|
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 ... |
1668-2053 |
3.04e-153 |
|
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: 477.49 E-value: 3.04e-153
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1668 GFPAQKQRLQQLYQRMVAVMKKVETKIYEqhgsrfnlgssqavakvlglhrkakgrvTTSRQVLEKLN--SPISHLILGY 1745
Cdd:cd08638 1 GIGFDPEELERQRALLQAKLKELEEEAYR----------------------------STSKEVLEQLKrlHPLPKLILEY 52
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1746 RKLSGLLAKSIQPLMECC------QADRIHGQSI-TYTATGRISMTEPNLQNVAKEFSIQV--------GSDVVHISCRS 1810
Cdd:cd08638 53 RKLSKLLTTYVEPLLLLCklssslQMYRIHPTWNqTGTATGRLSSSEPNLQNVPKDFEIKDapsppagsEGDIPTISLRH 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1811 PFMPTdESRCLLSADFCQLEMRILAHMSQDKALLEVMKSSQDLFIAIAAHWNKIEESEVTQDLRNSTKQVCYGIVYGMGM 1890
Cdd:cd08638 133 AFIPP-PGRVLLSADYSQLELRILAHLSGDPALIELLNSGGDVFKMIAAQWLGKPVEEVTDEERQQAKQLVYGILYGMGA 211
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1891 RSLAESLNCSEQEARMISDQFHQAYKGIRDYTTRVVNFARSKGFVETITGRRRYLENINSDVEHLKNQAERQAVNSTIQG 1970
Cdd:cd08638 212 KSLAEQLGVSEEEAKQFIESFKNAYPGVRRFIRETIERARRNGFVETLTGRRRYLPEINSGNSSERAQAERQAVNTVIQG 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1971 SAADIAKNAILKMEKNIERYREKLALGDnsVDLVMHLHDELIFEVPTGKAKKIAKVLSLTMENCVKLSVPLKVKLRIGRS 2050
Cdd:cd08638 292 SAADIMKIAMINIHEKLHSLLPNLPAGR--ARLVLQIHDELLFEVPESDVDEVARIIKRSMENAAKLSVPLPVKVSIGKS 369
|
...
gi 17933644 2051 WGE 2053
Cdd:cd08638 370 WGS 372
|
|
| DNA_pol_A |
pfam00476 |
DNA polymerase family A; |
1687-2053 |
2.05e-127 |
|
DNA polymerase family A;
Pssm-ID: 459825 Cd Length: 368 Bit Score: 405.28 E-value: 2.05e-127
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1687 MKKVETKIYEQHGSRFNLGSSQAVAKVL----GLH--RKAKGRVTTSRQVLEKLNS---PISHLILGYRKLSGLLAKSIQ 1757
Cdd:pfam00476 3 LKELEQEIYELAGEEFNINSPKQLGEILfeklGLPpgKKTKTGYSTDAEVLEKLAAdehPIPKLILEYRQLAKLKSTYVD 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1758 PLMECCQAD--RIHGQ-SITYTATGRISMTEPNLQN--VAKEFSIQVgsdvvhiscRSPFMPTDESrCLLSADFCQLEMR 1832
Cdd:pfam00476 83 ALPKLINPDtgRIHTSfNQTVTATGRLSSSDPNLQNipIRTEEGRRI---------RKAFVAEPGW-VLLSADYSQIELR 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1833 ILAHMSQDKALLEVMKSSQDLFIAIAAHWNKIEESEVTQDLRNSTKQVCYGIVYGMGMRSLAESLNCSEQEARMISDQFH 1912
Cdd:pfam00476 153 ILAHLSGDENLIEAFRNGEDIHTATASEVFGVPLEEVTPEQRRRAKAINFGIIYGMSAFGLAQQLGISRKEAKEYIDRYF 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1913 QAYKGIRDYTTRVVNFARSKGFVETITGRRRYLENINSDVEHLKNQAERQAVNSTIQGSAADIAKNAILKMEKNIERYRE 1992
Cdd:pfam00476 233 ERYPGVKEYMEETVEEAREKGYVETLLGRRRYLPDINSSNRNLRSFAERAAINAPIQGSAADIIKLAMIRVDEALKEEGL 312
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17933644 1993 KlalgdnsVDLVMHLHDELIFEVPTGKAKKIAKVLSLTMENC--VKLSVPLKVKLRIGRSWGE 2053
Cdd:pfam00476 313 K-------ARLLLQVHDELVFEVPEEEVEEVAALVKEEMENEnaVKLSVPLKVDVGIGKNWGE 368
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
216-779 |
8.07e-118 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 384.25 E-value: 8.07e-118
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 216 LPMSIQAEYKKKGVVDMFDWQVECLskPRLLFEHCNLVYSAPTSAGKTLVSEILMLKTvLERGKKVLLILPFISVVREKM 295
Cdd:COG1204 7 PLEKVIEFLKERGIEELYPPQAEAL--EAGLLEGKNLVVSAPTASGKTLIAELAILKA-LLNGGKALYIVPLRALASEKY 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 296 FYMQDLLTPAGYRVEGFYGGYTPPGG-FESLHVAICTIEKANSIVNKlmEQGKLETIGMVVVDEVHLISDKGRGYILELL 374
Cdd:COG1204 84 REFKRDFEELGIKVGVSTGDYDSDDEwLGRYDILVATPEKLDSLLRN--GPSWLRDVDLVVVDEAHLIDDESRGPTLEVL 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 375 LAKIlymsRRNGLQIQVITMSATLENVQLLQSWLDAELYITNYRPVALKEmikvGtVIYDHRLKLVRdvakqkvllkGLE 454
Cdd:COG1204 162 LARL----RRLNPEAQIVALSATIGNAEEIAEWLDAELVKSDWRPVPLNE----G-VLYDGVLRFDD----------GSR 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 455 NDSDDVALLCIETLLEGCSVIVFCPSKDWCENLAVQLATAIhvqiksetvlgQRLRTNLNPRAIAEVKQQLRDI--PTGL 532
Cdd:COG1204 223 RSKDPTLALALDLLEEGGQVLVFVSSRRDAESLAKKLADEL-----------KRRLTPEEREELEELAEELLEVseETHT 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 533 DGVMSKAITYACAFHHAGLTTEERDIIEASFKAGALKVLVATSTLSSGVNLPARRVLIRSP-LFGGKQMSSLTYRQMIGR 611
Cdd:COG1204 292 NEKLADCLEKGVAFHHAGLPSELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRDTkRGGMVPIPVLEFKQMAGR 371
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 612 AGRMGKDTLGESILICN---EINARMGRdLVVSELQPITSCLDMDGSthLKRALLEVISSGVANTKEDIDFFVNCTLLSA 688
Cdd:COG1204 372 AGRPGYDPYGEAILVAKssdEADELFER-YILGEPEPIRSKLANESA--LRTHLLALIASGFANSREELLDFLENTFYAY 448
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 689 QKafhakekppDEESDANYINDALDFLVEYEFVrlqrneERETAVYVATRLGAACLASSMPPTDGLILFAELQKSRRSFv 768
Cdd:COG1204 449 QY---------DKGDLEEVVDDALEFLLENGFI------EEDGDRLRATKLGKLVSRLYIDPLTAAELVDGLRKADEEF- 512
|
570
....*....|.
gi 17933644 769 leSELHAVYLV 779
Cdd:COG1204 513 --TDLGLLHLI 521
|
|
| PolA |
COG0749 |
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ... |
1487-2053 |
2.22e-109 |
|
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and repair];
Pssm-ID: 440512 [Multi-domain] Cd Length: 575 Bit Score: 361.68 E-value: 2.22e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1487 ISGVSFCLADNVAYYWNMQIDERAAYqgvPTPLKVQELCNLMARKDLTLVMHDGKEQLKMLRKAIPQLKRIsakLEDAKV 1566
Cdd:COG0749 20 LVGISFAVEPGEAAYIPLAHGAPEQL---DLDEVLAALKPLLEDPAIPKIGQNLKYDLHVLARYGIELAGV---AFDTML 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1567 ANWLLQPDKT-VNFLNMCQTF-APECTGLANLCGSGRGYSSYGLDTSSAILPRIrtAIESCVTLHILQGQTENLSRIGng 1644
Cdd:COG0749 94 ASYLLNPGRRrHGLDDLAERYlGHETISYEELAGKGKKQLTFDQVPLEEAAEYA--AEDADITLRLHEVLKPELEEEG-- 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1645 dLLKFFHDIEMPIQLTLCQMELVGFPAQKQRLQQLYQRMVAVMKKVETKIYEQHGSRFNLGSSQAVAKVL----GL--HR 1718
Cdd:COG0749 170 -LLKLYEEIELPLVPVLARMERNGILVDRELLAELSAELAKRLAELEQEIYELAGEEFNLNSPKQLGEILfeklGLpvGK 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1719 KAKGRVTTSRQVLEKL--NSPISHLILGYRKLSGLlaKS--IQPLMECCQAD--RIHGqsiTY----TATGRISMTEPNL 1788
Cdd:COG0749 249 KTKTGYSTDAEVLEKLaeDHPIPALILEYRQLSKL--KStyVDALPKLINPDtgRIHT---SFnqtvTATGRLSSSDPNL 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1789 QN--VAKEFSIQVgsdvvhiscRSPFMPTDESrCLLSADFCQLEMRILAHMSQDKALLEVMKSSQDLFIAIAAHWNKIEE 1866
Cdd:COG0749 324 QNipIRTEEGRRI---------RKAFVAPEGY-VLLSADYSQIELRILAHLSGDEGLIEAFREGEDIHAATAAEVFGVPL 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1867 SEVTQDLRNSTKQVCYGIVYGMGMRSLAESLNCSEQEARMISDQFHQAYKGIRDYTTRVVNFARSKGFVETITGRRRYLE 1946
Cdd:COG0749 394 EEVTSEQRRRAKAINFGIIYGMSAFGLARQLGISRKEAKEYIDRYFERYPGVKDYMEETVEEAREKGYVETLFGRRRYLP 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1947 NINSDVEHLKNQAERQAVNSTIQGSAADIAKNAILKMEKNIEryREKLalgdnSVDLVMHLHDELIFEVPTGKAKKIAKV 2026
Cdd:COG0749 474 DINSSNRNRRSFAERAAINAPIQGSAADIIKLAMIRVDRALK--EEGL-----KSRMLLQVHDELVFEVPEDELEEVKEL 546
|
570 580
....*....|....*....|....*..
