRLAELEQEIYELAGEEFNLNSPKQLGE 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2136 VLFLELKLPpnremknqGSKKTlgstrrgidngrKlrlgRQFSTSKDVLNKLKALHPLPGLILEWRRI-------TNAIT 2208
Cdd:COG0749 237 ILFEKLGLP--------VGKKT------------K----TGYSTDAEVLEKLAEDHPIPALILEYRQLsklkstyVDALP 292
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2209 KVVfplqrekclNPFLGmeRIYPV-SQSHTATGRITFTEPNIQNVPrdfeIKmptlvgesppsqavgkglLPMGRGkykk 2287
Cdd:COG0749 293 KLI---------NPDTG--RIHTSfNQTVTATGRLSSSDPNLQNIP----IR------------------TEEGRR---- 335
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2288 gfsvnprcqaqmeeraadrgmpfsisMRHAFVPFPGGSILAADYSQLELRILAHLSHDRRLIQVLNTGADVFRSIAAEwk 2367
Cdd:COG0749 336 --------------------------IRKAFVAPEGYVLLSADYSQIELRILAHLSGDEGLIEAFREGEDIHAATAAE-- 387
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2368 M--IEPESVGDDLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYTGINQFMTETVKNCKRDGFVQTILG 2445
Cdd:COG0749 388 VfgVPLEEVTSEQRRRAKAINFGIIYGMSAFGLARQLGISRKEAKEYIDRYFERYPGVKDYMEETVEEAREKGYVETLFG 467
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2446 RRRYLPGIKDNNPYRKAHAERQAINTIVQGSAADIVKIATVNIQKQLetfhstfkshghregmlqsdqtglsRKRKLQG- 2524
Cdd:COG0749 468 RRRYLPDINSSNRNRRSFAERAAINAPIQGSAADIIKLAMIRVDRAL-------------------------KEEGLKSr 522
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 139394648 2525 MfcpirggffILQLHDELLYEVAEEDVVQVAQIVKNEMESAVKLSVKLKVKVKIGASWGELK 2586
Cdd:COG0749 523 M---------LLQVHDELVFEVPEDELEEVKELVKEVMENAVELSVPLVVDVGVGKNWDEAH 575
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
76-661 |
5.22e-121 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 394.26 E-value: 5.22e-121
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 76 LPKAVLEKYHSFGVKKMFEWQAECLLLGqVLEGKNLVYSAPTSAGKTLVAELLILKRVLEmRKKALFILPFVSVAKEKKY 155
Cdd:COG1204 7 PLEKVIEFLKERGIEELYPPQAEALEAG-LLEGKNLVVSAPTASGKTLIAELAILKALLN-GGKALYIVPLRALASEKYR 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 156 YLQSLFQEVGIKVDGYMGS-TSPSRHFSSLDIAVCTIERANGLINRliEENKMDLLGMVVVDELHMLGDSHRGYLLELLL 234
Cdd:COG1204 85 EFKRDFEELGIKVGVSTGDyDSDDEWLGRYDILVATPEKLDSLLRN--GPSWLRDVDLVVVDEAHLIDDESRGPTLEVLL 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 235 TKIcyitrksascqadlaSSLSNAVQIVGMSATLPNLELVASWLNAELYHTDFRPVPLLESVKVGNSIYdssmklvreFE 314
Cdd:COG1204 163 ARL---------------RRLNPEAQIVALSATIGNAEEIAEWLDAELVKSDWRPVPLNEGVLYDGVLR---------FD 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 315 PMLQVKGDEdhVVSLCYETICDNHSVLLFCPSKKWCEKLADIIAREFynlhhqAEGLVKPsecppvilEQKELLEVMDQL 394
Cdd:COG1204 219 DGSRRSKDP--TLALALDLLEEGGQVLVFVSSRRDAESLAKKLADEL------KRRLTPE--------EREELEELAEEL 282
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 395 RRL--PSGLDSVLQKTVPWGVAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIRTP-IFGGRPLDI 471
Cdd:COG1204 283 LEVseETHTNEKLADCLEKGVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRDTkRGGMVPIPV 362
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 472 LTYKQMVGRAGRKGVDTVGESILICKNSEKSKGIA--LLQGSLKPVRSCLqrreGEEVtgSMIRAILEIIVGGVASTSQD 549
Cdd:COG1204 363 LEFKQMAGRAGRPGYDPYGEAILVAKSSDEADELFerYILGEPEPIRSKL----ANES--ALRTHLLALIASGFANSREE 436
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 550 MHTYAACTFLAasmkegkqgIQRNQESVQlGAIEACVMWLLENEFIQsteasdgTEGKVYHPTHLGSATLSSSLSPaDTL 629
Cdd:COG1204 437 LLDFLENTFYA---------YQYDKGDLE-EVVDDALEFLLENGFIE-------EDGDRLRATKLGKLVSRLYIDP-LTA 498
|
570 580 590
....*....|....*....|....*....|..
gi 139394648 630 DIFADLQRAMKGFVleNDLHILYLVTpMFEDW 661
Cdd:COG1204 499 AELVDGLRKADEEF--TDLGLLHLIL-ILRDW 527
|
|
| PRK05755 |
PRK05755 |
DNA polymerase I; Provisional |
1900-2586 |
3.99e-119 |
|
DNA polymerase I; Provisional
Pssm-ID: 235591 [Multi-domain] Cd Length: 880 Bit Score: 401.01 E-value: 3.99e-119
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 1900 VVGLAVCWGGRDAYYFSLqkEQKHSEISASLVPpsldpsltlkdrmWYlqsclrkeSDKECSVVIYDFIQSYKILLlSCG 1979
Cdd:PRK05755 334 LVGLSFAVEPGEAAYIPL--DQLDREVLAALKP-------------LL--------EDPAIKKVGQNLKYDLHVLA-RYG 389
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 1980 ISLEQSYEDPKVACWLLDPDSQEpTLHSIVTSFLPHELPLLEGMETSQ-GIQSLGLNAGSEHSGRyRASVesilIFNSMN 2058
Cdd:PRK05755 390 IELRGIAFDTMLASYLLDPGRRH-GLDSLAERYLGHKTISFEEVAGKQlTFAQVDLEEAAEYAAE-DADV----TLRLHE 463
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2059 QLNS-LLQKENLQDVFRKVEMPSQYCLALLELNGIGFSTAECESQKHIMQAKLDAIETQAYQLAGHSFSFTSSDDIAEVL 2137
Cdd:PRK05755 464 VLKPkLLEEPGLLELYEEIELPLVPVLARMERNGIKVDREYLKELSAELAQRLAELEQEIYELAGEEFNINSPKQLGEIL 543
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2138 FLELKLPPnremknqgSKKTlgstRRGidngrklrlgrqFSTSKDVLNKLKALHPLPGLILEWRritnAITK----VVFP 2213
Cdd:PRK05755 544 FEKLGLPV--------GKKT----KTG------------YSTDAEVLEKLADDHPIPDKILEYR----QLSKlkstYTDA 595
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2214 LQREKclNPFLGmeRIYP-VSQSHTATGRITFTEPNIQNVPrdfeIKmptlvgesppsqavgkglLPMGRgkykkgfsvn 2292
Cdd:PRK05755 596 LPKLI--NPDTG--RIHTsFNQTVTATGRLSSSDPNLQNIP----IR------------------TEEGR---------- 639
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2293 prcqaqmeeraadrgmpfsiSMRHAFVPFPGGSILAADYSQLELRILAHLSHDRRLIQVLNTGADVFRSIAAEWKMIEPE 2372
Cdd:PRK05755 640 --------------------RIRKAFVAPEGYKLLSADYSQIELRILAHLSGDEGLIEAFAEGEDIHTATASEVFGVPLE 699
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2373 SVGDDLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYTGINQFMTETVKNCKRDGFVQTILGRRRYLPG 2452
Cdd:PRK05755 700 EVTSEQRRRAKAINFGIIYGMSAFGLAQQLGISRKEAKEYIDRYFERYPGVKEYMERTVEQAREKGYVETLFGRRRYLPD 779
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2453 IKDNNPYRKAHAERQAINTIVQGSAADIVKIATVNIQKQLEtfhstfkshghrEGMLQSdqtglsrkrKLqgmfcpirgg 2532
Cdd:PRK05755 780 INSRNGNRRAFAERAAINAPIQGSAADIIKLAMIRVDKALK------------EEGLKS---------RM---------- 828
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....
gi 139394648 2533 ffILQLHDELLYEVAEEDVVQVAQIVKNEMESAVKLSVKLKVKVKIGASWGELK 2586
Cdd:PRK05755 829 --LLQVHDELVFEVPEDELEEVKKLVKEVMENAVELSVPLVVDVGVGDNWDEAH 880
|
|
| DNA_pol_A_pol_I_C |
cd08637 |
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ... |
2106-2583 |
6.71e-114 |
|
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and DNA polymerase activity to fill in the resulting gap. A combination of phylogenomic and signature sequence-based (or phonetic) approaches is used to understand the evolutionary relationships among bacteria. DNA polymerase I is one of the conserved proteins that is used to search for protein signatures. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains.
Pssm-ID: 176474 Cd Length: 377 Bit Score: 367.52 E-value: 6.71e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2106 MQAKLDAIETQAYQLAGHSFSFTSSDDIAEVLFLELKLPPnremknqgSKKTlgstRRGidngrklrlgrqFSTSKDVLN 2185
Cdd:cd08637 12 LEKELAELEEEIYELAGEEFNINSPKQLGEVLFEKLGLPV--------GKKT----KTG------------YSTDAEVLE 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2186 KLKALHPLPGLILEWRRITNAITKVVFPLQreKCLNPFLGmeRIYPV-SQSHTATGRITFTEPNIQNVPrdfeIKMPtlv 2264
Cdd:cd08637 68 KLADEHPIVELILEYRELTKLKSTYVDALP--KLINPKTG--RIHTSfNQTVTATGRLSSSDPNLQNIP----IRTE--- 136
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2265 gesppsqavgkgllpMGRgkykkgfsvnprcqaqmeeraadrgmpfsiSMRHAFVPFPGGSILAADYSQLELRILAHLSH 2344
Cdd:cd08637 137 ---------------EGR------------------------------EIRKAFVAEEGWVLLSADYSQIELRILAHLSG 171
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2345 DRRLIQVLNTGADVFRSIAAEWKMIEPESVGDDLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYTGIN 2424
Cdd:cd08637 172 DEALIEAFKNGEDIHTRTAAEVFGVPPEEVTPEMRRIAKAVNFGIIYGISAFGLSQQLGISRKEAKEYIDRYFARYPGVK 251
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2425 QFMTETVKNCKRDGFVQTILGRRRYLPGIKDNNPYRKAHAERQAINTIVQGSAADIVKIATVNIQKQLEtfhstfkshgh 2504
Cdd:cd08637 252 EYMEETVEEAREKGYVETLFGRRRYIPEINSKNRNVRAFAERIAINTPIQGTAADIIKLAMIRVHKALK----------- 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2505 regmlqsdqtglsrKRKLQG-MfcpirggffILQLHDELLYEVAEEDVVQVAQIVKNEMESAVKLSVKLKVKVKIGASWG 2583
Cdd:cd08637 321 --------------EEGLKArM---------LLQVHDELVFEVPEEELEEVAALVKEEMENAVELSVPLKVDVGVGKNWG 377
|
|
| DEXHc_POLQ-like |
cd18026 |
DEXH-box helicase domain of DNA polymerase theta; DNA polymerase theta (POLQ) is important in ... |
76-289 |
8.30e-111 |
|
DEXH-box helicase domain of DNA polymerase theta; DNA polymerase theta (POLQ) is important in the repair of genomic double-strand breaks (DSBs). POLQ contains an N-terminal type II DEAD box helicase domain which contains the ATP-binding region.
