|
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 ... |
1878-2370 |
1.02e-172 |
|
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: 534.11 E-value: 1.02e-172
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1878 GIGFSTAECETQKHIMQAKLDAIETQAYQlaghsfsftsaddiaqvlflelklppngemktqggrktlgstrrgtesdrk 1957
Cdd:cd08638 1 GIGFDPEELERQRALLQAKLKELEEEAYR--------------------------------------------------- 29
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1958 lrlgrrfSTSKDILNKLKDLHPLPGLILEWRRISNAITKVVFPLQREKHLNPFLRMERIYPV-SQSHTATGRITFTEPNI 2036
Cdd:cd08638 30 -------STSKEVLEQLKRLHPLPKLILEYRKLSKLLTTYVEPLLLLCKLSSSLQMYRIHPTwNQTGTATGRLSSSEPNL 102
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2037 QNVPRDFEIKMPTLVRESppsqasgkgqlamarqnqkvyglhpgqrtvlektsDRGVPFSVSMRHAFVPFPGGLILAADY 2116
Cdd:cd08638 103 QNVPKDFEIKDAPSPPAG-----------------------------------SEGDIPTISLRHAFIPPPGRVLLSADY 147
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2117 SQLELRILAHLSRDCRLIQVLNSGADVFRSIAAEWKMIEPDAVGDNLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAAC 2196
Cdd:cd08638 148 SQLELRILAHLSGDPALIELLNSGGDVFKMIAAQWLGKPVEEVTDEERQQAKQLVYGILYGMGAKSLAEQLGVSEEEAKQ 227
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2197 YIDSFKSRYKGINHFMRDTVKNCRRDGFVETILGRRRYLPGIKDNNPYHKAHAERQAINTTVQGSAADIVKVATVNIQKQ 2276
Cdd:cd08638 228 FIESFKNAYPGVRRFIRETIERARRNGFVETLTGRRRYLPEINSGNSSERAQAERQAVNTVIQGSAADIMKIAMINIHEK 307
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2277 LETFHPTfkshghresmlqsdragllpkrkvkgmfCPMRGGFFILQLHDELLYEVAEEDVVQVAQIVKNEMECAIKLSVK 2356
Cdd:cd08638 308 LHSLLPN----------------------------LPAGRARLVLQIHDELLFEVPESDVDEVARIIKRSMENAAKLSVP 359
|
490
....*....|....
gi 1958664953 2357 LKVKVKIGASWGEL 2370
Cdd:cd08638 360 LPVKVSIGKSWGSL 373
|
|
| DNA_pol_A |
pfam00476 |
DNA polymerase family A; |
1895-2369 |
3.47e-132 |
|
DNA polymerase family A;
Pssm-ID: 459825 Cd Length: 368 Bit Score: 419.54 E-value: 3.47e-132
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1895 AKLDAIETQAYQLAGHSFSFTSADDIAQVLFLELKLPPNGEMKTQggrktlgstrrgtesdrklrlgrrFSTSKDILNKL 1974
Cdd:pfam00476 1 ERLKELEQEIYELAGEEFNINSPKQLGEILFEKLGLPPGKKTKTG------------------------YSTDAEVLEKL 56
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1975 -KDLHPLPGLILEWRRISNAITKVVFPLQreKHLNPflRMERIYP-VSQSHTATGRITFTEPNIQNVPrdfeikmptlVR 2052
Cdd:pfam00476 57 aADEHPIPKLILEYRQLAKLKSTYVDALP--KLINP--DTGRIHTsFNQTVTATGRLSSSDPNLQNIP----------IR 122
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2053 EsppsqasgkgqlamarqnqkvyglhpgqrtvlektsdrgvPFSVSMRHAFVPFPGGLILAADYSQLELRILAHLSRDCR 2132
Cdd:pfam00476 123 T----------------------------------------EEGRRIRKAFVAEPGWVLLSADYSQIELRILAHLSGDEN 162
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2133 LIQVLNSGADVFRSIAAEWKMIEPDAVGDNLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYKGINHFM 2212
Cdd:pfam00476 163 LIEAFRNGEDIHTATASEVFGVPLEEVTPEQRRRAKAINFGIIYGMSAFGLAQQLGISRKEAKEYIDRYFERYPGVKEYM 242
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2213 RDTVKNCRRDGFVETILGRRRYLPGIKDNNPYHKAHAERQAINTTVQGSAADIVKVATVNIQKQLETFHPTFKshghres 2292
Cdd:pfam00476 243 EETVEEAREKGYVETLLGRRRYLPDINSSNRNLRSFAERAAINAPIQGSAADIIKLAMIRVDEALKEEGLKAR------- 315
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958664953 2293 MlqsdragllpkrkvkgmfcpmrggffILQLHDELLYEVAEEDVVQVAQIVKNEMEC--AIKLSVKLKVKVKIGASWGE 2369
Cdd:pfam00476 316 L--------------------------LLQVHDELVFEVPEEEVEEVAALVKEEMENenAVKLSVPLKVDVGIGKNWGE 368
|
|
| PolA |
COG0749 |
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ... |
1685-2371 |
9.69e-124 |
|
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and repair];
Pssm-ID: 440512 [Multi-domain] Cd Length: 575 Bit Score: 403.66 E-value: 9.69e-124
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1685 AVVVGLAVCWGGKDAYYLSLQKEqkqsemspslAPPPLDATLTVKERMEYLQsclqkksDQERSVVTYDFIQTYKVLLlS 1764
Cdd:COG0749 18 AELVGISFAVEPGEAAYIPLAHG----------APEQLDLDEVLAALKPLLE-------DPAIPKIGQNLKYDLHVLA-R 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1765 CGISLEPSYEDPKVACWLLDPDSKEPTLHSIVTSFLPHELALLEGIeTGPGIQSLGLN-VNTDHSGRYrASVESVLIFNS 1843
Cdd:COG0749 80 YGIELAGVAFDTMLASYLLNPGRRRHGLDDLAERYLGHETISYEEL-AGKGKKQLTFDqVPLEEAAEY-AAEDADITLRL 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1844 MNQLNSMLQKENLHDIFCKVEMPSQYCLALLELNGIGFSTAECETQKHIMQAKLDAIETQAYQLAGHSFSFTSADDIAQV 1923
Cdd:COG0749 158 HEVLKPELEEEGLLKLYEEIELPLVPVLARMERNGILVDRELLAELSAELAKRLAELEQEIYELAGEEFNLNSPKQLGEI 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1924 LFLELKLPPNGEMKTQggrktlgstrrgtesdrklrlgrrFSTSKDILNKLKDLHPLPGLILEWRRISnaitKV----VF 1999
Cdd:COG0749 238 LFEKLGLPVGKKTKTG------------------------YSTDAEVLEKLAEDHPIPALILEYRQLS----KLkstyVD 289
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2000 PLQreKHLNPflRMERIYPV-SQSHTATGRITFTEPNIQNVPrdfeikmptlVResppsqasgkgqLAMARQnqkvyglh 2078
Cdd:COG0749 290 ALP--KLINP--DTGRIHTSfNQTVTATGRLSSSDPNLQNIP----------IR------------TEEGRR-------- 335
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2079 pgqrtvlektsdrgvpfsvsMRHAFVPFPGGLILAADYSQLELRILAHLSRDCRLIQVLNSGADVFRSIAAEwkM--IEP 2156
Cdd:COG0749 336 --------------------IRKAFVAPEGYVLLSADYSQIELRILAHLSGDEGLIEAFREGEDIHAATAAE--VfgVPL 393
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2157 DAVGDNLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYKGINHFMRDTVKNCRRDGFVETILGRRRYLP 2236
Cdd:COG0749 394 EEVTSEQRRRAKAINFGIIYGMSAFGLARQLGISRKEAKEYIDRYFERYPGVKDYMEETVEEAREKGYVETLFGRRRYLP 473
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2237 GIKDNNPYHKAHAERQAINTTVQGSAADIVKVATVNIQKQLetfhptfkshghRESMLQSdragllpkRkvkgmfcpMrg 2316
Cdd:COG0749 474 DINSSNRNRRSFAERAAINAPIQGSAADIIKLAMIRVDRAL------------KEEGLKS--------R--------M-- 523
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*
gi 1958664953 2317 gffILQLHDELLYEVAEEDVVQVAQIVKNEMECAIKLSVKLKVKVKIGASWGELK 2371
Cdd:COG0749 524 ---LLQVHDELVFEVPEDELEEVKELVKEVMENAVELSVPLVVDVGVGKNWDEAH 575
|
|
| PRK05755 |
PRK05755 |
DNA polymerase I; Provisional |
1685-2371 |
2.50e-115 |
|
DNA polymerase I; Provisional
Pssm-ID: 235591 [Multi-domain] Cd Length: 880 Bit Score: 389.84 E-value: 2.50e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1685 AVVVGLAVCWGGKDAYYLSLqkEQKQSEMSPSLAPppldatltvkermeYLQsclqkksDQERSVVTYDFIQTYKVLLlS 1764
Cdd:PRK05755 332 AELVGLSFAVEPGEAAYIPL--DQLDREVLAALKP--------------LLE-------DPAIKKVGQNLKYDLHVLA-R 387
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1765 CGISLEPSYEDPKVACWLLDPDSKEpTLHSIVTSFLPHELALLEGIE-TGPGIQSLGLNVNTDHSGRyRASVESVLIFNS 1843
Cdd:PRK05755 388 YGIELRGIAFDTMLASYLLDPGRRH-GLDSLAERYLGHKTISFEEVAgKQLTFAQVDLEEAAEYAAE-DADVTLRLHEVL 465
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1844 MNQLnsmLQKENLHDIFCKVEMPSQYCLALLELNGIGFSTAECETQKHIMQAKLDAIETQAYQLAGHSFSFTSADDIAQV 1923
Cdd:PRK05755 466 KPKL---LEEPGLLELYEEIELPLVPVLARMERNGIKVDREYLKELSAELAQRLAELEQEIYELAGEEFNINSPKQLGEI 542
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1924 LFLELKLPPngemktqgGRKTlgstRRGtesdrklrlgrrFSTSKDILNKLKDLHPLPGLILEWRrisnAITK----VVF 1999
Cdd:PRK05755 543 LFEKLGLPV--------GKKT----KTG------------YSTDAEVLEKLADDHPIPDKILEYR----QLSKlkstYTD 594
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2000 PLQreKHLNPflRMERIYP-VSQSHTATGRITFTEPNIQNVPrdfeikmptlVResppsqasgkgqLAMARQnqkvyglh 2078
Cdd:PRK05755 595 ALP--KLINP--DTGRIHTsFNQTVTATGRLSSSDPNLQNIP----------IR------------TEEGRR-------- 640
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2079 pgqrtvlektsdrgvpfsvsMRHAFVPFPGGLILAADYSQLELRILAHLSRDCRLIQVLNSGADVFRSIAAEWKMIEPDA 2158
Cdd:PRK05755 641 --------------------IRKAFVAPEGYKLLSADYSQIELRILAHLSGDEGLIEAFAEGEDIHTATASEVFGVPLEE 700
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2159 VGDNLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYKGINHFMRDTVKNCRRDGFVETILGRRRYLPGI 2238
Cdd:PRK05755 701 VTSEQRRRAKAINFGIIYGMSAFGLAQQLGISRKEAKEYIDRYFERYPGVKEYMERTVEQAREKGYVETLFGRRRYLPDI 780
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2239 KDNNPYHKAHAERQAINTTVQGSAADIVKVATVNIQKQLEtfhptfkshghresmlqsdRAGLLPKrkvkgmfcpMrggf 2318
Cdd:PRK05755 781 NSRNGNRRAFAERAAINAPIQGSAADIIKLAMIRVDKALK-------------------EEGLKSR---------M---- 828
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|...