gi 17933644 2027 LSLTMENCVKLSVPLKVKLRIGRSWGE 2053
Cdd:COG0749 547 VKEVMENAVELSVPLVVDVGVGKNWDE 573
|
|
| PRK05755 |
PRK05755 |
DNA polymerase I; Provisional |
1487-2055 |
9.24e-108 |
|
DNA polymerase I; Provisional
Pssm-ID: 235591 [Multi-domain] Cd Length: 880 Bit Score: 367.11 E-value: 9.24e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1487 ISGVSFCLADNVAYYwnmqIDERAAYQGVPTPLKvqelcNLMARKDLTLVMHDGKEQLKMLRKAIPQLKRISaklEDAKV 1566
Cdd:PRK05755 334 LVGLSFAVEPGEAAY----IPLDQLDREVLAALK-----PLLEDPAIKKVGQNLKYDLHVLARYGIELRGIA---FDTML 401
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1567 ANWLLQPDKTVNFLNMCQTFAP-ECTGLANLCGSGRGYSSYGLDTSSAILprirtAIESCVTLHILQGQTENLsrIGNGD 1645
Cdd:PRK05755 402 ASYLLDPGRRHGLDSLAERYLGhKTISFEEVAGKQLTFAQVDLEEAAEYA-----AEDADVTLRLHEVLKPKL--LEEPG 474
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1646 LLKFFHDIEMPIQLTLCQMELVGFPAQKQRLQQLYQRMVAVMKKVETKIYEQHGSRFNLGSSQAVAKVL----GLH--RK 1719
Cdd:PRK05755 475 LLELYEEIELPLVPVLARMERNGIKVDREYLKELSAELAQRLAELEQEIYELAGEEFNINSPKQLGEILfeklGLPvgKK 554
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1720 AKGRVTTSRQVLEKL--NSPISHLILGYRKLSGLlaKS--IQPLMECCQAD--RIHGqsiTY----TATGRISMTEPNLQ 1789
Cdd:PRK05755 555 TKTGYSTDAEVLEKLadDHPIPDKILEYRQLSKL--KStyTDALPKLINPDtgRIHT---SFnqtvTATGRLSSSDPNLQ 629
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1790 N--VAKEFSIQVgsdvvhiscRSPFMPTDESrCLLSADFCQLEMRILAHMSQDKALLEVMKSSQDLFIAIAAHWNKIEES 1867
Cdd:PRK05755 630 NipIRTEEGRRI---------RKAFVAPEGY-KLLSADYSQIELRILAHLSGDEGLIEAFAEGEDIHTATASEVFGVPLE 699
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1868 EVTQDLRNSTKQVCYGIVYGMGMRSLAESLNCSEQEARMISDQFHQAYKGIRDYTTRVVNFARSKGFVETITGRRRYLEN 1947
Cdd:PRK05755 700 EVTSEQRRRAKAINFGIIYGMSAFGLAQQLGISRKEAKEYIDRYFERYPGVKEYMERTVEQAREKGYVETLFGRRRYLPD 779
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1948 INSDVEHLKNQAERQAVNSTIQGSAADIAKNAILKMEKnieryreKLALGDNSVDLVMHLHDELIFEVPTGKAKKIAKVL 2027
Cdd:PRK05755 780 INSRNGNRRAFAERAAINAPIQGSAADIIKLAMIRVDK-------ALKEEGLKSRMLLQVHDELVFEVPEDELEEVKKLV 852
|
570 580
....*....|....*....|....*...
gi 17933644 2028 SLTMENCVKLSVPLKVKLRIGRSWGEFK 2055
Cdd:PRK05755 853 KEVMENAVELSVPLVVDVGVGDNWDEAH 880
|
|
| DEXHc_POLQ-like |
cd18026 |
DEXH-box helicase domain of DNA polymerase theta; DNA polymerase theta (POLQ) is important in ... |
216-419 |
3.20e-105 |
|
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: 334.57 E-value: 3.20e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 216 LPMSIQAEYKKKGVVDMFDWQVECLSKPRLLfEHCNLVYSAPTSAGKTLVSEILMLKTVLERGKKVLLILPFISVVREKM 295
Cdd:cd18026 1 LPDAVREAYAKKGIKKLYDWQKECLSLPGLL-EGRNLVYSLPTSGGKTLVAEILMLKRLLERRKKALFVLPYVSIVQEKV 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 296 FYMQDLLTPAGYRVEGFYGGYT--PPGGFESLHVAICTIEKANSIVNKLMEQGKLETIGMVVVDEVHLISDKGRGYILEL 373
Cdd:cd18026 80 DALSPLFEELGFRVEGYAGNKGrsPPKRRKSLSVAVCTIEKANSLVNSLIEEGRLDELGLVVVDELHMLGDGHRGALLEL 159
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 17933644 374 LLAKILYMSRRNglqIQVITMSATLENVQLLQSWLDAELYITNYRP 419
Cdd:cd18026 160 LLTKLLYAAQKN---IQIVGMSATLPNLEELASWLRAELYTTNFRP 202
|
|
| DNA_pol_A_pol_I_C |
cd08637 |
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ... |
1673-2052 |
1.77e-97 |
|
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: 319.75 E-value: 1.77e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1673 KQRLQQLYQRMVAVMKKVETKIYEQHGSRFNLGSSQAVAKVL----GLH--RKAKGRVTTSRQVLEKL--NSPISHLILG 1744
Cdd:cd08637 2 TEYLEELSEELEKELAELEEEIYELAGEEFNINSPKQLGEVLfeklGLPvgKKTKTGYSTDAEVLEKLadEHPIVELILE 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1745 YRKLSGLLAKSIQPLMECCQAD--RIH---GQsiTYTATGRISMTEPNLQN--VAKEFSIQVgsdvvhiscRSPFMPtDE 1817
Cdd:cd08637 82 YRELTKLKSTYVDALPKLINPKtgRIHtsfNQ--TVTATGRLSSSDPNLQNipIRTEEGREI---------RKAFVA-EE 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1818 SRCLLSADFCQLEMRILAHMSQDKALLEVMKSSQDLFIAIAAHWNKIEESEVTQDLRNSTKQVCYGIVYGMGMRSLAESL 1897
Cdd:cd08637 150 GWVLLSADYSQIELRILAHLSGDEALIEAFKNGEDIHTRTAAEVFGVPPEEVTPEMRRIAKAVNFGIIYGISAFGLSQQL 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1898 NCSEQEARMISDQFHQAYKGIRDYTTRVVNFARSKGFVETITGRRRYLENINSDVEHLKNQAERQAVNSTIQGSAADIAK 1977
Cdd:cd08637 230 GISRKEAKEYIDRYFARYPGVKEYMEETVEEAREKGYVETLFGRRRYIPEINSKNRNVRAFAERIAINTPIQGTAADIIK 309
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17933644 1978 NAILKMEKNIERYREKlalgdnsVDLVMHLHDELIFEVPTGKAKKIAKVLSLTMENCVKLSVPLKVKLRIGRSWG 2052
Cdd:cd08637 310 LAMIRVHKALKEEGLK-------ARMLLQVHDELVFEVPEEELEEVAALVKEEMENAVELSVPLKVDVGVGKNWG 377
|
|
| pola |
TIGR00593 |
DNA polymerase I; All proteins in this family for which functions are known are DNA ... |
1536-2055 |
1.54e-96 |
|
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: 334.31 E-value: 1.54e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1536 VMHDGKEQLKML-RKAIPQLKRIsaklEDAKVANWLLQPDKTVNFLNMCQTFAPECTGLAnlcgsgrgYSSYGLDTSSAI 1614
Cdd:TIGR00593 382 IGHDAKFLMHLLkREGIELGGVI----FDTMLAAYLLDPAQVSTLDTLARRYLVEELILD--------EKIGGKLAKFAF 449
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1615 LPR---IRTAIESCVTLHILQGQTenLSRIGNGDLLKFFHDIEMPIQLTLCQMELVGFPAQKQRLQQLYQRMVAVMKKVE 1691
Cdd:TIGR00593 450 PPLeeaTEYLARRAAATKRLAEEL--LKELDENKLLSLYREIELPLSKVLAEMEKTGIKVDADYLQELSQEFGEEIADLE 527
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1692 TKIYEQHGSRFNLGSSQAVAKVL----GL--HRKAKGRVTTSRQVLEKL--NSPISHLILGYRKLSGLLAKSIQPLMECC 1763
Cdd:TIGR00593 528 EEIYELAGEEFNINSPKQLGEVLfeklGLpvGKKTKTGYSTDADVLEKLreKHPIIALILEYRQLTKLKSTYVDGLPELV 607
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1764 --QADRIHGQSI-TYTATGRISMTEPNLQN--VAKEFSIQVgsdvvhiscRSPFMPTDESrCLLSADFCQLEMRILAHMS 1838
Cdd:TIGR00593 608 npDTGRIHTTFNqTGTATGRLSSSNPNLQNipIRSEEGRKI---------RKAFVAEKGW-LLISADYSQIELRVLAHLS 677
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1839 QDKALLEVMKSSQDLFIAIAAHWNKIEESEVTQDLRNSTKQVCYGIVYGMGMRSLAESLNCSEQEARMISDQFHQAYKGI 1918
Cdd:TIGR00593 678 QDENLIEAFQNGEDIHTETASRLFGVEIEDVTPNMRRIAKTINFGVVYGMSAFGLAQELGISRKEAKEFIERYFARYPGV 757
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1919 RDYTTRVVNFARSKGFVETITGRRRYLENINSDVEHLKNQAERQAVNSTIQGSAADIAKNAILKMEKNIERYREKlalgd 1998
Cdd:TIGR00593 758 KDYIENTVEEARKKGYVETLFGRRRYIPDINSRNRNVREAAERMAINAPIQGSAADIMKIAMIKLDKRLKERKLK----- 832
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*..