Pssm-ID: 350784 [Multi-domain] Cd Length: 202 Bit Score: 351.13 E-value: 8.30e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 76 LPKAVLEKYHSFGVKKMFEWQAECLLLGQVLEGKNLVYSAPTSAGKTLVAELLILKRVLEMRKKALFILPFVSVAKEKKY 155
Cdd:cd18026 1 LPDAVREAYAKKGIKKLYDWQKECLSLPGLLEGRNLVYSLPTSGGKTLVAEILMLKRLLERRKKALFVLPYVSIVQEKVD 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 156 YLQSLFQEVGIKVDGYMGS--TSPSRHFSSLDIAVCTIERANGLINRLIEENKMDLLGMVVVDELHMLGDSHRGYLLELL 233
Cdd:cd18026 81 ALSPLFEELGFRVEGYAGNkgRSPPKRRKSLSVAVCTIEKANSLVNSLIEEGRLDELGLVVVDELHMLGDGHRGALLELL 160
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*.
gi 139394648 234 LTKICYITRKSascqadlasslsnaVQIVGMSATLPNLELVASWLNAELYHTDFRP 289
Cdd:cd18026 161 LTKLLYAAQKN--------------IQIVGMSATLPNLEELASWLRAELYTTNFRP 202
|
|
| pola |
TIGR00593 |
DNA polymerase I; All proteins in this family for which functions are known are DNA ... |
1979-2586 |
1.22e-102 |
|
DNA polymerase I; All proteins in this family for which functions are known are DNA polymerases Many also have an exonuclease motif. 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: 273160 [Multi-domain] Cd Length: 887 Bit Score: 352.80 E-value: 1.22e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 1979 GISLEQSYEDPKVACWLLDPdSQEPTLHSIVTSFLPHELPLLEGMETSQGIQSlglNAGSEHSGRYrASVESILIFNSMN 2058
Cdd:TIGR00593 397 GIELGGVIFDTMLAAYLLDP-AQVSTLDTLARRYLVEELILDEKIGGKLAKFA---FPPLEEATEY-LARRAAATKRLAE 471
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2059 QLNSLLQKENLQDVFRKVEMPSQYCLALLELNGIGFSTAECES-QKHIMQaKLDAIETQAYQLAGHSFSFTSSDDIAEVL 2137
Cdd:TIGR00593 472 ELLKELDENKLLSLYREIELPLSKVLAEMEKTGIKVDADYLQElSQEFGE-EIADLEEEIYELAGEEFNINSPKQLGEVL 550
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2138 FLELKLPPnremknqgskktlgstrrgidnGRKLRLGRqfSTSKDVLNKLKALHPLPGLILEWRRITNAITKVVFPLQRE 2217
Cdd:TIGR00593 551 FEKLGLPV----------------------GKKTKTGY--STDADVLEKLREKHPIIALILEYRQLTKLKSTYVDGLPEL 606
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2218 kcLNPFLGmeRIYPV-SQSHTATGRITFTEPNIQNVPrdfeIKmptlvgesppsqavgkglLPMGRgkykkgfsvnprcq 2296
Cdd:TIGR00593 607 --VNPDTG--RIHTTfNQTGTATGRLSSSNPNLQNIP----IR------------------SEEGR-------------- 646
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2297 aqmeeraadrgmpfsiSMRHAFVPFPGGSILAADYSQLELRILAHLSHDRRLIQVLNTGADVFRSIAAEWKMIEPESVGD 2376
Cdd:TIGR00593 647 ----------------KIRKAFVAEKGWLLISADYSQIELRVLAHLSQDENLIEAFQNGEDIHTETASRLFGVEIEDVTP 710
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2377 DLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYTGINQFMTETVKNCKRDGFVQTILGRRRYLPGIKDN 2456
Cdd:TIGR00593 711 NMRRIAKTINFGVVYGMSAFGLAQELGISRKEAKEFIERYFARYPGVKDYIENTVEEARKKGYVETLFGRRRYIPDINSR 790
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2457 NPYRKAHAERQAINTIVQGSAADIVKIATVNIQKQletfhstFKSHGHREGMLqsdqtglsrkrklqgmfcpirggffiL 2536
Cdd:TIGR00593 791 NRNVREAAERMAINAPIQGSAADIMKIAMIKLDKR-------LKERKLKARLL--------------------------L 837
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|
gi 139394648 2537 QLHDELLYEVAEEDVVQVAQIVKNEMESAVKLSVKLKVKVKIGASWGELK 2586
Cdd:TIGR00593 838 QVHDELIFEAPEEEAEEVAALVKEVMEHAYPLAVPLEVEVGTGKNWGEAK 887
|
|
| PRK02362 |
PRK02362 |
ATP-dependent DNA helicase; |
76-833 |
2.32e-99 |
|
ATP-dependent DNA helicase;
Pssm-ID: 235032 [Multi-domain] Cd Length: 737 Bit Score: 338.86 E-value: 2.32e-99
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 76 LPKAVLEKYHSFGVKKMFEWQAECLLLGqVLEGKNLVYSAPTSAGKTLVAELLILKRVLEmRKKALFILPFVSVAKEKKY 155
Cdd:PRK02362 8 LPEGVIEFYEAEGIEELYPPQAEAVEAG-LLDGKNLLAAIPTASGKTLIAELAMLKAIAR-GGKALYIVPLRALASEKFE 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 156 YLQSlFQEVGIKV----------DGYMGSTspsrhfsslDIAVCTIERANGLInrlieENK---MDLLGMVVVDELHMLG 222
Cdd:PRK02362 86 EFER-FEELGVRVgistgdydsrDEWLGDN---------DIIVATSEKVDSLL-----RNGapwLDDITCVVVDEVHLID 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 223 DSHRGYLLELLLTKIcyitRKsascqadlassLSNAVQIVGMSATLPNLELVASWLNAELYHTDFRPVPLLESVKVGNSI 302
Cdd:PRK02362 151 SANRGPTLEVTLAKL----RR-----------LNPDLQVVALSATIGNADELADWLDAELVDSEWRPIDLREGVFYGGAI 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 303 -YDSSMKLVRefepmlQVKGDEDhvVSLCYETICDNHSVLLFCPSKKWCE----KLADIIAREFYNLhhqaeglvkpsec 377
Cdd:PRK02362 216 hFDDSQREVE------VPSKDDT--LNLVLDTLEEGGQCLVFVSSRRNAEgfakRAASALKKTLTAA------------- 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 378 ppvilEQKELLEVMDQLRRL-PSGLDSVLQKTVPWGVAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPARR 456
Cdd:PRK02362 275 -----ERAELAELAEEIREVsDTETSKDLADCVAKGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARR 349
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 457 VIIR-----TPIFGGRPLDILTYKQMVGRAGRKGVDTVGESILICKNSEKSKgiALLQ----GSLKPVRSCLqrreGEEv 527
Cdd:PRK02362 350 VIIRdyrryDGGAGMQPIPVLEYHQMAGRAGRPGLDPYGEAVLLAKSYDELD--ELFEryiwADPEDVRSKL----ATE- 422
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 528 tGSMIRAILEIIVGGVASTSQDMHTYAACTFLAAsmkegKQGIQRNQESVqlgaIEACVMWLLENEFIQSteasdgtEGK 607
Cdd:PRK02362 423 -PALRTHVLSTIASGFARTRDGLLEFLEATFYAT-----QTDDTGRLERV----VDDVLDFLERNGMIEE-------DGE 485
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 608 VYHPTHLGSatLSSSL-----SPADTLDifadlqrAMKGFVLENDLHILYLV--TP-MFE------DWTtidWYRFFC-- 671
Cdd:PRK02362 486 TLEATELGH--LVSRLyidplSAAEIID-------GLEAAKKPTDLGLLHLVcsTPdMYElylrsgDYE---WLNEYLye 553
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 672 ----LWEKLPTSMKRVAelvgvEEGFLaRCVKgkvvarterqhrqmaihkrffTSLVLLDLISEVPLREINQKYGCNRGQ 747
Cdd:PRK02362 554 hedeLLGDVPSEFEDDE-----FEDFL-SAVK---------------------TALLLEDWIDEVDEERITERYGVGPGD 606
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 748 IQSLQQSAAVYAGMITVFSNRLGWHnMELLLSQFQKRLTFGIQRELCDLVRVSLLNAQRARVLYASGFHTVADLARANIV 827
Cdd:PRK02362 607 IRGKVETAEWLLHAAERLASELDLD-LARAARELEKRVEYGVREELLDLVGLRGVGRVRARRLYNAGIESRADLRAADKS 685
|
....*.
gi 139394648 828 EVEVIL 833
Cdd:PRK02362 686 VVLAIL 691
|
|
| POLAc |
smart00482 |
DNA polymerase A domain; |
2311-2550 |
4.98e-88 |
|
DNA polymerase A domain;
Pssm-ID: 214687 Cd Length: 207 Bit Score: 286.06 E-value: 4.98e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2311 SISMRHAFVPFPGGSILAADYSQLELRILAHLSHDRRLIQVLNTGADVFRSIAAEWKMIEPESVGDDLRQQAKQICYGII 2390
Cdd:smart00482 1 GREIRRAFIAPPGYVLVSADYSQIELRILAHLSGDENLIEAFNNGGDIHTKTAAQVFGVPEEEVTPELRRAAKAINFGII 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2391 YGMGAKSLGEQMGIKENDAACYIDSFKSRYTGINQFMTETVKNCKRDGFVQTILGRRRYLPGIKDNNPYRKAHAERQAIN 2470
Cdd:smart00482 81 YGMGAKGLAEQLGISEAEAKELIKKYFARFPGVRRYIDRTLEEARRKGYVTTLFGRRRYIPDIDSRNPVLRAAAERAAVN 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2471 TIVQGSAADIVKIATVNIQKQLETFHStfkshghregmlqsdqtglsrkrklqgmfcpirGGFFILQLHDELLYEVAEED 2550
Cdd:smart00482 161 TPIQGSAADILKLAMIKMDEALKEFGL---------------------------------RARLLLQVHDELVFEVPEEE 207
|
|
| DNA_pol_A |
cd06444 |
Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and ... |
2186-2582 |
6.51e-81 |
|
Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; DNA polymerase family A, 5'-3' polymerase domain. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gamma, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic polymerase I (pol I) has two functional domains located on the same polypeptide; a 5'-3' polymerase and a 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and the DNA polymerase activity to fill in the resulting gap. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains.
Pssm-ID: 176473 [Multi-domain] Cd Length: 347 Bit Score: 271.21 E-value: 6.51e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2186 KLKAL-HPLPGLILEWRRITNAITKVVFPLQREKclnpfLGMERIYPVSQSH-TATGRITFTEPNIQNVPRDFeikmptl 2263
Cdd:cd06444 20 ELELLaHPAVPLLLEYKKLAKLWSANGWPWLDQW-----VRDGRFHPEYVPGgTVTGRWASRGGNAQQIPRRD------- 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2264 vgesppsqavgkgllpmgrgkykkgfsvnprcqaqmeeraadrgmPFSISMRHAFVPFPGGSILAADYSQLELRILAHLS 2343
Cdd:cd06444 88 ---------------------------------------------PLGRDIRQAFVADPGWTLVVADASQLELRVLAALS 122
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2344 HDRRLIQVLNTGADVFRSIAAEWKMIepeSVGDDLRQQAKQICYGIIYG----MGAKSLGEQMGIKENDAACYIDSFKSR 2419
Cdd:cd06444 123 GDEALAEAFGRGGDLYTATASAMFGV---PVGGGERQHAKIANLGAMYGatsgISARLLAQLRRISTKEAAALIELFFSR 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2420 YTGINQFMTETVKNCKRD---GFVQTILGRRRYLPGIKDN-----------NPYRKAHAERQAINTIVQGSAADIVKIAT 2485
Cdd:cd06444 200 FPAFPKAMEYVEDAARRGergGYVRTLLGRRSPPPDIRWTevvsdpaaasrARRVRRAAGRFARNFVVQGTAADWAKLAM 279
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2486 VNIQKQLETFhstfkshghregmlqsdqtglsrkrklqgmfcpIRGGFFILQLHDELLYEVAEEDVVQVAQIVKNEMESA 2565
Cdd:cd06444 280 VALRRRLEEL---------------------------------ALDARLVFFVHDEVVLHCPKEEAEAVAAIVREAAEQA 326
|
410 420
....*....|....*....|
gi 139394648 2566 VKL---SVKLKVKVKIGASW 2582
Cdd:cd06444 327 VRLlfgSVPVRFPVKIGVVW 346
|
|
| PRK00254 |
PRK00254 |
ski2-like helicase; Provisional |
78-829 |
1.61e-78 |
|
ski2-like helicase; Provisional
Pssm-ID: 234702 [Multi-domain] Cd Length: 720 Bit Score: 277.08 E-value: 1.61e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 78 KAVLEKYhsfGVKKMFEWQAECLLLGqVLEGKNLVYSAPTSAGKTLVAELLILKRVLEMRKKALFILPFVSVAKEKKYYL 157
Cdd:PRK00254 13 KRVLKER---GIEELYPPQAEALKSG-VLEGKNLVLAIPTASGKTLVAEIVMVNKLLREGGKAVYLVPLKALAEEKYREF 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 158 QSlFQEVGIKVDGYMGS-TSPSRHFSSLDIAVCTIERANGLI---NRLIEENKMdllgmVVVDELHMLGDSHRGYLLELL 233
Cdd:PRK00254 89 KD-WEKLGLRVAMTTGDyDSTDEWLGKYDIIIATAEKFDSLLrhgSSWIKDVKL-----VVADEIHLIGSYDRGATLEMI 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 234 LTKicyitrksascqadlassLSNAVQIVGMSATLPNLELVASWLNAELYHTDFRPVPLLESV-KVGNSIYD--SSMKLV 310
Cdd:PRK00254 163 LTH------------------MLGRAQILGLSATVGNAEELAEWLNAELVVSDWRPVKLRKGVfYQGFLFWEdgKIERFP 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 311 REFEpmlqvkgdedhvvSLCYETICDNHSVLLFCPSKKWCEKLADIIAREFYNLhhqaegLVKPsecppvilEQKELLEV 390
Cdd:PRK00254 225 NSWE-------------SLVYDAVKKGKGALVFVNTRRSAEKEALELAKKIKRF------LTKP--------ELRALKEL 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 391 MDQLRRLPSglDSVLQKTVPWGVAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIRTPI----FGG 466
Cdd:PRK00254 278 ADSLEENPT--NEKLKKALRGGVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKrysnFGW 355
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 467 RPLDILTYKQMVGRAGRKGVDTVGESILICKNSEKSKGIA-LLQGSLKPVRSCLQRRegeevtgSMIRA-ILEIIVGGVA 544
Cdd:PRK00254 356 EDIPVLEIQQMMGRAGRPKYDEVGEAIIVATTEEPSKLMErYIFGKPEKLFSMLSNE-------SAFRSqVLALITNFGV 428
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 545 STSQDMHTYAACTFLAAsmkegkqgiQRNQESVQLGAIEACVMWLLENEFIQSTEASDgtegkvYHPTHLGSATLSSSLS 624
Cdd:PRK00254 429 SNFKELVNFLERTFYAH---------QRKDLYSLEEKAKEIVYFLLENEFIDIDLEDR------FIPLPLGIRTSQLYID 493
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 625 PAdTLDIFAD-LQRAMKGfvlENDLHILYLV--TPmfeDWTTidwyrffclwekLPTSMKRVAELVGveegfLARCVKGK 701
Cdd:PRK00254 494 PL-TAKKFKDaFPKIEKN---PNPLGIFQLIasTP---DMTP------------LNYSRKEMEDLLD-----EAYEMEDR 549
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 702 VVART--ERQHRQMAIHKRFFTSLVLLDLISEVPLREINQKYGCNRGQIQSLQQSAA--VYAgMITVFsnRLGWHNMELL 777
Cdd:PRK00254 550 LYFNIpyWEDYKFQKFLRAFKTAKVLLDWINEVPEGEIVETYNIDPGDLYRILELADwlMYS-LIELY--KLFEPKQEVL 626
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|....