gi 1958664953 2319 fILQLHDELLYEVAEEDVVQVAQIVKNEMECAIKLSVKLKVKVKIGASWGELK 2371
Cdd:PRK05755 829 -LLQVHDELVFEVPEDELEEVKKLVKEVMENAVELSVPLVVDVGVGDNWDEAH 880
|
|
| pola |
TIGR00593 |
DNA polymerase I; All proteins in this family for which functions are known are DNA ... |
1759-2371 |
2.15e-102 |
|
DNA polymerase I; All proteins in this family for which functions are known are DNA polymerases Many also have an exonuclease motif. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273160 [Multi-domain] Cd Length: 887 Bit Score: 352.03 E-value: 2.15e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1759 KVLLLSCGISLEPSYEDPKVACWLLDPdSKEPTLHSIVTSFLPHELALLEGI-ETGPGIQSLGLNVNTDHSGRyrasvES 1837
Cdd:TIGR00593 390 MHLLKREGIELGGVIFDTMLAAYLLDP-AQVSTLDTLARRYLVEELILDEKIgGKLAKFAFPPLEEATEYLAR-----RA 463
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1838 VLIFNSMNQLNSMLQKENLHDIFCKVEMPSQYCLALLELNGIGFSTAECET-QKHIMQaKLDAIETQAYQLAGHSFSFTS 1916
Cdd:TIGR00593 464 AATKRLAEELLKELDENKLLSLYREIELPLSKVLAEMEKTGIKVDADYLQElSQEFGE-EIADLEEEIYELAGEEFNINS 542
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1917 ADDIAQVLFLELKLPPNGEMKTqggrktlgstrrgtesdrklrlGRrfSTSKDILNKLKDLHPLPGLILEWRRISNAITK 1996
Cdd:TIGR00593 543 PKQLGEVLFEKLGLPVGKKTKT----------------------GY--STDADVLEKLREKHPIIALILEYRQLTKLKST 598
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1997 VVFPLQREkhLNPflRMERIYPV-SQSHTATGRITFTEPNIQNVPrdfeikmptlVResppsqaSGKGQLamarqnqkvy 2075
Cdd:TIGR00593 599 YVDGLPEL--VNP--DTGRIHTTfNQTGTATGRLSSSNPNLQNIP----------IR-------SEEGRK---------- 647
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2076 glhpgqrtvlektsdrgvpfsvsMRHAFVPFPGGLILAADYSQLELRILAHLSRDCRLIQVLNSGADVFRSIAAEWKMIE 2155
Cdd:TIGR00593 648 -----------------------IRKAFVAEKGWLLISADYSQIELRVLAHLSQDENLIEAFQNGEDIHTETASRLFGVE 704
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2156 PDAVGDNLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYKGINHFMRDTVKNCRRDGFVETILGRRRYL 2235
Cdd:TIGR00593 705 IEDVTPNMRRIAKTINFGVVYGMSAFGLAQELGISRKEAKEFIERYFARYPGVKDYIENTVEEARKKGYVETLFGRRRYI 784
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2236 PGIKDNNPYHKAHAERQAINTTVQGSAADIVKVATVNIQKQletfhptFKSHGHRESMLqsdragllpkrkvkgmfcpmr 2315
Cdd:TIGR00593 785 PDINSRNRNVREAAERMAINAPIQGSAADIMKIAMIKLDKR-------LKERKLKARLL--------------------- 836
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*.
gi 1958664953 2316 ggffiLQLHDELLYEVAEEDVVQVAQIVKNEMECAIKLSVKLKVKVKIGASWGELK 2371
Cdd:TIGR00593 837 -----LQVHDELIFEAPEEEAEEVAALVKEVMEHAYPLAVPLEVEVGTGKNWGEAK 887
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
14-488 |
4.52e-95 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 319.15 E-value: 4.52e-95
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 14 DVAVCTIERANGLINRliEENKMDLLGTVVVDELHMLGDSHRGYLLELLLTKvcfvtrksascqadsASALACAVQIVGM 93
Cdd:COG1204 115 DILVATPEKLDSLLRN--GPSWLRDVDLVVVDEAHLIDDESRGPTLEVLLAR---------------LRRLNPEAQIVAL 177
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 94 SATLPNLQLVASWLNAELYHTDFRPVPLLESIKVGNSIYdssmklvreFQPLLQVKGDEdhIVSLCYETVRDNHSVLVFC 173
Cdd:COG1204 178 SATIGNAEEIAEWLDAELVKSDWRPVPLNEGVLYDGVLR---------FDDGSRRSKDP--TLALALDLLEEGGQVLVFV 246
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 174 PSKKWCEKVADIIAREFYNLHHQPEglvkssefppvildQKSLLEVIDQLKR--SPSGLDSVLKNTVPWGVAFHHAGLTF 251
Cdd:COG1204 247 SSRRDAESLAKKLADELKRRLTPEE--------------REELEELAEELLEvsEETHTNEKLADCLEKGVAFHHAGLPS 312
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 252 EERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIRTP-VFGGQPLDILTYKQMVGRAGRKGVDTMGESILVCKNSEK 330
Cdd:COG1204 313 ELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRDTkRGGMVPIPVLEFKQMAGRAGRPGYDPYGEAILVAKSSDE 392
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 331 SKGIA--LLQGSLEPVHSCLQSQgevtSTMIRAILEIIVSGVASTSQDMQTYAACTFLAadvkegkqgIQRNRDDVQRgA 408
Cdd:COG1204 393 ADELFerYILGEPEPIRSKLANE----SALRTHLLALIASGFANSREELLDFLENTFYA---------YQYDKGDLEE-V 458
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 409 VDACVTWLLENEFIQaaepsdgTGGKVYHPTHLGSATLSSSLSPtDTLDIFADLQRAMKGFVleNDLHIVYLVTpVFEDW 488
Cdd:COG1204 459 VDDALEFLLENGFIE-------EDGDRLRATKLGKLVSRLYIDP-LTAAELVDGLRKADEEF--TDLGLLHLIL-ILRDW 527
|
|
| POLAc |
smart00482 |
DNA polymerase A domain; |
2098-2335 |
3.12e-85 |
|
DNA polymerase A domain;
Pssm-ID: 214687 Cd Length: 207 Bit Score: 277.97 E-value: 3.12e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2098 SMRHAFVPFPGGLILAADYSQLELRILAHLSRDCRLIQVLNSGADVFRSIAAEWKMIEPDAVGDNLRQQAKQICYGIIYG 2177
Cdd:smart00482 3 EIRRAFIAPPGYVLVSADYSQIELRILAHLSGDENLIEAFNNGGDIHTKTAAQVFGVPEEEVTPELRRAAKAINFGIIYG 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2178 MGAKSLGEQMGIKENDAACYIDSFKSRYKGINHFMRDTVKNCRRDGFVETILGRRRYLPGIKDNNPYHKAHAERQAINTT 2257
Cdd:smart00482 83 MGAKGLAEQLGISEAEAKELIKKYFARFPGVRRYIDRTLEEARRKGYVTTLFGRRRYIPDIDSRNPVLRAAAERAAVNTP 162
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958664953 2258 VQGSAADIVKVATVNIQKQLETFHPtfkshghresmlqsdragllpkrkvkgmfcpmrGGFFILQLHDELLYEVAEED 2335
Cdd:smart00482 163 IQGSAADILKLAMIKMDEALKEFGL---------------------------------RARLLLQVHDELVFEVPEEE 207
|
|
| PRK02362 |
PRK02362 |
ATP-dependent DNA helicase; |
14-660 |
2.24e-76 |
|
ATP-dependent DNA helicase;
Pssm-ID: 235032 [Multi-domain] Cd Length: 737 Bit Score: 271.06 E-value: 2.24e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 14 DVAVCTIERANGLInrlieENK---MDLLGTVVVDELHMLGDSHRGYLLELLLTKVcfvtRKsascqadsasaLACAVQI 90
Cdd:PRK02362 115 DIIVATSEKVDSLL-----RNGapwLDDITCVVVDEVHLIDSANRGPTLEVTLAKL----RR-----------LNPDLQV 174
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 91 VGMSATLPNLQLVASWLNAELYHTDFRPVPLLESIKVGNSI-YDSSMKLVRefqpllQVKGDEDhiVSLCYETVRDNHSV 169
Cdd:PRK02362 175 VALSATIGNADELADWLDAELVDSEWRPIDLREGVFYGGAIhFDDSQREVE------VPSKDDT--LNLVLDTLEEGGQC 246
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 170 LVFCPSKKWCE----KVADIIAREFYNLhhqpeglvkssefppvilDQKSLLEVIDQLKR-SPSGLDSVLKNTVPWGVAF 244
Cdd:PRK02362 247 LVFVSSRRNAEgfakRAASALKKTLTAA------------------ERAELAELAEEIREvSDTETSKDLADCVAKGAAF 308
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 245 HHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIR-----TPVFGGQPLDILTYKQMVGRAGRKGVDTMG 319
Cdd:PRK02362 309 HHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRdyrryDGGAGMQPIPVLEYHQMAGRAGRPGLDPYG 388
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 320 ESILVCKNSEKSKgiALLQ----GSLEPVHSCLQsqgevTSTMIRA-ILEIIVSGVASTSQDMQTYAACTFLAAdvkegK 394
Cdd:PRK02362 389 EAVLLAKSYDELD--ELFEryiwADPEDVRSKLA-----TEPALRThVLSTIASGFARTRDGLLEFLEATFYAT-----Q 456
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 395 QGIQRNRDDVqrgaVDACVTWLLENEFIQAAepsdgtgGKVYHPTHLGSATLSSSLSPTDTLDIfADLQRAMKGFVLEND 474
Cdd:PRK02362 457 TDDTGRLERV----VDDVLDFLERNGMIEED-------GETLEATELGHLVSRLYIDPLSAAEI-IDGLEAAKKPTDLGL 524
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 475 LHIVyLVTP----VFEDWTSIDWYRFFC------LWEKLPTSMKRVAelvgvEEGFLaRCVKgkvvarterqhrqmaihk 544
Cdd:PRK02362 525 LHLV-CSTPdmyeLYLRSGDYEWLNEYLyehedeLLGDVPSEFEDDE-----FEDFL-SAVK------------------ 579
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 545 rffTSLVLLDLISEIPLKEINQKYGCNRGQIQSLQQSAAVYAGMITVFSNRLGWHnMELLLSQFQKRLTFGIQRELCDLI 624
Cdd:PRK02362 580 ---TALLLEDWIDEVDEERITERYGVGPGDIRGKVETAEWLLHAAERLASELDLD-LARAARELEKRVEYGVREELLDLV 655
|
650 660 670
....*....|....*....|....*....|....*.
gi 1958664953 625 RVSSLNAQRARFLYASGFLTVADLARADTVEVEAAL 660
Cdd:PRK02362 656 GLRGVGRVRARRLYNAGIESRADLRAADKSVVLAIL 691
|
|
| SF2_C_Ski2 |
cd18795 |
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
117-326 |
1.28e-57 |
|
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: 196.62 E-value: 1.28e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 117 RPVPLLESIKVGNSIYDSSMKLVREfqpllqvKGDEDHIVSLCYETVRDNHSVLVFCPSKKWCEKVADIIArefynlhhq 196
Cdd:cd18795 1 RPVPLEEYVLGFNGLGIKLRVDVMN-------KFDSDIIVLLKIETVSEGKPVLVFCSSRKECEKTAKDLA--------- 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 197 peglvkssefppvildqksllevidqlkrspsgldsvlkntvpwGVAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLS 276
Cdd:cd18795 65 --------------------------------------------GIAFHHAGLTREDRELVEELFREGLIKVLVATSTLA 100
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 1958664953 277 SGVNLPARRVIIR-TPVFGG---QPLDILTYKQMVGRAGRKGVDTMGESILVCK 326
Cdd:cd18795 101 AGVNLPARTVIIKgTQRYDGkgyRELSPLEYLQMIGRAGRPGFDTRGEAIIMTK 154
|
|
| HTH_61 |
pfam20470 |
Helix-turn-helix domain; This entry represents a presumed helix-turn-helix domain found in DNA ... |
319-423 |
4.49e-31 |
|
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: 118.03 E-value: 4.49e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 319 GESILVCKNSEKSKGIALLQGSLEPVHSCLQSQgevTSTMIRAILEIIVSGVASTSQDMQTYAACTFLAADVKEGKQGIQ 398
Cdd:pfam20470 1 GESILICKEKDLEKVAELLRAELPPVYSCLLPE---KRGIKRALLEIIALGLATSPEDVDEYMSCTLLSVQQKELDVEKS 77
|
90 100
....*....|....*....|....*
gi 1958664953 399 rnrddvqrgaVDACVTWLLENEFIQ 423
Cdd:pfam20470 78 ----------IESSLEELVENGLIT 92
|
|
| phage_DpoZ_1 |
NF038380 |
aminoadenine-incorporating DNA polymerase DpoZ; |
1853-2369 |
1.71e-17 |
|
aminoadenine-incorporating DNA polymerase DpoZ;
Pssm-ID: 468497 [Multi-domain] Cd Length: 604 Bit Score: 88.95 E-value: 1.71e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1853 KENLHDIfCKVEMPSQYCLALLELNGIGFSTAECETQKHIMQAKLDAIETQAYQLAGHSFSFTSADDIAQvlFLELKLPP 1932
Cdd:NF038380 173 RQGLQRV-VELERRLFPVLIDMEWRGIRVDLEAAEAAIPELDKVIDQLQKELNEIAGFEFNVNSSPQIRK--LFKPKKIS 249
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1933 NGEMKTQGGrKTLGSTRRGTESdrklrlgrrfsTSKDILNKLKdlHPLPGLILEWRriSNAITKVVFPLqreKHLNPFLR 2012
Cdd:NF038380 250 KGQWVAIDG-TPLETTDAGKPS-----------LGADALREIK--HPAAAKILELR--KLIKTRDTFLR---GHVLGHAV 310
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2013 MERIYP-VSQS------HTATGRITFTEPNIQNVP-RDFEIkmptlvresppsqASgkgqlamarqnqkvyglhpgqrtv 2084
Cdd:NF038380 311 GGGVHPnINQTkgedggGTGTGRLSYTDPALQQIPsRDKAI-------------AA------------------------ 353
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2085 lektsdrgvpfsvSMRHAFVPFPGGLILAADYSQLELRILAHLSRDCRLIQV--LNSGADvFRSIAAEWKMI--EPDAVG 2160
Cdd:NF038380 354 -------------IVRPIFLPDEGQVWLCSDLAQFEFRIFAHLVNNPSIIAAyaEDPELD-FHQIVADMTGLprNATYSG 419
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2161 DnlrQQAKQICYGIIYGMGAKSLGEQMG----IKEND--------------AACYIDSFKSRYKGINHFMRDTVKNCRRD 2222
Cdd:NF038380 420 Q---ANAKQINLGMIFNMGNGKLADKMGmpyeWEEFTfgkevrrykkagpeAMAVIENYHRKLPGVKELADRAKAVAKER 496
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2223 GFVETILGRRRYLPGIKdnnpyhKAHAerqAINTTVQGSAADIVKVATVNIQKQLETfhptfkshghresmlqsdragll 2302
Cdd:NF038380 497 GYVRTAMGRRLRFPGGM------KTYK---ASGLLIQATAADLNKENLLEIDEVLGS----------------------- 544
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958664953 2303 pkrkvkgmfcpmRGGFFILQLHDELLYEVAEEDVVQ-VAQIVKNEMEcaiKLSVKLKVKVKI-----GASWGE 2369
Cdd:NF038380 545 ------------LDGRLLLNTHDEYSMSLPEDDVRKpIKERVKLFIE---DSSPWLRVPIILelsgfGRNWWE 602
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
241-314 |
1.58e-16 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 76.48 E-value: 1.58e-16
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958664953 241 GVAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLP-ARRVIIRTPvfggqPLDILTYKQMVGRAGRKG 314
Cdd:smart00490 13 KVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPgVDLVIIYDL-----PWSPASYIQRIGRAGRAG 82
|
|
| DNA_polA_I_Bacillus_like_exo |
cd06140 |
inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and ... |
1672-1872 |
6.97e-06 |
|
inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases; Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.
