|
Name |
Accession |
Description |
Interval |
E-value |
| PRK07726 |
PRK07726 |
DNA topoisomerase 3; |
3-658 |
0e+00 |
|
DNA topoisomerase 3;
Pssm-ID: 236078 [Multi-domain] Cd Length: 658 Bit Score: 560.94 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 3 ILIIAEKPNQVKKYVEALGNsFNNKDGYIEleselfDKKVIVTWCVGHLIQLAHMEDYDSNLKQWSKDTLPFIPEDFIFK 82
Cdd:PRK07726 2 RLFIAEKPSVGRDIADVLKP-HKKGDGYIE------GNGYIVTWAIGHLLELAEPEAYDERYKRWRLEDLPIIPEKWKLV 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 83 VSDYGSKQFKIIKELcenLNSDSEIIIATDPDREGEAIARYVLNKIPCTKNLKlkRLWANTQEPEGLKLAFKNLKDADDT 162
Cdd:PRK07726 75 VKKKTAKQFNVVKKL---LKQATEIVIATDADREGELIAREILDYCGVRKPIK--RLWISSLTDKAIKRAFANLKPGKET 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 163 YRFYLEAEARSIADWLVGMNFTRYVTLEMKQLGIDeGVFSVGRVQTPTLYMVYKRNNEIKNFESKTYYEMVAKDKENENA 242
Cdd:PRK07726 150 IPLYYSALARSRADWLVGINMTRAYTLLGRKAGYN-GVLSVGRVQTPTLALVVRRDEEIENFVPKPYWEVEAHLTPGERF 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 243 VFKSEHKFDSIDEFEQFLNEN---NLNCECEG---EIKEISISEKRKVAPNLFKLGGIQKVANQKWGYTLDKTLSIVQSL 316
Cdd:PRK07726 229 TAKWQPSEPYQDEEGRLLDRPlaeQVVARIQGqpaKVTEVETKRKKEYAPLLYDLSELQIDANKRFGLSAKETLDIAQSL 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 317 YDK-GYLSYPRTDCSLITHSEFEYLKD------NFSSYCKLLNieiEQKNIEPRTQYVNDSKVLEHYAIIPTKQIPEndv 389
Cdd:PRK07726 309 YEThKLITYPRTDSRYLPEDMVATLPEvlnaisKVDPYLLLAP---PVLDPSIRSRAWNDKKVTAHHAIIPTEQPPN--- 382
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 390 YNNFSDDEKKIYDEVVKRTMLMFMEDYIYSETKIVLCIENVEFKLTGNVAKEQGWK-LLDSENKNSKEK-LLPNYKENEK 467
Cdd:PRK07726 383 LSKLSEDERKVYDLIARRYLAQFLPPAEYDKTTIELEIAGGTFIAKGKQVVEAGWKaLLGKKEEDEEKEqPLPVLAKGDE 462
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 468 LSLNLVP-KELNTKPPKYLTEATLGGeggLMENCSKFIENEELKGNLKEVHGIGTPATRSSIVKSLIDRGYLETKKKHLM 546
Cdd:PRK07726 463 LKVEKGEvKEGQTQPPKRFTEGTLLS---AMENIARFVQDKELKKTLKETDGLGTEATRAGIIEKLFKRGYLEKKGKYIH 539
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 547 ITPKGTLLCSALeNTNLVSVEMTANWESTLKDISEKghRIRQNEFIDSIKQYIKQMINsDNKLLKLESNDKNIEKAieqs 626
Cdd:PRK07726 540 ATDKGKQLIDAL-PEELTSPDMTAKWEQALDQISEG--QLSYQDFMQPLKQWLKQLVE-QAKQSSEKYKFDNLTGP---- 611
|
650 660 670
....*....|....*....|....*....|..
gi 488415014 627 ticNCPKCsnGRIKKLLSKNKKLFYACSNKDC 658
Cdd:PRK07726 612 ---KCPDC--GKPMLKVKGKNGKMLVCQDREC 638
|
|
| topB |
TIGR01056 |
DNA topoisomerase III, bacteria and conjugative plasmid; This model describes topoisomerase ... |
4-638 |
1.28e-160 |
|
DNA topoisomerase III, bacteria and conjugative plasmid; This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273419 [Multi-domain] Cd Length: 660 Bit Score: 478.95 E-value: 1.28e-160
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 4 LIIAEKPNQVKKYVEALGNSfNNKDGYIELeselfDKKVIVTWCVGHLIQLAHMEDYDSNLKQWSKDTLPFIPEDFIFKV 83
Cdd:TIGR01056 3 LVLCEKPSQARDLATVLAKK-KKGNGYLEI-----GVGGFVTWAVGHLVELAEPEEYDEKYKNWRTYDLPLEPEDWQLVV 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 84 SDYGSKQFKIIKELCENLNSDsEIIIATDPDREGEAIARYVLNKIPCTKNLKLKRLWANTQEPEGLKLAFKNLKDADDTY 163
Cdd:TIGR01056 77 SDKTKKQFNVIKRILKENKVD-EVVIATDPDREGELIAREILDYLKVTDKVTIKRLWISSLVDSSIRKAFKNLRPKSETE 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 164 RFYLEAEARSIADWLVGMNFTRYVTLEMKQLGIDeGVFSVGRVQTPTLYMVYKRNNEIKNFESKTYYEMVAKDKENEnAV 243
Cdd:TIGR01056 156 GLYKSGVARARADWLVGINLTRAFTKLGREAGND-GVLSVGRVQTPTLAMVVKRENEIKNFVGKPFYEVSATINKDE-QE 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 244 FKSE---HKFDSIDEFEQFLNENNLNcECEGE---IKEISISEKRKVAPNLFKLGGIQKVANQKWGYTLDKTLSIVQSLY 317
Cdd:TIGR01056 234 FTTEwqpYKDEEERELHEFLAENVVT-DLTQKpalVTDIEKERKKTSAPLFYDLSALQEDANKRFGISAKRTLDIAQKLY 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 318 DKGYL-SYPRTDCSLITHSEFEYLKDNFS--SYCKLLNIEIEQKNIEPRTQYVNDSKVLEHYAIIPTKqipENDVYNNFS 394
Cdd:TIGR01056 313 ETHKLiTYPRTDSRYLPEDEKEMLLEVLDalKVITPALLPIKKRDELTNNRLWNDKKIEDHHAIIPTG---NDFNLSDLS 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 395 DDEKKIYDEVVKRTMLMFMEDYIYSETKIVLCIENVEFKLTGNVAKEQGWKLLDSENKNSKE---KLLPNYKENEKLSL- 470
Cdd:TIGR01056 390 EEERNVYKLIAQNYLMQFMPKEEYETTTIEIAIGKLMFEAKGKILQDNGWKALLGKQEEDEEtedTTLPAFQKGDELDVe 469
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 471 NLVPKELNTKPPKYLTEATLGGEgglMENCSKFIENEELKGNLKEVHGIGTPATRSSIVKSLIDRGYLETKKKHLMITPK 550
Cdd:TIGR01056 470 TLELLEKQTKPPARYTEGTLLSA---MTNPAAFVQDKGLKKTLKETKGLGTEATRADIIENLFKRGFIQKKKNKIYITKN 546
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 551 GTLLCSALENTnLVSVEMTANWESTLKDISEKghRIRQNEFIDSIKQYIKQMINsdnkllKLESNDKNIEKAIEQSTICN 630
Cdd:TIGR01056 547 GKLLCLLLPEL-LTKPDLTAQWEQYLNGISAG--EKDDDDFINTINEMIKQTIN------EEKKNPETIQKVAKEPVSCG 617
|
650
....*....|..
gi 488415014 631 ----CPKCSNGR 638
Cdd:TIGR01056 618 giakCPAKDNGR 629
|
|
| TopA |
COG0550 |
DNA topoisomerase IA [Replication, recombination and repair]; |
3-604 |
8.27e-136 |
|
DNA topoisomerase IA [Replication, recombination and repair];
Pssm-ID: 440316 [Multi-domain] Cd Length: 541 Bit Score: 410.64 E-value: 8.27e-136
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 3 ILIIAEKPNQVKKYVEALGNSFnnkdgyieleselfdkkvIVTWCVGHLIQLAHME-DYDSNLKqwskdtlpFIPEdfiF 81
Cdd:COG0550 2 KLVIVESPAKAKTIAKYLGKDY------------------VVTASVGHLRDLPKPElDVDVEND--------FEPK---Y 52
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 82 KVSDYGSKQFKIIKELcenLNSDSEIIIATDPDREGEAIARYVLNKIPCTKnlKLKRLWANTQEPEGLKLAFKNLKDADd 161
Cdd:COG0550 53 EVIPGKKKQVKELKKL---AKKADEVILATDPDREGEAIAWHLLELLGDKK--PVKRVVFNEITKKAIKEAFKNPRDID- 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 162 tYRFYLEAEARSIADWLVGMNFTRYVTLEMKQLgidegvFSVGRVQTPTLYMVYKRNNEIKNFESKTYYEMVAKDKeNEN 241
Cdd:COG0550 127 -MNLVDAQQARRILDRLVGYNLSPLLWKKVKRG------LSAGRVQSPALRLIVEREREIEAFVPEEYWTIEATFK-TGG 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 242 AVFKSEH------KFDSIDEFEQFLNEnnlnceCEG---EIKEISISEKRKVAPNLFKLGGIQKVANQKWGYTLDKTLSI 312
Cdd:COG0550 199 GEFTAKLvkidgkKILDEEEAEAILAA------LKGktfTVTSVEKKPKKRNPPPPFTTSTLQQEASRKLGFSAKKTMSI 272
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 313 VQSLYDKGYLSYPRTDCSLITHSEF----EYLKDNFSSyckllnieiEQKNIEPRTQYVNDSKVLEHYAIIPTKQIPEND 388
Cdd:COG0550 273 AQRLYEVGLITYMRTDSVRLSEDAVaaarEYIEALYGK---------EYLPEKPRVYKTSKNAQEAHEAIRPTGVTRTPE 343
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 389 vynNFSDDEKKIYDEVVKRTMLMFMEDYIYSETKIVLCIENVEFKLTGNVAKEQGWKLL----DSENKNSKEKLLPNYKE 464
Cdd:COG0550 344 ---SLSGDEFKLYDLIWKRFLASQMPPAEYETTTVTIEVGGEEFRASGKVIKFPGFLKVygegKDDEEEEEEKRLPPLKE 420
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 465 NEKLSLN-LVPKELNTKPPKYLTEATLGGEgglMENCskfieneelkgnlkevhGIGTPATRSSIVKSLIDRGYLETKKK 543
Cdd:COG0550 421 GEKLKLKkIEPEQHFTKPPPRYTEASLVKA---MEEL-----------------GIGRPSTYASIIETLQDRGYVEREGK 480
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488415014 544 HLMITPKGTLLCSALEN--TNLVSVEMTANWESTLKDISEKghRIRQNEFIDSIKQYIKQMIN 604
Cdd:COG0550 481 RLVPTELGFIVIDLLEEhfPDLVDYEFTAKMEEKLDEIAEG--KLDWKDVLEEFYKPFKELVE 541
|
|
| Topoisom_bac |
pfam01131 |
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ... |
166-593 |
5.24e-109 |
|
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA.