gi 139394648 778 --LSQFQKRLTFGIQRELCDLVRVSLLNAQRARVLYASGFHTVADLARANIVEV 829
Cdd:PRK00254 627 dyLETLHLRVKHGVREELLELMRLPMIGRKRARALYNAGFRSIEDIVNAKPSEL 680
|
|
| PRK01172 |
PRK01172 |
ATP-dependent DNA helicase; |
104-844 |
5.40e-73 |
|
ATP-dependent DNA helicase;
Pssm-ID: 100801 [Multi-domain] Cd Length: 674 Bit Score: 259.43 E-value: 5.40e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 104 QVLEGKNLVYSAPTSAGKTLVAELLILKRVLEmRKKALFILPFVSVAKEKKYYLQSLfQEVGIKVDGYMGSTSPSRHF-S 182
Cdd:PRK01172 33 QLRKGENVIVSVPTAAGKTLIAYSAIYETFLA-GLKSIYIVPLRSLAMEKYEELSRL-RSLGMRVKISIGDYDDPPDFiK 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 183 SLDIAVCTIERANGLINRliEENKMDLLGMVVVDELHMLGDSHRGYLLELLLTKICYITRKsascqadlasslsnaVQIV 262
Cdd:PRK01172 111 RYDVVILTSEKADSLIHH--DPYIINDVGLIVADEIHIIGDEDRGPTLETVLSSARYVNPD---------------ARIL 173
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 263 GMSATLPNLELVASWLNAELYHTDFRPVPLLESVKVGNSIYDSSMKlvrefepmlqvKGDEDhVVSLCYETICDNHSVLL 342
Cdd:PRK01172 174 ALSATVSNANELAQWLNASLIKSNFRPVPLKLGILYRKRLILDGYE-----------RSQVD-INSLIKETVNDGGQVLV 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 343 FCPSKKWCEKLADIIAREFynlhhqaeglvkpsecpPVILEQKELLEVMDqlrrlpsGLDSVLQKTVPWGVAFHHAGLTF 422
Cdd:PRK01172 242 FVSSRKNAEDYAEMLIQHF-----------------PEFNDFKVSSENNN-------VYDDSLNEMLPHGVAFHHAGLSN 297
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 423 EERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIRTPI----FGGRPLDILTYKQMVGRAGRKGVDTVGESIlICKN 498
Cdd:PRK01172 298 EQRRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIVRDITrygnGGIRYLSNMEIKQMIGRAGRPGYDQYGIGY-IYAA 376
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 499 SEKSKGIA--LLQGSLKPVRSCLQRREgeevtgSMIRAILEIIVGGVASTSQDMHTYAACTFLAAsmkegkqgiqRNQES 576
Cdd:PRK01172 377 SPASYDAAkkYLSGEPEPVISYMGSQR------KVRFNTLAAISMGLASSMEDLILFYNETLMAI----------QNGVD 440
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 577 VQLGAIEACVMWLLENEFIQSTEASDGTE-GKVyhpthlgsatlssslspadTLDIFADLQRAMkgfvlendlhilyLVT 655
Cdd:PRK01172 441 EIDYYIESSLKFLKENGFIKGDVTLRATRlGKL-------------------TSDLYIDPESAL-------------ILK 488
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 656 PMFEDWTTIDWYRFF-CLW-EKLPTSMKrvaELVGVEEgFLARC--VKGKVVARTerqhrqmaihkrffTSLVLLDLISE 731
Cdd:PRK01172 489 SAFDHDYDEDLALYYiSLCrEIIPANTR---DDYYAME-FLEDIgvIDGDISAAK--------------TAMVLRGWISE 550
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 732 VPLREINQKYGCNRGQIQSLQQSA----AVYAGMITVFSNRlgwhnMELLLSQFQKRLTFGIQRELCDLVRVSLLNAQRA 807
Cdd:PRK01172 551 ASMQKITDTYGIAPGDVQARASSAdwisYSLARLSSIYKPE-----MRRKLEILNIRIKEGIREDLIDLVLIPKVGRVRA 625
|
730 740 750 760
....*....|....*....|....*....|....*....|...
gi 139394648 808 RVLYASGFHTVADLARANIVEVEVI------LKNAVpFKSARK 844
Cdd:PRK01172 626 RRLYDAGFKTVDDIARSSPERIKKIygfsdtLANAI-VNRAMK 667
|
|
| DNA_pol_A_plastid_like |
cd08640 |
DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in ... |
2197-2584 |
4.81e-60 |
|
DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication; DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). The three-dimensional structure of plastid DNA polymerase has substantial similarity to Pol I. The structure of Pol I resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains.
Pssm-ID: 176477 Cd Length: 371 Bit Score: 211.87 E-value: 4.81e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2197 ILEWRRITNAITKVVFPLQreKCLNPFLGmeRIYPVSQSHTATGRITFTEPNIQNVPRdfeikmptlvgesppsqavgkg 2276
Cdd:cd08640 48 LKEIKSISTLLSTFIIPLQ--ELLNDSTG--RIHCSLNINTETGRLSSRNPNLQNQPA---------------------- 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2277 llpMGRGKYKkgfsvnprcqaqmeeraadrgmpfsisMRHAFVPFPGGSILAADYSQLELRILAHLSHDRRLIQVLNTGA 2356
Cdd:cd08640 102 ---LEKDRYK---------------------------IRKAFIASPGNTLIVADYSQLELRLLAHMTRCKSMIEAFNAGG 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2357 D------------VFRSIAAEWKMIEPESVGDDL-----------RQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYI 2413
Cdd:cd08640 152 DfhsrtasgmyphVAEAVANGEVLLEWKSEGKPPapllkdkfkseRRKAKVLNFSIAYGKTAHGLAKDWKVKLKEAERTV 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2414 DSFKSRYTGINQFMTETVKNCKRDGFVQTILGRRRYLPGIKDNNPYRKAHAERQAINTIVQGSAADIVKIATVNIQKQLE 2493
Cdd:cd08640 232 DAWYSDRPEVEQWQKKTKKEARERGYTRTLLGRYRYLPDIKSRNRKKRGHAERAAINTPIQGSAADIAMKAMLRIYRNLR 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2494 tfhstfkshghregmlqsdqtglsrkrklqgmfcPIRGGF-FILQLHDELLYEVAEEDVVQVAQIVKNEMES--AVKLSV 2570
Cdd:cd08640 312 ----------------------------------LKRLGWkLLLQIHDEVILEGPEEKADEALKIVKDCMENpfFGPLDV 357
|
410
....*....|....
gi 139394648 2571 KLKVKVKIGASWGE 2584
Cdd:cd08640 358 PLEVDGSVGYNWYE 371
|
|
| SF2_C_Ski2 |
cd18795 |
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
288-497 |
3.39e-56 |
|
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. This family includes spliceosomal Brr2 RNA helicase, ASCC3 (involved in the repair of N-alkylated nucleotides), Mtr4 (involved in processing of structured RNAs), DDX60 (involved in viral RNA degradation), and other proteins. Ski2-like RNA helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350182 [Multi-domain] Cd Length: 154 Bit Score: 192.38 E-value: 3.39e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 288 RPVPLLESVKVGNSIYDSSMKLVREfepmlqvKGDEDHVVSLCYETICDNHSVLLFCPSKKWCEKLADIIArefynlhhq 367
Cdd:cd18795 1 RPVPLEEYVLGFNGLGIKLRVDVMN-------KFDSDIIVLLKIETVSEGKPVLVFCSSRKECEKTAKDLA--------- 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 368 aeglvkpsecppvileqkellevmdqlrrlpsgldsvlqktvpwGVAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLS 447
Cdd:cd18795 65 --------------------------------------------GIAFHHAGLTREDRELVEELFREGLIKVLVATSTLA 100
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 139394648 448 SGVNLPARRVIIR-TPIFGG---RPLDILTYKQMVGRAGRKGVDTVGESILICK 497
Cdd:cd18795 101 AGVNLPARTVIIKgTQRYDGkgyRELSPLEYLQMIGRAGRPGFDTRGEAIIMTK 154
|
|
| PRK14975 |
PRK14975 |
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional |
2058-2586 |
6.79e-52 |
|
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Pssm-ID: 237876 [Multi-domain] Cd Length: 553 Bit Score: 193.66 E-value: 6.79e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2058 NQLNSLLQKEN---LQDVFrKVEMPSQYCLALLELNGIGFSTAEcesqkhiMQAKLDAIETQAYQLAGHSFSFTssdDIA 2134
Cdd:PRK14975 142 DQLNRIAAAAHpgrLRLLA-AAESAGALAAAEMELAGLPWDTDV-------HEALLAELLGPRPAAGGRPARLA---ELA 210
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2135 EVLFLELKLPPnremKNQGSKKTLGstrrgidngRKL-RLG-RQFSTSKDVLNKLKalHPLPGLILEWRRITNAITKVVF 2212
Cdd:PRK14975 211 AEIREALGRPR----LNPDSPQQVL---------RALrRAGiELPSTRKWELREID--HPAVEPLLEYRKLSKLLSANGW 275
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2213 PLQREKCLNpflgmERIYPV-SQSHTATGRITFTEPNIQNVPRDfeikmptlvgesppsqavgkgllpmgrgkykkgfsv 2291
Cdd:PRK14975 276 AWLDYWVRD-----GRFHPEyVPGGVVTGRWASRGPNAQQIPRD------------------------------------ 314
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2292 nprcqaqmeeraadrgmpfsisMRHAFVPFPGGSILAADYSQLELRILAHLSHDRRLIQVLNTGADVFRSIAAEWKMIEP 2371
Cdd:PRK14975 315 ----------------------IRSAFVADPGWKLVVADASQIELRVLAAYSGDERMIEAFRTGGDLHRLTASVGFGKPE 372
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2372 ESVGDdlRQQAKQICYGIIYGMGAKSLGEQMGiKENDAACYIDSFKSRYTGINQFMTETVKNCKRDGFVQTILGRRRYLP 2451
Cdd:PRK14975 373 EEKEE--RALAKAANFGAIYGATSKGLQEYAK-NYGEAARLLERLRRAYPRAVGWVERAAREGERGGVVRTLLGRTSPPP 449
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2452 GIKDNNPYRKAHAERQAINTIVQGSAADIVKIATVNIQKQLetfhstfkshghREGMlqsdqtglsrkrklqgmfcpirG 2531
Cdd:PRK14975 450 GFAWRARRRARSRGRFTRNFPVQGTAADWAKLALALLRRRL------------AEGL----------------------D 495
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*...
gi 139394648 2532 GFFILQLHDELLYEVAEEDVVQVAQIVKNEMESAVKL---SVKLKVKVKIGASWGELK 2586
Cdd:PRK14975 496 AELVFFVHDEVVVECPEEEAEEVAAAIEEAMEEAGRLlfgPVPFPVEVAVVESYAEAK 553
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
92-286 |
2.42e-50 |
|
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: 177.07 E-value: 2.42e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 92 MFEWQAECLLLGqVLEGKNLVYSAPTSAGKTLVAELLILKRVLEMRKKALFILPFVSVAKEKKYYLQSLFQEVGIKVDGY 171
Cdd:cd17921 2 LNPIQREALRAL-YLSGDSVLVSAPTSSGKTLIAELAILRALATSGGKAVYIAPTRALVNQKEADLRERFGPLGKNVGLL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 172 MGSTSPSR-HFSSLDIAVCTIERANGLINRLiEENKMDLLGMVVVDELHMLGDSHRGYLLELLLTKICYITRKsascqad 250
Cdd:cd17921 81 TGDPSVNKlLLAEADILVATPEKLDLLLRNG-GERLIQDVRLVVVDEAHLIGDGERGVVLELLLSRLLRINKN------- 152
|
170 180 190
....*....|....*....|....*....|....*..
gi 139394648 251 lasslsnaVQIVGMSATLPNLELVASWLNAE-LYHTD 286
Cdd:cd17921 153 --------ARFVGLSATLPNAEDLAEWLGVEdLIRFD 181
|
|
| DNA_pol_A_Aquificae_like |
cd08639 |
Phylum Aquificae Pol A is different from Escherichia coli Pol A by three signature sequences; ... |
2191-2583 |
2.33e-41 |
|
Phylum Aquificae Pol A is different from Escherichia coli Pol A by three signature sequences; Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and DNA polymerase activity to fill in the resulting gap. A combination of phylogenomic and signature sequence-based (or phonetic) approaches is used to understand the evolutionary relationships among bacteria. DNA polymerase I is one of the conserved proteins that is used for phylogenetic anaylsis of bacteria. Species of the phylum Aquificae grow in extreme thermophilic environments. The Aquificae are non-spore-forming, Gram-negative rods and strictly thermophilic. Phylum Aquificae Pol A is different from E. coli Pol I by three signature sequences consisting of a 2 amino acids (aa) insert, a 5-6 aa insert and a 6 aa deletion. These signature sequences may provide a molecular marker for the family Aquificaceae and related species.