Pssm-ID: 176652 [Multi-domain] Cd Length: 178 Bit Score: 48.80 E-value: 6.97e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1672 VEDDGFPVHGSDcavVVGLAVcWGGKDAYYLSLQKEQKQSEmspslappPLDATLtvkermeylqsclqkkSDQERSVVT 1751
Cdd:cd06140 10 VELLGENYHTAD---IIGLAL-ANGGGAYYIPLELALLDLA--------ALKEWL----------------EDEKIPKVG 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1752 YDFIQTYkVLLLSCGISLEPSYEDPKVACWLLDPDSKEPTLHSIVTSFLPHEL-ALLEGIETGPGIQSLGLNVNTDHSGR 1830
Cdd:cd06140 62 HDAKRAY-VALKRHGIELAGVAFDTMLAAYLLDPTRSSYDLADLAKRYLGRELpSDEEVYGKGAKFAVPDEEVLAEHLAR 140
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 1958664953 1831 yRASVesvlIFNSMNQLNSMLQKENLHDIFCKVEMPSQYCLA 1872
Cdd:cd06140 141 -KAAA----IARLAPKLEEELEENEQLELYYEVELPLAEVLA 177
|
|
| |
|
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 ... |
1878-2370 |
1.02e-172 |
|
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: 534.11 E-value: 1.02e-172
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1878 GIGFSTAECETQKHIMQAKLDAIETQAYQlaghsfsftsaddiaqvlflelklppngemktqggrktlgstrrgtesdrk 1957
Cdd:cd08638 1 GIGFDPEELERQRALLQAKLKELEEEAYR--------------------------------------------------- 29
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1958 lrlgrrfSTSKDILNKLKDLHPLPGLILEWRRISNAITKVVFPLQREKHLNPFLRMERIYPV-SQSHTATGRITFTEPNI 2036
Cdd:cd08638 30 -------STSKEVLEQLKRLHPLPKLILEYRKLSKLLTTYVEPLLLLCKLSSSLQMYRIHPTwNQTGTATGRLSSSEPNL 102
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2037 QNVPRDFEIKMPTLVRESppsqasgkgqlamarqnqkvyglhpgqrtvlektsDRGVPFSVSMRHAFVPFPGGLILAADY 2116
Cdd:cd08638 103 QNVPKDFEIKDAPSPPAG-----------------------------------SEGDIPTISLRHAFIPPPGRVLLSADY 147
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2117 SQLELRILAHLSRDCRLIQVLNSGADVFRSIAAEWKMIEPDAVGDNLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAAC 2196
Cdd:cd08638 148 SQLELRILAHLSGDPALIELLNSGGDVFKMIAAQWLGKPVEEVTDEERQQAKQLVYGILYGMGAKSLAEQLGVSEEEAKQ 227
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2197 YIDSFKSRYKGINHFMRDTVKNCRRDGFVETILGRRRYLPGIKDNNPYHKAHAERQAINTTVQGSAADIVKVATVNIQKQ 2276
Cdd:cd08638 228 FIESFKNAYPGVRRFIRETIERARRNGFVETLTGRRRYLPEINSGNSSERAQAERQAVNTVIQGSAADIMKIAMINIHEK 307
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2277 LETFHPTfkshghresmlqsdragllpkrkvkgmfCPMRGGFFILQLHDELLYEVAEEDVVQVAQIVKNEMECAIKLSVK 2356
Cdd:cd08638 308 LHSLLPN----------------------------LPAGRARLVLQIHDELLFEVPESDVDEVARIIKRSMENAAKLSVP 359
|
490
....*....|....
gi 1958664953 2357 LKVKVKIGASWGEL 2370
Cdd:cd08638 360 LPVKVSIGKSWGSL 373
|
|
| DNA_pol_A |
pfam00476 |
DNA polymerase family A; |
1895-2369 |
3.47e-132 |
|
DNA polymerase family A;
Pssm-ID: 459825 Cd Length: 368 Bit Score: 419.54 E-value: 3.47e-132
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1895 AKLDAIETQAYQLAGHSFSFTSADDIAQVLFLELKLPPNGEMKTQggrktlgstrrgtesdrklrlgrrFSTSKDILNKL 1974
Cdd:pfam00476 1 ERLKELEQEIYELAGEEFNINSPKQLGEILFEKLGLPPGKKTKTG------------------------YSTDAEVLEKL 56
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1975 -KDLHPLPGLILEWRRISNAITKVVFPLQreKHLNPflRMERIYP-VSQSHTATGRITFTEPNIQNVPrdfeikmptlVR 2052
Cdd:pfam00476 57 aADEHPIPKLILEYRQLAKLKSTYVDALP--KLINP--DTGRIHTsFNQTVTATGRLSSSDPNLQNIP----------IR 122
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2053 EsppsqasgkgqlamarqnqkvyglhpgqrtvlektsdrgvPFSVSMRHAFVPFPGGLILAADYSQLELRILAHLSRDCR 2132
Cdd:pfam00476 123 T----------------------------------------EEGRRIRKAFVAEPGWVLLSADYSQIELRILAHLSGDEN 162
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2133 LIQVLNSGADVFRSIAAEWKMIEPDAVGDNLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYKGINHFM 2212
Cdd:pfam00476 163 LIEAFRNGEDIHTATASEVFGVPLEEVTPEQRRRAKAINFGIIYGMSAFGLAQQLGISRKEAKEYIDRYFERYPGVKEYM 242
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2213 RDTVKNCRRDGFVETILGRRRYLPGIKDNNPYHKAHAERQAINTTVQGSAADIVKVATVNIQKQLETFHPTFKshghres 2292
Cdd:pfam00476 243 EETVEEAREKGYVETLLGRRRYLPDINSSNRNLRSFAERAAINAPIQGSAADIIKLAMIRVDEALKEEGLKAR------- 315
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958664953 2293 MlqsdragllpkrkvkgmfcpmrggffILQLHDELLYEVAEEDVVQVAQIVKNEMEC--AIKLSVKLKVKVKIGASWGE 2369
Cdd:pfam00476 316 L--------------------------LLQVHDELVFEVPEEEVEEVAALVKEEMENenAVKLSVPLKVDVGIGKNWGE 368
|
|
| PolA |
COG0749 |
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and ... |
1685-2371 |
9.69e-124 |
|
DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and repair];
Pssm-ID: 440512 [Multi-domain] Cd Length: 575 Bit Score: 403.66 E-value: 9.69e-124
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1685 AVVVGLAVCWGGKDAYYLSLQKEqkqsemspslAPPPLDATLTVKERMEYLQsclqkksDQERSVVTYDFIQTYKVLLlS 1764
Cdd:COG0749 18 AELVGISFAVEPGEAAYIPLAHG----------APEQLDLDEVLAALKPLLE-------DPAIPKIGQNLKYDLHVLA-R 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1765 CGISLEPSYEDPKVACWLLDPDSKEPTLHSIVTSFLPHELALLEGIeTGPGIQSLGLN-VNTDHSGRYrASVESVLIFNS 1843
Cdd:COG0749 80 YGIELAGVAFDTMLASYLLNPGRRRHGLDDLAERYLGHETISYEEL-AGKGKKQLTFDqVPLEEAAEY-AAEDADITLRL 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1844 MNQLNSMLQKENLHDIFCKVEMPSQYCLALLELNGIGFSTAECETQKHIMQAKLDAIETQAYQLAGHSFSFTSADDIAQV 1923
Cdd:COG0749 158 HEVLKPELEEEGLLKLYEEIELPLVPVLARMERNGILVDRELLAELSAELAKRLAELEQEIYELAGEEFNLNSPKQLGEI 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1924 LFLELKLPPNGEMKTQggrktlgstrrgtesdrklrlgrrFSTSKDILNKLKDLHPLPGLILEWRRISnaitKV----VF 1999
Cdd:COG0749 238 LFEKLGLPVGKKTKTG------------------------YSTDAEVLEKLAEDHPIPALILEYRQLS----KLkstyVD 289
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2000 PLQreKHLNPflRMERIYPV-SQSHTATGRITFTEPNIQNVPrdfeikmptlVResppsqasgkgqLAMARQnqkvyglh 2078
Cdd:COG0749 290 ALP--KLINP--DTGRIHTSfNQTVTATGRLSSSDPNLQNIP----------IR------------TEEGRR-------- 335
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2079 pgqrtvlektsdrgvpfsvsMRHAFVPFPGGLILAADYSQLELRILAHLSRDCRLIQVLNSGADVFRSIAAEwkM--IEP 2156
Cdd:COG0749 336 --------------------IRKAFVAPEGYVLLSADYSQIELRILAHLSGDEGLIEAFREGEDIHAATAAE--VfgVPL 393
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2157 DAVGDNLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYKGINHFMRDTVKNCRRDGFVETILGRRRYLP 2236
Cdd:COG0749 394 EEVTSEQRRRAKAINFGIIYGMSAFGLARQLGISRKEAKEYIDRYFERYPGVKDYMEETVEEAREKGYVETLFGRRRYLP 473
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2237 GIKDNNPYHKAHAERQAINTTVQGSAADIVKVATVNIQKQLetfhptfkshghRESMLQSdragllpkRkvkgmfcpMrg 2316
Cdd:COG0749 474 DINSSNRNRRSFAERAAINAPIQGSAADIIKLAMIRVDRAL------------KEEGLKS--------R--------M-- 523
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*
gi 1958664953 2317 gffILQLHDELLYEVAEEDVVQVAQIVKNEMECAIKLSVKLKVKVKIGASWGELK 2371
Cdd:COG0749 524 ---LLQVHDELVFEVPEDELEEVKELVKEVMENAVELSVPLVVDVGVGKNWDEAH 575
|
|
| PRK05755 |
PRK05755 |
DNA polymerase I; Provisional |
1685-2371 |
2.50e-115 |
|
DNA polymerase I; Provisional
Pssm-ID: 235591 [Multi-domain] Cd Length: 880 Bit Score: 389.84 E-value: 2.50e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1685 AVVVGLAVCWGGKDAYYLSLqkEQKQSEMSPSLAPppldatltvkermeYLQsclqkksDQERSVVTYDFIQTYKVLLlS 1764
Cdd:PRK05755 332 AELVGLSFAVEPGEAAYIPL--DQLDREVLAALKP--------------LLE-------DPAIKKVGQNLKYDLHVLA-R 387
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1765 CGISLEPSYEDPKVACWLLDPDSKEpTLHSIVTSFLPHELALLEGIE-TGPGIQSLGLNVNTDHSGRyRASVESVLIFNS 1843
Cdd:PRK05755 388 YGIELRGIAFDTMLASYLLDPGRRH-GLDSLAERYLGHKTISFEEVAgKQLTFAQVDLEEAAEYAAE-DADVTLRLHEVL 465
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1844 MNQLnsmLQKENLHDIFCKVEMPSQYCLALLELNGIGFSTAECETQKHIMQAKLDAIETQAYQLAGHSFSFTSADDIAQV 1923
Cdd:PRK05755 466 KPKL---LEEPGLLELYEEIELPLVPVLARMERNGIKVDREYLKELSAELAQRLAELEQEIYELAGEEFNINSPKQLGEI 542
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1924 LFLELKLPPngemktqgGRKTlgstRRGtesdrklrlgrrFSTSKDILNKLKDLHPLPGLILEWRrisnAITK----VVF 1999
Cdd:PRK05755 543 LFEKLGLPV--------GKKT----KTG------------YSTDAEVLEKLADDHPIPDKILEYR----QLSKlkstYTD 594
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2000 PLQreKHLNPflRMERIYP-VSQSHTATGRITFTEPNIQNVPrdfeikmptlVResppsqasgkgqLAMARQnqkvyglh 2078
Cdd:PRK05755 595 ALP--KLINP--DTGRIHTsFNQTVTATGRLSSSDPNLQNIP----------IR------------TEEGRR-------- 640
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2079 pgqrtvlektsdrgvpfsvsMRHAFVPFPGGLILAADYSQLELRILAHLSRDCRLIQVLNSGADVFRSIAAEWKMIEPDA 2158
Cdd:PRK05755 641 --------------------IRKAFVAPEGYKLLSADYSQIELRILAHLSGDEGLIEAFAEGEDIHTATASEVFGVPLEE 700
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2159 VGDNLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYKGINHFMRDTVKNCRRDGFVETILGRRRYLPGI 2238
Cdd:PRK05755 701 VTSEQRRRAKAINFGIIYGMSAFGLAQQLGISRKEAKEYIDRYFERYPGVKEYMERTVEQAREKGYVETLFGRRRYLPDI 780
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2239 KDNNPYHKAHAERQAINTTVQGSAADIVKVATVNIQKQLEtfhptfkshghresmlqsdRAGLLPKrkvkgmfcpMrggf 2318
Cdd:PRK05755 781 NSRNGNRRAFAERAAINAPIQGSAADIIKLAMIRVDKALK-------------------EEGLKSR---------M---- 828
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|...