gi 17933644 1999 nsVDLVMHLHDELIFEVPTGKAKKIAKVLSLTMENCVKLSVPLKVKLRIGRSWGEFK 2055
Cdd:TIGR00593 833 --ARLLLQVHDELIFEAPEEEAEEVAALVKEVMEHAYPLAVPLEVEVGTGKNWGEAK 887
|
|
| PRK02362 |
PRK02362 |
ATP-dependent DNA helicase; |
211-956 |
1.47e-84 |
|
ATP-dependent DNA helicase;
Pssm-ID: 235032 [Multi-domain] Cd Length: 737 Bit Score: 294.94 E-value: 1.47e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 211 ISAWNLPMSIQAEYKKKGVVDMFDWQVECLSKPrlLFEHCNLVYSAPTSAGKTLVSEILMLKTVlERGKKVLLILPFISV 290
Cdd:PRK02362 3 IAELPLPEGVIEFYEAEGIEELYPPQAEAVEAG--LLDGKNLLAAIPTASGKTLIAELAMLKAI-ARGGKALYIVPLRAL 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 291 VREKmFYMQDLLTPAGYRVegfyGGYTppGGFES---------LHVAicTIEKANSIVNKlmEQGKLETIGMVVVDEVHL 361
Cdd:PRK02362 80 ASEK-FEEFERFEELGVRV----GIST--GDYDSrdewlgdndIIVA--TSEKVDSLLRN--GAPWLDDITCVVVDEVHL 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 362 ISDKGRGYILELLLAKILYMSRrnglQIQVITMSATLENVQLLQSWLDAELYITNYRPVALKEmikvgTVIYDHRLKLVR 441
Cdd:PRK02362 149 IDSANRGPTLEVTLAKLRRLNP----DLQVVALSATIGNADELADWLDAELVDSEWRPIDLRE-----GVFYGGAIHFDD 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 442 DVAKQKVLLKglendsDDVALLCIETLLEGCSVIVFCPSKDWCENLAVQLATAihvqiksetvLGQRLRTNLNPrAIAEV 521
Cdd:PRK02362 220 SQREVEVPSK------DDTLNLVLDTLEEGGQCLVFVSSRRNAEGFAKRAASA----------LKKTLTAAERA-ELAEL 282
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 522 KQQLRDI-PTGLDGVMSKAITYACAFHHAGLTTEERDIIEASFKAGALKVLVATSTLSSGVNLPARRVLIR-----SPLF 595
Cdd:PRK02362 283 AEEIREVsDTETSKDLADCVAKGAAFHHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRdyrryDGGA 362
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 596 GGKQMSSLTYRQMIGRAGRMGKDTLGESILICNeiNARMGRDL----VVSELQPITSCLDMDGS--THlkraLLEVISSG 669
Cdd:PRK02362 363 GMQPIPVLEYHQMAGRAGRPGLDPYGEAVLLAK--SYDELDELferyIWADPEDVRSKLATEPAlrTH----VLSTIASG 436
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 670 VANTKEDIDFFVNCTLLSAQKafhakekpPDEESDANYINDALDFLVEYEFVrlqrneERETAVYVATRLGAacLASSM- 748
Cdd:PRK02362 437 FARTRDGLLEFLEATFYATQT--------DDTGRLERVVDDVLDFLERNGMI------EEDGETLEATELGH--LVSRLy 500
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 749 -PPTDGLILFAELQKSRRSfvleSELHAVYLV--TPysvcyqlqDIdWLLYVHmweklSSPMKKVGELVGVR-DAFLYKA 824
Cdd:PRK02362 501 iDPLSAAEIIDGLEAAKKP----TDLGLLHLVcsTP--------DM-YELYLR-----SGDYEWLNEYLYEHeDELLGDV 562
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 825 LRGQTKLDYKQmqihkrFY----IALALEELVNETPINVVVHKYKCHRG-----------MLQSLQQMASTFAgivtafc 889
Cdd:PRK02362 563 PSEFEDDEFED------FLsavkTALLLEDWIDEVDEERITERYGVGPGdirgkvetaewLLHAAERLASELD------- 629
|
730 740 750 760 770 780
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17933644 890 nsLQWSTLaliVSQFKDRLFFGIHRDLIDLMRIPDLSQKRARALFDAGITSLVELAGADPVELEKVL 956
Cdd:PRK02362 630 --LDLARA---ARELEKRVEYGVREELLDLVGLRGVGRVRARRLYNAGIESRADLRAADKSVVLAIL 691
|
|
| POLAc |
smart00482 |
DNA polymerase A domain; |
1805-2019 |
1.65e-83 |
|
DNA polymerase A domain;
Pssm-ID: 214687 Cd Length: 207 Bit Score: 272.58 E-value: 1.65e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1805 HISCRSPFMPTDESrCLLSADFCQLEMRILAHMSQDKALLEVMKSSQDLFIAIAAHWNKIEESEVTQDLRNSTKQVCYGI 1884
Cdd:smart00482 1 GREIRRAFIAPPGY-VLVSADYSQIELRILAHLSGDENLIEAFNNGGDIHTKTAAQVFGVPEEEVTPELRRAAKAINFGI 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1885 VYGMGMRSLAESLNCSEQEARMISDQFHQAYKGIRDYTTRVVNFARSKGFVETITGRRRYLENINSDVEHLKNQAERQAV 1964
Cdd:smart00482 80 IYGMGAKGLAEQLGISEAEAKELIKKYFARFPGVRRYIDRTLEEARRKGYVTTLFGRRRYIPDIDSRNPVLRAAAERAAV 159
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 17933644 1965 NSTIQGSAADIAKNAILKMEKNIERYREKlalgdnsVDLVMHLHDELIFEVPTGK 2019
Cdd:smart00482 160 NTPIQGSAADILKLAMIKMDEALKEFGLR-------ARLLLQVHDELVFEVPEEE 207
|
|
| PRK01172 |
PRK01172 |
ATP-dependent DNA helicase; |
251-955 |
7.86e-70 |
|
ATP-dependent DNA helicase;
Pssm-ID: 100801 [Multi-domain] Cd Length: 674 Bit Score: 249.80 E-value: 7.86e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 251 NLVYSAPTSAGKTLVSEILMLKTVLeRGKKVLLILPFISVVREKMFYMQDLLTpAGYRVEGFYGGY-TPPGGFESLHVAI 329
Cdd:PRK01172 39 NVIVSVPTAAGKTLIAYSAIYETFL-AGLKSIYIVPLRSLAMEKYEELSRLRS-LGMRVKISIGDYdDPPDFIKRYDVVI 116
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 330 CTIEKANSIVNKlmEQGKLETIGMVVVDEVHLISDKGRGYILELLLAKILYMSRrnglQIQVITMSATLENVQLLQSWLD 409
Cdd:PRK01172 117 LTSEKADSLIHH--DPYIINDVGLIVADEIHIIGDEDRGPTLETVLSSARYVNP----DARILALSATVSNANELAQWLN 190
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 410 AELYITNYRPVALKemikVGtVIYDHRLklvrdvakqkvLLKGLENDSDDVALLCIETLLEGCSVIVFCPSKDWCENLAV 489
Cdd:PRK01172 191 ASLIKSNFRPVPLK----LG-ILYRKRL-----------ILDGYERSQVDINSLIKETVNDGGQVLVFVSSRKNAEDYAE 254
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 490 QLAtaihvQIKSEtvlgqrlrtnlnpraIAEVKQQLRDiPTGLDGVMSKAITYACAFHHAGLTTEERDIIEASFKAGALK 569
Cdd:PRK01172 255 MLI-----QHFPE---------------FNDFKVSSEN-NNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIK 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 570 VLVATSTLSSGVNLPARRVLIRSPL----FGGKQMSSLTYRQMIGRAGRMGKDTLGESILICNEINA-RMGRDLVVSELQ 644
Cdd:PRK01172 314 VIVATPTLAAGVNLPARLVIVRDITrygnGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAASPASyDAAKKYLSGEPE 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 645 PITSclDMDGSTHLKRALLEVISSGVANTKEDIDFFVNCTLLSAQKafhakekppDEESDANYINDALDFLVEYEFVrlq 724
Cdd:PRK01172 394 PVIS--YMGSQRKVRFNTLAAISMGLASSMEDLILFYNETLMAIQN---------GVDEIDYYIESSLKFLKENGFI--- 459
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 725 rneeRETAVYVATRLGAACLASSMPPTDGLILFAELQKSrrsfvlESELHAVYLVtpySVCYQLQDIDWLLYVHMWEKLS 804
Cdd:PRK01172 460 ----KGDVTLRATRLGKLTSDLYIDPESALILKSAFDHD------YDEDLALYYI---SLCREIIPANTRDDYYAMEFLE 526
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 805 SpmkkvgelVGVRDAFLYKAlrgqtkldykqmqihkrfYIALALEELVNETPINVVVHKYKCHRGMLQSLQQMAstfagi 884
Cdd:PRK01172 527 D--------IGVIDGDISAA------------------KTAMVLRGWISEASMQKITDTYGIAPGDVQARASSA------ 574
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 885 vtafcNSLQWStLALIVSQFKD-----------RLFFGIHRDLIDLMRIPDLSQKRARALFDAGITSLVELAGADPVELE 953
Cdd:PRK01172 575 -----DWISYS-LARLSSIYKPemrrkleilniRIKEGIREDLIDLVLIPKVGRVRARRLYDAGFKTVDDIARSSPERIK 648
|
..
gi 17933644 954 KV 955
Cdd:PRK01172 649 KI 650
|
|
| PRK00254 |
PRK00254 |
ski2-like helicase; Provisional |
220-955 |
2.72e-67 |
|
ski2-like helicase; Provisional
Pssm-ID: 234702 [Multi-domain] Cd Length: 720 Bit Score: 243.19 E-value: 2.72e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 220 IQAEYKKKGVVDMFDWQVECLSKPRLlfEHCNLVYSAPTSAGKTLVSEILMLKTVLERGKKVLLILPFISVVREKMFYMQ 299
Cdd:PRK00254 12 IKRVLKERGIEELYPPQAEALKSGVL--EGKNLVLAIPTASGKTLVAEIVMVNKLLREGGKAVYLVPLKALAEEKYREFK 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 300 DLlTPAGYRVEGFYGGYTPP----GGFEslhVAICTIEKANSivnkLMEQGK--LETIGMVVVDEVHLISDKGRGYILEL 373
Cdd:PRK00254 90 DW-EKLGLRVAMTTGDYDSTdewlGKYD---IIIATAEKFDS----LLRHGSswIKDVKLVVADEIHLIGSYDRGATLEM 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 374 LLAKILYmsrrnglQIQVITMSATLENVQLLQSWLDAELYITNYRPVAL-KEMIKVGTVIYDHrlklvrdvakqkvllKG 452
Cdd:PRK00254 162 ILTHMLG-------RAQILGLSATVGNAEELAEWLNAELVVSDWRPVKLrKGVFYQGFLFWED---------------GK 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 453 LENDSDDVALLCIETLLEGCSVIVFCPSKDWCENLAVQLATAIhvqiksetvlgQRLRTNLNPRAIAEVKQQLRDIPTgl 532
Cdd:PRK00254 220 IERFPNSWESLVYDAVKKGKGALVFVNTRRSAEKEALELAKKI-----------KRFLTKPELRALKELADSLEENPT-- 286
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 533 DGVMSKAITYACAFHHAGLTTEERDIIEASFKAGALKVLVATSTLSSGVNLPARRVLIRSPL----FGGKQMSSLTYRQM 608
Cdd:PRK00254 287 NEKLKKALRGGVAFHHAGLGRTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDTKrysnFGWEDIPVLEIQQM 366
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 609 IGRAGRMGKDTLGESILIC--NEINARMGRdLVVSELQPITSCLDMDGSthLKRALLEVISS-GVANTKEDIDFFvnctl 685
Cdd:PRK00254 367 MGRAGRPKYDEVGEAIIVAttEEPSKLMER-YIFGKPEKLFSMLSNESA--FRSQVLALITNfGVSNFKELVNFL----- 438
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 686 lsaQKAFHAKEKpPDEESDANYINDALDFLVEYEFVRLQRNEEretavYVATRLGAACLASSMPPTDGLIL---FAELQK 762
Cdd:PRK00254 439 ---ERTFYAHQR-KDLYSLEEKAKEIVYFLLENEFIDIDLEDR-----FIPLPLGIRTSQLYIDPLTAKKFkdaFPKIEK 509
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 763 SRRSFVLeseLHAVYLvTPysvcyqlqDIDWLLY----VHMWEKLSSPMKKvgelvgvrdaFLYKALRGQTklDYKQMQI 838
Cdd:PRK00254 510 NPNPLGI---FQLIAS-TP--------DMTPLNYsrkeMEDLLDEAYEMED----------RLYFNIPYWE--DYKFQKF 565
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 839 HKRFYIALALEELVNETPINVVVHKYKCHRGMLQSLQQMASTFAGIVTAFCNSLQWSTLAL-IVSQFKDRLFFGIHRDLI 917
Cdd:PRK00254 566 LRAFKTAKVLLDWINEVPEGEIVETYNIDPGDLYRILELADWLMYSLIELYKLFEPKQEVLdYLETLHLRVKHGVREELL 645
|
730 740 750
....*....|....*....|....*....|....*...