Pssm-ID: 176476 Cd Length: 324 Bit Score: 156.29 E-value: 2.33e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2191 HPLPGLILEWRRITNAITKvvFPLQREKCLNPFLGmeRIYP-VSQSHTATGRITFTEPNIQNVPRDFEikmptlvgespp 2269
Cdd:cd08639 29 HPAVRLLLEYRKLNKLIST--FGEKLPKHIHPVTG--RIHPsFNQIGAASGRMSCSNPNLQQIPRERE------------ 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2270 sqavgkgllpmgrgkykkgfsvnprcqaqmeeraadrgmpfsisMRHAFVPFPGGSILAADYSQLELRILAHLSHDRRLI 2349
Cdd:cd08639 93 --------------------------------------------FRRCFVAPEGNKLIIADYSQIELRIAAEISGDERMI 128
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2350 QVLNTGADVFRSIAAEWKMIEPESVGDDLRQQAKQICYGIIYGMGAKSLGEQMGIKEN------DAACYIDSFKSRYTGI 2423
Cdd:cd08639 129 SAYQKGEDLHRLTASLITGKPIEEITKEERQLAKAVNFGLIYGMSAKGLREYARTNYGvemsleEAEKFRESFFFFYKGI 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2424 NQfmTETVKNCKRDGFVQTILGRRRylpgIKDNNPYRKahaerqAINTIVQGSAADIVKIATVNIQkqletfhstfkshg 2503
Cdd:cd08639 209 LR--WHHRLKAKGPIEVRTLLGRRR----VFEYFTFTE------ALNYPIQGTGADILKLALALLV-------------- 262
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2504 hregmlqsdqtglSRKRKLqgmfcpirGGFFILQLHDELLYEVAEEDVVQVAQIVKNEMESAVKL---SVKLKVKVKIGA 2580
Cdd:cd08639 263 -------------DRLKDL--------DAKIVLCVHDEIVLEVPEDEAEEAKKILESSMEEAGKRilkKVPVEVEVSISD 321
|
...
gi 139394648 2581 SWG 2583
Cdd:cd08639 322 SWA 324
|
|
| Dob10 |
COG4581 |
Superfamily II RNA helicase [Replication, recombination and repair]; |
105-493 |
1.68e-39 |
|
Superfamily II RNA helicase [Replication, recombination and repair];
Pssm-ID: 443638 [Multi-domain] Cd Length: 751 Bit Score: 159.72 E-value: 1.68e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 105 VLEGKNLVYSAPTSAGKTLVAELLILKRVLEMRK-------KALfilpfvsvAKEKKYYLQSLF--QEVGIkvdgyM-GS 174
Cdd:COG4581 37 LEAGRSVLVAAPTGSGKTLVAEFAIFLALARGRRsfytapiKAL--------SNQKFFDLVERFgaENVGL-----LtGD 103
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 175 TSPSRHfssLDIAVCTIERangLINRLIEE-NKMDLLGMVVVDELHMLGDSHRGYLLELLltkICYITRKsascqadlas 253
Cdd:COG4581 104 ASVNPD---APIVVMTTEI---LRNMLYREgADLEDVGVVVMDEFHYLADPDRGWVWEEP---IIHLPAR---------- 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 254 slsnaVQIVGMSATLPNLELVASWLNA-----ELYHTDFRPVPLLESVKVGNSIYDssmklVREFEPMLQVKGDEDHVVS 328
Cdd:COG4581 165 -----VQLVLLSATVGNAEEFAEWLTRvrgetAVVVSEERPVPLEFHYLVTPRLFP-----LFRVNPELLRPPSRHEVIE 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 329 LCYETicDNHSVLLFCPSKKWCEKLADIIAREfynlhhqaeGLVKPSEcppvileQKELLEVMDQLRRLPSGLD-SVLQK 407
Cdd:COG4581 235 ELDRG--GLLPAIVFIFSRRGCDEAAQQLLSA---------RLTTKEE-------RAEIREAIDEFAEDFSVLFgKTLSR 296
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 408 TVPWGVAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIRTPI-FGGRPLDILT---YKQMVGRAGR 483
Cdd:COG4581 297 LLRRGIAVHHAGMLPKYRRLVEELFQAGLLKVVFATDTLAVGINMPARTVVFTKLSkFDGERHRPLTareFHQIAGRAGR 376
|
410
....*....|
gi 139394648 484 KGVDTVGESI 493
Cdd:COG4581 377 RGIDTEGHVV 386
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
91-286 |
2.20e-36 |
|
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play an important role in RNA degradation, processing and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350786 [Multi-domain] Cd Length: 177 Bit Score: 136.70 E-value: 2.20e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 91 KMFEWQAECLLLGqVLEGKNLVYSAPTSAGKTLVAELLILKRVLEmRKKALFILPFVSVAKEK-----KYYLQSLfqEVG 165
Cdd:cd18028 1 ELYPPQAEAVRAG-LLKGENLLISIPTASGKTLIAEMAMVNTLLE-GGKALYLVPLRALASEKyeefkKLEEIGL--KVG 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 166 IKVDGYmgsTSPSRHFSSLDIAVCTIERANGLINRliEENKMDLLGMVVVDELHMLGDSHRGYLLELLLTKIcyitrksa 245
Cdd:cd18028 77 ISTGDY---DEDDEWLGDYDIIVATYEKFDSLLRH--SPSWLRDVGVVVVDEIHLISDEERGPTLESIVARL-------- 143
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 139394648 246 scqadlaSSLSNAVQIVGMSATLPNLELVASWLNAELYHTD 286
Cdd:cd18028 144 -------RRLNPNTQIIGLSATIGNPDELAEWLNAELVESD 177
|
|
| HTH_61 |
pfam20470 |
Helix-turn-helix domain; This entry represents a presumed helix-turn-helix domain found in DNA ... |
490-596 |
8.96e-33 |
|
Helix-turn-helix domain; This entry represents a presumed helix-turn-helix domain found in DNA polymerase theta.
Pssm-ID: 466619 [Multi-domain] Cd Length: 92 Bit Score: 123.04 E-value: 8.96e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 490 GESILICKNSEKSKGIALLQGSLKPVRSCLQRRegeevTGSMIRAILEIIVGGVASTSQDMHTYAACTFLAASMKEGKQG 569
Cdd:pfam20470 1 GESILICKEKDLEKVAELLRAELPPVYSCLLPE-----KRGIKRALLEIIALGLATSPEDVDEYMSCTLLSVQQKELDVE 75
|
90 100
....*....|....*....|....*..
gi 139394648 570 IQrnqesvqlgaIEACVMWLLENEFIQ 596
Cdd:pfam20470 76 KS----------IESSLEELVENGLIT 92
|
|
| COG1202 |
COG1202 |
Superfamily II helicase, archaea-specific [Replication, recombination and repair]; |
90-516 |
2.15e-30 |
|
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
Pssm-ID: 440815 [Multi-domain] Cd Length: 790 Bit Score: 131.17 E-value: 2.15e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 90 KKMFEWQAECLLLGQV-------LEGKN-LVYSApTSAGKTLVAELLILKRVLEMRKKALFILPFVSVAKEKkyYLQslF 161
Cdd:COG1202 200 KDLLEGRGEELLPVQSlavenglLEGKDqLVVSA-TATGKTLIGELAGIKNALEGKGKMLFLVPLVALANQK--YED--F 274
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 162 QE-------VGIKVdgymGST---SPSRHFS-SLDIAVCTIEranGLINRLIEENKMDLLGMVVVDELHMLGDSHRGYLL 230
Cdd:COG1202 275 KDrygdgldVSIRV----GASrirDDGTRFDpNADIIVGTYE---GIDHALRTGRDLGDIGTVVIDEVHMLEDPERGHRL 347
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 231 ELLLTKICYITRKSascqadlasslsnavQIVGMSATLPNLELVASWLNAELYHTDFRPVPL---------LESVKVGNs 301
Cdd:COG1202 348 DGLIARLKYYCPGA---------------QWIYLSATVGNPEELAKKLGAKLVEYEERPVPLerhltfadgREKIRIIN- 411
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 302 iydssmKLV-REFepmlqvkgdeDHVVSLCY--ETIcdnhsvlLFCPSKKWCEKLADIIarefynlhhqaeglvkpsecp 378
Cdd:COG1202 412 ------KLVkREF----------DTKSSKGYrgQTI-------IFTNSRRRCHEIARAL--------------------- 447
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 379 pvileqkellevmdqlrrlpsGLDSvlqktvpwgvAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVI 458
Cdd:COG1202 448 ---------------------GYKA----------APYHAGLDYGERKKVERRFADQELAAVVTTAALAAGVDFPASQVI 496
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 139394648 459 IRTPIFGGRPLDILTYKQMVGRAGRKGVDTVGESILI----------CKNSEKSKGIALLQGSLKPVR 516
Cdd:COG1202 497 FDSLAMGIEWLSVQEFHQMLGRAGRPDYHDRGKVYLLvepgksyhrsMEMTEDEVAFKLLKGEMEDVA 564
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
96-274 |
2.16e-21 |
|
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.
Pssm-ID: 425570 [Multi-domain] Cd Length: 165 Bit Score: 93.46 E-value: 2.16e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 96 QAECLLLgqVLEGKNLVYSAPTSAGKTLVAELLILKRVLEMR--KKALFILPFVSVAKEKKYYLQSLFQEVGIKVDGYMG 173
Cdd:pfam00270 4 QAEAIPA--ILEGRDVLVQAPTGSGKTLAFLLPALEALDKLDngPQALVLAPTRELAEQIYEELKKLGKGLGLKVASLLG 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 174 STSPSRHFSSL---DIAVCTIERangLINRLIEENKMDLLGMVVVDELHMLGDSHRGYLLELLLtkicyitrksascqad 250
Cdd:pfam00270 82 GDSRKEQLEKLkgpDILVGTPGR---LLDLLQERKLLKNLKLLVLDEAHRLLDMGFGPDLEEIL---------------- 142
|
170 180
....*....|....*....|....*
gi 139394648 251 laSSLSNAVQIVGMSATLP-NLELV 274
Cdd:pfam00270 143 --RRLPKKRQILLLSATLPrNLEDL 165
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
85-285 |
3.62e-20 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 91.01 E-value: 3.62e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 85 HSFGVKKMFEWQAECLLlgQVLEG-KNLVYSAPTSAGKTLVAELLILKRVLE-MRKKALFILPFVSVAKEKKYYLQSLFQ 162
Cdd:smart00487 2 EKFGFEPLRPYQKEAIE--ALLSGlRDVILAAPTGSGKTLAALLPALEALKRgKGGRVLVLVPTRELAEQWAEELKKLGP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 163 EVGIKVDGYMGSTSPSRHFSSL-----DIAVCTIERanglINRLIEENKMDL--LGMVVVDELHMLGDSHRGYLLELLLT 235
Cdd:smart00487 80 SLGLKVVGLYGGDSKREQLRKLesgktDILVTTPGR----LLDLLENDKLSLsnVDLVILDEAHRLLDGGFGDQLEKLLK 155
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|
gi 139394648 236 KicyitrksascqadlassLSNAVQIVGMSATLPNLELVASWLNAELYHT 285
Cdd:smart00487 156 L------------------LPKNVQLLLLSATPPEEIENLLELFLNDPVF 187
|
|
| phage_DpoZ_1 |
NF038380 |
aminoadenine-incorporating DNA polymerase DpoZ; |
2066-2584 |
2.55e-19 |
|
aminoadenine-incorporating DNA polymerase DpoZ;
Pssm-ID: 468497 [Multi-domain] Cd Length: 604 Bit Score: 94.73 E-value: 2.55e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2066 KENLQDVFRkVEMPSQYCLALLELNGIGFSTAECESQKHIMQAKLDAIETQAYQLAGHSFSFTSSDDIAEVLflelKLPP 2145
Cdd:NF038380 173 RQGLQRVVE-LERRLFPVLIDMEWRGIRVDLEAAEAAIPELDKVIDQLQKELNEIAGFEFNVNSSPQIRKLF----KPKK 247
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2146 NREMKNQGSKKT-LGSTRRGidngrklrlgrQFSTSKDVLNKLKalHPLPGLILEWRRITnaitkvvfplqreKCLNPFL 2224
Cdd:NF038380 248 ISKGQWVAIDGTpLETTDAG-----------KPSLGADALREIK--HPAAAKILELRKLI-------------KTRDTFL 301
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2225 G--------MERIYP-VSQS------HTATGRITFTEPNIQNVP-RDFEIkmptlvgesppsqavgkgllpmgrgkykkg 2288
Cdd:NF038380 302 RghvlghavGGGVHPnINQTkgedggGTGTGRLSYTDPALQQIPsRDKAI------------------------------ 351
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2289 fsvnprcqaqmeerAAdrgmpfsiSMRHAFVPFPGGSILAADYSQLELRILAHLSHDRRLIQV--LNTGADvFRSIAAEW 2366
Cdd:NF038380 352 --------------AA--------IVRPIFLPDEGQVWLCSDLAQFEFRIFAHLVNNPSIIAAyaEDPELD-FHQIVADM 408
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2367 KMIePESVGDDLRQQAKQICYGIIYGMGAKSLGEQMG----IKEND--------------AACYIDSFKSRYTGINQFMT 2428
Cdd:NF038380 409 TGL-PRNATYSGQANAKQINLGMIFNMGNGKLADKMGmpyeWEEFTfgkevrrykkagpeAMAVIENYHRKLPGVKELAD 487
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2429 ETVKNCKRDGFVQTILGRRRYLPGIKdnnpyrKAHAerqAINTIVQGSAADIVKIATVNIQKQLETfhstfkshghregm 2508
Cdd:NF038380 488 RAKAVAKERGYVRTAMGRRLRFPGGM------KTYK---ASGLLIQATAADLNKENLLEIDEVLGS-------------- 544
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2509 lqsdqtglsrkrklqgmfcpiRGGFFILQLHDELLYEVAEEDVVQ-VAQIVKNEMESAvklSVKLKVKVKI-----GASW 2582
Cdd:NF038380 545 ---------------------LDGRLLLNTHDEYSMSLPEDDVRKpIKERVKLFIEDS---SPWLRVPIILelsgfGRNW 600
|
..