gi 1958664953 2319 fILQLHDELLYEVAEEDVVQVAQIVKNEMECAIKLSVKLKVKVKIGASWGELK 2371
Cdd:PRK05755 829 -LLQVHDELVFEVPEDELEEVKKLVKEVMENAVELSVPLVVDVGVGDNWDEAH 880
|
|
| DNA_pol_A_pol_I_C |
cd08637 |
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ... |
1887-2368 |
5.28e-112 |
|
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: 361.74 E-value: 5.28e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1887 ETQKHIMQAKLDAIETQAYQLAGHSFSFTSADDIAQVLFLELKLPPngemktqgGRKTlgstRRGtesdrklrlgrrFST 1966
Cdd:cd08637 6 EELSEELEKELAELEEEIYELAGEEFNINSPKQLGEVLFEKLGLPV--------GKKT----KTG------------YST 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1967 SKDILNKLKDLHPLPGLILEWRRISNAITKVVFPLQreKHLNPflRMERIYPV-SQSHTATGRITFTEPNIQNVPrdfei 2045
Cdd:cd08637 62 DAEVLEKLADEHPIVELILEYRELTKLKSTYVDALP--KLINP--KTGRIHTSfNQTVTATGRLSSSDPNLQNIP----- 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2046 kmptlVResppsqasgkgqLAMARQnqkvyglhpgqrtvlektsdrgvpfsvsMRHAFVPFPGGLILAADYSQLELRILA 2125
Cdd:cd08637 133 -----IR------------TEEGRE----------------------------IRKAFVAEEGWVLLSADYSQIELRILA 167
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2126 HLSRDCRLIQVLNSGADVFRSIAAEWKMIEPDAVGDNLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRY 2205
Cdd:cd08637 168 HLSGDEALIEAFKNGEDIHTRTAAEVFGVPPEEVTPEMRRIAKAVNFGIIYGISAFGLSQQLGISRKEAKEYIDRYFARY 247
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2206 KGINHFMRDTVKNCRRDGFVETILGRRRYLPGIKDNNPYHKAHAERQAINTTVQGSAADIVKVATVNIQKQLetfhptfK 2285
Cdd:cd08637 248 PGVKEYMEETVEEAREKGYVETLFGRRRYIPEINSKNRNVRAFAERIAINTPIQGTAADIIKLAMIRVHKAL-------K 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2286 SHGHRESMlqsdragllpkrkvkgmfcpmrggffILQLHDELLYEVAEEDVVQVAQIVKNEMECAIKLSVKLKVKVKIGA 2365
Cdd:cd08637 321 EEGLKARM--------------------------LLQVHDELVFEVPEEELEEVAALVKEEMENAVELSVPLKVDVGVGK 374
|
...
gi 1958664953 2366 SWG 2368
Cdd:cd08637 375 NWG 377
|
|
| pola |
TIGR00593 |
DNA polymerase I; All proteins in this family for which functions are known are DNA ... |
1759-2371 |
2.15e-102 |
|
DNA polymerase I; All proteins in this family for which functions are known are DNA polymerases Many also have an exonuclease motif. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273160 [Multi-domain] Cd Length: 887 Bit Score: 352.03 E-value: 2.15e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1759 KVLLLSCGISLEPSYEDPKVACWLLDPdSKEPTLHSIVTSFLPHELALLEGI-ETGPGIQSLGLNVNTDHSGRyrasvES 1837
Cdd:TIGR00593 390 MHLLKREGIELGGVIFDTMLAAYLLDP-AQVSTLDTLARRYLVEELILDEKIgGKLAKFAFPPLEEATEYLAR-----RA 463
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1838 VLIFNSMNQLNSMLQKENLHDIFCKVEMPSQYCLALLELNGIGFSTAECET-QKHIMQaKLDAIETQAYQLAGHSFSFTS 1916
Cdd:TIGR00593 464 AATKRLAEELLKELDENKLLSLYREIELPLSKVLAEMEKTGIKVDADYLQElSQEFGE-EIADLEEEIYELAGEEFNINS 542
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1917 ADDIAQVLFLELKLPPNGEMKTqggrktlgstrrgtesdrklrlGRrfSTSKDILNKLKDLHPLPGLILEWRRISNAITK 1996
Cdd:TIGR00593 543 PKQLGEVLFEKLGLPVGKKTKT----------------------GY--STDADVLEKLREKHPIIALILEYRQLTKLKST 598
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1997 VVFPLQREkhLNPflRMERIYPV-SQSHTATGRITFTEPNIQNVPrdfeikmptlVResppsqaSGKGQLamarqnqkvy 2075
Cdd:TIGR00593 599 YVDGLPEL--VNP--DTGRIHTTfNQTGTATGRLSSSNPNLQNIP----------IR-------SEEGRK---------- 647
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2076 glhpgqrtvlektsdrgvpfsvsMRHAFVPFPGGLILAADYSQLELRILAHLSRDCRLIQVLNSGADVFRSIAAEWKMIE 2155
Cdd:TIGR00593 648 -----------------------IRKAFVAEKGWLLISADYSQIELRVLAHLSQDENLIEAFQNGEDIHTETASRLFGVE 704
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2156 PDAVGDNLRQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYIDSFKSRYKGINHFMRDTVKNCRRDGFVETILGRRRYL 2235
Cdd:TIGR00593 705 IEDVTPNMRRIAKTINFGVVYGMSAFGLAQELGISRKEAKEFIERYFARYPGVKDYIENTVEEARKKGYVETLFGRRRYI 784
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2236 PGIKDNNPYHKAHAERQAINTTVQGSAADIVKVATVNIQKQletfhptFKSHGHRESMLqsdragllpkrkvkgmfcpmr 2315
Cdd:TIGR00593 785 PDINSRNRNVREAAERMAINAPIQGSAADIMKIAMIKLDKR-------LKERKLKARLL--------------------- 836
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*.
gi 1958664953 2316 ggffiLQLHDELLYEVAEEDVVQVAQIVKNEMECAIKLSVKLKVKVKIGASWGELK 2371
Cdd:TIGR00593 837 -----LQVHDELIFEAPEEEAEEVAALVKEVMEHAYPLAVPLEVEVGTGKNWGEAK 887
|
|
| BRR2 |
COG1204 |
Replicative superfamily II helicase [Replication, recombination and repair]; |
14-488 |
4.52e-95 |
|
Replicative superfamily II helicase [Replication, recombination and repair];
Pssm-ID: 440817 [Multi-domain] Cd Length: 529 Bit Score: 319.15 E-value: 4.52e-95
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 14 DVAVCTIERANGLINRliEENKMDLLGTVVVDELHMLGDSHRGYLLELLLTKvcfvtrksascqadsASALACAVQIVGM 93
Cdd:COG1204 115 DILVATPEKLDSLLRN--GPSWLRDVDLVVVDEAHLIDDESRGPTLEVLLAR---------------LRRLNPEAQIVAL 177
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 94 SATLPNLQLVASWLNAELYHTDFRPVPLLESIKVGNSIYdssmklvreFQPLLQVKGDEdhIVSLCYETVRDNHSVLVFC 173
Cdd:COG1204 178 SATIGNAEEIAEWLDAELVKSDWRPVPLNEGVLYDGVLR---------FDDGSRRSKDP--TLALALDLLEEGGQVLVFV 246
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 174 PSKKWCEKVADIIAREFYNLHHQPEglvkssefppvildQKSLLEVIDQLKR--SPSGLDSVLKNTVPWGVAFHHAGLTF 251
Cdd:COG1204 247 SSRRDAESLAKKLADELKRRLTPEE--------------REELEELAEELLEvsEETHTNEKLADCLEKGVAFHHAGLPS 312
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 252 EERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIRTP-VFGGQPLDILTYKQMVGRAGRKGVDTMGESILVCKNSEK 330
Cdd:COG1204 313 ELRRLVEDAFREGLIKVLVATPTLAAGVNLPARRVIIRDTkRGGMVPIPVLEFKQMAGRAGRPGYDPYGEAILVAKSSDE 392
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 331 SKGIA--LLQGSLEPVHSCLQSQgevtSTMIRAILEIIVSGVASTSQDMQTYAACTFLAadvkegkqgIQRNRDDVQRgA 408
Cdd:COG1204 393 ADELFerYILGEPEPIRSKLANE----SALRTHLLALIASGFANSREELLDFLENTFYA---------YQYDKGDLEE-V 458
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 409 VDACVTWLLENEFIQaaepsdgTGGKVYHPTHLGSATLSSSLSPtDTLDIFADLQRAMKGFVleNDLHIVYLVTpVFEDW 488
Cdd:COG1204 459 VDDALEFLLENGFIE-------EDGDRLRATKLGKLVSRLYIDP-LTAAELVDGLRKADEEF--TDLGLLHLIL-ILRDW 527
|
|
| POLAc |
smart00482 |
DNA polymerase A domain; |
2098-2335 |
3.12e-85 |
|
DNA polymerase A domain;
Pssm-ID: 214687 Cd Length: 207 Bit Score: 277.97 E-value: 3.12e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2098 SMRHAFVPFPGGLILAADYSQLELRILAHLSRDCRLIQVLNSGADVFRSIAAEWKMIEPDAVGDNLRQQAKQICYGIIYG 2177
Cdd:smart00482 3 EIRRAFIAPPGYVLVSADYSQIELRILAHLSGDENLIEAFNNGGDIHTKTAAQVFGVPEEEVTPELRRAAKAINFGIIYG 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2178 MGAKSLGEQMGIKENDAACYIDSFKSRYKGINHFMRDTVKNCRRDGFVETILGRRRYLPGIKDNNPYHKAHAERQAINTT 2257
Cdd:smart00482 83 MGAKGLAEQLGISEAEAKELIKKYFARFPGVRRYIDRTLEEARRKGYVTTLFGRRRYIPDIDSRNPVLRAAAERAAVNTP 162
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958664953 2258 VQGSAADIVKVATVNIQKQLETFHPtfkshghresmlqsdragllpkrkvkgmfcpmrGGFFILQLHDELLYEVAEED 2335
Cdd:smart00482 163 IQGSAADILKLAMIKMDEALKEFGL---------------------------------RARLLLQVHDELVFEVPEEE 207
|
|
| DNA_pol_A |
cd06444 |
Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and ... |
1978-2367 |
1.67e-81 |
|
Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication; DNA polymerase family A, 5'-3' polymerase domain. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gamma, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic polymerase I (pol I) has two functional domains located on the same polypeptide; a 5'-3' polymerase and a 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and the DNA polymerase activity to fill in the resulting gap. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains.