gi 17933644 918 DLMRIPDLSQKRARALFDAGITSLVELAGADPVELEKV 955
Cdd:PRK00254 646 ELMRLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKV 683
|
|
| PRK14975 |
PRK14975 |
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional |
1628-2055 |
2.84e-56 |
|
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Pssm-ID: 237876 [Multi-domain] Cd Length: 553 Bit Score: 206.38 E-value: 2.84e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1628 LHILQGQTENLSRIGNGDLLKFFHDIEMPIQLTLCQMELVGFPAQKQRLQQLYQRM----------VAVMKKVETKIYEQ 1697
Cdd:PRK14975 137 YAVLADQLNRIAAAAHPGRLRLLAAAESAGALAAAEMELAGLPWDTDVHEALLAELlgprpaaggrPARLAELAAEIREA 216
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1698 HGS-RFNLGSSQAVAKVLglhRKAKGRV-TTSRQVLEKLNSPISHLILGYRKLSGLLAKSIQPLMECCQAD-RIHGQsit 1774
Cdd:PRK14975 217 LGRpRLNPDSPQQVLRAL---RRAGIELpSTRKWELREIDHPAVEPLLEYRKLSKLLSANGWAWLDYWVRDgRFHPE--- 290
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1775 Y----TATGRISMTEPNLQNVAKEFsiqvgsdvvhiscRSPFMPtDESRCLLSADFCQLEMRILAHMSQDKALLEVMKSS 1850
Cdd:PRK14975 291 YvpggVVTGRWASRGPNAQQIPRDI-------------RSAFVA-DPGWKLVVADASQIELRVLAAYSGDERMIEAFRTG 356
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1851 QDLFIAIAAHWNKIEESEVTQdlRNSTKQVCYGIVYGMGMRSLAESLNcSEQEARMISDQFHQAYKGIRDYTTRVVNFAR 1930
Cdd:PRK14975 357 GDLHRLTASVGFGKPEEEKEE--RALAKAANFGAIYGATSKGLQEYAK-NYGEAARLLERLRRAYPRAVGWVERAAREGE 433
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1931 SKGFVETITGRRRYLENINSDVEHLKNQAERQAVNSTIQGSAADIAKNAILKMeknieryREKLALGDnSVDLVMHLHDE 2010
Cdd:PRK14975 434 RGGVVRTLLGRTSPPPGFAWRARRRARSRGRFTRNFPVQGTAADWAKLALALL-------RRRLAEGL-DAELVFFVHDE 505
|
410 420 430 440
....*....|....*....|....*....|....*....|....*...
gi 17933644 2011 LIFEVPTGKAKKIAKVLSLTMENCVKL---SVPLKVKLRIGRSWGEFK 2055
Cdd:PRK14975 506 VVVECPEEEAEEVAAAIEEAMEEAGRLlfgPVPFPVEVAVVESYAEAK 553
|
|
| DNA_pol_A_plastid_like |
cd08640 |
DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in ... |
1745-2053 |
2.60e-54 |
|
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: 194.92 E-value: 2.60e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1745 YRKLSGLLAKSIQPLME--CCQADRIHGQSITYTATGRISMTEPNLQNV-AKEfsiqvgSDVVHIscRSPFMPTdESRCL 1821
Cdd:cd08640 51 IKSISTLLSTFIIPLQEllNDSTGRIHCSLNINTETGRLSSRNPNLQNQpALE------KDRYKI--RKAFIAS-PGNTL 121
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1822 LSADFCQLEMRILAHMSQDKALLEVMKSSQDL------------FIAIAAHWNKIE---ESEVTQDL--------RNSTK 1878
Cdd:cd08640 122 IVADYSQLELRLLAHMTRCKSMIEAFNAGGDFhsrtasgmyphvAEAVANGEVLLEwksEGKPPAPLlkdkfkseRRKAK 201
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1879 QVCYGIVYGMGMRSLAESLNCSEQEARMISDQFHQAYKGIRDYTTRVVNFARSKGFVETITGRRRYLENINSDVEHLKNQ 1958
Cdd:cd08640 202 VLNFSIAYGKTAHGLAKDWKVKLKEAERTVDAWYSDRPEVEQWQKKTKKEARERGYTRTLLGRYRYLPDIKSRNRKKRGH 281
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1959 AERQAVNSTIQGSAADIAKNAILKMEKNieryrekLALGDNSVDLVMHLHDELIFEVPTGKAKKIAKVLSLTMEN--CVK 2036
Cdd:cd08640 282 AERAAINTPIQGSAADIAMKAMLRIYRN-------LRLKRLGWKLLLQIHDEVILEGPEEKADEALKIVKDCMENpfFGP 354
|
330
....*....|....*..
gi 17933644 2037 LSVPLKVKLRIGRSWGE 2053
Cdd:cd08640 355 LDVPLEVDGSVGYNWYE 371
|
|
| SF2_C_Ski2 |
cd18795 |
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
418-627 |
2.59e-52 |
|
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: 181.21 E-value: 2.59e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 418 RPVALKEMIKVGTVIYDHRLKLVRdvakqkvllkgLENDSDDVALLCIETLLEGCSVIVFCPSKDWCENLAVQLAtaihv 497
Cdd:cd18795 1 RPVPLEEYVLGFNGLGIKLRVDVM-----------NKFDSDIIVLLKIETVSEGKPVLVFCSSRKECEKTAKDLA----- 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 498 qiksetvlgqrlrtnlnpraiaevkqqlrdiptgldGVmskaityacAFHHAGLTTEERDIIEASFKAGALKVLVATSTL 577
Cdd:cd18795 65 ------------------------------------GI---------AFHHAGLTREDRELVEELFREGLIKVLVATSTL 99
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 17933644 578 SSGVNLPARRVLIRSPLFGG----KQMSSLTYRQMIGRAGRMGKDTLGESILIC 627
Cdd:cd18795 100 AAGVNLPARTVIIKGTQRYDgkgyRELSPLEYLQMIGRAGRPGFDTRGEAIIMT 153
|
|
| DNA_pol_A |
cd06444 |
Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and ... |
1737-2051 |
1.19e-50 |
|
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: 183.77 E-value: 1.19e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1737 PISHLILGYRKLSGLLAKSIQPLMECCQAD-RIHGQSIT-YTATGRISMTEPNLQNVAKEFSIQVgsdvvhiSCRSPFMP 1814
Cdd:cd06444 27 PAVPLLLEYKKLAKLWSANGWPWLDQWVRDgRFHPEYVPgGTVTGRWASRGGNAQQIPRRDPLGR-------DIRQAFVA 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1815 tDESRCLLSADFCQLEMRILAHMSQDKALLEVMKSSQDLFIAIAAHWNKIeesEVTQDLRNSTKQVCYGIVYG----MGM 1890
Cdd:cd06444 100 -DPGWTLVVADASQLELRVLAALSGDEALAEAFGRGGDLYTATASAMFGV---PVGGGERQHAKIANLGAMYGatsgISA 175
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1891 RSLAESLNCSEQEARMISDQFHQAYKGIRDYTTRVVNFARSK---GFVETITGRRRYLENI-----------NSDVEHLK 1956
Cdd:cd06444 176 RLLAQLRRISTKEAAALIELFFSRFPAFPKAMEYVEDAARRGergGYVRTLLGRRSPPPDIrwtevvsdpaaASRARRVR 255
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1957 NQAERQAVNSTIQGSAADIAKNAILKMeknieryREKLALGDNSVDLVMHLHDELIFEVPTGKAKKIAKVLSLTMENCVK 2036
Cdd:cd06444 256 RAAGRFARNFVVQGTAADWAKLAMVAL-------RRRLEELALDARLVFFVHDEVVLHCPKEEAEAVAAIVREAAEQAVR 328
|
330
....*....|....*...
gi 17933644 2037 L---SVPLKVKLRIGRSW 2051
Cdd:cd06444 329 LlfgSVPVRFPVKIGVVW 346
|
|
| Dob10 |
COG4581 |
Superfamily II RNA helicase [Replication, recombination and repair]; |
231-648 |
1.80e-40 |
|
Superfamily II RNA helicase [Replication, recombination and repair];
Pssm-ID: 443638 [Multi-domain] Cd Length: 751 Bit Score: 162.42 E-value: 1.80e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 231 DMFDWQVE-CLSkprlLFEHCNLVYSAPTSAGKTLVSEILMLKtVLERGKKVLLILPFISVVREKMFYMQD--------L 301
Cdd:COG4581 25 ELDPFQEEaILA----LEAGRSVLVAAPTGSGKTLVAEFAIFL-ALARGRRSFYTAPIKALSNQKFFDLVErfgaenvgL 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 302 LTpagyrvegfyggytppgGFESLH----VAICTIEkansIV-NKLMEQG-KLETIGMVVVDEVHLISDKGRGYILElll 375
Cdd:COG4581 100 LT-----------------GDASVNpdapIVVMTTE----ILrNMLYREGaDLEDVGVVVMDEFHYLADPDRGWVWE--- 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 376 AKILYMSRRnglqIQVITMSATLENVQLLQSWL-----DAELYITNYRPVALKEMIKVGTVIYDhrLKLVRDVAKQKVLL 450
Cdd:COG4581 156 EPIIHLPAR----VQLVLLSATVGNAEEFAEWLtrvrgETAVVVSEERPVPLEFHYLVTPRLFP--LFRVNPELLRPPSR 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 451 KGLendsddvallcIETLLEG--CSVIVFCPSKDWCENLAVQLATAihvqiksetvlgqRLRTNLNPRAIAEVKQQLRDI 528
Cdd:COG4581 230 HEV-----------IEELDRGglLPAIVFIFSRRGCDEAAQQLLSA-------------RLTTKEERAEIREAIDEFAED 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 529 PTGLDG-VMSKAITYACAFHHAGLTTEERDIIEASFKAGALKVLVATSTLSSGVNLPARRVLI-RSPLFGGKQMSSLT-- 604
Cdd:COG4581 286 FSVLFGkTLSRLLRRGIAVHHAGMLPKYRRLVEELFQAGLLKVVFATDTLAVGINMPARTVVFtKLSKFDGERHRPLTar 365
|
410 420 430 440
....*....|....*....|....*....|....*....|....*.
gi 17933644 605 -YRQMIGRAGRMGKDTLGESILICNE-INARMGRDLVVSELQPITS 648
Cdd:COG4581 366 eFHQIAGRAGRRGIDTEGHVVVLAPEhDDPKKFARLASARPEPLRS 411
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
231-416 |
3.07e-40 |
|
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: 147.79 E-value: 3.07e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 231 DMFDWQVECLSkpRLLFEHCNLVYSAPTSAGKTLVSEILMLKTVLERGKKVLLILPFISVVREKMFYMQDLLTPAGYRVE 310
Cdd:cd17921 1 LLNPIQREALR--ALYLSGDSVLVSAPTSSGKTLIAELAILRALATSGGKAVYIAPTRALVNQKEADLRERFGPLGKNVG 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 311 GFYGGYTPPGGFES-LHVAICTIEKANSIVNKLmEQGKLETIGMVVVDEVHLISDKGRGYILELLLAKILYMSRrnglQI 389
Cdd:cd17921 79 LLTGDPSVNKLLLAeADILVATPEKLDLLLRNG-GERLIQDVRLVVVDEAHLIGDGERGVVLELLLSRLLRINK----NA 153
|
170 180
....*....|....*....|....*..