Pssm-ID: 426069 [Multi-domain] Cd Length: 410 Bit Score: 336.91 E-value: 5.24e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 166 YLEAEARSIADWLVGMNFTRYVTLEMKqlgiDEGVFSVGRVQTPTLYMVYKRNNEIKNFESKTYYEMVA---KDKENENA 242
Cdd:pfam01131 7 VDAQLARRELDWLIGFNLSRLLTLKLK----GNKLLSAGRVQTPTLALIVEREREIENFVPEPYWTIEAtlkDGGGVFAN 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 243 VFKSEHKFDSIDEFEQFLNennlNCEC-EGEIKEISISEKRKVAPNLFKLGGIQKVANQKWGYTLDKTLSIVQSLYDK-G 320
Cdd:pfam01131 83 AKWKRGRIFDKEEAEAILE----KLKKgTAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQKLYEKhG 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 321 YLSYPRTDCSLITHSEF-----EYLKDNFSSYCKLLNIEIeqkNIEPRTQYVNDSKVLEHYAIIPTKQIPendVYNNFSD 395
Cdd:pfam01131 159 LITYPRTDSTYLSDDATlkailEYLTKNYGKYLPYAPRLL---KKTKGKLTVGNAKVTAHEAIRPTGDIP---VLPELSD 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 396 DEKKIYDEVVKRTMLMFMEDYIYSETKIVLCIENVEFKLTGNVAKEQGWKLLDSENKNSKEKLLPNYKENEKLSL-NLVP 474
Cdd:pfam01131 233 DERKLYELIVRRFLASQMPPAVYETTTVVLEVGGEEFRASGKVILEDGWLKVYPYEKKEDEEELPELKEGEELKVtQVEV 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 475 KELNTKPPKYLTEATLGGeggLMENCskfieneelkgnlkevhGIGTPATRSSIVKSLIDRGYLETKKKHLMITPKGTLL 554
Cdd:pfam01131 313 EEKKTKPPPRYTEASLIK---AMEKA-----------------GIGTPATRATIIETLLERGYVERKKKSLVPTELGKAL 372
|
410 420 430 440
....*....|....*....|....*....|....*....|
gi 488415014 555 CSALENT-NLVSVEMTANWESTLKDISEkgHRIRQNEFID 593
Cdd:pfam01131 373 VEALEKFpDLVDPELTAELEEKLDEIAE--GKLDWKDVLA 410
|
|
| TOP1Ac |
cd00186 |
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ... |
163-603 |
3.70e-94 |
|
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.
Pssm-ID: 238110 [Multi-domain] Cd Length: 381 Bit Score: 297.21 E-value: 3.70e-94
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 163 YRFYLEAEARSIADWLVGMNFTRYVTLEMKQlgidEGVFSVGRVQTPTLYMVYKRNNEIKNFESKTYYEmvakdkenena 242
Cdd:cd00186 1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRR----KGVLSAGRVQSPTLGLIVEREREIKAFVPEDYWE----------- 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 243 vfksehkfdsIDEFEqflnennlncecegeIKEISISEKRKVAPNLFKLGGIQKVANQKWGYTLDKTLSIVQSLYDKGYL 322
Cdd:cd00186 66 ----------IKEAV---------------VVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGLI 120
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 323 SYPRTDCSLITHSEFEYLKDNFSSYCKLLNIEIEQKnIEPRTQYVNDSKVLEHYAIIPTKQIPENDVYNNFSDDEKKIYD 402
Cdd:cd00186 121 TYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPL-LGRRNPKRGKKEQGAHEAIRPTKVAPTPELEANLSEDEFKLYE 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 403 EVVKRTMLMFMEDYIYSETKIVLCIENVEFKLTGNVAKEQGWKLLDSENKNSKEKLLPNYKENEKLSLNLV-PKELNTKP 481
Cdd:cd00186 200 LIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKLEEVeLEEKETQP 279
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 482 PKYLTEATLggeGGLMENcskfieneelkgnlkevHGIGTPATRSSIVKSLIDRGYLETKKKHLMITPKGTLLCSALENT 561
Cdd:cd00186 280 PPRYTEASL---IKLMEK-----------------RGIGRPSTYASIIETLLDRGYVEKEKKKLIPTELGFAVIELLEKH 339
|
410 420 430 440
....*....|....*....|....*....|....*....|....
gi 488415014 562 --NLVSVEMTANWESTLKDISEKghRIRQNEFIDSIKQYIKQMI 603
Cdd:cd00186 340 fpELVDPEFTAKLEEKLDEIAEG--KKDYQEVLEEFYEEFKKIV 381
|
|
| TOP1Ac |
smart00437 |
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ... |
280-551 |
1.32e-60 |
|
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Pssm-ID: 214663 [Multi-domain] Cd Length: 259 Bit Score: 204.40 E-value: 1.32e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 280 EKRKVAPNLFKLGGIQKVANQKWGYTLDKTLSIVQSLYDKGYLSYPRTDCSLITHSEFEYLKDNFSSYCKLLNIEIEQKN 359
Cdd:smart00437 4 EKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGKEYLDLAVVL 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 360 IEPRTQYVNDSKVLEHYAIIPTKQIPENDVYNNFSDDEKKIYDEVVKRTMLMFMEDYIYSETKIVLCIENVEFKLTGNVA 439
Cdd:smart00437 84 LKPRKPRKGKKAQGAHEAIRPTKPIFTPELEKELSEDEFKLYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAKGKTL 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 440 KEQGWKLLDSENKNSKEKLLPNYKENEKLSLNLV-PKELNTKPPKYLTEATLGGEgglMENcskfieneelkgnlkevHG 518
Cdd:smart00437 164 LFDGWLKVYPEEKKEEEIELPTLKKGDELKVEEVeVEEKETKPPARYTEASLIKL---MEK-----------------RG 223
|
250 260 270
....*....|....*....|....*....|...
gi 488415014 519 IGTPATRSSIVKSLIDRGYLETKKKHLMITPKG 551
Cdd:smart00437 224 IGRPSTYASIIETLLDRGYVTKKKKKLIPTELG 256
|
|
| Toprim_Crpt |
pfam13342 |
C-terminal repeat of topoisomerase; |
657-714 |
1.84e-18 |
|
C-terminal repeat of topoisomerase;
Pssm-ID: 463851 [Multi-domain] Cd Length: 60 Bit Score: 79.44 E-value: 1.84e-18
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 488415014 657 DCDFIIFGMISNKNITPQIVKEIIEKGKTKTIKGFTSKAGKKFNAKLKLTE-KGVEFDF 714
Cdd:pfam13342 1 GCGFSIGKTIAGKKLSEEQVKELLTKGKTGLIKGFKSKKGKKFDAYLVLDDdEKVEFDF 59
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK07726 |
PRK07726 |
DNA topoisomerase 3; |
3-658 |
0e+00 |
|
DNA topoisomerase 3;
Pssm-ID: 236078 [Multi-domain] Cd Length: 658 Bit Score: 560.94 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 3 ILIIAEKPNQVKKYVEALGNsFNNKDGYIEleselfDKKVIVTWCVGHLIQLAHMEDYDSNLKQWSKDTLPFIPEDFIFK 82
Cdd:PRK07726 2 RLFIAEKPSVGRDIADVLKP-HKKGDGYIE------GNGYIVTWAIGHLLELAEPEAYDERYKRWRLEDLPIIPEKWKLV 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 83 VSDYGSKQFKIIKELcenLNSDSEIIIATDPDREGEAIARYVLNKIPCTKNLKlkRLWANTQEPEGLKLAFKNLKDADDT 162
Cdd:PRK07726 75 VKKKTAKQFNVVKKL---LKQATEIVIATDADREGELIAREILDYCGVRKPIK--RLWISSLTDKAIKRAFANLKPGKET 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 163 YRFYLEAEARSIADWLVGMNFTRYVTLEMKQLGIDeGVFSVGRVQTPTLYMVYKRNNEIKNFESKTYYEMVAKDKENENA 242
Cdd:PRK07726 150 IPLYYSALARSRADWLVGINMTRAYTLLGRKAGYN-GVLSVGRVQTPTLALVVRRDEEIENFVPKPYWEVEAHLTPGERF 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 243 VFKSEHKFDSIDEFEQFLNEN---NLNCECEG---EIKEISISEKRKVAPNLFKLGGIQKVANQKWGYTLDKTLSIVQSL 316
Cdd:PRK07726 229 TAKWQPSEPYQDEEGRLLDRPlaeQVVARIQGqpaKVTEVETKRKKEYAPLLYDLSELQIDANKRFGLSAKETLDIAQSL 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 317 YDK-GYLSYPRTDCSLITHSEFEYLKD------NFSSYCKLLNieiEQKNIEPRTQYVNDSKVLEHYAIIPTKQIPEndv 389
Cdd:PRK07726 309 YEThKLITYPRTDSRYLPEDMVATLPEvlnaisKVDPYLLLAP---PVLDPSIRSRAWNDKKVTAHHAIIPTEQPPN--- 382
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 390 YNNFSDDEKKIYDEVVKRTMLMFMEDYIYSETKIVLCIENVEFKLTGNVAKEQGWK-LLDSENKNSKEK-LLPNYKENEK 467
Cdd:PRK07726 383 LSKLSEDERKVYDLIARRYLAQFLPPAEYDKTTIELEIAGGTFIAKGKQVVEAGWKaLLGKKEEDEEKEqPLPVLAKGDE 462
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 468 LSLNLVP-KELNTKPPKYLTEATLGGeggLMENCSKFIENEELKGNLKEVHGIGTPATRSSIVKSLIDRGYLETKKKHLM 546
Cdd:PRK07726 463 LKVEKGEvKEGQTQPPKRFTEGTLLS---AMENIARFVQDKELKKTLKETDGLGTEATRAGIIEKLFKRGYLEKKGKYIH 539
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 547 ITPKGTLLCSALeNTNLVSVEMTANWESTLKDISEKghRIRQNEFIDSIKQYIKQMINsDNKLLKLESNDKNIEKAieqs 626
Cdd:PRK07726 540 ATDKGKQLIDAL-PEELTSPDMTAKWEQALDQISEG--QLSYQDFMQPLKQWLKQLVE-QAKQSSEKYKFDNLTGP---- 611
|
650 660 670
....*....|....*....|....*....|..