Pssm-ID: 176473 [Multi-domain] Cd Length: 347 Bit Score: 272.76 E-value: 1.67e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1978 HPLPGLILEWRRISNAITKVVFPLQREKHlnpflRMERIYPVSQSH-TATGRITFTEPNIQNVPRDFeikmptlvrespp 2056
Cdd:cd06444 26 HPAVPLLLEYKKLAKLWSANGWPWLDQWV-----RDGRFHPEYVPGgTVTGRWASRGGNAQQIPRRD------------- 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2057 sqasgkgqlamarqnqkvyglhpgqrtvlektsdrgvPFSVSMRHAFVPFPGGLILAADYSQLELRILAHLSRDCRLIQV 2136
Cdd:cd06444 88 -------------------------------------PLGRDIRQAFVADPGWTLVVADASQLELRVLAALSGDEALAEA 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2137 LNSGADVFRSIAAEWKMIepdAVGDNLRQQAKQICYGIIYG----MGAKSLGEQMGIKENDAACYIDSFKSRYKGINHFM 2212
Cdd:cd06444 131 FGRGGDLYTATASAMFGV---PVGGGERQHAKIANLGAMYGatsgISARLLAQLRRISTKEAAALIELFFSRFPAFPKAM 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2213 RDTVKNCRRD---GFVETILGRRRYLPGIKDN-----------NPYHKAHAERQAINTTVQGSAADIVKVATVNIQKQLE 2278
Cdd:cd06444 208 EYVEDAARRGergGYVRTLLGRRSPPPDIRWTevvsdpaaasrARRVRRAAGRFARNFVVQGTAADWAKLAMVALRRRLE 287
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2279 TFHPtfkshghresmlqsdragllpkrkvkgmfcpmrGGFFILQLHDELLYEVAEEDVVQVAQIVKNEMECAIKL---SV 2355
Cdd:cd06444 288 ELAL---------------------------------DARLVFFVHDEVVLHCPKEEAEAVAAIVREAAEQAVRLlfgSV 334
|
410
....*....|..
gi 1958664953 2356 KLKVKVKIGASW 2367
Cdd:cd06444 335 PVRFPVKIGVVW 346
|
|
| PRK02362 |
PRK02362 |
ATP-dependent DNA helicase; |
14-660 |
2.24e-76 |
|
ATP-dependent DNA helicase;
Pssm-ID: 235032 [Multi-domain] Cd Length: 737 Bit Score: 271.06 E-value: 2.24e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 14 DVAVCTIERANGLInrlieENK---MDLLGTVVVDELHMLGDSHRGYLLELLLTKVcfvtRKsascqadsasaLACAVQI 90
Cdd:PRK02362 115 DIIVATSEKVDSLL-----RNGapwLDDITCVVVDEVHLIDSANRGPTLEVTLAKL----RR-----------LNPDLQV 174
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 91 VGMSATLPNLQLVASWLNAELYHTDFRPVPLLESIKVGNSI-YDSSMKLVRefqpllQVKGDEDhiVSLCYETVRDNHSV 169
Cdd:PRK02362 175 VALSATIGNADELADWLDAELVDSEWRPIDLREGVFYGGAIhFDDSQREVE------VPSKDDT--LNLVLDTLEEGGQC 246
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 170 LVFCPSKKWCE----KVADIIAREFYNLhhqpeglvkssefppvilDQKSLLEVIDQLKR-SPSGLDSVLKNTVPWGVAF 244
Cdd:PRK02362 247 LVFVSSRRNAEgfakRAASALKKTLTAA------------------ERAELAELAEEIREvSDTETSKDLADCVAKGAAF 308
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 245 HHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIR-----TPVFGGQPLDILTYKQMVGRAGRKGVDTMG 319
Cdd:PRK02362 309 HHAGLSREHRELVEDAFRDRLIKVISSTPTLAAGLNLPARRVIIRdyrryDGGAGMQPIPVLEYHQMAGRAGRPGLDPYG 388
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 320 ESILVCKNSEKSKgiALLQ----GSLEPVHSCLQsqgevTSTMIRA-ILEIIVSGVASTSQDMQTYAACTFLAAdvkegK 394
Cdd:PRK02362 389 EAVLLAKSYDELD--ELFEryiwADPEDVRSKLA-----TEPALRThVLSTIASGFARTRDGLLEFLEATFYAT-----Q 456
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 395 QGIQRNRDDVqrgaVDACVTWLLENEFIQAAepsdgtgGKVYHPTHLGSATLSSSLSPTDTLDIfADLQRAMKGFVLEND 474
Cdd:PRK02362 457 TDDTGRLERV----VDDVLDFLERNGMIEED-------GETLEATELGHLVSRLYIDPLSAAEI-IDGLEAAKKPTDLGL 524
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 475 LHIVyLVTP----VFEDWTSIDWYRFFC------LWEKLPTSMKRVAelvgvEEGFLaRCVKgkvvarterqhrqmaihk 544
Cdd:PRK02362 525 LHLV-CSTPdmyeLYLRSGDYEWLNEYLyehedeLLGDVPSEFEDDE-----FEDFL-SAVK------------------ 579
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 545 rffTSLVLLDLISEIPLKEINQKYGCNRGQIQSLQQSAAVYAGMITVFSNRLGWHnMELLLSQFQKRLTFGIQRELCDLI 624
Cdd:PRK02362 580 ---TALLLEDWIDEVDEERITERYGVGPGDIRGKVETAEWLLHAAERLASELDLD-LARAARELEKRVEYGVREELLDLV 655
|
650 660 670
....*....|....*....|....*....|....*.
gi 1958664953 625 RVSSLNAQRARFLYASGFLTVADLARADTVEVEAAL 660
Cdd:PRK02362 656 GLRGVGRVRARRLYNAGIESRADLRAADKSVVLAIL 691
|
|
| PRK01172 |
PRK01172 |
ATP-dependent DNA helicase; |
14-658 |
5.45e-63 |
|
ATP-dependent DNA helicase;
Pssm-ID: 100801 [Multi-domain] Cd Length: 674 Bit Score: 229.77 E-value: 5.45e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 14 DVAVCTIERANGLINRliEENKMDLLGTVVVDELHMLGDSHRGYLLELLLTKVCFVTRKsascqadsasalacaVQIVGM 93
Cdd:PRK01172 113 DVVILTSEKADSLIHH--DPYIINDVGLIVADEIHIIGDEDRGPTLETVLSSARYVNPD---------------ARILAL 175
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 94 SATLPNLQLVASWLNAELYHTDFRPVPLLESIKVGNSIYDSSMKlvrefqpllqvKGDEDhIVSLCYETVRDNHSVLVFC 173
Cdd:PRK01172 176 SATVSNANELAQWLNASLIKSNFRPVPLKLGILYRKRLILDGYE-----------RSQVD-INSLIKETVNDGGQVLVFV 243
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 174 PSKKWCEKVADIIAREFynlhhqpeglvkssefpPVILDQKSLLEVIDqlkrspsGLDSVLKNTVPWGVAFHHAGLTFEE 253
Cdd:PRK01172 244 SSRKNAEDYAEMLIQHF-----------------PEFNDFKVSSENNN-------VYDDSLNEMLPHGVAFHHAGLSNEQ 299
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 254 RDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIRTPV----FGGQPLDILTYKQMVGRAGRKGVDTMGESILVCKnSE 329
Cdd:PRK01172 300 RRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIVRDITrygnGGIRYLSNMEIKQMIGRAGRPGYDQYGIGYIYAA-SP 378
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 330 KSKGIA--LLQGSLEPVHSCLQSQGEVTSTmiraILEIIVSGVASTSQDMQTYAACTFLAAdvkegkqgiqRNRDDVQRG 407
Cdd:PRK01172 379 ASYDAAkkYLSGEPEPVISYMGSQRKVRFN----TLAAISMGLASSMEDLILFYNETLMAI----------QNGVDEIDY 444
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 408 AVDACVTWLLENEFIQaaepsdgtGGKVYHPTHLGSAtlssslsptdTLDIFADLQRAMkgfvlendlhivyLVTPVFED 487
Cdd:PRK01172 445 YIESSLKFLKENGFIK--------GDVTLRATRLGKL----------TSDLYIDPESAL-------------ILKSAFDH 493
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 488 WTSIDWYRFF-CLW-EKLPTSMKrvaELVGVEEgFLARC--VKGKVVARTerqhrqmaihkrffTSLVLLDLISEIPLKE 563
Cdd:PRK01172 494 DYDEDLALYYiSLCrEIIPANTR---DDYYAME-FLEDIgvIDGDISAAK--------------TAMVLRGWISEASMQK 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 564 INQKYGCNRGQIQSLQQSA----AVYAGMITVFSNRlgwhnMELLLSQFQKRLTFGIQRELCDLIRVSSLNAQRARFLYA 639
Cdd:PRK01172 556 ITDTYGIAPGDVQARASSAdwisYSLARLSSIYKPE-----MRRKLEILNIRIKEGIREDLIDLVLIPKVGRVRARRLYD 630
|
650
....*....|....*....
gi 1958664953 640 SGFLTVADLARADTVEVEA 658
Cdd:PRK01172 631 AGFKTVDDIARSSPERIKK 649
|
|
| DNA_pol_A_plastid_like |
cd08640 |
DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in ... |
1984-2369 |
7.90e-60 |
|
DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication; DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). The three-dimensional structure of plastid DNA polymerase has substantial similarity to Pol I. The structure of Pol I resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains.
Pssm-ID: 176477 Cd Length: 371 Bit Score: 211.49 E-value: 7.90e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1984 ILEWRRISNAITKVVFPLQreKHLN-PFlrmERIYPVSQSHTATGRITFTEPNIQNVPRdfeikmptlvresppsqasgk 2062
Cdd:cd08640 48 LKEIKSISTLLSTFIIPLQ--ELLNdST---GRIHCSLNINTETGRLSSRNPNLQNQPA--------------------- 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2063 gqlamarqnqkvyglhpgqrtvLEKtsDRgvpfsVSMRHAFVPFPGGLILAADYSQLELRILAHLSRDCRLIQVLNSGAD 2142
Cdd:cd08640 102 ----------------------LEK--DR-----YKIRKAFIASPGNTLIVADYSQLELRLLAHMTRCKSMIEAFNAGGD 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2143 ------------VFRSIAAEWKMIEPDAVGDNL-----------RQQAKQICYGIIYGMGAKSLGEQMGIKENDAACYID 2199
Cdd:cd08640 153 fhsrtasgmyphVAEAVANGEVLLEWKSEGKPPapllkdkfkseRRKAKVLNFSIAYGKTAHGLAKDWKVKLKEAERTVD 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2200 SFKSRYKGINHFMRDTVKNCRRDGFVETILGRRRYLPGIKDNNPYHKAHAERQAINTTVQGSAADIVKVAtvniqkqlet 2279
Cdd:cd08640 233 AWYSDRPEVEQWQKKTKKEARERGYTRTLLGRYRYLPDIKSRNRKKRGHAERAAINTPIQGSAADIAMKA---------- 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2280 fhptfkshghresMLQSDRaGLLPKRkvkgmfcpmrGGF-FILQLHDELLYEVAEEDVVQVAQIVKNEME--CAIKLSVK 2356
Cdd:cd08640 303 -------------MLRIYR-NLRLKR----------LGWkLLLQIHDEVILEGPEEKADEALKIVKDCMEnpFFGPLDVP 358
|
410
....*....|...