gi 139394648 2583 GE 2584
Cdd:NF038380 601 WE 602
|
|
| DEXHc_HFM1 |
cd18023 |
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box ... |
109-289 |
4.33e-18 |
|
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box helicase, required for crossover formation and complete synapsis of homologous chromosomes during meiosis. HFM1 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: 350781 [Multi-domain] Cd Length: 206 Bit Score: 85.10 E-value: 4.33e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 109 KNLVYSAPTSAGKTLVAELLILkRVL-------EMRKKALFILPFVSVAKEKKYYLQSLFQEVGIKVDGYMGSTS--PSR 179
Cdd:cd18023 18 KNFVVSAPTGSGKTVLFELAIL-RLLkernplpWGNRKVVYIAPIKALCSEKYDDWKEKFGPLGLSCAELTGDTEmdDTF 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 180 HFSSLDIAVCTIERANGLINRLIEENKM-DLLGMVVVDELHMLGDShRGYLLELLLTKICYITRKSASCQADLASslsna 258
Cdd:cd18023 97 EIQDADIILTTPEKWDSMTRRWRDNGNLvQLVALVLIDEVHIIKEN-RGATLEVVVSRMKTLSSSSELRGSTVRP----- 170
|
170 180 190
....*....|....*....|....*....|....*.
gi 139394648 259 VQIVGMSATLPNLELVASWLNAE-----LYHTDFRP 289
Cdd:cd18023 171 MRFVAVSATIPNIEDLAEWLGDNpagcfSFGESFRP 206
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
108-267 |
2.11e-17 |
|
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: 81.30 E-value: 2.11e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 108 GKNLVYSAPTSAGKTLVAELLILKRVLEMRKKALFILPFVSVAKEKKYYLQSLFQEvGIKVDGYMGSTSPSRHFS----S 183
Cdd:cd00046 1 GENVLITAPTGSGKTLAALLAALLLLLKKGKKVLVLVPTKALALQTAERLRELFGP-GIRVAVLVGGSSAEEREKnklgD 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 184 LDIAVCTIERANGLINRLIEENKMDlLGMVVVDELHMLGDSHRGYLLEllltkicyitrksasCQADLASSLSNaVQIVG 263
Cdd:cd00046 80 ADIIIATPDMLLNLLLREDRLFLKD-LKLIIVDEAHALLIDSRGALIL---------------DLAVRKAGLKN-AQVIL 142
|
....
gi 139394648 264 MSAT 267
Cdd:cd00046 143 LSAT 146
|
|
| DNA_pol_A_pol_I_B |
cd08643 |
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ... |
2307-2584 |
2.45e-17 |
|
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and DNA polymerase activity to fill in the resulting gap. A combination of phylogenomic and signature sequence-based (or phonetic) approaches is used to understand the evolutionary relationships among bacteria. DNA polymerase I is one of the conserved proteins that is used to search for protein signatures. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains.
Pssm-ID: 176480 Cd Length: 429 Bit Score: 87.49 E-value: 2.45e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2307 GMPFSISMRHAFVPFPGGSILAADYSQLELRILAHLSHDrrliqvLNTGADVFRSIAAEWKMIEPESVGDDLRQQAKQIC 2386
Cdd:cd08643 170 GSPYGKECRELFGVPPGWSLVGADASGLELRCLAHYLAR------YDGGAYTRKVLGGDIHWANAQAMGLLSRDGAKTFI 243
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2387 YGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYTGINQFMTETVKNCK-RDGF-------------VQTILGRRRYLPG 2452
Cdd:cd08643 244 YAFLYGAGDEKLGQIVGDDLRTAKNLNAEWPQTKKGTIKKIADKAKGRVvRANFlkglpalgklikkVKEAAKKRGHLVG 323
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2453 IKDNNPY-RKAHAerqAINTIVQGSAADIVKIATVNIQKQLETFHSTfksHGHREGmlqsdqtglsrkrklqgmfcpirg 2531
Cdd:cd08643 324 LDGRRIRvRSAHA---ALNTLLQSAGAILMKKWLVLLDDELTAKGGV---WGGDFE------------------------ 373
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*.
gi 139394648 2532 gfFILQLHDELLYEVAEEDVVQVAQIVKNEMESAVK---LSVKLKVKVKIGASWGE 2584
Cdd:cd08643 374 --YCAWVHDEVQIECRKGIAEEVGKIAVEAAEKAGEhfnFRCPLAGEFDIGRNWAE 427
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
412-485 |
1.48e-16 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 76.48 E-value: 1.48e-16
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 139394648 412 GVAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLP-ARRVIIRtpifgGRPLDILTYKQMVGRAGRKG 485
Cdd:smart00490 13 KVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPgVDLVIIY-----DLPWSPASYIQRIGRAGRAG 82
|
|
| DEXHc_LHR-like |
cd17922 |
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ... |
108-278 |
4.91e-15 |
|
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases from 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: 350680 [Multi-domain] Cd Length: 166 Bit Score: 74.93 E-value: 4.91e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 108 GKNLVYSAPTSAGKTLVAELLILKRVLEMRKK---ALFILPFVSVAKEKKYYLQSLFQE--VGIKVDGYMGSTSPSRHFS 182
Cdd:cd17922 1 GRNVLIAAPTGSGKTEAAFLPALSSLADEPEKgvqVLYISPLKALINDQERRLEEPLDEidLEIPVAVRHGDTSQSEKAK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 183 SL----DIAVCTIERANGLINRLIEENKMDLLGMVVVDELHMLGDSHRGYLLELLLTKICYITRKSAscqadlasslsna 258
Cdd:cd17922 81 QLknppGILITTPESLELLLVNKKLRELFAGLRYVVVDEIHALLGSKRGVQLELLLERLRKLTGRPL------------- 147
|
170 180
....*....|....*....|
gi 139394648 259 vQIVGMSATLPNLELVASWL 278
Cdd:cd17922 148 -RRIGLSATLGNLEEAAAFL 166
|
|
| DEXHc_Brr2_1 |
cd18019 |
N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD ... |
110-278 |
5.12e-15 |
|
N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD box helicase that mediates spliceosome catalytic activation. It is a stable subunit of the spliceosome, required during splicing catalysis and spliceosome disassembly. Brr2 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: 350777 [Multi-domain] Cd Length: 214 Bit Score: 76.25 E-value: 5.12e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 110 NLVYSAPTSAGKTLVAELLILKRVLEMRK----------KALFILPFVSVAKEKKYYLQSLFQEVGIKVDGYMGSTSPSR 179
Cdd:cd18019 35 NLLLCAPTGAGKTNVALLTILREIGKHRNpdgtinldafKIVYIAPMKALVQEMVGNFSKRLAPYGITVAELTGDQQLTK 114
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 180 -HFSSLDIAVCTIERANGLINRLIEENKMDLLGMVVVDELHMLGDShRGYLLELLLTKIcyiTRKSASCQADlasslsna 258
Cdd:cd18019 115 eQISETQIIVTTPEKWDIITRKSGDRTYTQLVRLIIIDEIHLLHDD-RGPVLESIVART---IRQIEQTQEY-------- 182
|
170 180
....*....|....*....|
gi 139394648 259 VQIVGMSATLPNLELVASWL 278
Cdd:cd18019 183 VRLVGLSATLPNYEDVATFL 202
|
|
| DEXHc_ASCC3_2 |
cd18022 |
C-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ... |
109-279 |
1.11e-14 |
|
C-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; Activating signal cointegrator 1 complex subunit 3 (ASCC3) is a type II DEAD box helicase that plays a role in the repair of N-alkylated nucleotides. ASCC3 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: 350780 [Multi-domain] Cd Length: 189 Bit Score: 74.72 E-value: 1.11e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 109 KNLVYSAPTSAGKTLVAELLILkRVLEMR--KKALFILPFVSVAKEK-KYYLQSLFQEVGIKVDGYMGSTSPS-RHFSSL 184
Cdd:cd18022 18 NNVLLGAPTGSGKTIAAELAMF-RAFNKYpgSKVVYIAPLKALVRERvDDWKKRFEEKLGKKVVELTGDVTPDmKALADA 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 185 DIAVCTIERANGLINRLIEENKMDLLGMVVVDELHMLGdSHRGYLLELLLTKICYITRKSascqadlasslSNAVQIVGM 264
Cdd:cd18022 97 DIIITTPEKWDGISRSWQTREYVQQVSLIIIDEIHLLG-SDRGPVLEVIVSRMNYISSQT-----------EKPVRLVGL 164
|
170
....*....|....*
gi 139394648 265 SATLPNLELVASWLN 279
Cdd:cd18022 165 STALANAGDLANWLG 179
|
|
| YprA |
COG1205 |
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ... |
75-485 |
3.62e-14 |
|
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, recombination and repair];
Pssm-ID: 440818 [Multi-domain] Cd Length: 758 Bit Score: 78.72 E-value: 3.62e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 75 GLPKAVLEKYHSFGVKKMFEWQAECLllGQVLEGKNLVYSAPTSAGKTLVAELLILKRVLEMRK-KALFILPFVSVAKEK 153
Cdd:COG1205 40 WLPPELRAALKKRGIERLYSHQAEAI--EAARAGKNVVIATPTASGKSLAYLLPVLEALLEDPGaTALYLYPTKALARDQ 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 154 KYYLQSLFQEVG--IKVDGYMGSTSPS-RH--FSSLDIAVCT-------IERANGLINRLIEEnkmdlLGMVVVDELHM- 220
Cdd:COG1205 118 LRRLRELAEALGlgVRVATYDGDTPPEeRRwiREHPDIVLTNpdmlhygLLPHHTRWARFFRN-----LRYVVIDEAHTy 192
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 221 ---LGdSHRGYLLELLLtKICyitrksascqADLASSlsnaVQIVGMSATLPN-LELVASWLNAELYH--TDFRPVP--- 291
Cdd:COG1205 193 rgvFG-SHVANVLRRLR-RIC----------RHYGSD----PQFILASATIGNpAEHAERLTGRPVTVvdEDGSPRGert 256
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 292 --LLESVKVGNSIYDSSMKLVREfepmlqvkgdedhvvsLCYETICDNHSVLLFCPSKKWCEKLADIIAREFynlhhqAE 369
Cdd:COG1205 257 fvLWNPPLVDDGIRRSALAEAAR----------------LLADLVREGLRTLVFTRSRRGAELLARYARRAL------RE 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 370 GLVKPSecppvileqkellevmdqlrrlpsgldsvlqktvpwgVAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSG 449
Cdd:COG1205 315 PDLADR-------------------------------------VAAYRAGYLPEERREIERGLRSGELLGVVSTNALELG 357
|
410 420 430
....*....|....*....|....*....|....*....