gi 488415014 627 ticNCPKCsnGRIKKLLSKNKKLFYACSNKDC 658
Cdd:PRK07726 612 ---KCPDC--GKPMLKVKGKNGKMLVCQDREC 638
|
|
| topB |
TIGR01056 |
DNA topoisomerase III, bacteria and conjugative plasmid; This model describes topoisomerase ... |
4-638 |
1.28e-160 |
|
DNA topoisomerase III, bacteria and conjugative plasmid; This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273419 [Multi-domain] Cd Length: 660 Bit Score: 478.95 E-value: 1.28e-160
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 4 LIIAEKPNQVKKYVEALGNSfNNKDGYIELeselfDKKVIVTWCVGHLIQLAHMEDYDSNLKQWSKDTLPFIPEDFIFKV 83
Cdd:TIGR01056 3 LVLCEKPSQARDLATVLAKK-KKGNGYLEI-----GVGGFVTWAVGHLVELAEPEEYDEKYKNWRTYDLPLEPEDWQLVV 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 84 SDYGSKQFKIIKELCENLNSDsEIIIATDPDREGEAIARYVLNKIPCTKNLKLKRLWANTQEPEGLKLAFKNLKDADDTY 163
Cdd:TIGR01056 77 SDKTKKQFNVIKRILKENKVD-EVVIATDPDREGELIAREILDYLKVTDKVTIKRLWISSLVDSSIRKAFKNLRPKSETE 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 164 RFYLEAEARSIADWLVGMNFTRYVTLEMKQLGIDeGVFSVGRVQTPTLYMVYKRNNEIKNFESKTYYEMVAKDKENEnAV 243
Cdd:TIGR01056 156 GLYKSGVARARADWLVGINLTRAFTKLGREAGND-GVLSVGRVQTPTLAMVVKRENEIKNFVGKPFYEVSATINKDE-QE 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 244 FKSE---HKFDSIDEFEQFLNENNLNcECEGE---IKEISISEKRKVAPNLFKLGGIQKVANQKWGYTLDKTLSIVQSLY 317
Cdd:TIGR01056 234 FTTEwqpYKDEEERELHEFLAENVVT-DLTQKpalVTDIEKERKKTSAPLFYDLSALQEDANKRFGISAKRTLDIAQKLY 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 318 DKGYL-SYPRTDCSLITHSEFEYLKDNFS--SYCKLLNIEIEQKNIEPRTQYVNDSKVLEHYAIIPTKqipENDVYNNFS 394
Cdd:TIGR01056 313 ETHKLiTYPRTDSRYLPEDEKEMLLEVLDalKVITPALLPIKKRDELTNNRLWNDKKIEDHHAIIPTG---NDFNLSDLS 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 395 DDEKKIYDEVVKRTMLMFMEDYIYSETKIVLCIENVEFKLTGNVAKEQGWKLLDSENKNSKE---KLLPNYKENEKLSL- 470
Cdd:TIGR01056 390 EEERNVYKLIAQNYLMQFMPKEEYETTTIEIAIGKLMFEAKGKILQDNGWKALLGKQEEDEEtedTTLPAFQKGDELDVe 469
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 471 NLVPKELNTKPPKYLTEATLGGEgglMENCSKFIENEELKGNLKEVHGIGTPATRSSIVKSLIDRGYLETKKKHLMITPK 550
Cdd:TIGR01056 470 TLELLEKQTKPPARYTEGTLLSA---MTNPAAFVQDKGLKKTLKETKGLGTEATRADIIENLFKRGFIQKKKNKIYITKN 546
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 551 GTLLCSALENTnLVSVEMTANWESTLKDISEKghRIRQNEFIDSIKQYIKQMINsdnkllKLESNDKNIEKAIEQSTICN 630
Cdd:TIGR01056 547 GKLLCLLLPEL-LTKPDLTAQWEQYLNGISAG--EKDDDDFINTINEMIKQTIN------EEKKNPETIQKVAKEPVSCG 617
|
650
....*....|..
gi 488415014 631 ----CPKCSNGR 638
Cdd:TIGR01056 618 giakCPAKDNGR 629
|
|
| TopA |
COG0550 |
DNA topoisomerase IA [Replication, recombination and repair]; |
3-604 |
8.27e-136 |
|
DNA topoisomerase IA [Replication, recombination and repair];
Pssm-ID: 440316 [Multi-domain] Cd Length: 541 Bit Score: 410.64 E-value: 8.27e-136
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 3 ILIIAEKPNQVKKYVEALGNSFnnkdgyieleselfdkkvIVTWCVGHLIQLAHME-DYDSNLKqwskdtlpFIPEdfiF 81
Cdd:COG0550 2 KLVIVESPAKAKTIAKYLGKDY------------------VVTASVGHLRDLPKPElDVDVEND--------FEPK---Y 52
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 82 KVSDYGSKQFKIIKELcenLNSDSEIIIATDPDREGEAIARYVLNKIPCTKnlKLKRLWANTQEPEGLKLAFKNLKDADd 161
Cdd:COG0550 53 EVIPGKKKQVKELKKL---AKKADEVILATDPDREGEAIAWHLLELLGDKK--PVKRVVFNEITKKAIKEAFKNPRDID- 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 162 tYRFYLEAEARSIADWLVGMNFTRYVTLEMKQLgidegvFSVGRVQTPTLYMVYKRNNEIKNFESKTYYEMVAKDKeNEN 241
Cdd:COG0550 127 -MNLVDAQQARRILDRLVGYNLSPLLWKKVKRG------LSAGRVQSPALRLIVEREREIEAFVPEEYWTIEATFK-TGG 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 242 AVFKSEH------KFDSIDEFEQFLNEnnlnceCEG---EIKEISISEKRKVAPNLFKLGGIQKVANQKWGYTLDKTLSI 312
Cdd:COG0550 199 GEFTAKLvkidgkKILDEEEAEAILAA------LKGktfTVTSVEKKPKKRNPPPPFTTSTLQQEASRKLGFSAKKTMSI 272
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 313 VQSLYDKGYLSYPRTDCSLITHSEF----EYLKDNFSSyckllnieiEQKNIEPRTQYVNDSKVLEHYAIIPTKQIPEND 388
Cdd:COG0550 273 AQRLYEVGLITYMRTDSVRLSEDAVaaarEYIEALYGK---------EYLPEKPRVYKTSKNAQEAHEAIRPTGVTRTPE 343
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 389 vynNFSDDEKKIYDEVVKRTMLMFMEDYIYSETKIVLCIENVEFKLTGNVAKEQGWKLL----DSENKNSKEKLLPNYKE 464
Cdd:COG0550 344 ---SLSGDEFKLYDLIWKRFLASQMPPAEYETTTVTIEVGGEEFRASGKVIKFPGFLKVygegKDDEEEEEEKRLPPLKE 420
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 465 NEKLSLN-LVPKELNTKPPKYLTEATLGGEgglMENCskfieneelkgnlkevhGIGTPATRSSIVKSLIDRGYLETKKK 543
Cdd:COG0550 421 GEKLKLKkIEPEQHFTKPPPRYTEASLVKA---MEEL-----------------GIGRPSTYASIIETLQDRGYVEREGK 480
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488415014 544 HLMITPKGTLLCSALEN--TNLVSVEMTANWESTLKDISEKghRIRQNEFIDSIKQYIKQMIN 604
Cdd:COG0550 481 RLVPTELGFIVIDLLEEhfPDLVDYEFTAKMEEKLDEIAEG--KLDWKDVLEEFYKPFKELVE 541
|
|
| Topoisom_bac |
pfam01131 |
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ... |
166-593 |
5.24e-109 |
|
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA.