gi 1958664953 2357 LKVKVKIGASWGE 2369
Cdd:cd08640 359 LEVDGSVGYNWYE 371
|
|
| SF2_C_Ski2 |
cd18795 |
C-terminal helicase domain of the Ski2 family helicases; Ski2-like RNA helicases play an ... |
117-326 |
1.28e-57 |
|
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: 196.62 E-value: 1.28e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 117 RPVPLLESIKVGNSIYDSSMKLVREfqpllqvKGDEDHIVSLCYETVRDNHSVLVFCPSKKWCEKVADIIArefynlhhq 196
Cdd:cd18795 1 RPVPLEEYVLGFNGLGIKLRVDVMN-------KFDSDIIVLLKIETVSEGKPVLVFCSSRKECEKTAKDLA--------- 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 197 peglvkssefppvildqksllevidqlkrspsgldsvlkntvpwGVAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLS 276
Cdd:cd18795 65 --------------------------------------------GIAFHHAGLTREDRELVEELFREGLIKVLVATSTLA 100
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 1958664953 277 SGVNLPARRVIIR-TPVFGG---QPLDILTYKQMVGRAGRKGVDTMGESILVCK 326
Cdd:cd18795 101 AGVNLPARTVIIKgTQRYDGkgyRELSPLEYLQMIGRAGRPGFDTRGEAIIMTK 154
|
|
| PRK00254 |
PRK00254 |
ski2-like helicase; Provisional |
14-656 |
2.87e-57 |
|
ski2-like helicase; Provisional
Pssm-ID: 234702 [Multi-domain] Cd Length: 720 Bit Score: 213.53 E-value: 2.87e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 14 DVAVCTIERANGLI---NRLIEENKMdllgtVVVDELHMLGDSHRGYLLELLLTKvcfvtrksascqadsasaLACAVQI 90
Cdd:PRK00254 116 DIIIATAEKFDSLLrhgSSWIKDVKL-----VVADEIHLIGSYDRGATLEMILTH------------------MLGRAQI 172
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 91 VGMSATLPNLQLVASWLNAELYHTDFRPVPLLESIKVGNSIYDSSMKLVREfqpllqvkgdEDHIVSLCYETVRDNHSVL 170
Cdd:PRK00254 173 LGLSATVGNAEELAEWLNAELVVSDWRPVKLRKGVFYQGFLFWEDGKIERF----------PNSWESLVYDAVKKGKGAL 242
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 171 VFCPSKKWCEKVADIIAREFYNLHHQPEglvkssefppvildQKSLLEVIDQLKRSPSglDSVLKNTVPWGVAFHHAGLT 250
Cdd:PRK00254 243 VFVNTRRSAEKEALELAKKIKRFLTKPE--------------LRALKELADSLEENPT--NEKLKKALRGGVAFHHAGLG 306
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 251 FEERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIRT----PVFGGQPLDILTYKQMVGRAGRKGVDTMGESILVCK 326
Cdd:PRK00254 307 RTERVLIEDAFREGLIKVITATPTLSAGINLPAFRVIIRDtkrySNFGWEDIPVLEIQQMMGRAGRPKYDEVGEAIIVAT 386
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 327 NSEKSKGIA-LLQGSLEPVHSCLQSQGEVTSTmiraILEIIVSGVASTSQDMQTYAACTFLAAdvkegkqgiQRNRDDVQ 405
Cdd:PRK00254 387 TEEPSKLMErYIFGKPEKLFSMLSNESAFRSQ----VLALITNFGVSNFKELVNFLERTFYAH---------QRKDLYSL 453
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 406 RGAVDACVTWLLENEFIqaaepsDGTGGKVYHPTHLGSATLSSSLSPTdTLDIFAD-LQRAMKGfvlENDLHIVYLV--T 482
Cdd:PRK00254 454 EEKAKEIVYFLLENEFI------DIDLEDRFIPLPLGIRTSQLYIDPL-TAKKFKDaFPKIEKN---PNPLGIFQLIasT 523
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 483 PvfeDWTSidwyrffclwekLPTSMKRVAELVGveegfLARCVKGKVVART--ERQHRQMAIHKRFFTSLVLLDLISEIP 560
Cdd:PRK00254 524 P---DMTP------------LNYSRKEMEDLLD-----EAYEMEDRLYFNIpyWEDYKFQKFLRAFKTAKVLLDWINEVP 583
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 561 LKEINQKYGCNRGQIQSLQQSAA--VYAgMITVFsnRLGWHNMELL--LSQFQKRLTFGIQRELCDLIRVSSLNAQRARF 636
Cdd:PRK00254 584 EGEIVETYNIDPGDLYRILELADwlMYS-LIELY--KLFEPKQEVLdyLETLHLRVKHGVREELLELMRLPMIGRKRARA 660
|
650 660
....*....|....*....|
gi 1958664953 637 LYASGFLTVADLARADTVEV 656
Cdd:PRK00254 661 LYNAGFRSIEDIVNAKPSEL 680
|
|
| DEXHc_POLQ-like |
cd18026 |
DEXH-box helicase domain of DNA polymerase theta; DNA polymerase theta (POLQ) is important in ... |
3-118 |
9.11e-52 |
|
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: 181.64 E-value: 9.11e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 3 STSPTGRFSSLDVAVCTIERANGLINRLIEENKMDLLGTVVVDELHMLGDSHRGYLLELLLTKVCFVTRKSascqadsas 82
Cdd:cd18026 101 GRSPPKRRKSLSVAVCTIEKANSLVNSLIEEGRLDELGLVVVDELHMLGDGHRGALLELLLTKLLYAAQKN--------- 171
|
90 100 110
....*....|....*....|....*....|....*.
gi 1958664953 83 alacaVQIVGMSATLPNLQLVASWLNAELYHTDFRP 118
Cdd:cd18026 172 -----IQIVGMSATLPNLEELASWLRAELYTTNFRP 202
|
|
| PRK14975 |
PRK14975 |
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional |
1845-2371 |
8.54e-51 |
|
bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Pssm-ID: 237876 [Multi-domain] Cd Length: 553 Bit Score: 190.20 E-value: 8.54e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1845 NQLNSMLQKENLH--DIFCKVEMPSQYCLALLELNGIGFSTAEcetqkhiMQAKLDAIETQAYQLAGHSFSFTsadDIAQ 1922
Cdd:PRK14975 142 DQLNRIAAAAHPGrlRLLAAAESAGALAAAEMELAGLPWDTDV-------HEALLAELLGPRPAAGGRPARLA---ELAA 211
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1923 VLFLELKLP---PN-----GEMKTQGGRKtLGSTRRGTesdrklrlgrrfstskdilnkLKDL-HPLPGLILEWRRISNA 1993
Cdd:PRK14975 212 EIREALGRPrlnPDspqqvLRALRRAGIE-LPSTRKWE---------------------LREIdHPAVEPLLEYRKLSKL 269
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1994 ITKVVFPLQREKHLNpflrmERIYPV-SQSHTATGRITFTEPNIQNVPRDfeikmptlvresppsqasgkgqlamarqnq 2072
Cdd:PRK14975 270 LSANGWAWLDYWVRD-----GRFHPEyVPGGVVTGRWASRGPNAQQIPRD------------------------------ 314
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2073 kvyglhpgqrtvlektsdrgvpfsvsMRHAFVPFPGGLILAADYSQLELRILAHLSRDCRLIQVLNSGADVFRSIAAEWK 2152
Cdd:PRK14975 315 --------------------------IRSAFVADPGWKLVVADASQIELRVLAAYSGDERMIEAFRTGGDLHRLTASVGF 368
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2153 MIEPDAVGDnlRQQAKQICYGIIYGMGAKSLGEQMGiKENDAACYIDSFKSRYKGINHFMRDTVKNCRRDGFVETILGRR 2232
Cdd:PRK14975 369 GKPEEEKEE--RALAKAANFGAIYGATSKGLQEYAK-NYGEAARLLERLRRAYPRAVGWVERAAREGERGGVVRTLLGRT 445
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2233 RYLPGIKDNNPYHKAHAERQAINTTVQGSAADIVKVATVNIqkqletfhptfkshghRESMLQSDRAGLlpkrkvkgmfc 2312
Cdd:PRK14975 446 SPPPGFAWRARRRARSRGRFTRNFPVQGTAADWAKLALALL----------------RRRLAEGLDAEL----------- 498
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958664953 2313 pmrggffILQLHDELLYEVAEEDVVQVAQIVKNEMECAIKL---SVKLKVKVKIGASWGELK 2371
Cdd:PRK14975 499 -------VFFVHDEVVVECPEEEAEEVAAAIEEAMEEAGRLlfgPVPFPVEVAVVESYAEAK 553
|
|
| DNA_pol_A_Aquificae_like |
cd08639 |
Phylum Aquificae Pol A is different from Escherichia coli Pol A by three signature sequences; ... |
1978-2368 |
1.15e-42 |
|
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: 160.14 E-value: 1.15e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1978 HPLPGLILEWRRISNAITKvvFPLQREKHLNPflRMERIYP-VSQSHTATGRITFTEPNIQNVPRDFEikmptlvrespp 2056
Cdd:cd08639 29 HPAVRLLLEYRKLNKLIST--FGEKLPKHIHP--VTGRIHPsFNQIGAASGRMSCSNPNLQQIPRERE------------ 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2057 sqasgkgqlamarqnqkvyglhpgqrtvlektsdrgvpfsvsMRHAFVPFPGGLILAADYSQLELRILAHLSRDCRLIQV 2136
Cdd:cd08639 93 ------------------------------------------FRRCFVAPEGNKLIIADYSQIELRIAAEISGDERMISA 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2137 LNSGADVFRSIAAEWKMIEPDAVGDNLRQQAKQICYGIIYGMGAKSLGEQMGIKEN------DAACYIDSFKSRYKGINH 2210
Cdd:cd08639 131 YQKGEDLHRLTASLITGKPIEEITKEERQLAKAVNFGLIYGMSAKGLREYARTNYGvemsleEAEKFRESFFFFYKGILR 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2211 FMRDTVKNcrRDGFVETILGRRRylpgIKDNNPYhkahaeRQAINTTVQGSAADIVKVATVniqkqletfhptfkshghr 2290
Cdd:cd08639 211 WHHRLKAK--GPIEVRTLLGRRR----VFEYFTF------TEALNYPIQGTGADILKLALA------------------- 259
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2291 esMLQSDRAGLlpkrkvkgmfcpmrGGFFILQLHDELLYEVAEEDVVQVAQIVKNEMECAIKL---SVKLKVKVKIGASW 2367
Cdd:cd08639 260 --LLVDRLKDL--------------DAKIVLCVHDEIVLEVPEDEAEEAKKILESSMEEAGKRilkKVPVEVEVSISDSW 323
|
.
gi 1958664953 2368 G 2368
Cdd:cd08639 324 A 324
|
|
| Dob10 |
COG4581 |
Superfamily II RNA helicase [Replication, recombination and repair]; |
15-364 |
1.33e-32 |
|
Superfamily II RNA helicase [Replication, recombination and repair];
Pssm-ID: 443638 [Multi-domain] Cd Length: 751 Bit Score: 137.76 E-value: 1.33e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 15 VAVCTIERangLINRLIEE-NKMDLLGTVVVDELHMLGDSHRGYLLEL-LLTkvcfvtrksascqadsasaLACAVQIVG 92
Cdd:COG4581 112 IVVMTTEI---LRNMLYREgADLEDVGVVVMDEFHYLADPDRGWVWEEpIIH-------------------LPARVQLVL 169
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 93 MSATLPNLQLVASWLNA-----ELYHTDFRPVPLLESIKVGNSIYdssmklvrefqPLLQVKGDEDHIVSLcYETV---- 163
Cdd:COG4581 170 LSATVGNAEEFAEWLTRvrgetAVVVSEERPVPLEFHYLVTPRLF-----------PLFRVNPELLRPPSR-HEVIeeld 237
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 164 -RDNHSVLVFCPSKKWCEKVADIIAREfynlhhqpeGLVKSSEfppvildQKSLLEVIDQLKRSPSGLD-SVLKNTVPWG 241
Cdd:COG4581 238 rGGLLPAIVFIFSRRGCDEAAQQLLSA---------RLTTKEE-------RAEIREAIDEFAEDFSVLFgKTLSRLLRRG 301
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 242 VAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIRTPV-FGGQPLDILT---YKQMVGRAGRKGVDT 317
Cdd:COG4581 302 IAVHHAGMLPKYRRLVEELFQAGLLKVVFATDTLAVGINMPARTVVFTKLSkFDGERHRPLTareFHQIAGRAGRRGIDT 381
|
330 340 350 360
....*....|....*....|....*....|....*....|....*...
gi 1958664953 318 MGESILVCKNSEKSKGIA-LLQGSLEPvhscLQSQGEVTSTMIRAILE 364
Cdd:COG4581 382 EGHVVVLAPEHDDPKKFArLASARPEP----LRSSFRPSYNMVLNLLA 425
|
|
| HTH_61 |
pfam20470 |
Helix-turn-helix domain; This entry represents a presumed helix-turn-helix domain found in DNA ... |
319-423 |
4.49e-31 |
|
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: 118.03 E-value: 4.49e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 319 GESILVCKNSEKSKGIALLQGSLEPVHSCLQSQgevTSTMIRAILEIIVSGVASTSQDMQTYAACTFLAADVKEGKQGIQ 398
Cdd:pfam20470 1 GESILICKEKDLEKVAELLRAELPPVYSCLLPE---KRGIKRALLEIIALGLATSPEDVDEYMSCTLLSVQQKELDVEKS 77
|
90 100
....*....|....*....|....*
gi 1958664953 399 rnrddvqrgaVDACVTWLLENEFIQ 423
Cdd:pfam20470 78 ----------IESSLEELVENGLIT 92
|
|
| DEXHc_Ski2 |
cd17921 |
DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins; Ski2-like RNA helicases ... |
1-115 |
3.53e-21 |
|
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: 93.10 E-value: 3.53e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1 MGSTSPTGR-FSSLDVAVCTIERANGLINRLiEENKMDLLGTVVVDELHMLGDSHRGYLLELLLTKVCFVTRKsascqad 79
Cdd:cd17921 81 TGDPSVNKLlLAEADILVATPEKLDLLLRNG-GERLIQDVRLVVVDEAHLIGDGERGVVLELLLSRLLRINKN------- 152
|
90 100 110
....*....|....*....|....*....|....*..