gi 17933644 390 QVITMSATLENVQLLQSWLDAELYITN 416
Cdd:cd17921 154 RFVGLSATLPNAEDLAEWLGVEDLIRF 180
|
|
| DNA_pol_A_Aquificae_like |
cd08639 |
Phylum Aquificae Pol A is different from Escherichia coli Pol A by three signature sequences; ... |
1710-2052 |
2.18e-38 |
|
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: 147.43 E-value: 2.18e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1710 VAKVLGLHRKAKGRVTTSRQVLEKLNSPISHLILGYRKLSGLLAKSIQPLMECCQAD--RIHGqsiTY----TATGRISM 1783
Cdd:cd08639 3 LERWKELEKELERERQEAAKELYIEEHPAVRLLLEYRKLNKLISTFGEKLPKHIHPVtgRIHP---SFnqigAASGRMSC 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1784 TEPNLQNVAKEFSIqvgsdvvhiscRSPFMPtDESRCLLSADFCQLEMRILAHMSQDKALLEVMKSSQDLFIAIAAHWNK 1863
Cdd:cd08639 80 SNPNLQQIPREREF-----------RRCFVA-PEGNKLIIADYSQIELRIAAEISGDERMISAYQKGEDLHRLTASLITG 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1864 IEESEVTQDLRNSTKQVCYGIVYGMGMRSLAE------SLNCSEQEARMISDQFHQAYKGIRDYTTRVVnfARSKGFVET 1937
Cdd:cd08639 148 KPIEEITKEERQLAKAVNFGLIYGMSAKGLREyartnyGVEMSLEEAEKFRESFFFFYKGILRWHHRLK--AKGPIEVRT 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1938 ITGRRRYLENInsdvehlknqAERQAVNSTIQGSAADIAKNAILKMEKNieryreklaLGDNSVDLVMHLHDELIFEVPT 2017
Cdd:cd08639 226 LLGRRRVFEYF----------TFTEALNYPIQGTGADILKLALALLVDR---------LKDLDAKIVLCVHDEIVLEVPE 286
|
330 340 350
....*....|....*....|....*....|....*...
gi 17933644 2018 GKAKKIAKVLSLTMENCVKL---SVPLKVKLRIGRSWG 2052
Cdd:cd08639 287 DEAEEAKKILESSMEEAGKRilkKVPVEVEVSISDSWA 324
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
236-416 |
4.30e-30 |
|
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: 118.59 E-value: 4.30e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 236 QVECLSKprLLFEHCNLVYSAPTSAGKTLVSEILMLKTVLErGKKVLLILPFISVVREKMFYMQDLlTPAGYRVEGFYGG 315
Cdd:cd18028 6 QAEAVRA--GLLKGENLLISIPTASGKTLIAEMAMVNTLLE-GGKALYLVPLRALASEKYEEFKKL-EEIGLKVGISTGD 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 316 Y-TPPGGFESLHVAICTIEKANSIVNKlmEQGKLETIGMVVVDEVHLISDKGRGYILELLLAKIlymsRRNGLQIQVITM 394
Cdd:cd18028 82 YdEDDEWLGDYDIIVATYEKFDSLLRH--SPSWLRDVGVVVVDEIHLISDEERGPTLESIVARL----RRLNPNTQIIGL 155
|
170 180
....*....|....*....|..
gi 17933644 395 SATLENVQLLQSWLDAELYITN 416
Cdd:cd18028 156 SATIGNPDELAEWLNAELVESD 177
|
|
| phage_DpoZ_1 |
NF038380 |
aminoadenine-incorporating DNA polymerase DpoZ; |
1482-2053 |
6.93e-27 |
|
aminoadenine-incorporating DNA polymerase DpoZ;
Pssm-ID: 468497 [Multi-domain] Cd Length: 604 Bit Score: 118.61 E-value: 6.93e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1482 DDTNFISGVSFCLADNVAYYWnmqiDERAayqgvpTPLKVQELCNLMARKDLTLVMHDGKEQLKMLRKA---IPqlkris 1558
Cdd:NF038380 18 LDKAFGFSVALSLPDGRSWYW----DIRD------QPNALQWLRDILLRSYRLVVNHHASFDYQMLRAAginIP------ 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1559 akledakVANWllqpDKTVnfLNMCQTFAPECT-GLANLCGSGRGYSSY------------GLDTSSAILPRIRTAIESC 1625
Cdd:NF038380 82 -------LDNW----DCTM--IRACLINEHLLSyDLDSLAKKYLGASKDneiyeelaaifgGKPTRKAQMPNLARAPPEI 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1626 V----------TLHILQGQTENLSRIGNGDLLKFfhdiEMPIQLTLCQMELVGFPAQKQRLQQLYQRMVAVMKKVETKIY 1695
Cdd:NF038380 149 VapyaksdarlALELWLWQQEEIERQGLQRVVEL----ERRLFPVLIDMEWRGIRVDLEAAEAAIPELDKVIDQLQKELN 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1696 EQHGSRFNLGSSQAVAKVLG----------------LHRKAKGRVTTSRQVLEKLNSPISHLILGYRKLSGL----LAKS 1755
Cdd:NF038380 225 EIAGFEFNVNSSPQIRKLFKpkkiskgqwvaidgtpLETTDAGKPSLGADALREIKHPAAAKILELRKLIKTrdtfLRGH 304
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1756 IqplMECCQADRIH-------GQSITYTATGRISMTEPNLQNVAKEfsiqvGSDVVHIsCRSPFMPtDESRCLLSADFCQ 1828
Cdd:NF038380 305 V---LGHAVGGGVHpninqtkGEDGGGTGTGRLSYTDPALQQIPSR-----DKAIAAI-VRPIFLP-DEGQVWLCSDLAQ 374
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1829 LEMRILAHMSQDKALLEVMKSSQDL-FIAIAAhwnkieesEVTQDLRNST-------KQVCYGIVYGMGMRSLAESLNC- 1899
Cdd:NF038380 375 FEFRIFAHLVNNPSIIAAYAEDPELdFHQIVA--------DMTGLPRNATysgqanaKQINLGMIFNMGNGKLADKMGMp 446
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1900 -----------------SEQEARMISDQFHQAYKGIRDYTTRVVNFARSKGFVETITGRR-RYLENINSdvehlknqaeR 1961
Cdd:NF038380 447 yeweeftfgkevrrykkAGPEAMAVIENYHRKLPGVKELADRAKAVAKERGYVRTAMGRRlRFPGGMKT----------Y 516
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1962 QAVNSTIQGSAADIAKNAILkmekNIERYreklaLGDNSVDLVMHLHDELIFEVP-TGKAKKIAKVLSLTME-NCVKLSV 2039
Cdd:NF038380 517 KASGLLIQATAADLNKENLL----EIDEV-----LGSLDGRLLLNTHDEYSMSLPeDDVRKPIKERVKLFIEdSSPWLRV 587
|
650
....*....|....*
gi 17933644 2040 PLKVKL-RIGRSWGE 2053
Cdd:NF038380 588 PIILELsGFGRNWWE 602
|
|
| HTH_61 |
pfam20470 |
Helix-turn-helix domain; This entry represents a presumed helix-turn-helix domain found in DNA ... |
621-722 |
3.13e-22 |
|
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: 92.61 E-value: 3.13e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 621 GESILICNEINARMGRDLVVSELQPITSCLDMDGSThLKRALLEVISSGVANTKEDIDFFVNCTLLSAQKafhakekppD 700
Cdd:pfam20470 1 GESILICKEKDLEKVAELLRAELPPVYSCLLPEKRG-IKRALLEIIALGLATSPEDVDEYMSCTLLSVQQ---------K 70
|
90 100
....*....|....*....|..
gi 17933644 701 EESDANYINDALDFLVEYEFVR 722
Cdd:pfam20470 71 ELDVEKSIESSLEELVENGLIT 92
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
225-424 |
3.37e-21 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 93.71 E-value: 3.37e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 225 KKKGVVDMFDWQVECLskPRLLFEHCNLVYSAPTSAGKTLVSEILMLKTVLER-GKKVLLILPFISVVREKMFYMQDLLT 303
Cdd:smart00487 2 EKFGFEPLRPYQKEAI--EALLSGLRDVILAAPTGSGKTLAALLPALEALKRGkGGRVLVLVPTRELAEQWAEELKKLGP 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 304 PAGYRVEGFYGGYTPPGGFESL-----HVAICTIEKANSIVNKlmEQGKLETIGMVVVDEVHLISDKGRGYILELLLAKI 378
Cdd:smart00487 80 SLGLKVVGLYGGDSKREQLRKLesgktDILVTTPGRLLDLLEN--DKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLL 157
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 17933644 379 LYMsrrnglqIQVITMSATL-ENVQLLQSWLDAELYITNYRPVALKE 424
Cdd:smart00487 158 PKN-------VQLLLLSATPpEEIENLLELFLNDPVFIDVGFTPLEP 197
|
|
| COG1202 |
COG1202 |
Superfamily II helicase, archaea-specific [Replication, recombination and repair]; |
252-614 |
1.84e-19 |
|
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
Pssm-ID: 440815 [Multi-domain] Cd Length: 790 Bit Score: 95.73 E-value: 1.84e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 252 LVYSApTSAGKTLVSEILMLKTVLERGKKVLLILPFISVVREKmfYMQdlltpagyrvegFYGGYTPpggfeSLHVAI-- 329
Cdd:COG1202 229 LVVSA-TATGKTLIGELAGIKNALEGKGKMLFLVPLVALANQK--YED------------FKDRYGD-----GLDVSIrv 288
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 330 ----------CTIEKANSIV------NKLMEQGK-LETIGMVVVDEVHLISDKGRGYILELLLAKILYMSRrnglQIQVI 392
Cdd:COG1202 289 gasrirddgtRFDPNADIIVgtyegiDHALRTGRdLGDIGTVVIDEVHMLEDPERGHRLDGLIARLKYYCP----GAQWI 364
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 393 TMSATLENVQLLQSWLDAELYITNYRPVAL-------KEMIKVGTViydhrLKLVRDVAKQKVLlKGLENDSddvallci 465
Cdd:COG1202 365 YLSATVGNPEELAKKLGAKLVEYEERPVPLerhltfaDGREKIRII-----NKLVKREFDTKSS-KGYRGQT-------- 430
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 466 etllegcsvIVFCPSKDWCENLAvqlataihvqiksetvlgqrlrtnlnpraiaevkqqlrdiptgldgvmsKAITYACA 545
Cdd:COG1202 431 ---------IIFTNSRRRCHEIA-------------------------------------------------RALGYKAA 452
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17933644 546 FHHAGLTTEERDIIEASFKAGALKVLVATSTLSSGVNLPARRVLIRSPLFGGKQMSSLTYRQMIGRAGR 614
Cdd:COG1202 453 PYHAGLDYGERKKVERRFADQELAAVVTTAALAAGVDFPASQVIFDSLAMGIEWLSVQEFHQMLGRAGR 521
|
|
| DEXHc_ASCC3_2 |
cd18022 |
C-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ... |
250-408 |
2.88e-19 |
|
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: 87.81 E-value: 2.88e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 250 CNLVYSAPTSAGKTLVSEILMLKTVLER-GKKVLLILPFISVVREKMF-YMQDLLTPAGYRVEGFYGGYTP-PGGFESLH 326
Cdd:cd18022 18 NNVLLGAPTGSGKTIAAELAMFRAFNKYpGSKVVYIAPLKALVRERVDdWKKRFEEKLGKKVVELTGDVTPdMKALADAD 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 327 VAICTIEKANSIVNKLMEQGKLETIGMVVVDEVHLISDKgRGYILELLLAKILYMSRRNGLQIQVITMSATLENVQLLQS 406
Cdd:cd18022 98 IIITTPEKWDGISRSWQTREYVQQVSLIIIDEIHLLGSD-RGPVLEVIVSRMNYISSQTEKPVRLVGLSTALANAGDLAN 176
|
..