Pssm-ID: 426069 [Multi-domain] Cd Length: 410 Bit Score: 336.91 E-value: 5.24e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 166 YLEAEARSIADWLVGMNFTRYVTLEMKqlgiDEGVFSVGRVQTPTLYMVYKRNNEIKNFESKTYYEMVA---KDKENENA 242
Cdd:pfam01131 7 VDAQLARRELDWLIGFNLSRLLTLKLK----GNKLLSAGRVQTPTLALIVEREREIENFVPEPYWTIEAtlkDGGGVFAN 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 243 VFKSEHKFDSIDEFEQFLNennlNCEC-EGEIKEISISEKRKVAPNLFKLGGIQKVANQKWGYTLDKTLSIVQSLYDK-G 320
Cdd:pfam01131 83 AKWKRGRIFDKEEAEAILE----KLKKgTAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQKLYEKhG 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 321 YLSYPRTDCSLITHSEF-----EYLKDNFSSYCKLLNIEIeqkNIEPRTQYVNDSKVLEHYAIIPTKQIPendVYNNFSD 395
Cdd:pfam01131 159 LITYPRTDSTYLSDDATlkailEYLTKNYGKYLPYAPRLL---KKTKGKLTVGNAKVTAHEAIRPTGDIP---VLPELSD 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 396 DEKKIYDEVVKRTMLMFMEDYIYSETKIVLCIENVEFKLTGNVAKEQGWKLLDSENKNSKEKLLPNYKENEKLSL-NLVP 474
Cdd:pfam01131 233 DERKLYELIVRRFLASQMPPAVYETTTVVLEVGGEEFRASGKVILEDGWLKVYPYEKKEDEEELPELKEGEELKVtQVEV 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 475 KELNTKPPKYLTEATLGGeggLMENCskfieneelkgnlkevhGIGTPATRSSIVKSLIDRGYLETKKKHLMITPKGTLL 554
Cdd:pfam01131 313 EEKKTKPPPRYTEASLIK---AMEKA-----------------GIGTPATRATIIETLLERGYVERKKKSLVPTELGKAL 372
|
410 420 430 440
....*....|....*....|....*....|....*....|
gi 488415014 555 CSALENT-NLVSVEMTANWESTLKDISEkgHRIRQNEFID 593
Cdd:pfam01131 373 VEALEKFpDLVDPELTAELEEKLDEIAE--GKLDWKDVLA 410
|
|
| PRK08173 |
PRK08173 |
DNA topoisomerase III; Validated |
3-714 |
6.23e-105 |
|
DNA topoisomerase III; Validated
Pssm-ID: 236172 [Multi-domain] Cd Length: 862 Bit Score: 340.11 E-value: 6.23e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 3 ILIIAEKPNQVKKYVEALGnSFNNKDGYieLESELFdkkvIVTWCVGHLIQLAHMEDYDSNLKQWSKDTLPFIPEDFIFK 82
Cdd:PRK08173 4 ALIIAEKPSVANDIARALG-GFTKHDEY--FESDEY----VLSSAVGHLLEIAAPEEYEVKRGKWSFAHLPVIPPHFDLN 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 83 VSDYGSKQFKIIKELCENLNSDsEIIIATDPDREGEAIARYVLNKIPCTKnlKLKRLWANTQEPEGLKLAFKNLKDADDT 162
Cdd:PRK08173 77 PIAKTESRLKVLTKLIKRKDVT-RLINACDAGREGELIFRLIAQHAKAKK--PVKRLWLQSMTPQAIRDGFANLRSDEDM 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 163 YRFYLEAEARSIADWLVGMNFTRYVTLEMKQLGideGVF--SVGRVQTPTLYMVYKRNNEIKNFESKTYYEMVAkDKENE 240
Cdd:PRK08173 154 QPLADAARCRSEADWLVGINGTRAMTAFNSKGG---GFFltTVGRVQTPTLSIVVEREEKIRRFVPRDYWEVRA-EFVAA 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 241 NAVFKS---EHKFdSIDEFEQFLNENNLNCE---------CEGeiKEISISEKRK----VAPNLFKLGGIQKVANQKWGY 304
Cdd:PRK08173 230 AGFYEGrwfDPKF-KKDEFDPEKRASRLWSEaaaeaivaaCRG--KPGTVTEESKpstqLSPLLFDLTSLQREANGRFGF 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 305 TLDKTLSIVQSLYDK-GYLSYPRTDCS------LITHSE-FEYLKDNfSSYCKLLNIEIEQKNIEPRTQYVNDSKVLEHY 376
Cdd:PRK08173 307 SAKNTLGLAQALYEKhKVLTYPRTDSRalpedyLGTVKQtLEMLKES-NNYLPHAKQILDKGWVKPNKRIFDNSKISDHF 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 377 AIIPTKQIPEndvynNFSDDEKKIYDEVVKRTMLMFMEDYIYSETKIVLCIENVEFKLTGNVAKEQGWKLLDSENKNSKE 456
Cdd:PRK08173 386 AIIPTLQAPK-----SLSEPEQKLYDLVVKRFLAVFFPAAEFLVTTRITEVAGHHFKTEGKVLVNPGWLAVYGKEAQGAD 460
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 457 KLLPNYKENEK-LSLNLVPKELNTKPPKYLTEATLggeGGLMENCSKFIENEELKGNLKEvHGIGTPATRSSIVKSLIDR 535
Cdd:PRK08173 461 ANLVPVQKGEKvKTDKIEAVALTTKPPARYNEATL---LSAMEGAGKLVEDDELREAMAE-KGLGTPATRAAIIEGLLGE 536
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 536 GYLETKKKHLMITPKG----TLLcSALENTNLVSVEMTANWESTLKDIsEKGhRIRQNEFIDSIKQYIKQMInsdnKLLK 611
Cdd:PRK08173 537 KYLVREGRELIPTAKAfqlmTLL-RGLGVEELTSPELTGEWEYKLSQI-ERG-KLSRDAFMQEIAQMTQQIV----KRAK 609
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 612 lESNDKNI--EKAIEQSTicnCPKCSnGRIKKLLSKnkklfYACSnkDCDFIIFGMISNKNITPQIVKEIIEKGKTKTIK 689
Cdd:PRK08173 610 -EYDSDTIpgDYATLQTP---CPNCG-GVVKENYRR-----FACT--KCDFSISKIPGGRQFEIAEVEELLRKKEIGPLS 677
|
730 740
....*....|....*....|....*....
gi 488415014 690 GFTSKAGKKFNAKLKLTEKG----VEFDF 714
Cdd:PRK08173 678 GFRSKMGRPFSAILKLSDETknykLEFDF 706
|
|
| TOP1Ac |
cd00186 |
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ... |
163-603 |
3.70e-94 |
|
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.
Pssm-ID: 238110 [Multi-domain] Cd Length: 381 Bit Score: 297.21 E-value: 3.70e-94
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 163 YRFYLEAEARSIADWLVGMNFTRYVTLEMKQlgidEGVFSVGRVQTPTLYMVYKRNNEIKNFESKTYYEmvakdkenena 242
Cdd:cd00186 1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRR----KGVLSAGRVQSPTLGLIVEREREIKAFVPEDYWE----------- 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 243 vfksehkfdsIDEFEqflnennlncecegeIKEISISEKRKVAPNLFKLGGIQKVANQKWGYTLDKTLSIVQSLYDKGYL 322
Cdd:cd00186 66 ----------IKEAV---------------VVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGLI 120
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 323 SYPRTDCSLITHSEFEYLKDNFSSYCKLLNIEIEQKnIEPRTQYVNDSKVLEHYAIIPTKQIPENDVYNNFSDDEKKIYD 402
Cdd:cd00186 121 TYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPL-LGRRNPKRGKKEQGAHEAIRPTKVAPTPELEANLSEDEFKLYE 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 403 EVVKRTMLMFMEDYIYSETKIVLCIENVEFKLTGNVAKEQGWKLLDSENKNSKEKLLPNYKENEKLSLNLV-PKELNTKP 481
Cdd:cd00186 200 LIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKLEEVeLEEKETQP 279
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 482 PKYLTEATLggeGGLMENcskfieneelkgnlkevHGIGTPATRSSIVKSLIDRGYLETKKKHLMITPKGTLLCSALENT 561
Cdd:cd00186 280 PPRYTEASL---IKLMEK-----------------RGIGRPSTYASIIETLLDRGYVEKEKKKLIPTELGFAVIELLEKH 339
|
410 420 430 440
....*....|....*....|....*....|....*....|....