gi 139394648 450 VNLP---ArrVIIRtpifgGRPLDILTYKQMVGRAGRKG 485
Cdd:COG1205 358 IDIGgldA--VVLA-----GYPGTRASFWQQAGRAGRRG 389
|
|
| DEXHc_Brr2_2 |
cd18021 |
C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type ... |
110-285 |
9.48e-14 |
|
C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD box helicase that mediates spliceosome catalytic activation. It is a stable subunit of the spliceosome, required during splicing catalysis and spliceosome disassembly. Brr2 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: 350779 [Multi-domain] Cd Length: 191 Bit Score: 71.91 E-value: 9.48e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 110 NLVYSAPTSAGKTLVAELLILKRVLEMRK-KALFILPFVSVAKEKKYYLQSLFQEV-GIKVDGYMGSTSPS-RHFSSLDI 186
Cdd:cd18021 21 NVFVGAPTGSGKTVCAELALLRHWRQNPKgRAVYIAPMQELVDARYKDWRAKFGPLlGKKVVKLTGETSTDlKLLAKSDV 100
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 187 AVCTIERANGLINRLIEENKMDLLGMVVVDELHMLGDSHrGYLLELLLTKICYItrksascqadlASSLSNAVQIVGMSA 266
Cdd:cd18021 101 ILATPEQWDVLSRRWKQRKNVQSVELFIADELHLIGGEN-GPVYEVVVSRMRYI-----------SSQLEKPIRIVGLSS 168
|
170
....*....|....*....
gi 139394648 267 TLPNLELVASWLNAELYHT 285
Cdd:cd18021 169 SLANARDVGEWLGASKSTI 187
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
403-485 |
2.66e-13 |
|
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 68.39 E-value: 2.66e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 403 SVLQKTVPWGVAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIrtpIFGGrPLDILTYKQMVGRAG 482
Cdd:pfam00271 31 ELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVI---NYDL-PWNPASYIQRIGRAG 106
|
...
gi 139394648 483 RKG 485
Cdd:pfam00271 107 RAG 109
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
91-484 |
3.90e-10 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 65.43 E-value: 3.90e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 91 KMFEWQAECL---LLGQVLEGKNLVYSAPTSAGKTLVAeLLILKRVLEmRKKALFILPFVSVAKekkyylQSL--FQEVG 165
Cdd:COG1061 80 ELRPYQQEALealLAALERGGGRGLVVAPTGTGKTVLA-LALAAELLR-GKRVLVLVPRRELLE------QWAeeLRRFL 151
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 166 IKVDGYMGSTSPSRhfsslDIAVCTIeraNGLINRLIEENKMDLLGMVVVDELHMLG-DSHRGyLLELLltkicyitrks 244
Cdd:COG1061 152 GDPLAGGGKKDSDA-----PITVATY---QSLARRAHLDELGDRFGLVIIDEAHHAGaPSYRR-ILEAF----------- 211
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 245 ascqadlasslsNAVQIVGMSAT---LPNLELVASWLNAELYHTDFR----------------PVPLLESVKVGNSIYDS 305
Cdd:COG1061 212 ------------PAAYRLGLTATpfrSDGREILLFLFDGIVYEYSLKeaiedgylappeyygiRVDLTDERAEYDALSER 279
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 306 SMKLVREFEPMLqvkgdeDHVVSLCYETICDNHSVLLFCPSKKWCEKLADIIAREFYNlhhqaeglvkpsecppvileqk 385
Cdd:COG1061 280 LREALAADAERK------DKILRELLREHPDDRKTLVFCSSVDHAEALAELLNEAGIR---------------------- 331
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 386 ellevmdqlrrlpsgldsvlqktvpwgVAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLP-ARRVIIRTPIf 464
Cdd:COG1061 332 ---------------------------AAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPrLDVAILLRPT- 383
|
410 420
....*....|....*....|
gi 139394648 465 gGRPldiLTYKQMVGRAGRK 484
Cdd:COG1061 384 -GSP---REFIQRLGRGLRP 399
|
|
| PRK09751 |
PRK09751 |
putative ATP-dependent helicase Lhr; Provisional |
115-484 |
5.60e-10 |
|
putative ATP-dependent helicase Lhr; Provisional
Pssm-ID: 137505 [Multi-domain] Cd Length: 1490 Bit Score: 65.33 E-value: 5.60e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 115 APTSAGKTLVAELLILKRVL--------EMRKKA----LFILPF----VSVAKEKKYYLQSLFQE--------VGIKVDG 170
Cdd:PRK09751 3 APTGSGKTLAAFLYALDRLFreggedtrEAHKRKtsriLYISPIkalgTDVQRNLQIPLKGIADErrrrgeteVNLRVGI 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 171 YMGSTsPSRHFSSL-----DIAVCTIEranGLINRLIEENKMDLLGM--VVVDELHMLGDSHRGYLLELLLTKicyitrk 243
Cdd:PRK09751 83 RTGDT-PAQERSKLtrnppDILITTPE---SLYLMLTSRARETLRGVetVIIDEVHAVAGSKRGAHLALSLER------- 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 244 sascqadLASSLSNAVQIVGMSATLPNLELVASWLNAElyhtdfRPVPLLESvkvgNSIYDSSMKLVREFEPMLQVK--- 320
Cdd:PRK09751 152 -------LDALLHTSAQRIGLSATVRSASDVAAFLGGD------RPVTVVNP----PAMRHPQIRIVVPVANMDDVSsva 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 321 ---GDED----------HVVSLCYETICDNHSVLLFCPSKKWCEKLAdiiAR--EFYnlhhqAEGLvkpSECPPVILEQK 385
Cdd:PRK09751 215 sgtGEDShagregsiwpYIETGILDEVLRHRSTIVFTNSRGLAEKLT---ARlnELY-----AARL---QRSPSIAVDAA 283
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 386 ELLEVMDQLRRLPSGLDSVLQKTvpwgvafHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIRTpifg 465
Cdd:PRK09751 284 HFESTSGATSNRVQSSDVFIARS-------HHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQV---- 352
|
410
....*....|....*....
gi 139394648 466 GRPLDILTYKQMVGRAGRK 484
Cdd:PRK09751 353 ATPLSVASGLQRIGRAGHQ 371
|
|
| DEXHc_ASCC3_1 |
cd18020 |
N-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ... |
109-283 |
6.64e-09 |
|
N-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; Activating signal cointegrator 1 complex subunit 3 (ASCC3) is a type II DEAD box helicase that plays a role in the repair of N-alkylated nucleotides. ASCC3 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: 350778 [Multi-domain] Cd Length: 199 Bit Score: 58.21 E-value: 6.64e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 109 KNLVYSAPTSAGKTLVAELLIL----KRVLEMRK------KALFILPFVSVAKEKKYYLQSLFQEVGIKVDGYMGSTSPS 178
Cdd:cd18020 18 ENMLICAPTGAGKTNIAMLTILheirQHVNQGGVikkddfKIVYIAPMKALAAEMVEKFSKRLAPLGIKVKELTGDMQLT 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 179 R-HFSSLDIAVCTIERANGLINRLIEENKM-DLLGMVVVDELHMLGDShRGYLLELLLTKIcyiTRKSASCQAdlassls 256
Cdd:cd18020 98 KkEIAETQIIVTTPEKWDVVTRKSSGDVALsQLVRLLIIDEVHLLHDD-RGPVIESLVART---LRQVESTQS------- 166
|
170 180
....*....|....*....|....*..
gi 139394648 257 nAVQIVGMSATLPNLELVASWLNAELY 283
Cdd:cd18020 167 -MIRIVGLSATLPNYLDVADFLRVNPY 192
|
|
| DEADc |
cd00268 |
DEAD-box helicase domain of DEAD box helicases; DEAD-box helicases comprise a diverse family ... |
88-279 |
7.43e-08 |
|
DEAD-box helicase domain of 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. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region.
Pssm-ID: 350669 [Multi-domain] Cd Length: 196 Bit Score: 55.14 E-value: 7.43e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 88 GVKKMFEWQAECLLLgqVLEGKNLVYSAPTSAGKTLvAELL-ILKRVLEMRKK------ALFILP----FVSVAKEkkyy 156
Cdd:cd00268 9 GFEKPTPIQAQAIPL--ILSGRDVIGQAQTGSGKTL-AFLLpILEKLLPEPKKkgrgpqALVLAPtrelAMQIAEV---- 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 157 LQSLFQEVGIKVDGYMGSTSPSRHFSSL----DIAVCTIERanglINRLIEENKMDL--LGMVVVDEL-HMLGDSHRGYL 229
Cdd:cd00268 82 ARKLGKGTGLKVAAIYGGAPIKKQIEALkkgpDIVVGTPGR----LLDLIERGKLDLsnVKYLVLDEAdRMLDMGFEEDV 157
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 139394648 230 LELLltkicyitrksascqadlaSSLSNAVQIVGMSATLPN--LELVASWLN 279
Cdd:cd00268 158 EKIL-------------------SALPKDRQTLLFSATLPEevKELAKKFLK 190
|
|
| Lhr |
COG1201 |
Lhr-like helicase [Replication, recombination and repair]; |
213-446 |
1.09e-07 |
|
Lhr-like helicase [Replication, recombination and repair];
Pssm-ID: 440814 [Multi-domain] Cd Length: 850 Bit Score: 57.42 E-value: 1.09e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 213 VVVDELHMLGDSHRGYLLELLLtkicyitrksascqADLASSLSNAVQIVGMSATLPNLELVASWLnaeLYHTDFRPVPL 292
Cdd:COG1201 165 VIVDEIHALAGSKRGVHLALSL--------------ERLRALAPRPLQRIGLSATVGPLEEVARFL---VGYEDPRPVTI 227
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 293 LEsVKVGNSIydsSMKLVREFEPMLQVKGDEDHVVSLCYETICD----NHSVLLFCPSKKWCEKLadiiareFYNLhhqa 368
Cdd:COG1201 228 VD-AGAGKKP---DLEVLVPVEDLIERFPWAGHLWPHLYPRVLDlieaHRTTLVFTNTRSQAERL-------FQRL---- 292
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 139394648 369 eglvkpsecppvileqkellevmdqLRRLPSGLDSvlqktvpwgVAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTL 446
Cdd:COG1201 293 -------------------------NELNPEDALP---------IAAHHGSLSREQRLEVEEALKAGELRAVVATSSL 336
|
|
| DEADc_DDX28 |
cd17948 |
DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box ... |
105-269 |
2.12e-07 |
|
DEAD-box helicase domain of DEAD box protein 28; DDX28 (also called mitochondrial DEAD-box polypeptide 28) plays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function. DDX28 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: 350706 [Multi-domain] Cd Length: 231 Bit Score: 54.29 E-value: 2.12e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 105 VLEGKNLVYSAPTSAGKTLVAELLILKRVLEMRKK---------ALFILPFVSVAKEKKYYLQSLFQEVGIKVDGYMGST 175
Cdd:cd17948 24 ILRGRNTLCAAETGSGKTLTYLLPIIQRLLRYKLLaegpfnaprGLVITPSRELAEQIGSVAQSLTEGLGLKVKVITGGR 103
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 176 SPSR----HFSSLDIAVCTIeranGLINRLIEEN--KMDLLGMVVVDELH-MLGDShrgyLLELLLtkicYITRKS--AS 246
Cdd:cd17948 104 TKRQirnpHFEEVDILVATP----GALSKLLTSRiySLEQLRHLVLDEADtLLDDS----FNEKLS----HFLRRFplAS 171
|
170 180
....*....|....*....|...
gi 139394648 247 CQADLASSLSNAVQIVGMSATLP 269
Cdd:cd17948 172 RRSENTDGLDPGTQLVLVSATMP 194
|
|
| DEXHc_Mtr4-like |
cd18024 |
DEXH-box helicase domain of ATP-dependent RNA helicase Mtr4; Mtr4 (also known as DOB1 or ... |
114-288 |
2.81e-07 |
|
DEXH-box helicase domain of ATP-dependent RNA helicase Mtr4; Mtr4 (also known as DOB1 or SKIV2L2) is a type II DEAD box helicase that plays a role in the processing of structured RNAs, including the maturation of 5.8S ribosomal RNA (rRNA)and is part of the TRAMP complex that is involved in exosome-mediated degradation of aberrant RNAs. Mtr4 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: 350782 [Multi-domain] Cd Length: 205 Bit Score: 53.60 E-value: 2.81e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 114 SAPTSAGKTLVAELLILKrVLEMRKKALFILPFVSVAKEKKYYLQSLFQEVGIKVdgymGSTSPSRHFSSLdiaVCTIER 193
Cdd:cd18024 53 SAHTSAGKTVVAEYAIAQ-SLRDKQRVIYTSPIKALSNQKYRELQEEFGDVGLMT----GDVTINPNASCL---VMTTEI 124
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 194 ANGLINRLIEenKMDLLGMVVVDELHMLGDSHRGYLLE--LLLtkicyitrksascqadlassLSNAVQIVGMSATLPNL 271
Cdd:cd18024 125 LRSMLYRGSE--IMREVAWVIFDEIHYMRDKERGVVWEetIIL--------------------LPDKVRYVFLSATIPNA 182
|
170 180
....*....|....*....|....