gi 17933644 407 WL 408
Cdd:cd18022 177 WL 178
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
251-404 |
1.62e-18 |
|
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: 84.60 E-value: 1.62e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 251 NLVYSAPTSAGKTLVSEILMLKTV--LERGKKVLLILPFISVVREKMFYMQDLLTPAGYRVEGFYGGYTPP---GGFESL 325
Cdd:pfam00270 16 DVLVQAPTGSGKTLAFLLPALEALdkLDNGPQALVLAPTRELAEQIYEELKKLGKGLGLKVASLLGGDSRKeqlEKLKGP 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 326 HVAICTIEKANSIvnkLMEQGKLETIGMVVVDEVHLISDKGRGYILELLLAKILYmsrrnglQIQVITMSATL-ENVQLL 404
Cdd:pfam00270 96 DILVGTPGRLLDL---LQERKLLKNLKLLVLDEAHRLLDMGFGPDLEEILRRLPK-------KRQILLLSATLpRNLEDL 165
|
|
| SF2-N |
cd00046 |
N-terminal DEAD/H-box helicase domain of superfamily 2 helicases; The DEAD/H-like superfamily ... |
256-397 |
1.03e-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: 81.68 E-value: 1.03e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 256 APTSAGKTLVSEILMLKTVLERGKKVLLILPFISVVREKMFYMQDLLTPaGYRVEGFYGGYTPPGGFE----SLHVAICT 331
Cdd:cd00046 8 APTGSGKTLAALLAALLLLLKKGKKVLVLVPTKALALQTAERLRELFGP-GIRVAVLVGGSSAEEREKnklgDADIIIAT 86
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17933644 332 IEKansIVNKLMEQGKLET--IGMVVVDEVHLISDKGRgYILELLLAKILYMSrrngLQIQVITMSAT 397
Cdd:cd00046 87 PDM---LLNLLLREDRLFLkdLKLIIVDEAHALLIDSR-GALILDLAVRKAGL----KNAQVILLSAT 146
|
|
| DNA_pol_A_pol_I_B |
cd08643 |
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ... |
1692-2053 |
3.22e-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: 86.72 E-value: 3.22e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1692 TKIYEQHgsrFNLGSSQAVAKVLGLHRKAKGRVTTSR-------QVLEKLNSPISHLILGY---RKLSGLLAKSIQPLME 1761
Cdd:cd08643 58 TKIKLVT---FNPSSRKHIAKRLKAKYGWEPQEFTESgepkvdeDVLSKLDYPEAKLLAEYllvQKRLGQLADGNNAWLK 134
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1762 CCQAD-RIHGQSITY-TATGRISMTEPNLQNVAKefsiqVGSDVVHiSCRSPFMPTDESRcLLSADFCQLEMRILAHM-- 1837
Cdd:cd08643 135 LVHEDgRIHGAVNTNgAVTGRATHFSPNMAQVPA-----VGSPYGK-ECRELFGVPPGWS-LVGADASGLELRCLAHYla 207
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1838 SQDKALLEVMKSSQDlfiaiaAHWNKIEESEVTQdlRNSTKQVCYGIVYGMGMRSLAESLNCSEQEARMISDQFHQAYKG 1917
Cdd:cd08643 208 RYDGGAYTRKVLGGD------IHWANAQAMGLLS--RDGAKTFIYAFLYGAGDEKLGQIVGDDLRTAKNLNAEWPQTKKG 279
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1918 IRDYTT-----RVV--NFARS-KGF------VETITGRRRYLENInsDVEHLKNQAERQAVNSTIQGSAADIAKNAILKM 1983
Cdd:cd08643 280 TIKKIAdkakgRVVraNFLKGlPALgklikkVKEAAKKRGHLVGL--DGRRIRVRSAHAALNTLLQSAGAILMKKWLVLL 357
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17933644 1984 EKNIEryrEKLALGDNSVDLVMHLHDELIFEVPTGKAKKIAKVLSLTMENCVK---LSVPLKVKLRIGRSWGE 2053
Cdd:cd08643 358 DDELT---AKGGVWGGDFEYCAWVHDEVQIECRKGIAEEVGKIAVEAAEKAGEhfnFRCPLAGEFDIGRNWAE 427
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
542-616 |
3.88e-16 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 74.94 E-value: 3.88e-16
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17933644 542 YACAFHHAGLTTEERDIIEASFKAGALKVLVATSTLSSGVNLP-ARRVLIRSPLFggkqmSSLTYRQMIGRAGRMG 616
Cdd:smart00490 12 IKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPgVDLVIIYDLPW-----SPASYIQRIGRAGRAG 82
|
|
| SSL2 |
COG1061 |
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]; |
232-620 |
2.24e-15 |
|
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
Pssm-ID: 440681 [Multi-domain] Cd Length: 566 Bit Score: 81.61 E-value: 2.24e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 232 MFDWQVECLSKPRLLFE--HCNLVYSAPTSAGKTLVSEILMLKtvLERGKKVLLILPFISVVR--EKMFymqdlltPAGY 307
Cdd:COG1061 81 LRPYQQEALEALLAALErgGGRGLVVAPTGTGKTVLALALAAE--LLRGKRVLVLVPRRELLEqwAEEL-------RRFL 151
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 308 RVEGFYGGYTPPGGfeslHVAICTIekaNSIVNKLMEQGKLETIGMVVVDEVHLISDKGRGYILELLLAKILYmsrrnGL 387
Cdd:COG1061 152 GDPLAGGGKKDSDA----PITVATY---QSLARRAHLDELGDRFGLVIIDEAHHAGAPSYRRILEAFPAAYRL-----GL 219
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 388 qiqvitmSATLENvqllqswLDA-ELYITNYRPVA----LKEMIKVGTV----IYDHRLKLVRDVAKQKVLLKGLEN--- 455
Cdd:COG1061 220 -------TATPFR-------SDGrEILLFLFDGIVyeysLKEAIEDGYLappeYYGIRVDLTDERAEYDALSERLREala 285
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 456 DSDDVALLCIETLLE----GCSVIVFCPSKDwcenlavqlataiHVQiksetvlgqrlrtnlnpraiaEVKQQLRDIPtg 531
Cdd:COG1061 286 ADAERKDKILRELLRehpdDRKTLVFCSSVD-------------HAE---------------------ALAELLNEAG-- 329
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 532 ldgvmskaitYACAFHHAGLTTEERDIIEASFKAGALKVLVATSTLSSGVNLPARRVLIrspLFGGKQmSSLTYRQMIGR 611
Cdd:COG1061 330 ----------IRAAVVTGDTPKKEREEILEAFRDGELRILVTVDVLNEGVDVPRLDVAI---LLRPTG-SPREFIQRLGR 395
|
410
....*....|.
gi 17933644 612 AGRM--GKDTL 620
Cdd:COG1061 396 GLRPapGKEDA 406
|
|
| DEXHc_HFM1 |
cd18023 |
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box ... |
236-411 |
2.33e-15 |
|
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: 77.01 E-value: 2.33e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 236 QVECLskPRLLFEHCNLVYSAPTSAGKTLVSEILMLKTVLERG------KKVLLILPFISVVREKMFYMQDLLTPAGYRV 309
Cdd:cd18023 6 QSEVF--PDLLYSDKNFVVSAPTGSGKTVLFELAILRLLKERNplpwgnRKVVYIAPIKALCSEKYDDWKEKFGPLGLSC 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 310 EGFYGGYTPPGGFE--SLHVAICTIEKANSIVNKLMEQGKL-ETIGMVVVDEVHLISDKgRGYILELLLA--KILYMSRR 384
Cdd:cd18023 84 AELTGDTEMDDTFEiqDADIILTTPEKWDSMTRRWRDNGNLvQLVALVLIDEVHIIKEN-RGATLEVVVSrmKTLSSSSE 162
|
170 180 190
....*....|....*....|....*....|.
gi 17933644 385 -NGLQ---IQVITMSATLENVQLLQSWLDAE 411
Cdd:cd18023 163 lRGSTvrpMRFVAVSATIPNIEDLAEWLGDN 193
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
542-616 |
4.00e-14 |
|
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 70.32 E-value: 4.00e-14
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17933644 542 YACAFHHAGLTTEERDIIEASFKAGALKVLVATSTLSSGVNLPARRVLIrsplFGGKQMSSLTYRQMIGRAGRMG 616
Cdd:pfam00271 39 IKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVI----NYDLPWNPASYIQRIGRAGRAG 109
|
|
| DEXHc_Brr2_1 |
cd18019 |
N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD ... |
251-408 |
2.88e-13 |
|
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: 70.86 E-value: 2.88e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 251 NLVYSAPTSAGKTLVSEILML----KTVLERGK------KVLLILPFISVVREKMFYMQDLLTPAGYRVEGFYGGYTPPG 320
Cdd:cd18019 35 NLLLCAPTGAGKTNVALLTILreigKHRNPDGTinldafKIVYIAPMKALVQEMVGNFSKRLAPYGITVAELTGDQQLTK 114
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 321 G-FESLHVAICTIEKANSIVNKLMEQGKLETIGMVVVDEVHLISDKgRGYILELLLAKILYMSRRNGLQIQVITMSATLE 399
Cdd:cd18019 115 EqISETQIIVTTPEKWDIITRKSGDRTYTQLVRLIIIDEIHLLHDD-RGPVLESIVARTIRQIEQTQEYVRLVGLSATLP 193
|
....*....
gi 17933644 400 NVQLLQSWL 408
Cdd:cd18019 194 NYEDVATFL 202
|
|
| Lhr |
COG1201 |
Lhr-like helicase [Replication, recombination and repair]; |
317-617 |
6.64e-12 |
|
Lhr-like helicase [Replication, recombination and repair];
Pssm-ID: 440814 [Multi-domain] Cd Length: 850 Bit Score: 70.90 E-value: 6.64e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 317 TPpggfESLHVAIcTIEKAnsivnklmeQGKLETIGMVVVDEVH-LISDKgRGYILELLLAKIlymSRRNGLQIQVITMS 395
Cdd:COG1201 142 TP----ESLALLL-TSPDA---------RELLRGVRTVIVDEIHaLAGSK-RGVHLALSLERL---RALAPRPLQRIGLS 203
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 396 ATLENVQLLQSWLDAElyiTNYRPVALkemIKVGtviydhrlkLVRDVakqkvllkglendsdDVALLCIETLLEGcsvi 475
Cdd:COG1201 204 ATVGPLEEVARFLVGY---EDPRPVTI---VDAG---------AGKKP---------------DLEVLVPVEDLIE---- 249
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 476 vfcpSKDWCENLAVQLATAIHVQIKSEtvlgqrlRTNL---NPRAIAE-VKQQLRDIPTGLDGVMskaityacAFHHAGL 551
Cdd:COG1201 250 ----RFPWAGHLWPHLYPRVLDLIEAH-------RTTLvftNTRSQAErLFQRLNELNPEDALPI--------AAHHGSL 310
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17933644 552 TTEERDIIEASFKAGALKVLVATSTLSSGVNLPA--RRVLIRSPlfggKQMSSLtyRQMIGRAG-RMGK 617
Cdd:COG1201 311 SREQRLEVEEALKAGELRAVVATSSLELGIDIGDvdLVIQVGSP----KSVARL--LQRIGRAGhRVGE 373
|
|
| SF2_C_LHR |
cd18796 |
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
505-614 |
2.17e-10 |
|
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: 60.74 E-value: 2.17e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 505 LGQRLRTNL---NPRAIAE-VKQQLRDIPTglDGVMSKAItyacAFHHAGLTTEERDIIEASFKAGALKVLVATSTLSSG 580
Cdd:cd18796 34 LLERHKSTLvftNTRSQAErLAQRLRELCP--DRVPPDFI----ALHHGSLSRELREEVEAALKRGDLKVVVATSSLELG 107
|
90 100 110
....*....|....*....|....*....|....*.