gi 488415014 562 --NLVSVEMTANWESTLKDISEKghRIRQNEFIDSIKQYIKQMI 603
Cdd:cd00186 340 fpELVDPEFTAKLEEKLDEIAEG--KKDYQEVLEEFYEEFKKIV 381
|
|
| PRK14724 |
PRK14724 |
DNA topoisomerase III; Provisional |
1-718 |
6.06e-83 |
|
DNA topoisomerase III; Provisional
Pssm-ID: 237803 [Multi-domain] Cd Length: 987 Bit Score: 283.38 E-value: 6.06e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 1 MTILIIAEKPNQVKKYVEAL---GNSFNNKDGYIELESelfdkkVIVTWCVGHLIQLAHMEDYDSNLKQWSKDTLPFIPE 77
Cdd:PRK14724 1 TKTLVIAEKPSVAQDIVRALtpvAGKFEKHDEHFESDS------YVVTSAVGHLVEIQAPEEFDVKRGKWSFANLPVIPP 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 78 DFIFKVSDYGSKQFKIIKELCENLNSDsEIIIATDPDREGEAIAR----YVLNKIPcTKNLKLKRLWANTQEPEGLKLAF 153
Cdd:PRK14724 75 YFDLKPVDKTKTRLNAVVKLAKRKDVT-ELVNACDAGREGELIFRlieqYAGGAKG-GLGKPVKRLWLQSMTPQAIRDGF 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 154 KNLKDADDTYRFYLEAEARSIADWLVGMNFTRYVTLEMKQlgiDEGVF--SVGRVQTPTLYMVYKRNNEIKNFESKTYYE 231
Cdd:PRK14724 153 DNLRSDAQMQGLASAARSRSEADWLVGINGTRAMTAFNSR---DGGFFltTVGRVQTPTLSLVVEREEKIRKFVSRDYWE 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 232 MvakdkeneNAVFKSEHK------FDSidEFEQFLNENNLNCE---CEGEIKEI---------SISEKRK----VAPNLF 289
Cdd:PRK14724 230 I--------HAGFHAEAGeylgkwFDP--QWKKASDDPEARADrvwSEREARAIadavrgkaaTVTEESKpttqASPLLF 299
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 290 KLGGIQKVANQKWGYTLDKTLSIVQSLYDK-GYLSYPRTDCSLITHSEFEYLKDNFSSYCK--------LLNIEIEQKNI 360
Cdd:PRK14724 300 DLTSLQREANGKFGFSAKTTLALAQSLYERhKALTYPRTDSRALPEDYLPVAKQTFEMLATsgmrhlapFAQQALDGNYV 379
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 361 EPRTQYVNDSKVLEHYAIIPTKQIPendvyNNFSDDEKKIYDEVVKRTMLMFMEDYIYSETKIVLCIENVEFKLTGNVAK 440
Cdd:PRK14724 380 RPSKRIFDNSKVSDHFAIIPTTQAP-----SGLSEAEQKLYDLVVRRFMAVFFPSAEYQVTTRISQVVGHSFKTEGKVLV 454
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 441 EQGW----------KLLDSENKNSKEKLLPnYKENEKLSLNLV-PKELNTKPPKYLTEATLGGEgglMENCSKFIENEEL 509
Cdd:PRK14724 455 KPGWlaiygkeaanEVEDAKDGDKGQPLVP-VKPGEMVRTEFAeAKGLKTKPPARYSEATLLGA---MESAGKQIDDDEL 530
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 510 KGNLKEvHGIGTPATRSSIVKSLIDRGYLETKKKHLMITPKG----TLLcSALENTNLVSVEMTANWESTLKDIsEKGHR 585
Cdd:PRK14724 531 REAMQE-KGLGTPATRAAIIEGLLTEKYMLREGRELIPTAKAfqlmTLL-RGLGVEELSRAELTGEWEYKLAQM-EKGQL 607
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 586 IRQnEFIDSIKQYIKQMINsdnkllKLESNDKNIEKAIEQSTICNCPKCSnGRIKKLLSKnkklfYACSNKD-----CDF 660
Cdd:PRK14724 608 SRE-AFMQQIAAMTEKLVK------KAKEYDRDTIPGDYATLSTPCPNCG-GVVKENYRR-----YACTGANgagegCGF 674
|
730 740 750 760 770 780
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488415014 661 IIFGMISNKNITPQIVKEIIEKGKTKTIKGFTSKAGKKFNAK--LKLTEKG----VEFDFNKKK 718
Cdd:PRK14724 675 SFTKSPAGRTFETAEAEQLLRDRRIGPLEGFRSKAGWPFTAEvvIKRDEEAknykLEFDFGDDK 738
|
|
| PRK07219 |
PRK07219 |
DNA topoisomerase I; Validated |
2-660 |
4.65e-80 |
|
DNA topoisomerase I; Validated
Pssm-ID: 235971 [Multi-domain] Cd Length: 822 Bit Score: 272.26 E-value: 4.65e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 2 TILIIAEKPNQVKKYVEALGN-----SFNNKDGYIELESElfDKKVIVTWCVGHLIQLahmeDYDSNLKQWSKdtlpFIP 76
Cdd:PRK07219 1 TELIIAEKNNAARRIADILSGgkakkKRVNGVPYYEFERK--GEKWIVIGLSGHIVTV----DFPEEYGDWRD----VDP 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 77 EDFIFKVSDYGSKQFKIIKELcENLNSDS-EIIIATDPDREGEAIARYVLNKIPCTKNLKLKRLWANTQEPEGLKLAFKN 155
Cdd:PRK07219 71 AELIDADPVKKITKQNYINAL-KKLAKDAdEIIIATDYDREGELIGKEAYHILREVCQVPVKRARFSSLTKKEIRKAFEN 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 156 LKDADdtYRFYLEAEARSIADWLVGMNFTRYVTLEMKQLGiDEGVFSVGRVQTPTLYMVYKRNNEIKNFESKTYYEMVAk 235
Cdd:PRK07219 150 PDEID--FNLADAGEARQIIDLYWGAALTRFLSLSVRQLG-RWDFLSVGRVQTPTLAFIVDREREIRAFDPEDYWKIEA- 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 236 DKENENAVFKSEhkFDSIDEFEQFLNE-------NNLNCECEGEIKEISISEKRKVAPNLFKLGGIQKVANQKWGYTLDK 308
Cdd:PRK07219 226 LLDKEAQYFYRD--LIGGHEAEKFWDEeeaeeiyEKLKGAKEATVSSVKKRERTISPPAPFNTTEFLREASKIFGISPKR 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 309 TLSIVQSLYDKGYLSYPRTDCSLI--THSEFEYLKD-----NFSSYCKLLnieIEQKNIEPRTqyvNDSKVLEHYAIIPT 381
Cdd:PRK07219 304 AMEIAEKLYTAGYISYPRTDNTVYpdDLDPKELLKKlskkkEYGPYAESI---LEQENIKPTE---GKKETTDHPPIHPV 377
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 382 KQIPENDVynnfSDDEKKIYDEVVKRTMLMFMEDYIYSETKIVLCIENVEFKLTGNVAKEQGWKLLdSENKNSKEKLLPN 461
Cdd:PRK07219 378 DVPKREEL----SDDEWKVYELIVRRFLATLADPAEWEYLKVELDVNGEIFKASGSRLVEEGWHEV-YPYEKFDEKELPD 452
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 462 YKENEKLSLN---LVPKElnTKPPKYLTEATLGGEgglMENcskfieneelkgnlkevHGIGTPATRSSIVKSLIDRGYL 538
Cdd:PRK07219 453 LEEGEKLKVNkieIEAKE--TQPPKRYTQSSLIKE---MEK-----------------RGLGTKATRHDIIEKLYKRGYV 510
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 539 eTKKKHLMITPKGTLLCSALENTN--LVSVEMTANWESTLKDIsEKGhRIRQNEFIDSIKQYIKQMINsdnkllKLESND 616
Cdd:PRK07219 511 -IEGDPPRPTDLGIAVIEALEKYApeIVSEEMTAQLEADMQAI-EDG-KKKKEDVTEESREMLKEILS------ELKEKR 581
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....
gi 488415014 617 KNIEKAIEQS---------TICNCPKCSnGRIKKLLSKNKKLFYACSN-KDCDF 660
Cdd:PRK07219 582 KEIGDHLAGSlkaenrslkTIGKCPECG-GDLIIIRTDKGSRFVGCSGyPDCRN 634
|
|
| topA_arch |
TIGR01057 |
DNA topoisomerase I, archaeal; This model describes topoisomerase I from archaea. These ... |
6-655 |
1.22e-69 |
|
DNA topoisomerase I, archaeal; This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273420 [Multi-domain] Cd Length: 618 Bit Score: 239.34 E-value: 1.22e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 6 IAEKPNQVKKYVEALGNSFNNK---DG--YIELESElfDKKVIVTWCVGHLIQLAhmEDYDSNLKQWSkdtLPFIPEDFI 80
Cdd:TIGR01057 1 IAEKPKVAAKIAGALSDGRVLKkseYGvpYWEVRRD--GKKIIVASAVGHLFGLH--PKSRGGYPVFD---IEWVPIFEF 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 81 FKVSDYGSKQFKIIKELcenLNSDSEIIIATDPDREGEAIARYVLnKIPCTKNlKLKRLWANTQEPEGLKLAFKNLKDAD 160
Cdd:TIGR01057 74 DKGKGYVSKYIKALSKL---AKGADEYINACDYDIEGEVIGFKAL-KYFCGVE-RAKRMKFSTLTKQDIRRAYANPEEID 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 161 dtYRFYLEAEARSIADWLVGMNFTRYVTLEMKQLGIDEGVFSVGRVQTPTLYMVYKRNNEIKNFESKTYYEMVAKDKENe 240
Cdd:TIGR01057 149 --YGMVDAGMARHILDWYWGINLSRALMEAIRAAAGRWVILSAGRVQGPTLAFLVEREREINLFVPKPYWVIKATLEKG- 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 241 NAVFKSEHKFDSIDEFEQflnENNLNCECEG----EIKEISISEKRKVAPNLFKLGGIQKVANQKWGYTLDKTLSIVQSL 316
Cdd:TIGR01057 226 GGVFDARPEKWKIWSEEE---AKSIKEELKKspwaAVEEVRSERSILKPPPPFDLGTLQREAYRIFGFSPKKTQSIAQEL 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 317 YDKGYLSYPRTDCSLITHS-EFEYLKDNFSS---YCKLLNIEIEQKNIEPRTQYVNDSKvleHYAIIPTKQIPENDVynn 392
Cdd:TIGR01057 303 YEEALISYPRTSSQKLPPSiNYRAILDNLAKgplYREAAERLLETGVLKPVEGKKEDPA---HPAIHPTGEIPSQEL--- 376
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 393 fSDDEKKIYDEVVKRTMLMFMEDYIYSETKIVLCIENVEFKLTGNVAKEQGWKlldSENKNSK--EKLLPNYKENEKLSL 470
Cdd:TIGR01057 377 -SKDEKKVYDLIVRRFLAAFSEEAIREKSKVLLRIGQEKFRLSGLRVVKLGWL---EYYHYSKfeEKELPPLDRGDKIKV 452
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 471 NLVPKELN-TKPPKYLTEATLGGEgglMENcskfieneelkgnlkevHGIGTPATRSSIVKSLIDRGYLETKKKhLMITP 549
Cdd:TIGR01057 453 VRVDVRVKeTQPPARYDKASLIRE---MES-----------------RGLGTKATRARIIETLYKRGYIEGKKS-IKVTP 511
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 550 KGTLLCSALEN--TNLVSVEMTANWESTLKDISEKghRIRQNEFIDSIKQYIKQMINSDNKllKLESNDKNIEKAIEQST 627
Cdd:TIGR01057 512 LGEAVIETLQRycPEIISEELTRRFESKLEDIMSG--RITKDEVIDEAKKRLRKILEEFKK--RLDDIGIELGKSLGSVE 587
|
650 660
....*....|....*....|....*....
gi 488415014 628 IC-NCPKCsnGRIKKLLSKNKKLFYACSN 655
Cdd:TIGR01057 588 VVgKCPKC--GGKLVSKYAKKGRFVGCSN 614
|
|
| TOP1Ac |
smart00437 |
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ... |
280-551 |
1.32e-60 |
|
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Pssm-ID: 214663 [Multi-domain] Cd Length: 259 Bit Score: 204.40 E-value: 1.32e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 280 EKRKVAPNLFKLGGIQKVANQKWGYTLDKTLSIVQSLYDKGYLSYPRTDCSLITHSEFEYLKDNFSSYCKLLNIEIEQKN 359
Cdd:smart00437 4 EKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGKEYLDLAVVL 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 360 IEPRTQYVNDSKVLEHYAIIPTKQIPENDVYNNFSDDEKKIYDEVVKRTMLMFMEDYIYSETKIVLCIENVEFKLTGNVA 439
Cdd:smart00437 84 LKPRKPRKGKKAQGAHEAIRPTKPIFTPELEKELSEDEFKLYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAKGKTL 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 440 KEQGWKLLDSENKNSKEKLLPNYKENEKLSLNLV-PKELNTKPPKYLTEATLGGEgglMENcskfieneelkgnlkevHG 518
Cdd:smart00437 164 LFDGWLKVYPEEKKEEEIELPTLKKGDELKVEEVeVEEKETKPPARYTEASLIKL---MEK-----------------RG 223
|
250 260 270
....*....|....*....|....*....|...