gi 139394648 272 ELVASWLnAELYH-------TDFR 288
Cdd:cd18024 183 RQFAEWI-CKIHKqpchvvyTDYR 205
|
|
| DEXHc_Hrq1-like |
cd17923 |
DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a ... |
96-270 |
4.52e-07 |
|
DEAH-box helicase domain of Hrq1 and similar proteins; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. Hrq1 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: 350681 [Multi-domain] Cd Length: 182 Bit Score: 52.20 E-value: 4.52e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 96 QAECLLLgqVLEGKNLVYSAPTSAGKTLVAELLILKRVL-EMRKKALFILPFVSVAKEKKYYLQSLFQEV--GIKVDGYM 172
Cdd:cd17923 5 QAEAIEA--ARAGRSVVVTTGTASGKSLCYQLPILEALLrDPGSRALYLYPTKALAQDQLRSLRELLEQLglGIRVATYD 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 173 GSTSPSrhfssldiavctiERANGLIN--RLIEEN-KM-------------DLLGM---VVVDELHM----LGdSHRGYL 229
Cdd:cd17923 83 GDTPRE-------------ERRAIIRNppRILLTNpDMlhyallphhdrwaRFLRNlryVVLDEAHTyrgvFG-SHVALL 148
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 139394648 230 LELLLtkicyitrksascqaDLASSLSNAVQIVGMSATLPN 270
Cdd:cd17923 149 LRRLR---------------RLCRRYGADPQFILTSATIGN 174
|
|
| SF2_C_Hrq |
cd18797 |
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ... |
413-495 |
1.46e-06 |
|
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350184 [Multi-domain] Cd Length: 146 Bit Score: 49.95 E-value: 1.46e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 413 VAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIRTpifgGRPLDILTYKQMVGRAGRKGVDTVgeS 492
Cdd:cd18797 69 VASYRAGYLAEDRREIEAELFNGELLGVVATNALELGIDIGGLDAVVLA----GYPGSLASLWQQAGRAGRRGKDSL--V 142
|
...
gi 139394648 493 ILI 495
Cdd:cd18797 143 ILV 145
|
|
| DEXHc_RLR |
cd18036 |
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
106-269 |
7.32e-06 |
|
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) 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: 350794 [Multi-domain] Cd Length: 204 Bit Score: 49.40 E-value: 7.32e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 106 LEGKNLVYSAPTSAGKTLVAeLLILKRVLEMRKKA------LFILPFVSVAKEKKYYLQSLFqEVGIKVDGYMGSTSPSR 179
Cdd:cd18036 15 LRGKNTIICAPTGSGKTRVA-VYICRHHLEKRRSAgekgrvVVLVNKVPLVEQQLEKFFKYF-RKGYKVTGLSGDSSHKV 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 180 HFSSL----DIAVCTierANGLINRLIEENKMDLL-----GMVVVDELHMLGDSHRGYLLELLLTKicyitrKSASCQAD 250
Cdd:cd18036 93 SFGQIvkasDVIICT---PQILINNLLSGREEERVylsdfSLLIFDECHHTQKEHPYNKIMRMYLD------KKLSSQGP 163
|
170
....*....|....*....
gi 139394648 251 LAsslsnavQIVGMSATLP 269
Cdd:cd18036 164 LP-------QILGLTASPG 175
|
|
| DNA_polA_I_Bacillus_like_exo |
cd06140 |
inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and ... |
1900-2085 |
1.24e-05 |
|
inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases; Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.
Pssm-ID: 176652 [Multi-domain] Cd Length: 178 Bit Score: 48.03 E-value: 1.24e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 1900 VVGLAVcWGGRDAYYFSLQKEQKHSEISASLVppsldpsltlkdrmwylqsclrkeSDKECSVVIYDFIQSYkILLLSCG 1979
Cdd:cd06140 22 IIGLAL-ANGGGAYYIPLELALLDLAALKEWL------------------------EDEKIPKVGHDAKRAY-VALKRHG 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 1980 ISLEQSYEDPKVACWLLDPDSQEPTLHSIVTSFLPHELPLLEGmETSQGIQSLGLNAG--SEHSGRyRASVesilIFNSM 2057
Cdd:cd06140 76 IELAGVAFDTMLAAYLLDPTRSSYDLADLAKRYLGRELPSDEE-VYGKGAKFAVPDEEvlAEHLAR-KAAA----IARLA 149
|
170 180
....*....|....*....|....*...
gi 139394648 2058 NQLNSLLQKENLQDVFRKVEMPSQYCLA 2085
Cdd:cd06140 150 PKLEEELEENEQLELYYEVELPLAEVLA 177
|
|
| SF2_C_RecQ |
cd18794 |
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ... |
329-485 |
1.97e-05 |
|
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. 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: 350181 [Multi-domain] Cd Length: 134 Bit Score: 46.43 E-value: 1.97e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 329 LCYETICDNH---SVLLFCPSKKWCEKLADiiarefynlhhqaeglvkpsecppvileqkellevmdQLRRLpsGLDSvl 405
Cdd:cd18794 19 DLLKRIKVEHlggSGIIYCLSRKECEQVAA-------------------------------------RLQSK--GISA-- 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 406 qktvpwgvAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPArrviIRTPIFGGRPLDILTYKQMVGRAGRKG 485
Cdd:cd18794 58 --------AAYHAGLEPSDRRDVQRKWLRDKIQVIVATVAFGMGIDKPD----VRFVIHYSLPKSMESYYQESGRAGRDG 125
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
90-267 |
2.28e-05 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 46.90 E-value: 2.28e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 90 KKMFEWQAECL--LLGQVLEG-KNLVYSAPTSAGKTLVAeLLILKRVLE--MRKKALFILPFVSVAKekkyylQSL--FQ 162
Cdd:pfam04851 2 LELRPYQIEAIenLLESIKNGqKRGLIVMATGSGKTLTA-AKLIARLFKkgPIKKVLFLVPRKDLLE------QALeeFK 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 163 EVGIKVDGYMGSTSPSRHFSSLD---IAVCTIERANGLINRLIEENKMDLLGMVVVDElhmlgdSHRGyllellltkicy 239
Cdd:pfam04851 75 KFLPNYVEIGEIISGDKKDESVDdnkIVVTTIQSLYKALELASLELLPDFFDVIIIDE------AHRS------------ 136
|
170 180
....*....|....*....|....*...
gi 139394648 240 itrkSASCQADLASSLSNAVQIvGMSAT 267
Cdd:pfam04851 137 ----GASSYRNILEYFKPAFLL-GLTAT 159
|
|
| SF2_C_LHR |
cd18796 |
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
413-485 |
3.74e-05 |
|
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases. LHR family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350183 [Multi-domain] Cd Length: 150 Bit Score: 46.10 E-value: 3.74e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 139394648 413 VAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPA-RRVI-IrtpifgGRPLDILTYKQMVGRAGRKG 485
Cdd:cd18796 71 IALHHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIGDvDLVIqI------GSPKSVARLLQRLGRSGHRP 139
|
|
| PRK11057 |
PRK11057 |
ATP-dependent DNA helicase RecQ; Provisional |
413-485 |
5.30e-05 |
|
ATP-dependent DNA helicase RecQ; Provisional
Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 48.56 E-value: 5.30e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 139394648 413 VAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIRTPIfggrPLDILTYKQMVGRAGRKG 485
Cdd:PRK11057 263 AAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDI----PRNIESYYQETGRAGRDG 331
|
|
| DNA_pol_A_pol_I_A |
cd08642 |
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ... |
2309-2407 |
6.49e-05 |
|
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and DNA polymerase activity to fill in the resulting gap. A combination of phylogenomic and signature sequence-based (or phonetic) approaches is used to understand the evolutionary relationships among bacteria. DNA polymerase I is one of the conserved proteins that is used to search for protein signatures. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains.
Pssm-ID: 176479 [Multi-domain] Cd Length: 378 Bit Score: 48.00 E-value: 6.49e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 2309 PFSIS--MRHAFVPFPGGSILAADYSQLELRILAHLSHDRRLIQVLNTGADVFRSIAAewKM----IEPESVGDDLRQQA 2382
Cdd:cd08642 153 PDVLSqlIRTAFIPSEGHRFIVSDFSAIEARVIAWLAGEQWRLDVFATHGKIYEASAS--QMfgvpVEKIGKNSHLRQKG 230
|
90 100 110
....*....|....*....|....*....|...
gi 139394648 2383 K--------QICYGIIYGMGAKslgeQMGIKEN 2407
Cdd:cd08642 231 KvaelalgyGGSVGALKAMGAL----EMGLTED 259
|
|
| DEXHc_RIG-I_DDX58 |
cd18073 |
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called ... |
90-268 |
1.10e-04 |
|
DEXH-box helicase domain of RIG-I; RIG-I (Retinoic acid-inducible gene I protein), also called DEAD box protein 58 (DDX58), is a pathogen-recognition receptor that recognizes viral 5'-triphosphates carrying double-stranded RNA. Upon binding to these microbe-associated molecular patterns (MAMPs), RIG-I forms oligomers and promotes downstream processes that result in type I interferon production and induction of an antiviral state. The optimal ligand for RIG-I has been found to be base-paired or double-stranded RNA (dsRNA) molecules containing a 5' triphosphate (5'-ppp-dsRNA). RIG-I contains two N-terminal caspase activation and recruitment domains (CARDs), which are required for interaction with IPS-1, a superfamily 2 helicase/translocase/ATPase (SF2) domain and a C-terminal regulatory/repressor domain (RD). RIG-I 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: 350831 [Multi-domain] Cd Length: 202 Bit Score: 45.58 E-value: 1.10e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 90 KKMFEWQAEclLLGQVLEGKNLVYSAPTSAGKTLVAeLLI----LKRVLEMRK-KALFILPFVSVAKEKKYYLQSLFQEV 164
Cdd:cd18073 1 FKPRNYQLE--LALPAMKGKNTIICAPTGCGKTFVS-LLIcehhLKKFPQGQKgKVVFFATKVPVYEQQKSVFSKYFERH 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 165 GIKVDGYMGSTSPSRHFSSL----DIAVCTierANGLINRLI--EENKMDLLGMVVVDELHMLGDSHRgylLELLLTKic 238
Cdd:cd18073 78 GYRVTGISGATAENVPVEQIiennDIIILT---PQILVNNLKkgTIPSLSIFTLMIFDECHNTSGNHP---YNMIMFR-- 149
|
170 180 190
....*....|....*....|....*....|
gi 139394648 239 YITRKsascqadLASSLSNAVQIVGMSATL 268
Cdd:cd18073 150 YLDQK-------LGGSSGPLPQIIGLTASV 172
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
439-496 |
1.77e-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: 41.92 E-value: 1.77e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 139394648 439 VLAATSTLSSGVNLP-ARRVIIRTPIFGGRpldilTYKQMVGRAGRKGvDTVGESILIC 496
Cdd:cd18785 25 ILVATNVLGEGIDVPsLDTVIFFDPPSSAA-----SYIQRVGRAGRGG-KDEGEVILFV 77
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
106-219 |
2.87e-04 |
|
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350685 [Multi-domain] Cd Length: 201 Bit Score: 44.35 E-value: 2.87e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 106 LEGKNLVYSAPTSAGKTLVAeLLILKRVLEM-----RKKALFILPFVSVAKEKKYYLQSLFQEVGIKVDGYMGSTSPS-- 178
Cdd:cd17927 15 LKGKNTIICLPTGSGKTFVA-VLICEHHLKKfpagrKGKVVFLANKVPLVEQQKEVFRKHFERPGYKVTGLSGDTSENvs 93
|
90 100 110 120
....*....|....*....|....*....|....*....|....*
gi 139394648 179 --RHFSSLDIAVCTierANGLINRLIEENKMDL--LGMVVVDELH 219
Cdd:cd17927 94 veQIVESSDVIIVT---PQILVNDLKSGTIVSLsdFSLLVFDECH 135
|
|
| SF2_C_suv3 |
cd18805 |
C-terminal helicase domain of ATP-dependent RNA helicase; The SUV3 (suppressor of Var 3) gene ... |
439-485 |
3.06e-04 |
|
C-terminal helicase domain of ATP-dependent RNA helicase; The SUV3 (suppressor of Var 3) gene encodes a DNA and RNA helicase, which is localized in mitochondria and is a subunit of the degradosome complex involved in regulation of RNA surveillance and turnover. SUV3 exhibits DNA and RNA-dependent ATPase, DNA and RNA-binding and DNA and RNA unwinding activities. SUV3 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: 350192 [Multi-domain] Cd Length: 135 Bit Score: 42.93 E-value: 3.06e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 139394648 439 VLAATSTLSSGVNLPARRVIIRTPI-FGGRPLDILT---YKQMVGRAGRKG 485
Cdd:cd18805 73 VLVASDAIGMGLNLNIRRVIFSSLSkFDGNEMRPLSpseVKQIAGRAGRFG 123
|
|
| DEXHc_SKIV2L |
cd18027 |
DEXH-box helicase domain of SKIV2L; Superkiller viralicidic activity 2-like (SKIV2L, also ... |
106-278 |
3.48e-04 |
|
DEXH-box helicase domain of SKIV2L; Superkiller viralicidic activity 2-like (SKIV2L, also called SKI2 or DHX13) plays a role in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. SKIV2L 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: 350785 [Multi-domain] Cd Length: 179 Bit Score: 43.79 E-value: 3.48e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 106 LEGKNLVY-SAPTSAGKTLVAELLILKRVLEMrKKALFILPFVSVAKEKKYYLQSLFQEVGIKVDGYMGSTSPSRHFSSL 184
Cdd:cd18027 20 LEAGDSVFvAAHTSAGKTVVAEYAIALAQKHM-TRTIYTSPIKALSNQKFRDFKNTFGDVGLITGDVQLNPEASCLIMTT 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 185 DIAVCTIERANGLInRLIEenkmdllgMVVVDELHMLGDSHRGYLLELLLTKicyitrksascqadlassLSNAVQIVGM 264
Cdd:cd18027 99 EILRSMLYNGSDVI-RDLE--------WVIFDEVHYINDAERGVVWEEVLIM------------------LPDHVSIILL 151
|
170
....*....|....