gi 17933644 581 VNLPA--RRVLIRSPlfggKQMSSLtyRQMIGRAGR 614
Cdd:cd18796 108 IDIGDvdLVIQIGSP----KSVARL--LQRLGRSGH 137
|
|
| DEXHc_LHR-like |
cd17922 |
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ... |
251-408 |
3.67e-09 |
|
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: 57.98 E-value: 3.67e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 251 NLVYSAPTSAGKTLVSEILMLKTVLERGKK---VLLILPFISVVREKMFYMQDLLT--PAGYRVEGFYGGYT-------- 317
Cdd:cd17922 3 NVLIAAPTGSGKTEAAFLPALSSLADEPEKgvqVLYISPLKALINDQERRLEEPLDeiDLEIPVAVRHGDTSqsekakql 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 318 --PPggfeslHVAICTIEKANSI-VNKLMEQgKLETIGMVVVDEVH-LISDKgRGYILELLLAKILYMSRRNglqIQVIT 393
Cdd:cd17922 83 knPP------GILITTPESLELLlVNKKLRE-LFAGLRYVVVDEIHaLLGSK-RGVQLELLLERLRKLTGRP---LRRIG 151
|
170
....*....|....*
gi 17933644 394 MSATLENVQLLQSWL 408
Cdd:cd17922 152 LSATLGNLEEAAAFL 166
|
|
| SF2_C_Hrq |
cd18797 |
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ... |
454-626 |
4.38e-09 |
|
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: 56.88 E-value: 4.38e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 454 ENDSDDVALLCIETLLEGCSVIVFCPSKDWCENLAvqlataihvqiksetvlgqrlrtnlnpraiAEVKQQLRDIPTGLD 533
Cdd:cd18797 18 GSARREAARLFADLVRAGVKTIVFCRSRKLAELLL------------------------------RYLKARLVEEGPLAS 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 534 GVMSkaityacafHHAGLTTEERDIIEASFKAGALKVLVATSTLSSGVNLPARRVLIRSPlFGGKQMSsltYRQMIGRAG 613
Cdd:cd18797 68 KVAS---------YRAGYLAEDRREIEAELFNGELLGVVATNALELGIDIGGLDAVVLAG-YPGSLAS---LWQQAGRAG 134
|
170
....*....|...
gi 17933644 614 RMGKDTLgeSILI 626
Cdd:cd18797 135 RRGKDSL--VILV 145
|
|
| YprA |
COG1205 |
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ... |
547-626 |
1.48e-08 |
|
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: 59.85 E-value: 1.48e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 547 HHAGLTTEERDIIEASFKAGALKVLVATSTLSSGVNLP---ArrVLIRSplFGGKQMSsltYRQMIGRAGRMGKDTLgeS 623
Cdd:COG1205 324 YRAGYLPEERREIERGLRSGELLGVVSTNALELGIDIGgldA--VVLAG--YPGTRAS---FWQQAGRAGRRGQDSL--V 394
|
...
gi 17933644 624 ILI 626
Cdd:COG1205 395 VLV 397
|
|
| DEXHc_Brr2_2 |
cd18021 |
C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type ... |
251-411 |
3.86e-08 |
|
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: 55.34 E-value: 3.86e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 251 NLVYSAPTSAGKTLVSEILMLKTVLERGK-KVLLILPfisvvrekmfyMQDLltpAGYRVEGFYGGYTPPGG-------- 321
Cdd:cd18021 21 NVFVGAPTGSGKTVCAELALLRHWRQNPKgRAVYIAP-----------MQEL---VDARYKDWRAKFGPLLGkkvvkltg 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 322 --------FESLHVAICTIEKANSIVNKLMEQGKLETIGMVVVDEVHLISDkGRGYILELLLAKILYMSRRNGLQIQVIT 393
Cdd:cd18021 87 etstdlklLAKSDVILATPEQWDVLSRRWKQRKNVQSVELFIADELHLIGG-ENGPVYEVVVSRMRYISSQLEKPIRIVG 165
|
170
....*....|....*...
gi 17933644 394 MSATLENVQLLQSWLDAE 411
Cdd:cd18021 166 LSSSLANARDVGEWLGAS 183
|
|
| DEXHc_ASCC3_1 |
cd18020 |
N-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ... |
251-400 |
4.03e-08 |
|
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: 55.51 E-value: 4.03e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 251 NLVYSAPTSAGKTLVSEILMLKTVLERGK----------KVLLILPFISVVREKMFYMQDLLTPAGYRVEGFYGGYT-PP 319
Cdd:cd18020 19 NMLICAPTGAGKTNIAMLTILHEIRQHVNqggvikkddfKIVYIAPMKALAAEMVEKFSKRLAPLGIKVKELTGDMQlTK 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 320 GGFESLHVAICTIEKANSIVNKLMEQGKL-ETIGMVVVDEVHLISDKgRGYILELLLAKILYMSRRNGLQIQVITMSATL 398
Cdd:cd18020 99 KEIAETQIIVTTPEKWDVVTRKSSGDVALsQLVRLLIIDEVHLLHDD-RGPVIESLVARTLRQVESTQSMIRIVGLSATL 177
|
..
gi 17933644 399 EN 400
Cdd:cd18020 178 PN 179
|
|
| SF2_C_RecQ |
cd18794 |
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ... |
456-617 |
3.59e-07 |
|
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: 51.06 E-value: 3.59e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 456 DSDDVALLCIETLLEGC---SVIVFCPSKDWCENLAVQLataihvqiksetvlgqrlrtnlnpraiaevkqqlrdiptgl 532
Cdd:cd18794 12 DKKDEKLDLLKRIKVEHlggSGIIYCLSRKECEQVAARL----------------------------------------- 50
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 533 dgvmsKAITYACAFHHAGLTTEERDIIEASFKAGALKVLVATSTLSSGVNLPARRVLIRSPLfgGKQMSSltYRQMIGRA 612
Cdd:cd18794 51 -----QSKGISAAAYHAGLEPSDRRDVQRKWLRDKIQVIVATVAFGMGIDKPDVRFVIHYSL--PKSMES--YYQESGRA 121
|
....*
gi 17933644 613 GRMGK 617
Cdd:cd18794 122 GRDGL 126
|
|
| PRK09751 |
PRK09751 |
putative ATP-dependent helicase Lhr; Provisional |
348-613 |
6.00e-07 |
|
putative ATP-dependent helicase Lhr; Provisional
Pssm-ID: 137505 [Multi-domain] Cd Length: 1490 Bit Score: 54.93 E-value: 6.00e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 348 LETIGMVVVDEVHLISDKGRGYILELLLAKI--LYMSRrnglqIQVITMSATLENVQLLQSWLDAELYITNYRPVALKEM 425
Cdd:PRK09751 122 LRGVETVIIDEVHAVAGSKRGAHLALSLERLdaLLHTS-----AQRIGLSATVRSASDVAAFLGGDRPVTVVNPPAMRHP 196
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 426 ikvgtviydhRLKLVRDVAKQKVLLKGLENDSDD------------VALLCIETLLEGCSVIVFCPSKDWCENLAVQLAT 493
Cdd:PRK09751 197 ----------QIRIVVPVANMDDVSSVASGTGEDshagregsiwpyIETGILDEVLRHRSTIVFTNSRGLAEKLTARLNE 266
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 494 AihvqiksetvLGQRLRTNLnprAIAEVKQQLRDIPTGLDGVMSKAITYACAFHHAGLTTEERDIIEASFKAGALKVLVA 573
Cdd:PRK09751 267 L----------YAARLQRSP---SIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQRAITEQALKSGELRCVVA 333
|
250 260 270 280
....*....|....*....|....*....|....*....|..
gi 17933644 574 TSTLSSGVNLPARRVLIR--SPLfggkqmSSLTYRQMIGRAG 613
Cdd:PRK09751 334 TSSLELGIDMGAVDLVIQvaTPL------SVASGLQRIGRAG 369
|
|
| DNA_pol_A_pol_I_A |
cd08642 |
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ... |
1809-2018 |
2.00e-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: 49.16 E-value: 2.00e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1809 RSPFMPTDESRcLLSADFCQLEMRILAHMSQDKALLEVMKSSQDLFIAIAAHWNK--IEESEVTQDLRNSTKQVCYGIVY 1886
Cdd:cd08642 161 RTAFIPSEGHR-FIVSDFSAIEARVIAWLAGEQWRLDVFATHGKIYEASASQMFGvpVEKIGKNSHLRQKGKVAELALGY 239
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1887 GMGMRSL----AESLNCSEQEARMISDQFHQAYKGIRDYTTRVVNFArskgfVETITGRR------RYLENInsdvehlk 1956
Cdd:cd08642 240 GGSVGALkamgALEMGLTEDELPGIVDAWRNANPNIVKLWWDVDKAA-----KKAVKERKtvklggKLVENI-------- 306
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17933644 1957 nqaerqavnstIQGSAADIAKNAILKMEKNieryreklalgdnSVDLVMHLHDELIFEVPTG 2018
Cdd:cd08642 307 -----------VQAIARDCLAEAMLRLEKA-------------GYDIVMHVHDEVVIEVPEG 344
|
|
| phage_DpoZ_2 |
NF038381 |
aminoadenine-incorporating DNA polymerase DpoZ; |
1776-2023 |
2.08e-05 |
|
aminoadenine-incorporating DNA polymerase DpoZ;
Pssm-ID: 468498 [Multi-domain] Cd Length: 753 Bit Score: 49.56 E-value: 2.08e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1776 TATGRISMTEPNLQNVAKEFSIQvGSDVVHISCrspfmPTD-------ESRCLLSADFCQLEMRILAHMSQDKALLEVMK 1848
Cdd:NF038381 458 TASGRFSVEEIQLQAIPADYKVK-GYGLDGIPS-----PRDligsgvpKGYELWEMDLAQAELRVAALFAKCQRMLDMID 531
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1849 SSQDLFIAIAAH-WNKIEESEVTQDLRNSTKQVCYGIVYGMGMRSLAESL------NCSEQEAR-MISD--QFHQAYKGI 1918
Cdd:NF038381 532 AGMDLHGETAKElFDASPDDENWGQRRQVAKRGNFSLIFGVGWATFQATLwkeagiDLSDREAQvLIKAwnALYPEYKRA 611
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 1919 RDYTTRVVNFARSK----GFVETITGRRRYLENINSDVEHLKNQAER----QAVNSTIQGSAADIAKNAILKMEKNI-ER 1989
Cdd:NF038381 612 INVHEARVMRRYDKygvgWILDMATGERRWFTKWDVEFFDQRRQELRegahKAFNQRVQPALAQYGIDRWLLEDRYLsSQ 691
|
250 260 270
....*....|....*....|....*....|....
gi 17933644 1990 YREKlALGDNSVDLVMHLHDELIFEVPTGKAKKI 2023
Cdd:NF038381 692 LTGE-ELEHGGAGLVLMVHDSSVLLLPNERAEEV 724
|
|
| ResIII |
pfam04851 |
Type III restriction enzyme, res subunit; |
232-382 |
2.53e-05 |
|
Type III restriction enzyme, res subunit;
Pssm-ID: 398492 [Multi-domain] Cd Length: 162 Bit Score: 46.51 E-value: 2.53e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 232 MFDWQVECLS---------KPRLLFEHcnlvysaPTSAGKTLVSEILMLKTVLERG-KKVLLILPFISVVrEKMF--YMQ 299
Cdd:pfam04851 4 LRPYQIEAIEnllesikngQKRGLIVM-------ATGSGKTLTAAKLIARLFKKGPiKKVLFLVPRKDLL-EQALeeFKK 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 300 dlLTPAGYRVEGFYGGYTPPGGFESLHVAICTIEKANSIVNKLMEQGKLETIGMVVVDEVHLISDKGRGYILELL-LAKI 378
Cdd:pfam04851 76 --FLPNYVEIGEIISGDKKDESVDDNKIVVTTIQSLYKALELASLELLPDFFDVIIIDEAHRSGASSYRNILEYFkPAFL 153
|
....