gi 488415014 519 IGTPATRSSIVKSLIDRGYLETKKKHLMITPKG 551
Cdd:smart00437 224 IGRPSTYASIIETLLDRGYVTKKKKKLIPTELG 256
|
|
| PRK05776 |
PRK05776 |
DNA topoisomerase I; Provisional |
1-634 |
3.70e-59 |
|
DNA topoisomerase I; Provisional
Pssm-ID: 235602 [Multi-domain] Cd Length: 670 Bit Score: 211.77 E-value: 3.70e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 1 MTILIIAEKPNQVKKYVEALGNSFNNKDGYIELESELFD--KKVIVTWCVGHLIQLAHMED----YDSnlkQWskdtlpf 74
Cdd:PRK05776 1 GYILVIAEKPKAARKIAEALSEKPIRCRIYGVPYWIVKRdgKKIVVAPAAGHLFGLHTKSKgfpvFDY---EW------- 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 75 IPEDFIFKVSDYGSKQFKIIKELCENLnsdSEIIIATDPDREGEAIArYVLNKIPCTKNlKLKRLWANTQEPEGLKLAFK 154
Cdd:PRK05776 71 KPLYEIDKGSKYTKKYYELLSSLSKYA---DEFINACDYDIEGSVIG-YLIIKYLGDPK-KAKRMKFSALTKSDIRRAFR 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 155 NLKDADdtyrfYLEAEA---RSIADWLVGMNFTRYVTLEMKQLGIDEGVFSVGRVQTPTLYMVYKRNNEIKNFESKTYYE 231
Cdd:PRK05776 146 NLETLD-----YEMINAgiaRHELDWLWGINVSRALMSSVRDASGKRVILSAGRVQSPTLKYVVEREIERNLFVPLPYFS 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 232 MVAKDKENeNAVFKSEH---KFDSIDEFEQFLNEnnlnCECEGEIKEISISEKRKV--APNLFKLGGIQKVANQKWGYTL 306
Cdd:PRK05776 221 VSIIIEKN-GYEFTLKYenkKFETKEEAKEILEE----IKKTGYLKVTKVEVKIEIlePPPPFNLGDLQVEAARIYGFSP 295
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 307 DKTLSIVQSLYDKGYLSYPRTdcslithsefeylkdNFSSYCKLLNIEIEQKNIEPRTQYVNDSKVL------------- 373
Cdd:PRK05776 296 YKTQSIAEDLYLDGLISYPRT---------------NSQKLPPTLNIRNILKGLSRSPQYRPLVNLLlketkgvlkpvqg 360
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 374 -----EHYAIIPTKQIPEndvynNFSDDEKKIYDEVVKRTMLMFMEDYIYSETKIVLCI--ENVEFKLTGNVAKEQGWkL 446
Cdd:PRK05776 361 pkddpAHPAIYPTGEPPK-----NLSKDEFKLYDLIVRRFLASFAAPAVLSNTIVTLRVpgFPLVFSASGQRIEERGW-L 434
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 447 LDSENKNSKEKLLPNYKENEKLSLNLVPKELN-TKPPKYLTEATLggegglmencskfieneelkgnLK--EVHGIGTPA 523
Cdd:PRK05776 435 KYYPFHKFDEEELPLLKKGERVKIVDVKVRKSyTKPPSRYSKASL----------------------LKwmESVGIGTEA 492
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 524 TRSSIVKSLIDRGYLETKKKHLMITPKGTLLCSALEN--TNLVSVEMTANWESTLKDISEKghRIRQNEFIDSIKQYIKQ 601
Cdd:PRK05776 493 TRARIIETLFKRGYLTSNGKYIEVTPLGFGVAEVLEKyfPDIVSVELTRDFEEKLEMIRTG--KATREEVIEEAKETLNK 570
|
650 660 670
....*....|....*....|....*....|....
gi 488415014 602 MINSDNKllKLESNDKNIEKAIEQSTICN-CPKC 634
Cdd:PRK05776 571 LLEEFKK--NKDEIGEELAKALGLIKPVGkCKIC 602
|
|
| PRK07220 |
PRK07220 |
DNA topoisomerase I; Validated |
4-662 |
1.50e-52 |
|
DNA topoisomerase I; Validated
Pssm-ID: 180892 [Multi-domain] Cd Length: 740 Bit Score: 194.21 E-value: 1.50e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 4 LIIAEKPNQVKKYVEALGNSFNNK---DGYIELESELFDKKVIVTWCVGHLIQLAHMEDYDSnlkqWSK-DTLPFIPEDF 79
Cdd:PRK07220 3 LIITEKNIAARRIAQILAPKKPKKtrvSGVDVYRYEDNGDDTVVVGLSGHIVNIDFPKEYNN----WQKvDARDLIDAEI 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 80 IFKVSdygskQFKIIKELCENLNSDSEIIIATDPDREGEAIARYVLNKI-PCTKNLKLKRLWANTQEPEGLKLAFKNLKD 158
Cdd:PRK07220 79 ITTPT-----QKKIVTALKKLGKEADRVTIATDYDREGELIGVEALNIIkKVNPDIKFDRVRYSAITKKEIERAFSNPVE 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 159 ADdtyrFYLEA--EARSIADWLVGMNFTRYVTLEMKQLGidEGVFSVGRVQTPTLYMVYKRNNEIKNFESKTYYEMVAkD 236
Cdd:PRK07220 154 VD----FNLADagHSRQVIDLVWGAALTRYISLAAGRLG--KMFLSVGRVQSPTLALIVDREKEREAFVPTPYWEIYA-T 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 237 KENENAVFKSEHKFDSIDEFEQFLNENNLNCEcEGEIKEISISEKRKVAPNLFKLGGIQKVANQkWGYTLDKTLSIVQSL 316
Cdd:PRK07220 227 LENNGETFVAQHSTRRFWEKEEADRVFEKLGK-TAEVTEVEKGTKTDKPPTPFNTTEFISAANS-IGFSAANAMRIAESL 304
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 317 YDKGYLSYPRTD-----CSLITHSEFEYLKDN-FSSYCKLLnieIEQKNIEPRTqyvNDSKVLEHYAIIPTKQIPENDVy 390
Cdd:PRK07220 305 YTNGYISYPRTDntvypESLDLREQIEIFAEGpFGEYAQKL---LEKGELVPTR---GKKETTDHPPIYPASLAKKSEL- 377
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 391 nnfSDDEKKIYDEVVKRTMLMFMEDYIYSETKIVLCIENVEFKLTGNVAKEQGWKLLDSENKnSKEKLLPNYKENEKLSL 470
Cdd:PRK07220 378 ---KEDEWKVYELVVRRFFATFAGPAEWETMKLRFDIGGEEFRANGSRLTEPGWRWYYPYNA-PEDRLLPELSEGEELKV 453
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 471 N---LVPKElnTKPP-KYlteatlgGEGGLMencskfieneelkgNLKEVHGIGTPATRSSIVKSLIDRGYLETKKkhLM 546
Cdd:PRK07220 454 KkkeMLDKE--TQPPgRY-------GQGRLI--------------KLMEDLGLGTKATRHEIISKLYSRAYIHGNP--IQ 508
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 547 ITPKGTLLCSALEN--TNLVSVEMTANWESTLKDISEKghRIRQNEFIDSIKQYIKQMINsdnkllKLESNDKNIEKAI- 623
Cdd:PRK07220 509 PTNTAFAVVDALEKyaPTITKPDMTSRLEEDMDKIAEG--KIKEDAVLEESREMLEQVFD------ELDKNREKIRESLr 580
|
650 660 670 680
....*....|....*....|....*....|....*....|....