gi 139394648 265 SATLPNLELVASWL 278
Cdd:cd18027 152 SATVPNTVEFADWI 165
|
|
| DEXHc_dicer |
cd18034 |
DEXH-box helicase domain of endoribonuclease Dicer; Dicer ribonucleases cleave double-stranded ... |
109-266 |
9.13e-04 |
|
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: 43.02 E-value: 9.13e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 109 KNLVYSAPTSAGKTLVAELLIlKRVLEM-------RKKALFILPFVSVAKEKKYYLQslfQEVGIKVDGYMGSTSPS--- 178
Cdd:cd18034 17 RNTIVVLPTGSGKTLIAVMLI-KEMGELnrkeknpKKRAVFLVPTVPLVAQQAEAIR---SHTDLKVGEYSGEMGVDkwt 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 179 -----RHFSSLDIAVCTierANGLINRLIEEN-KMDLLGMVVVDELHMLGDSH--RgyllelLLTKICYITRKSASCQad 250
Cdd:cd18034 93 kerwkEELEKYDVLVMT---AQILLDALRHGFlSLSDINLLIFDECHHATGDHpyA------RIMKEFYHLEGRTSRP-- 161
|
170
....*....|....*.
gi 139394648 251 lasslsnavQIVGMSA 266
Cdd:cd18034 162 ---------RILGLTA 168
|
|
| DEXQc_Suv3 |
cd17913 |
DEXQ-box helicase domain of Suv3; Suppressor of var1 3-like protein (Suv3) is a DNA/RNA ... |
116-228 |
1.03e-03 |
|
DEXQ-box helicase domain of Suv3; Suppressor of var1 3-like protein (Suv3) is a DNA/RNA unwinding enzyme belonging to the class of DexH-box helicases. It localizes predominantly in the mitochondria, where it forms an RNA-degrading complex called mitochondrial degradosome (mtEXO) with exonuclease PNP (polynucleotide phosphorylase), that degrades 3' overhang double-stranded RNA with a 3'-to-5' directionality in an ATP-dependent manner. Suv3 plays a role in the RNA surveillance system in mitochondria; it regulates the stability of mature mRNAs, the removal of aberrantly formed mRNAs and the rapid degradation of non coding processing intermediates. It also confers salinity and drought stress tolerance by maintaining both photosynthesis and antioxidant machinery, probably via an increase in plant hormone levels such as gibberellic acid (GA3), the cytokinin zeatin (Z), and indole-3-acetic acid (IAA). Suv3 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: 350671 [Multi-domain] Cd Length: 142 Bit Score: 41.77 E-value: 1.03e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 116 PTSAGKTLVAelliLKRvLEMRKKALFILPFVSVAKEkkyyLQSLFQEVGIKVDGYMG----STSPSRHFSsldiavCTI 191
Cdd:cd17913 9 PTNSGKTYHA----LQR-LKSAKSGVYCGPLRLLAWE----VYERLNAEGVPCDLVTGqerrEVEGATHVS------CTV 73
|
90 100 110
....*....|....*....|....*....|....*..
gi 139394648 192 ERANglINRLIEenkmdllgMVVVDELHMLGDSHRGY 228
Cdd:cd17913 74 EMAS--ISEPYD--------VAVIDEIQMIGDPQRGW 100
|
|
| cas3_core |
TIGR01587 |
CRISPR-associated helicase Cas3; This model represents the highly conserved core region of an ... |
111-271 |
1.17e-03 |
|
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: 43.98 E-value: 1.17e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 111 LVYSAPTSAGKTLVAeLLILKRVLEMRK--KALFILPFVSVAKEKKYYLQSLFqevGIKVDGYMGSTSPSRHFSSLD--- 185
Cdd:TIGR01587 2 LVIEAPTGYGKTEAA-LLWALHSIKSQKadRVIIALPTRATINAMYRRAKELF---GSELVGLHHSSSFSRIKEMGDsee 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 186 -------------------IAVCTIERANGLINRLIEENKMDLLGM----VVVDELHMLGDSHRGYLLELLltkicyitr 242
Cdd:TIGR01587 78 fehlfplyihsndklfldpITVCTIDQVLKSVFGEFGHYEFTLASIanslLIFDEVHFYDEYTLALILAVL--------- 148
|
170 180
....*....|....*....|....*....
gi 139394648 243 ksaSCQADlasslsNAVQIVGMSATLPNL 271
Cdd:TIGR01587 149 ---EVLKD------NDVPILLMSATLPKF 168
|
|
| RecQ |
COG0514 |
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
413-485 |
1.30e-03 |
|
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 43.98 E-value: 1.30e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 139394648 413 VAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPArrviIRTPIFGGRPLDILTYKQMVGRAGRKG 485
Cdd:COG0514 257 AAAYHAGLDAEEREANQDRFLRDEVDVIVATIAFGMGIDKPD----VRFVIHYDLPKSIEAYYQEIGRAGRDG 325
|
|
| DEXHc_RLR-3 |
cd18075 |
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of ... |
106-219 |
1.66e-03 |
|
DEXH-box helicase domain of RLR-3; RIG-I-like receptor 3 (RLR-3, also known as laboratory of genetics and physiology 2 or LGP2 and DHX58) appears to positively and negatively regulate MDA5 and RIG-I signaling, respectively. RLR-3 resembles a chimera combining a MDA5-like helicase domain and RIG-I like CTD supporting both stem and end binding. RNA binding is required for RLR-3-mediated enhancement of MDA5 activation. RLR-3 end-binding may promote nucleation of MDA5 oligomerization on dsRNA. RLR-3 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: 350833 [Multi-domain] Cd Length: 200 Bit Score: 42.15 E-value: 1.66e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 106 LEGKNLVYSAPTSAGKTLVAeLLILKRVLEMRKKALfilpfVSVAKEKKYYL-QSLFQEVGIKVDGYM-----GSTSPSR 179
Cdd:cd18075 15 LRGKNSIIWLPTGAGKTRAA-VYVARRHLETKRGAK-----VAVLVNKVHLVdQHLEKEFHVLLDKYTvtaisGDSSHKC 88
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 139394648 180 HFSSL----DIAVCTIERANGLINRLIEENKMDL--LGMVVVDELH 219
Cdd:cd18075 89 FFGQLargsDVVICTAQILQNALLSGEEEAHVELtdFSLLVIDECH 134
|
|
| PTZ00424 |
PTZ00424 |
helicase 45; Provisional |
417-505 |
2.31e-03 |
|
helicase 45; Provisional
Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 42.89 E-value: 2.31e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 417 HAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIRTPIfggrPLDILTYKQMVGRAGRKGVDTVGESILIC 496
Cdd:PTZ00424 298 HGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDL----PASPENYIHRIGRSGRFGRKGVAINFVTP 373
|
....*....
gi 139394648 497 KNSEKSKGI 505
Cdd:PTZ00424 374 DDIEQLKEI 382
|
|
| DEXHc_HrpB |
cd17990 |
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA ... |
107-280 |
2.51e-03 |
|
DEXH-box helicase domain of ATP-dependent helicase HrpB; HrpB is part of the HrpB-HrpA two-partner secretion (TPS) system, a secretion pathway important to the secretion of large virulence-associated proteins. HrpB belongs to 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: 438711 [Multi-domain] Cd Length: 174 Bit Score: 41.16 E-value: 2.51e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 107 EGKNLVYSAPTSAGKTLVAELLILKRVLEMRKKALFILPFVSVAKEKKYYLQSLFQE-----VGIKVDGYMGSTSPSRhf 181
Cdd:cd17990 16 AGGQVVLEAPPGAGKTTRVPLALLAELWIAGGKIIVLEPRRVAARAAARRLATLLGEapgetVGYRVRGESRVGRRTR-- 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 182 ssldIAVCTieraNG-LINRLIEENKMDLLGMVVVDELHmlgdsHRGYLLELLLtkicyitrksASCqADLASSLSNAVQ 260
Cdd:cd17990 94 ----VEVVT----EGvLLRRLQRDPELSGVGAVILDEFH-----ERSLDADLAL----------ALL-LEVQQLLRDDLR 149
|
170 180
....*....|....*....|
gi 139394648 261 IVGMSATLPNLELVASWLNA 280
Cdd:cd17990 150 LLAMSATLDGDGLAALLPEA 169
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
112-222 |
4.85e-03 |
|
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: 39.98 E-value: 4.85e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 112 VYSAPTSAGKTLVAELLILKRvleMRKKALFILPFVSVA---KEKkyylqsLFQEVGIKVDGYMGSTSpSRHFSSLDIAV 188
Cdd:cd17926 22 ILVLPTGSGKTLTALALIAYL---KELRTLIVVPTDALLdqwKER------FEDFLGDSSIGLIGGGK-KKDFDDANVVV 91
|
90 100 110
....*....|....*....|....*....|....*.
gi 139394648 189 CTIErangLINRLIEENKM--DLLGMVVVDELHMLG 222
Cdd:cd17926 92 ATYQ----SLSNLAEEEKDlfDQFGLLIVDEAHHLP 123
|
|
| SrmB |
COG0513 |
Superfamily II DNA and RNA helicase [Replication, recombination and repair]; |
75-279 |
5.75e-03 |
|
Superfamily II DNA and RNA helicase [Replication, recombination and repair];
Pssm-ID: 440279 [Multi-domain] Cd Length: 420 Bit Score: 41.67 E-value: 5.75e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 75 GLPKAVLEKYHSFGVKKMFEWQAECLLLgqVLEGKNLVYSAPTSAGKTLvAELL-ILKRVLEMRKK---ALFILP----F 146
Cdd:COG0513 8 GLSPPLLKALAELGYTTPTPIQAQAIPL--ILAGRDVLGQAQTGTGKTA-AFLLpLLQRLDPSRPRapqALILAPtrelA 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 147 VSVAKEkkyyLQSLFQEVGIKVDGYMGSTSPSRHFSSL----DIAVCTIERangLINrLIEENKMDL--LGMVVVDE--- 217
Cdd:COG0513 85 LQVAEE----LRKLAKYLGLRVATVYGGVSIGRQIRALkrgvDIVVATPGR---LLD-LIERGALDLsgVETLVLDEadr 156
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 139394648 218 -LHMlgdshrGYLLEllLTKIcyitrksascqadlASSLSNAVQIVGMSATLPN--LELVASWLN 279
Cdd:COG0513 157 mLDM------GFIED--IERI--------------LKLLPKERQTLLFSATMPPeiRKLAKRYLK 199
|
|
| DEXHc_RecQ |
cd17920 |
DEXH-box helicase domain of RecQ family proteins; The RecQ family of the type II DEAD box ... |
105-221 |
9.19e-03 |
|
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: 39.83 E-value: 9.19e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 105 VLEGKNLVYSAPTSAGKTLVAEL--LILKRVlemrkkALFILPFVSVAKEKKYYLQSLfqevGIKVDgYMGSTSPSRHFS 182
Cdd:cd17920 24 VLAGRDVLVVMPTGGGKSLCYQLpaLLLDGV------TLVVSPLISLMQDQVDRLQQL----GIRAA-ALNSTLSPEEKR 92
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|
gi 139394648 183 SLDIAV---------CTIERA--NGLINRLIEENKMDLLGMVVVDELHML 221
Cdd:cd17920 93 EVLLRIkngqykllyVTPERLlsPDFLELLQRLPERKRLALIVVDEAHCV 142
|
|
| DEADc_DDX55 |
cd17960 |
DEAD-box helicase domain of DEAD box protein 55; DDX55 is a member of the DEAD-box helicases, ... |
86-217 |
9.53e-03 |
|
DEAD-box helicase domain of DEAD box protein 55; DDX55 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: 350718 [Multi-domain] Cd Length: 202 Bit Score: 39.87 E-value: 9.53e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 139394648 86 SFGVKKMFEWQAECLLLgqVLEGKNLVYSAPTSAGKTL-----VAELLiLKRVLEMRKK---ALFILPFVSVAKEKKYYL 157
Cdd:cd17960 7 ELGFTSMTPVQAATIPL--FLSNKDVVVEAVTGSGKTLaflipVLEIL-LKRKANLKKGqvgALIISPTRELATQIYEVL 83
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 139394648 158 QSLFQEVGIKVDG--YMGSTSPSRHFSSL-----DIAVCTIERANGLINRLIEENKMDLLGMVVVDE 217
Cdd:cd17960 84 QSFLEHHLPKLKCqlLIGGTNVEEDVKKFkrngpNILVGTPGRLEELLSRKADKVKVKSLEVLVLDE 150
|
|
| |