gi 1958664953 80 sasalacaVQIVGMSATLPNLQLVASWLNAE-LYHTD 115
Cdd:cd17921 153 --------ARFVGLSATLPNAEDLAEWLGVEdLIRFD 181
|
|
| COG1202 |
COG1202 |
Superfamily II helicase, archaea-specific [Replication, recombination and repair]; |
40-344 |
1.23e-19 |
|
Superfamily II helicase, archaea-specific [Replication, recombination and repair];
Pssm-ID: 440815 [Multi-domain] Cd Length: 790 Bit Score: 96.50 E-value: 1.23e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 40 GTVVVDELHMLGDSHRGYLLELLLTKVCFVTRKSascqadsasalacavQIVGMSATLPNLQLVASWLNAELYHTDFRPV 119
Cdd:COG1202 328 GTVVIDEVHMLEDPERGHRLDGLIARLKYYCPGA---------------QWIYLSATVGNPEELAKKLGAKLVEYEERPV 392
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 120 PLlesikvgnsiydssmklvrefqpllqvkgdEDHivslcyetvrdnhsvLVFCPSKkwcEKVaDIIARefynlhhqpeg 199
Cdd:COG1202 393 PL------------------------------ERH---------------LTFADGR---EKI-RIINK----------- 412
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 200 LVKSsEFppvilDQKSllevidqlKRSPSGLDSVLKNT----------VPWGVAFHHAGLTFEERDIIEGAFRQGLIRVL 269
Cdd:COG1202 413 LVKR-EF-----DTKS--------SKGYRGQTIIFTNSrrrcheiaraLGYKAAPYHAGLDYGERKKVERRFADQELAAV 478
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 270 AATSTLSSGVNLPARRVIIRTPVFGGQPLDILTYKQMVGRAGRKGVDTMGES-ILV---------CKNSEKSKGIALLQG 339
Cdd:COG1202 479 VTTAALAAGVDFPASQVIFDSLAMGIEWLSVQEFHQMLGRAGRPDYHDRGKVyLLVepgksyhrsMEMTEDEVAFKLLKG 558
|
....*
gi 1958664953 340 SLEPV 344
Cdd:COG1202 559 EMEDV 563
|
|
| phage_DpoZ_1 |
NF038380 |
aminoadenine-incorporating DNA polymerase DpoZ; |
1853-2369 |
1.71e-17 |
|
aminoadenine-incorporating DNA polymerase DpoZ;
Pssm-ID: 468497 [Multi-domain] Cd Length: 604 Bit Score: 88.95 E-value: 1.71e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1853 KENLHDIfCKVEMPSQYCLALLELNGIGFSTAECETQKHIMQAKLDAIETQAYQLAGHSFSFTSADDIAQvlFLELKLPP 1932
Cdd:NF038380 173 RQGLQRV-VELERRLFPVLIDMEWRGIRVDLEAAEAAIPELDKVIDQLQKELNEIAGFEFNVNSSPQIRK--LFKPKKIS 249
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1933 NGEMKTQGGrKTLGSTRRGTESdrklrlgrrfsTSKDILNKLKdlHPLPGLILEWRriSNAITKVVFPLqreKHLNPFLR 2012
Cdd:NF038380 250 KGQWVAIDG-TPLETTDAGKPS-----------LGADALREIK--HPAAAKILELR--KLIKTRDTFLR---GHVLGHAV 310
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2013 MERIYP-VSQS------HTATGRITFTEPNIQNVP-RDFEIkmptlvresppsqASgkgqlamarqnqkvyglhpgqrtv 2084
Cdd:NF038380 311 GGGVHPnINQTkgedggGTGTGRLSYTDPALQQIPsRDKAI-------------AA------------------------ 353
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2085 lektsdrgvpfsvSMRHAFVPFPGGLILAADYSQLELRILAHLSRDCRLIQV--LNSGADvFRSIAAEWKMI--EPDAVG 2160
Cdd:NF038380 354 -------------IVRPIFLPDEGQVWLCSDLAQFEFRIFAHLVNNPSIIAAyaEDPELD-FHQIVADMTGLprNATYSG 419
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2161 DnlrQQAKQICYGIIYGMGAKSLGEQMG----IKEND--------------AACYIDSFKSRYKGINHFMRDTVKNCRRD 2222
Cdd:NF038380 420 Q---ANAKQINLGMIFNMGNGKLADKMGmpyeWEEFTfgkevrrykkagpeAMAVIENYHRKLPGVKELADRAKAVAKER 496
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2223 GFVETILGRRRYLPGIKdnnpyhKAHAerqAINTTVQGSAADIVKVATVNIQKQLETfhptfkshghresmlqsdragll 2302
Cdd:NF038380 497 GYVRTAMGRRLRFPGGM------KTYK---ASGLLIQATAADLNKENLLEIDEVLGS----------------------- 544
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958664953 2303 pkrkvkgmfcpmRGGFFILQLHDELLYEVAEEDVVQ-VAQIVKNEMEcaiKLSVKLKVKVKI-----GASWGE 2369
Cdd:NF038380 545 ------------LDGRLLLNTHDEYSMSLPEDDVRKpIKERVKLFIE---DSSPWLRVPIILelsgfGRNWWE 602
|
|
| DNA_pol_A_pol_I_B |
cd08643 |
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ... |
2092-2369 |
6.33e-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: 85.95 E-value: 6.33e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2092 GVPFSVSMRHAFVPFPGGLILAADYSQLELRILAHlsrdcrLIQVLNSGADVFRSIAAEWKMIEPDAVGDNLRQQAKQIC 2171
Cdd:cd08643 170 GSPYGKECRELFGVPPGWSLVGADASGLELRCLAH------YLARYDGGAYTRKVLGGDIHWANAQAMGLLSRDGAKTFI 243
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2172 YGIIYGMGAKSLGEQMGIKENDA----ACYIDSFKSRYKGINH----------FMRDTV--KNCRRDgfVETILGRRRYL 2235
Cdd:cd08643 244 YAFLYGAGDEKLGQIVGDDLRTAknlnAEWPQTKKGTIKKIADkakgrvvranFLKGLPalGKLIKK--VKEAAKKRGHL 321
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2236 PGIKDNNPYHK-AHAerqAINTTVQGSAADIVKVATVNIQKQLETfhptfkshghresmlqsdrAGLLPKRKVKgmfcpm 2314
Cdd:cd08643 322 VGLDGRRIRVRsAHA---ALNTLLQSAGAILMKKWLVLLDDELTA-------------------KGGVWGGDFE------ 373
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*...
gi 1958664953 2315 rggfFILQLHDELLYEVAEEDVVQVAQIVKNEMECAIK---LSVKLKVKVKIGASWGE 2369
Cdd:cd08643 374 ----YCAWVHDEVQIECRKGIAEEVGKIAVEAAEKAGEhfnFRCPLAGEFDIGRNWAE 427
|
|
| HELICc |
smart00490 |
helicase superfamily c-terminal domain; |
241-314 |
1.58e-16 |
|
helicase superfamily c-terminal domain;
Pssm-ID: 197757 [Multi-domain] Cd Length: 82 Bit Score: 76.48 E-value: 1.58e-16
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958664953 241 GVAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLP-ARRVIIRTPvfggqPLDILTYKQMVGRAGRKG 314
Cdd:smart00490 13 KVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPgVDLVIIYDL-----PWSPASYIQRIGRAGRAG 82
|
|
| DEXHc_archSki2 |
cd18028 |
DEXH-box helicase domain of archaeal Ski2-type helicase; Archaeal Ski2-type RNA helicases play ... |
14-115 |
1.16e-15 |
|
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: 76.99 E-value: 1.16e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 14 DVAVCTIERANGLINRliEENKMDLLGTVVVDELHMLGDSHRGYLLELLLTKvcfvtrksascqadsASALACAVQIVGM 93
Cdd:cd18028 93 DIIVATYEKFDSLLRH--SPSWLRDVGVVVVDEIHLISDEERGPTLESIVAR---------------LRRLNPNTQIIGL 155
|
90 100
....*....|....*....|..
gi 1958664953 94 SATLPNLQLVASWLNAELYHTD 115
Cdd:cd18028 156 SATIGNPDELAEWLNAELVESD 177
|
|
| Helicase_C |
pfam00271 |
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ... |
232-314 |
2.49e-13 |
|
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.
Pssm-ID: 459740 [Multi-domain] Cd Length: 109 Bit Score: 68.01 E-value: 2.49e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 232 SVLKNTVPWGVAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIrtpvFGGQPLDILTYKQMVGRAG 311
Cdd:pfam00271 31 ELLLEKEGIKVARLHGDLSQEEREEILEDFRKGKIDVLVATDVAERGLDLPDVDLVI----NYDLPWNPASYIQRIGRAG 106
|
...
gi 1958664953 312 RKG 314
Cdd:pfam00271 107 RAG 109
|
|
| DEXHc_HFM1 |
cd18023 |
DEXH-box helicase domain of ATP-dependent DNA helicase HFM1; HFM1 is a type II DEAD box ... |
6-118 |
8.26e-07 |
|
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: 51.97 E-value: 8.26e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 6 PTGRFSSLDVAVCTIERANGLINRLIEENKM-DLLGTVVVDELHMLGDShRGYLLELLLTKVcfvtrKSASCQADSASAL 84
Cdd:cd18023 94 DTFEIQDADIILTTPEKWDSMTRRWRDNGNLvQLVALVLIDEVHIIKEN-RGATLEVVVSRM-----KTLSSSSELRGST 167
|
90 100 110
....*....|....*....|....*....|....*....
gi 1958664953 85 ACAVQIVGMSATLPNLQLVASWLNAE-----LYHTDFRP 118
Cdd:cd18023 168 VRPMRFVAVSATIPNIEDLAEWLGDNpagcfSFGESFRP 206
|
|
| SF2_C_RecQ |
cd18794 |
C-terminal helicase domain of the RecQ family helicases; The RecQ helicase family is an ... |
158-314 |
9.36e-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: 50.28 E-value: 9.36e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 158 LCYETVRDNH---SVLVFCPSKKWCEKVADiiarefynlhhqpeglvkssefppvildqksllevidQLKRSpsGLDSvl 234
Cdd:cd18794 19 DLLKRIKVEHlggSGIIYCLSRKECEQVAA-------------------------------------RLQSK--GISA-- 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 235 kntvpwgvAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIRTpvfgGQPLDILTYKQMVGRAGRKG 314
Cdd:cd18794 58 --------AAYHAGLEPSDRRDVQRKWLRDKIQVIVATVAFGMGIDKPDVRFVIHY----SLPKSMESYYQESGRAGRDG 125
|
|
| Lhr |
COG1201 |
Lhr-like helicase [Replication, recombination and repair]; |
41-275 |
1.02e-06 |
|
Lhr-like helicase [Replication, recombination and repair];
Pssm-ID: 440814 [Multi-domain] Cd Length: 850 Bit Score: 54.34 E-value: 1.02e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 41 TVVVDELHMLGDSHRGYLLELLLtkvcfvTRKSASCQADsasalacaVQIVGMSATLPNLQLVASWL-------NAELYH 113
Cdd:COG1201 164 TVIVDEIHALAGSKRGVHLALSL------ERLRALAPRP--------LQRIGLSATVGPLEEVARFLvgyedprPVTIVD 229
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 114 TDFRPVPLLESIkvgnsIYDSSMKLVREFQPLLQvkgdeDHIVSLCYETVRDNHSVLVFCPSKKWCEKVadiiareFYNL 193
Cdd:COG1201 230 AGAGKKPDLEVL-----VPVEDLIERFPWAGHLW-----PHLYPRVLDLIEAHRTTLVFTNTRSQAERL-------FQRL 292
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 194 hhqpeglvkssefppvildqksllevidqLKRSPSGLDSvlkntvpwgVAFHHAGLTFEERDIIEGAFRQGLIRVLAATS 273
Cdd:COG1201 293 -----------------------------NELNPEDALP---------IAAHHGSLSREQRLEVEEALKAGELRAVVATS 334
|
..