gi 488415014 624 ----EQSTICNCPKCSNgRIKKLLSKNKKLFYACSN-KDCDFII 662
Cdd:PRK07220 581 eglrEDKIIGKCPLCGS-DLMVRRSKRGSRFIGCEGyPECTFSL 623
|
|
| TOPRIM_TopoIA_TopoIII |
cd03362 |
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type ... |
2-156 |
1.11e-50 |
|
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173782 [Multi-domain] Cd Length: 151 Bit Score: 173.57 E-value: 1.11e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 2 TILIIAEKPNQVKKYVEALGNSFNNKDGYIELESELFDKKVIVTWCVGHLIQLAHMEDYDSNLKQWSKDTlPFIPEDFIF 81
Cdd:cd03362 1 MVLIIAEKPSVAKAIAKILGGGSKKKGKGRYYEFYGEGGGYVVTWASGHLLELDFPEEYDPWDKVWPLED-PLFPAPFKL 79
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488415014 82 KVSDYGSKQFKIIKELcenLNSDSEIIIATDPDREGEAIARYVLNKIPCTKNLKLKRLWANTQEPEGLKLAFKNL 156
Cdd:cd03362 80 KVDKGKKKQFKVLKKL---AKRADEIVIATDADREGELIGREILEYAKCVKRKPVKRAWFSSLTPKAIRRAFKNL 151
|
|
| PRK06599 |
PRK06599 |
DNA topoisomerase I; Validated |
92-689 |
1.26e-47 |
|
DNA topoisomerase I; Validated
Pssm-ID: 235840 [Multi-domain] Cd Length: 675 Bit Score: 179.28 E-value: 1.26e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 92 KIIKELCENLNSDSEIIIATDPDREGEAIARYVLN--KIPCTKNLKLKRLWANTQEPEGLKLAFKNLKDADdtYRFYLEA 169
Cdd:PRK06599 62 KVVDALKKAAKKADAVYLATDPDREGEAIAWHIAEvlKEAKLKDKNVKRVVFNEITKKAVQEAIENPRDID--MDLVDAQ 139
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 170 EARSIADWLVGMNFTRYVTLEMKQlGIdegvfSVGRVQTPTLYMVYKRNNEIKNFESKTYYEMVAKDKENENAVFKSE-H 248
Cdd:PRK06599 140 QARRALDYLVGFKLSPLLWKKVRR-GL-----SAGRVQSVALRLICEREDEIEAFIPQEYWTIEADLATSNGEPFTAKlV 213
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 249 KFDSiDEFEQFL--NE---NNLNCECEG---EIKEISISEKRKVAPNLFKLGGIQKVANQKWGYTLDKTLSIVQSLYD-- 318
Cdd:PRK06599 214 EVNG-KKLEKFSitNEeqaKALVKALEGqayTVDKIEKKERKRNPPPPFITSTLQQEASRKLGFSAKKTMRIAQKLYEgi 292
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 319 ------KGYLSYPRTDC------------SLIThSEF--EYLKDNfssyckllnieieqkniePRtQYVNDSK-VLE-HY 376
Cdd:PRK06599 293 dlgegtVGLITYMRTDSvrlsnealdearKYIT-KKYgkEYLPAK------------------PR-VYKKKSKnAQEaHE 352
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 377 AIIPT--KQIPEnDVYNNFSDDEKKIYDEVVKRTMLMFMEDYIYSETKIVL--CIENVEFKLTGNVAKEQG----WKLLD 448
Cdd:PRK06599 353 AIRPTsiNRTPE-SLKPYLTPDQFKLYELIWKRTVASQMAPAILDQTSVDIasENGKYVFRATGSVILFPGflkvYGESK 431
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 449 SENKNSKEKLLPNYKENEKLSLN-LVPKELNTKPPKYLTEATLGGEgglMENcskfieneelkgnlkevHGIGTPATRSS 527
Cdd:PRK06599 432 DDEEEDDEKLLPPLKEGEKLKLDeLLPEQHFTEPPPRYSEASLVKK---LEE-----------------YGIGRPSTYAS 491
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 528 IVKSLIDRGYLETKKKHLMITPKGTLLCSALEN--TNLVSVEMTANWESTLKDISEkGHR-----IRQ--NEFIDSIKQY 598
Cdd:PRK06599 492 IISTLQDREYVELEKKRFIPTDLGRIVNDFLVEhfPKYVDYDFTAGLEDELDEIAE-GKKdwkpvLREfwEPFISNLEKV 570
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 599 IKQMINSDnklLKLESNDKniekaieqsticNCPKCsNGRIKKLLSKNKKLFYACSN-KDCDFIifgmisnKNITPQIVK 677
Cdd:PRK06599 571 EEDVRTEK---VTQEETDE------------TCPKC-GGGPLVLKLGKNGKFLGCSGyPECKYT-------KNITRDEDE 627
|
650
....*....|..
gi 488415014 678 EIIEKGKTKTIK 689
Cdd:PRK06599 628 PIEEEEIVEEEK 639
|
|
| PRK07561 |
PRK07561 |
DNA topoisomerase I subunit omega; Validated |
92-637 |
1.01e-39 |
|
DNA topoisomerase I subunit omega; Validated
Pssm-ID: 236048 [Multi-domain] Cd Length: 859 Bit Score: 157.26 E-value: 1.01e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 92 KIIKELCENLNSDSEIIIATDPDREGEAIA---------------RYVLNKIpcTKNlklkrlwANTQepeglklAFKNL 156
Cdd:PRK07561 75 KVVSELKKAAKDADELYLATDPDREGEAIAwhllevlggddvpvkRVVFNEI--TKN-------AIQE-------AFENP 138
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 157 KDAD----DTYrfyleaEARSIADWLVGmnFT------RYVtleMKQLgidegvfSVGRVQTPTLYMVYKRNNEIKNFES 226
Cdd:PRK07561 139 RELDinlvNAQ------QARRFLDRLVG--YMvspllwKKI---ARGL-------SAGRVQSVAVRLIVEREREIEAFVP 200
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 227 KTYYEMVAKDKENENAVFKSE-HKFDSiDEFEQFLNENnlncecEGEIKEI------------SISEK---RK-VAPnlF 289
Cdd:PRK07561 201 EEYWDIHADLTTPRGDAFEARlTHLDG-KKFAPVDLLN------EAQAEAAvaalegarysvaSVEDKpttRKpSAP--F 271
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 290 KLGGIQKVANQKWGYTLDKTLSIVQSLYDKGYLSYPRTDC------------SLIThSEF--EYLKDnfssyckllniei 355
Cdd:PRK07561 272 TTSTLQQEASRKLGFSVKKTMRIAQRLYEAGYITYMRTDStnlsqeainaarGYIG-DNYgkKYLPE------------- 337
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 356 eqkniEPRtQYVNDSK-VLE-HYAIIPTKQIPENDVYNNFSDDEKKIYDEVVKRTMLMFMEDYIYSETKIVLCIENVEFK 433
Cdd:PRK07561 338 -----KPR-QYSSKAKnAQEaHEAIRPSDVFRTPDQLKGLEGDAQRLYELIWKRFVASQMAPARYDSTTVTIAAGDAELR 411
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 434 LTGNVAKEQGW-KLLDSENKNS---KEKLLPNYKENEKLSLN-LVPKELNTKPPKYLTEATLGGEgglMEncskfieneE 508
Cdd:PRK07561 412 ATGRVLRFDGFlKVYVEGRDDAlddEDRRLPALKVGDALTLEkLDPTQHFTKPPARYSEASLVKE---LE---------K 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 509 LkgnlkevhGIGTPATRSSIVKSLIDRGYLETKKKHLMITPKGTLLCSALEN--TNLVSVEMTANWESTLKDISEkGHRI 586
Cdd:PRK07561 480 L--------GIGRPSTYASIISTIQDRGYVRLENRRFYPEKMGRIVTDRLEEffPRLVDYDFTARMEEELDDIAN-GEAD 550
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....
gi 488415014 587 RQ---NEFIDSIKQYIKQminsdnklLKLESNDKNIEKAIEQSTICNCPKCSNG 637
Cdd:PRK07561 551 WKpvlDDFYKDFSQQLEK--------AEELREEGGMRPNQMVITDRDCPTCGRG 596
|
|
| TOPRIM_TopoIA |
cd01028 |
TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
2-156 |
4.42e-39 |
|
TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173778 [Multi-domain] Cd Length: 142 Bit Score: 141.21 E-value: 4.42e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 2 TILIIAEKPNQVKKYVEALGNSFNNKDGYIEleselfDKKVIVTWCVGHLIQLAHMEDYDsnlKQWSKDTLPFIPEDFIF 81
Cdd:cd01028 1 KVLIIAEKPSKAKTIAKILGKGSKKKGFYGE------GGGYVVTASVGHLLELPFPEEYV---DWDKDWPLELFPFEPKY 71
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488415014 82 KVSDYGSKQFKIIKELCENLNsdsEIIIATDPDREGEAIARYVLNKIPCtKNLKLKRLWANTQEPEGLKLAFKNL 156
Cdd:cd01028 72 VVIPDKKKQLKALKKLAKKAD---EIVLATDPDREGELIAWEILEVLKC-DNKPVKRAWFSEITPKAIREAFKNL 142
|
|
| PRK14973 |
PRK14973 |
DNA topoisomerase I; Provisional |
4-662 |
4.15e-38 |
|
DNA topoisomerase I; Provisional
Pssm-ID: 184936 [Multi-domain] Cd Length: 936 Bit Score: 152.31 E-value: 4.15e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 4 LIIAEK---PNQV------KKYVEAlgnsfnNKDGYIELESelFDKKVIVTwCVGHLIQLAHMEDYDSnlkqWSKDTLP- 73
Cdd:PRK14973 3 LIIAEKniaANRIaqilagKTKVQV------KKDGGVSTYS--FDDTVVVG-LRGHVVEVDFEPGYTN----WRSEEHTp 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 74 --FIPEDFIFKVSDygSKQFKIIKELCENLNsdsEIIIATDPDREGEAIAR--YVLNKiPCTKNLKLKRLWANTQEPEGL 149
Cdd:PRK14973 70 rsLIDADTIKKPTE--KKIVGLIQKLAKKAD---RVTIATDFDTEGELIGKeaYELVR-AVNPKVPIDRARFSAITKEEI 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 150 KLAFKNLKDADdtyrFYLEA--EARSIADWLVGMNFTRYVTLEMKQLGidEGVFSVGRVQTPTLYMVYKRNNEIKNFESK 227
Cdd:PRK14973 144 VTAFAEPTDLD----FALAAagEARQIIDLIWGASLTRFISLAAHRGG--DNILSVGRVQSPTLAMIVDREKEIEAFVPE 217
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 228 TYYEM-VAKDKENENAVFKSEH-KFDSIDEFEqflnennlncECEGEIKE----ISISEKRKV--APNLFKLGGIqKVAN 299
Cdd:PRK14973 218 KYWMLsLATEKDGEGIEARHTHgRFTDSAAAE----------AAYDATKEplvvTEVKEGHKVdrAPTPFDTTTF-IVAA 286