gi 17933644 379 LYMS 382
Cdd:pfam04851 154 LGLT 157
|
|
| PLN00206 |
PLN00206 |
DEAD-box ATP-dependent RNA helicase; Provisional |
535-639 |
4.40e-05 |
|
DEAD-box ATP-dependent RNA helicase; Provisional
Pssm-ID: 215103 [Multi-domain] Cd Length: 518 Bit Score: 48.25 E-value: 4.40e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 535 VMSKAITYA----CAFHHAGLTTEERDIIEASFKAGALKVLVATSTLSSGVNL-PARRVLIrsplFggkQMSSLT--YRQ 607
Cdd:PLN00206 382 LLANAITVVtglkALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLlRVRQVII----F---DMPNTIkeYIH 454
|
90 100 110
....*....|....*....|....*....|..
gi 17933644 608 MIGRAGRMGKDtlGESILICNEINARMGRDLV 639
Cdd:PLN00206 455 QIGRASRMGEK--GTAIVFVNEEDRNLFPELV 484
|
|
| RecQ |
COG0514 |
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
542-625 |
4.74e-05 |
|
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 48.21 E-value: 4.74e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 542 YACAFHHAGLTTEERDIIEASFKAGALKVLVATSTLSSGVN-----------LParrvlirsplfggKQMSSltYRQMIG 610
Cdd:COG0514 255 IRAAAYHAGLDAEEREANQDRFLRDEVDVIVATIAFGMGIDkpdvrfvihydLP-------------KSIEA--YYQEIG 319
|
90
....*....|....*
gi 17933644 611 RAGRMGKDtlGESIL 625
Cdd:COG0514 320 RAGRDGLP--AEALL 332
|
|
| DEXHc_RE |
cd17926 |
DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins; This family ... |
232-377 |
6.16e-05 |
|
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: 44.99 E-value: 6.16e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 232 MFDWQVECLSKprlLFEHCN---LVYSAPTSAGKTLVseilMLKTVLERGKKVLLIL-PFIsVVREKMfyMQDLLTPAGY 307
Cdd:cd17926 1 LRPYQEEALEA---WLAHKNnrrGILVLPTGSGKTLT----ALALIAYLKELRTLIVvPTD-ALLDQW--KERFEDFLGD 70
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17933644 308 RVEG-FYGGYTPpgGFESLHVAICTIEKANSIVNKLMEQGKLEtiGMVVVDEVHLISDKGRGYILELLLAK 377
Cdd:cd17926 71 SSIGlIGGGKKK--DFDDANVVVATYQSLSNLAEEEKDLFDQF--GLLIVDEAHHLPAKTFSEILKELNAK 137
|
|
| PTZ00424 |
PTZ00424 |
helicase 45; Provisional |
542-617 |
8.66e-05 |
|
helicase 45; Provisional
Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 47.13 E-value: 8.66e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17933644 542 YACAFHHAGLTTEERDIIEASFKAGALKVLVATSTLSSGVNLPARRVLIRSPLfggkQMSSLTYRQMIGRAGRMGK 617
Cdd:PTZ00424 292 FTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDL----PASPENYIHRIGRSGRFGR 363
|
|
| PRK13767 |
PRK13767 |
ATP-dependent helicase; Provisional |
347-613 |
1.02e-04 |
|
ATP-dependent helicase; Provisional
Pssm-ID: 237497 [Multi-domain] Cd Length: 876 Bit Score: 47.57 E-value: 1.02e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 347 KLETIGMVVVDEVHLISDKGRGYILELLLAKILYMSRRNglqIQVITMSATLEnvqllqswldaelyitnyrPvaLKEmi 426
Cdd:PRK13767 169 KLRTVKWVIVDEIHSLAENKRGVHLSLSLERLEELAGGE---FVRIGLSATIE-------------------P--LEE-- 222
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 427 kvgtviydhrlklvrdVAKqkvLLKGLENDSDDVALLCIET-LLEGCSVIVFCPSKDWCENLAVQLATAIHVQIKSetvL 505
Cdd:PRK13767 223 ----------------VAK---FLVGYEDDGEPRDCEIVDArFVKPFDIKVISPVDDLIHTPAEEISEALYETLHE---L 280
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 506 GQRLRTNL---NPRAIAE-VKQQLRDI-PTGLDGVMSKAityacafHHAGLTTEERDIIEASFKAGALKVLVATSTLSSG 580
Cdd:PRK13767 281 IKEHRTTLiftNTRSGAErVLYNLRKRfPEEYDEDNIGA-------HHSSLSREVRLEVEEKLKRGELKVVVSSTSLELG 353
|
250 260 270
....*....|....*....|....*....|....*
gi 17933644 581 VNLPARR--VLIRSPlfggKQMSSLTyrQMIGRAG 613
Cdd:PRK13767 354 IDIGYIDlvVLLGSP----KSVSRLL--QRIGRAG 382
|
|
| SF2_C_suv3 |
cd18805 |
C-terminal helicase domain of ATP-dependent RNA helicase; The SUV3 (suppressor of Var 3) gene ... |
569-616 |
1.50e-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: 43.70 E-value: 1.50e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 17933644 569 KVLVATSTLSSGVNLPARRVlIRSPL--FGGKQMSSLT---YRQMIGRAGRMG 616
Cdd:cd18805 72 DVLVASDAIGMGLNLNIRRV-IFSSLskFDGNEMRPLSpseVKQIAGRAGRFG 123
|
|
| DEXHc_RIG-I |
cd17927 |
DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins; Members of the RIG-I ... |
234-411 |
2.66e-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: 2.66e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 234 DWQVEcLSKPRLLFEhcNLVYSAPTSAGKTLVSEILML----KTVLERGKKVLLILPFISVVREKMFYMQDLLTPAGYRV 309
Cdd:cd17927 5 NYQLE-LAQPALKGK--NTIICLPTGSGKTFVAVLICEhhlkKFPAGRKGKVVFLANKVPLVEQQKEVFRKHFERPGYKV 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 310 EGfYGGYTP-----PGGFESLHVAICTiekANSIVNKLM--EQGKLETIGMVVVDEVHLiSDKGRGY--ILELLLAKILY 380
Cdd:cd17927 82 TG-LSGDTSenvsvEQIVESSDVIIVT---PQILVNDLKsgTIVSLSDFSLLVFDECHN-TTKNHPYneIMFRYLDQKLG 156
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 17933644 381 MSRRNglqIQVITMSA------------TLENVQLLQSWLDAE 411
Cdd:cd17927 157 SSGPL---PQILGLTAspgvggaknteeALEHICKLCANLDIS 196
|
|
| SF2_C_XPB |
cd18789 |
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex ... |
553-626 |
4.93e-04 |
|
C-terminal helicase domain of XPB-like helicases; TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350176 [Multi-domain] Cd Length: 153 Bit Score: 42.62 E-value: 4.93e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17933644 553 TEERDIIEASFKAGALKVLVATSTLSSGVNLPARRVLIrsplfggkQMSSL--TYRQMIGRAGRM---GKDTLGESILI 626
Cdd:cd18789 80 QSEREEILQNFREGEYNTLVVSKVGDEGIDLPEANVAI--------QISGHggSRRQEAQRLGRIlrpKKGGGKNAFFY 150
|
|
| SF2_C_RecG |
cd18811 |
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a ... |
542-614 |
5.98e-04 |
|
C-terminal helicase domain of DNA helicase RecG; ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350198 [Multi-domain] Cd Length: 159 Bit Score: 42.33 E-value: 5.98e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 17933644 542 YACAFHHAGLTTEERDIIEASFKAGALKVLVATSTLSSGVNLP-ARRVLIRSP-LFGGKQMssltyRQMIGRAGR 614
Cdd:cd18811 62 LNVGLLHGRLKSDEKDAVMAEFREGEVDILVSTTVIEVGVDVPnATVMVIEDAeRFGLSQL-----HQLRGRVGR 131
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| DEXHc_RLR |
cd18036 |
DEXH-box helicase domain of RIG-I-like receptors; RIG-I-like receptors (RLRs) sense ... |
234-398 |
9.64e-04 |
|
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: 42.46 E-value: 9.64e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 234 DWQVEcLSKPRLlfEHCNLVYSAPTSAGKTLVSEILMLKTVLER-----GKKVLLILPFISVV---REKMF-YMQDlltp 304
Cdd:cd18036 5 NYQLE-LVLPAL--RGKNTIICAPTGSGKTRVAVYICRHHLEKRrsageKGRVVVLVNKVPLVeqqLEKFFkYFRK---- 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17933644 305 aGYRVEGFYGGYTPPGGFESL----HVAICTiekANSIVNKLM-----EQGKLETIGMVVVDEVHLiSDKGRGY--ILEL 373
Cdd:cd18036 78 -GYKVTGLSGDSSHKVSFGQIvkasDVIICT---PQILINNLLsgreeERVYLSDFSLLIFDECHH-TQKEHPYnkIMRM 152
|
170 180
....*....|....*....|....*
gi 17933644 374 LLAKILymsRRNGLQIQVITMSATL 398
Cdd:cd18036 153 YLDKKL---SSQGPLPQILGLTASP 174
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|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
568-627 |
3.60e-03 |
|
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: 38.07 E-value: 3.60e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17933644 568 LKVLVATSTLSSGVNLP-ARRVLIRSPlfggkQMSSLTYRQMIGRAGRMGKDTlGESILIC 627
Cdd:cd18785 23 LEILVATNVLGEGIDVPsLDTVIFFDP-----PSSAASYIQRVGRAGRGGKDE-GEVILFV 77
|
|
| SF2_C_RecG_TRCF |
cd18792 |
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family ... |
548-614 |
4.52e-03 |
|
C-terminal helicase domain of the RecG family helicases; The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350179 [Multi-domain] Cd Length: 160 Bit Score: 39.94 E-value: 4.52e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17933644 548 HAGLTTEERDIIEASFKAGALKVLVATSTLSSGVNLPARRVLI--RSPLFGGKQMssltyRQMIGRAGR 614
Cdd:cd18792 67 HGKMTEDEKEAVMLEFREGEYDILVSTTVIEVGIDVPNANTMIieDADRFGLSQL-----HQLRGRVGR 130
|
|
| DEXHc_RHA-like |
cd17917 |
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) ... |
341-406 |
6.95e-03 |
|
DEXH-box helicase domain of DEAD-like helicase RHA family proteins; The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family 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: 438707 [Multi-domain] Cd Length: 159 Bit Score: 39.37 E-value: 6.95e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17933644 341 KLMEQGKLETIGMVVVDEVH---LISDkgrgyILELLLAKILymSRRNGLqiQVITMSATLeNVQLLQS 406
Cdd:cd17917 91 ELLSDPLLSGYSHVILDEAHersLDTD-----FLLGLLKDLL--RKRPDL--KVILMSATL-DAEKFSS 149
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