gi 1958664953 274 TL 275
Cdd:COG1201 335 SL 336
|
|
| SF2_C_Hrq |
cd18797 |
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role ... |
158-314 |
1.39e-06 |
|
C-terminal helicase domain of HrQ family helicases; Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350184 [Multi-domain] Cd Length: 146 Bit Score: 49.95 E-value: 1.39e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 158 LCYETVRDNHSVLVFCPSKKWCEKVADIIAREfynlhhqpeglvkssefppvildqksLLEVIDQLKRspsgldsvlknt 237
Cdd:cd18797 27 LFADLVRAGVKTIVFCRSRKLAELLLRYLKAR--------------------------LVEEGPLASK------------ 68
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958664953 238 vpwgVAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIRTpvfgGQPLDILTYKQMVGRAGRKG 314
Cdd:cd18797 69 ----VASYRAGYLAEDRREIEAELFNGELLGVVATNALELGIDIGGLDAVVLA----GYPGSLASLWQQAGRAGRRG 137
|
|
| DEXHc_LHR-like |
cd17922 |
DEXH-box helicase domain of LHR; Large helicase-related protein (LHR) is a DNA ... |
39-107 |
2.14e-06 |
|
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: 49.89 E-value: 2.14e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958664953 39 LGTVVVDELHMLGDSHRGYLLELLLTKVcfvtRKsascqadsasALACAVQIVGMSATLPNLQLVASWL 107
Cdd:cd17922 112 LRYVVVDEIHALLGSKRGVQLELLLERL----RK----------LTGRPLRRIGLSATLGNLEEAAAFL 166
|
|
| YprA |
COG1205 |
ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, ... |
242-314 |
2.42e-06 |
|
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: 52.92 E-value: 2.42e-06
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958664953 242 VAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLP---ArrVIIRtpvfgGQPLDILTYKQMVGRAGRKG 314
Cdd:COG1205 321 VAAYRAGYLPEERREIERGLRSGELLGVVSTNALELGIDIGgldA--VVLA-----GYPGTRASFWQQAGRAGRRG 389
|
|
| PRK09751 |
PRK09751 |
putative ATP-dependent helicase Lhr; Provisional |
41-313 |
2.51e-06 |
|
putative ATP-dependent helicase Lhr; Provisional
Pssm-ID: 137505 [Multi-domain] Cd Length: 1490 Bit Score: 53.39 E-value: 2.51e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 41 TVVVDELHMLGDSHRGYLLELLLTKVcfvtrksascqadsASALACAVQIVGMSATLPNLQLVASWLNAElyhtdfRPV- 119
Cdd:PRK09751 127 TVIIDEVHAVAGSKRGAHLALSLERL--------------DALLHTSAQRIGLSATVRSASDVAAFLGGD------RPVt 186
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 120 ----PLLESIKVGNSIYDSSMKLVREFQPllqVKGDED----------HIVSLCYETVRDNHSVLVFCPSKKWCEKvadI 185
Cdd:PRK09751 187 vvnpPAMRHPQIRIVVPVANMDDVSSVAS---GTGEDShagregsiwpYIETGILDEVLRHRSTIVFTNSRGLAEK---L 260
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 186 IAR--EFYnlhhqPEGLVKSsefPPVILDQKSLLEVIDQLKRSPSGLDSVLKNTvpwgvafHHAGLTFEERDIIEGAFRQ 263
Cdd:PRK09751 261 TARlnELY-----AARLQRS---PSIAVDAAHFESTSGATSNRVQSSDVFIARS-------HHGSVSKEQRAITEQALKS 325
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|
gi 1958664953 264 GLIRVLAATSTLSSGVNLPARRVIIRTpvfgGQPLDILTYKQMVGRAGRK 313
Cdd:PRK09751 326 GELRCVVATSSLELGIDMGAVDLVIQV----ATPLSVASGLQRIGRAGHQ 371
|
|
| DNA_polA_I_Bacillus_like_exo |
cd06140 |
inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and ... |
1672-1872 |
6.97e-06 |
|
inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases; Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.
Pssm-ID: 176652 [Multi-domain] Cd Length: 178 Bit Score: 48.80 E-value: 6.97e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1672 VEDDGFPVHGSDcavVVGLAVcWGGKDAYYLSLQKEQKQSEmspslappPLDATLtvkermeylqsclqkkSDQERSVVT 1751
Cdd:cd06140 10 VELLGENYHTAD---IIGLAL-ANGGGAYYIPLELALLDLA--------ALKEWL----------------EDEKIPKVG 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1752 YDFIQTYkVLLLSCGISLEPSYEDPKVACWLLDPDSKEPTLHSIVTSFLPHEL-ALLEGIETGPGIQSLGLNVNTDHSGR 1830
Cdd:cd06140 62 HDAKRAY-VALKRHGIELAGVAFDTMLAAYLLDPTRSSYDLADLAKRYLGRELpSDEEVYGKGAKFAVPDEEVLAEHLAR 140
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 1958664953 1831 yRASVesvlIFNSMNQLNSMLQKENLHDIFCKVEMPSQYCLA 1872
Cdd:cd06140 141 -KAAA----IARLAPKLEEELEENEQLELYYEVELPLAEVLA 177
|
|
| DEAD |
pfam00270 |
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ... |
9-98 |
1.17e-05 |
|
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: 47.62 E-value: 1.17e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 9 RFSSLDVAVCTIERangLINRLIEENKMDLLGTVVVDELHMLGDSHRGYLLELLLtkvcfvtrksascqadsaSALACAV 88
Cdd:pfam00270 91 KLKGPDILVGTPGR---LLDLLQERKLLKNLKLLVLDEAHRLLDMGFGPDLEEIL------------------RRLPKKR 149
|
90
....*....|
gi 1958664953 89 QIVGMSATLP 98
Cdd:pfam00270 150 QILLLSATLP 159
|
|
| DEXHc_Brr2_1 |
cd18019 |
N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type II DEAD ... |
10-107 |
2.18e-05 |
|
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: 47.75 E-value: 2.18e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 10 FSSLDVAVCTIERANGLINRLIEENKMDLLGTVVVDELHMLGDShRGYLLELLLTKVcfvTRKSASCQADsasalacaVQ 89
Cdd:cd18019 117 ISETQIIVTTPEKWDIITRKSGDRTYTQLVRLIIIDEIHLLHDD-RGPVLESIVART---IRQIEQTQEY--------VR 184
|
90
....*....|....*...
gi 1958664953 90 IVGMSATLPNLQLVASWL 107
Cdd:cd18019 185 LVGLSATLPNYEDVATFL 202
|
|
| SF2_C_LHR |
cd18796 |
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a ... |
242-314 |
3.84e-05 |
|
C-terminal helicase domain of LHR family helicases; Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases. LHR family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350183 [Multi-domain] Cd Length: 150 Bit Score: 46.10 E-value: 3.84e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958664953 242 VAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPA-RRVI-IrtpvfgGQPLDILTYKQMVGRAGRKG 314
Cdd:cd18796 71 IALHHGSLSRELREEVEAALKRGDLKVVVATSSLELGIDIGDvDLVIqI------GSPKSVARLLQRLGRSGHRP 139
|
|
| PRK11057 |
PRK11057 |
ATP-dependent DNA helicase RecQ; Provisional |
242-314 |
2.03e-04 |
|
ATP-dependent DNA helicase RecQ; Provisional
Pssm-ID: 182933 [Multi-domain] Cd Length: 607 Bit Score: 46.63 E-value: 2.03e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958664953 242 VAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIRTPVfggqPLDILTYKQMVGRAGRKG 314
Cdd:PRK11057 263 AAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMGINKPNVRFVVHFDI----PRNIESYYQETGRAGRDG 331
|
|
| DNA_pol_A_pol_I_A |
cd08642 |
Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination ... |
2093-2228 |
2.72e-04 |
|
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: 45.69 E-value: 2.72e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2093 VPFSVS--MRHAFVPFPGGLILAADYSQLELRILAHLSRDCRLIQVLNSGADVFRSIAAewKM----IEPDAVGDNLRQQ 2166
Cdd:cd08642 152 VPDVLSqlIRTAFIPSEGHRFIVSDFSAIEARVIAWLAGEQWRLDVFATHGKIYEASAS--QMfgvpVEKIGKNSHLRQK 229
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 2167 AK--------QICYGIIYGMGAKslgeQMGIKENDAACYIDSFKSRYKGINHFMRDT---VKNCRRDG--------FVET 2227
Cdd:cd08642 230 GKvaelalgyGGSVGALKAMGAL----EMGLTEDELPGIVDAWRNANPNIVKLWWDVdkaAKKAVKERktvklggkLVEN 305
|
.
gi 1958664953 2228 I 2228
Cdd:cd08642 306 I 306
|
|
| SF2_C |
cd18785 |
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ... |
268-325 |
3.87e-04 |
|
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350172 [Multi-domain] Cd Length: 77 Bit Score: 41.15 E-value: 3.87e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 1958664953 268 VLAATSTLSSGVNLP-ARRVIIRTPVFggqplDILTYKQMVGRAGRKGvDTMGESILVC 325
Cdd:cd18785 25 ILVATNVLGEGIDVPsLDTVIFFDPPS-----SAASYIQRVGRAGRGG-KDEGEVILFV 77
|
|
| SF2_C_suv3 |
cd18805 |
C-terminal helicase domain of ATP-dependent RNA helicase; The SUV3 (suppressor of Var 3) gene ... |
268-314 |
3.92e-04 |
|
C-terminal helicase domain of ATP-dependent RNA helicase; The SUV3 (suppressor of Var 3) gene encodes a DNA and RNA helicase, which is localized in mitochondria and is a subunit of the degradosome complex involved in regulation of RNA surveillance and turnover. SUV3 exhibits DNA and RNA-dependent ATPase, DNA and RNA-binding and DNA and RNA unwinding activities. SUV3 is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.
Pssm-ID: 350192 [Multi-domain] Cd Length: 135 Bit Score: 42.55 E-value: 3.92e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 1958664953 268 VLAATSTLSSGVNLPARRVIIRTPV-FGGQPLDILT---YKQMVGRAGRKG 314
Cdd:cd18805 73 VLVASDAIGMGLNLNIRRVIFSSLSkFDGNEMRPLSpseVKQIAGRAGRFG 123
|
|
| DEXHc_Brr2_2 |
cd18021 |
C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase; Brr2 is a type ... |
14-114 |
4.09e-04 |
|
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: 43.79 E-value: 4.09e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 14 DVAVCTIERANGLINRLIEENKMDLLGTVVVDELHMLGDSHrGYLLELLLTKVCFVtrksascqadsASALACAVQIVGM 93
Cdd:cd18021 99 DVILATPEQWDVLSRRWKQRKNVQSVELFIADELHLIGGEN-GPVYEVVVSRMRYI-----------SSQLEKPIRIVGL 166
|
90 100
....*....|....*....|.
gi 1958664953 94 SATLPNLQLVASWLNAELYHT 114
Cdd:cd18021 167 SSSLANARDVGEWLGASKSTI 187
|
|
| DEXDc |
smart00487 |
DEAD-like helicases superfamily; |
1-123 |
4.26e-04 |
|
DEAD-like helicases superfamily;
Pssm-ID: 214692 [Multi-domain] Cd Length: 201 Bit Score: 44.02 E-value: 4.26e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958664953 1 MGSTSPTGRFSSL-----DVAVCTIERanglINRLIEENKMDL--LGTVVVDELHMLGDSHRGYLLELLLTKvcfvtrks 73
Cdd:smart00487 89 YGGDSKREQLRKLesgktDILVTTPGR----LLDLLENDKLSLsnVDLVILDEAHRLLDGGFGDQLEKLLKL-------- 156
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 1958664953 74 ascqadsasaLACAVQIVGMSATLP-NLQLVASWLNAELYHTDFRPVPLLE 123
Cdd:smart00487 157 ----------LPKNVQLLLLSATPPeEIENLLELFLNDPVFIDVGFTPLEP 197
|
|
| DEXHc_ASCC3_2 |
cd18022 |
C-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ... |
40-108 |
5.54e-04 |
|
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: 43.13 E-value: 5.54e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958664953 40 GTVVVDELHMLGdSHRGYLLELLLTKVCFVTRKSAScqadsasalacAVQIVGMSATLPNLQLVASWLN 108
Cdd:cd18022 123 SLIIIDEIHLLG-SDRGPVLEVIVSRMNYISSQTEK-----------PVRLVGLSTALANAGDLANWLG 179
|
|
| RecQ |
COG0514 |
Superfamily II DNA helicase RecQ [Replication, recombination and repair]; |
242-314 |
3.37e-03 |
|
Superfamily II DNA helicase RecQ [Replication, recombination and repair];
Pssm-ID: 440280 [Multi-domain] Cd Length: 489 Bit Score: 42.44 E-value: 3.37e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958664953 242 VAFHHAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLP-ARRVI---IrtpvfggqPLDILTYKQMVGRAGRKG 314
Cdd:COG0514 257 AAAYHAGLDAEEREANQDRFLRDEVDVIVATIAFGMGIDKPdVRFVIhydL--------PKSIEAYYQEIGRAGRDG 325
|
|
| PTZ00424 |
PTZ00424 |
helicase 45; Provisional |
246-315 |
4.66e-03 |
|
helicase 45; Provisional
Pssm-ID: 185609 [Multi-domain] Cd Length: 401 Bit Score: 41.74 E-value: 4.66e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958664953 246 HAGLTFEERDIIEGAFRQGLIRVLAATSTLSSGVNLPARRVIIRTPVfggqPLDILTYKQMVGRAGR---KGV 315
Cdd:PTZ00424 298 HGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDL----PASPENYIHRIGRSGRfgrKGV 366
|
|
| DEXHc_ASCC3_1 |
cd18020 |
N-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3; ... |
42-112 |
6.48e-03 |
|
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: 40.11 E-value: 6.48e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958664953 42 VVVDELHMLGDShRGYLLEllltkvCFVTRKSAscQADSASALacaVQIVGMSATLPNLQLVASWLNAELY 112
Cdd:cd18020 134 LIIDEVHLLHDD-RGPVIE------SLVARTLR--QVESTQSM---IRIVGLSATLPNYLDVADFLRVNPY 192
|
|
| |