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 300 QKWGYTLDKTLSIVQSLYDKGYLSYPRTDCSLithsefeylkdnfssYCKLLNIEiEQKNIEPRTQYVNDSK-VLEHYAI 378
Cdd:PRK14973 287 SRLGFSAANAMRIAEDLYMNGYISYPRTDNTI---------------YPKSLDLN-GVLATLAKGAFSKDVAwVKDNRRP 350
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 379 IPTKQIPEND----VY-------NNFSDDEKKIYDEVVKRTMLMFMEDYIYSETKIVLCIENVEFKLTGNVAKEQGWKLL 447
Cdd:PRK14973 351 VPTRGKKSSTdhppIHptgvatrEELGDDRWKLYELVVRRFLATLSPDAEWATMKVNFDAGGEPYTATGGRLLEAGWRTV 430
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 448 DSENKnSKEKLLPNYKENEKL---SLNLVPKElnTKPPKYLTEatlggegglmencSKFIEN-EELkgnlkevhGIGTPA 523
Cdd:PRK14973 431 YPYSE-AKENILPAFALGEKLpilAVNLEEKE--TQPPARYSQ-------------SRLIQRmEEL--------GLGTKS 486
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 524 TRSSIVKSLIDRGYLETKKkhLMITPKGTLLCSALEN--TNLVSVEMTANWESTLKDISEkGHRIRQNEFIDSikqyiKQ 601
Cdd:PRK14973 487 TRHEVIGKLVSRKYIEGNP--LRPTLVGRAVTESLEEhaGTITEPDMTQTLEEHMQQIKE-RKRTRDDVVTES-----RK 558
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 488415014 602 MINsdNKLLKLESNDKNI-----EKAIEQSTICNCPKCsnGRIKKLLSKNKKLFYACSN-KDCDFII 662
Cdd:PRK14973 559 MLH--RAFDELEANEAVIgrdimERTAEELTIGPCPVC--GKDLRIKHIGSSQFIGCSGyPDCTFNI 621
|
|
| PRK08780 |
PRK08780 |
DNA topoisomerase I; Provisional |
101-580 |
3.66e-31 |
|
DNA topoisomerase I; Provisional
Pssm-ID: 181555 [Multi-domain] Cd Length: 780 Bit Score: 130.27 E-value: 3.66e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 101 LNSDSEIIIATDPDREGEAIA---RYVLNKIPCTKNLKLKRLWANTQEPEGLKLAFKNLKD-ADDtyrfYLEA-EARSIA 175
Cdd:PRK08780 71 AKSADDLYLATDPDREGEAISwhlAEILKERGLLKDKPMQRVVFTEITPRAIKEAMAKPRDiASD----LVDAqQARRAL 146
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 176 DWLVGMNFTryvTLEMKQlgIDEGVfSVGRVQTPTLYMVYKRNNEIKNFESKTYYEMVAKDKENENAVFKSEHKFDSiDE 255
Cdd:PRK08780 147 DYLVGFNLS---PLLWRK--IQRGL-SAGRVQSPALRMIVEREEEIEAFIAREYWSIEADCAHPSQPFNAKLIKLDG-QK 219
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 256 FEQFLNENNLNCE---------CEGEIKEISISEK---RKVAPNlFKLGGIQKVANQKWGYTLDKTLSIVQSLYDK---- 319
Cdd:PRK08780 220 FEQFTITDGDTAEaarlriqqaAQGTLHVTDVESKerkRNPAPP-FTTSTLQQEASRKLGFTTRRTMQVAQKLYEGvdlg 298
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 320 -----GYLSYPRTDCSLITHSEFEYLKDnfssyckLLNIEIEQKNI--EPRTqYVNDSKVLE--HYAIIPTK--QIPEnD 388
Cdd:PRK08780 299 degsvGLITYMRTDSVNLSQDALAEIRD-------VIARDYGTASLpdQPNT-YKTKSKNAQeaHEAVRPTSalRTPA-Q 369
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 389 VYNNFSDDEKKIYDEVVKRTMLMFMEDYIYSETKIVLCI--ENVeFKLTGNVAKEQGWKLLDSENKNSK-------EKLL 459
Cdd:PRK08780 370 VARFLSDDQRRLYELIWKRAVACQMIPATLNTVSVDLAAgsEHV-FRATGSTVVVPGFLAVYEEGKDDKsaededeGRKL 448
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 460 PNYKENEKLSLN-LVPKELNTKPPKYLTEATLggegglmencSKFIENeelkgnlkevHGIGTPATRSSIVKSLIDRGYL 538
Cdd:PRK08780 449 PPMKEGDNVPLErIRAEQHFTEPPPRYTEASL----------VKALEE----------YGIGRPSTYASIISTLQFRKYV 508
|
490 500 510 520
....*....|....*....|....*....|....*....|....
gi 488415014 539 ETKKKHLMITPKGTLLCSALEN--TNLVSVEMTANWESTLKDIS 580
Cdd:PRK08780 509 EMEGRRFRPTDVGRAVNKFLTGhfTRYVDYDFTARLEDDLDAVS 552
|
|
| PRK06319 |
PRK06319 |
DNA topoisomerase I/SWI domain fusion protein; Validated |
4-660 |
1.25e-30 |
|
DNA topoisomerase I/SWI domain fusion protein; Validated
Pssm-ID: 235778 [Multi-domain] Cd Length: 860 Bit Score: 128.79 E-value: 1.25e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 4 LIIAEKPNQVKKYVEALGnsfnnkDGYIeLESELfdkkvivtwcvGHLIQLAHmedydsnlKQWSKDtlpfIPEDFIFKV 83
Cdd:PRK06319 5 LIIVESPAKIKTLQKLLG------EGFI-FASSL-----------GHIVDLPA--------KEFGID----IENDFEPDY 54
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 84 SDYGSKQfKIIKELCENLNSDSEIIIATDPDREGEAIARYVLNKIPctKNLKLKRLWANTQEPEGLKLAFKNLKDADdtY 163
Cdd:PRK06319 55 QILPDKE-EVINKICKLAKKCDVVYLSPDPDREGEAIAWHIANQLP--KNTKIQRISFNAITKGAVTEALKHPREID--M 129
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 164 RFYLEAEARSIADWLVGMNFTRYVTLEMKQLGideGVfSVGRVQTPTLYMVYKRNNEIKNF----------------ESK 227
Cdd:PRK06319 130 ALVNAQQARRLLDRIVGYKISPILSRKLQRRS---GV-SAGRVQSVALKLVVDREKAIEAFvpveywnirvhlkdpkTQK 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 228 TY----YEMVAKDKENENAVFKSEHKFDSIDEFEQFLNENNLNCECEGEIKEISISEKRKVAPNLFKLGGIQKVANQKWG 303
Cdd:PRK06319 206 TFwahlYSVDGKKWEKEIPEGKTEDEVLLINSKEKADHIVELLESATYTVTRVESKEKRRNAYPPFITSTLQQEASRHFR 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 304 YTLDKTLSIVQSLYD---------KGYLSYPRTDcSLITHSEF-----EYLKDNFSsyckllnieieqKNIEPRTQYVND 369
Cdd:PRK06319 286 FSSSRTMNIAQTLYEgvdldsegaTGLITYMRTD-SVRTDPEAlkqvrKYIEGTFG------------KEFLPSSPNVYT 352
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 370 SKVL---EHYAIIPTK-QIPENDVYNNFSDDEKKIYDEVVKRTMLMFMEDYIYSETKI-VLCIENVEFKLTGNVAKEQGW 444
Cdd:PRK06319 353 TKKMaqdAHEAIRPTDiTLTPEKLRSKLTEDQYKLYSLIWKRFVASQMIPAIYDTLAIrITTNKGIDLRATGSLLKFKGF 432
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 445 -----KLLDSENKNSKEKLLPNYKENEKLSLNLVPKELN-TKPPKYLTEATLGGEgglmencskfieneelkgnlKEVHG 518
Cdd:PRK06319 433 lavyeEKRDDEGDEEENIHLPKLHEQDVLTKEELSAEQAfTKPLPRFTEASLVKE--------------------LEKSG 492
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 519 IGTPATRSSIVKSLIDRGYLETKKKHLMITPKGTLLCSALEnTN---LVSVEMTANWESTLKdisekghRIRQNEfiDSI 595
Cdd:PRK06319 493 IGRPSTYATIMNKIQSREYTLKENQRLRPTELGKIISQFLE-TNfprIMDIGFTALMEDELE-------LIADNK--KPW 562
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488415014 596 KQYIKQMINSDNKLLKLESNDKNIEKAIeqsTICNCPKCSNGRIkKLLSKNKKLFYACSN-KDCDF 660
Cdd:PRK06319 563 KLLLQEFWELFLPVVVTAEKEAFIPRIV---TEIDCPKCHKGKL-VKIWAKNRYFYGCSEyPECDY 624
|
|
| PTZ00407 |
PTZ00407 |
DNA topoisomerase IA; Provisional |
4-583 |
1.80e-26 |
|
DNA topoisomerase IA; Provisional
Pssm-ID: 173597 [Multi-domain] Cd Length: 805 Bit Score: 115.81 E-value: 1.80e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 4 LIIAEKPNQVKKyVEALGN--------SFNN-KDGYIELESElfdkKVIVTWCVGHLIQLAHMedydsnlkQWSKDTLPF 74
Cdd:PTZ00407 12 LVIVESPNKVIK-VEGLLSdpkvipdwSFKQsHLRRIGTGAE----KAVAMATTGHFMALKEI--------TWSPQASSP 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 75 IP------EDFIFK--VSDY--------GSK-QFKIIKELCENLNSDSEIIIATDPDREGEAIARYVLNKIpctKNL--K 135
Cdd:PTZ00407 79 ASvvgagdEPFPSNgtLAEYtlewellpGRRiQETLERYIEEKADNVTEIILATDPDREGELIAVHALQTI---KRLypK 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 136 LK----RLWANTQEPEGLKLAFKN-LKDADDtYRFYLEAEARSIADWL---VGMNFTRYVTLEMKqlgidegvfSVGRVQ 207
Cdd:PTZ00407 156 LKvpfsRAYMHSITEDGIRKAMRErHVEACD-YDLANAAETRHAMDRIfgfLGSSVVRAANSQMR---------SIGRVQ 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 208 TPTLYMVYKRNNEIKNF--ESKTYYEMVAKdkenenAVFKSEH--KFDSI--------DEFEQFLNENNLNCECEG---- 271
Cdd:PTZ00407 226 TPALILINEREDKIKAFleSNKSTFEVQAM------CQFPSPHgtTFSQVvtitpdrkGGASHWATEAEARRCLEQwkln 299
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 272 EIKEISISEKRKVAPNL------FKLGGIQKVANQKWGYTLDKTLSIVQSLYDKGYLSYPRTDCSLITHS---------- 335
Cdd:PTZ00407 300 NCTGFSVPLEPKPQPSVvpppqpFTMATAIAKANRQLKYSSEMVSGCLQDLFQLGHITYPRTDSTRIDESalpdiyaavk 379
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 336 -----EFEYLKDNF---------SSYCKLLNIEIEQKNIEPRTQYVNDSkvleHYAIIPTKQIPENDVYnNFSDDEKKIY 401
Cdd:PTZ00407 380 kefgkEFLYRLEDRtvsaqegkgSKKTGKKRSTKQKKGADTPVGNVEDA----HEAIRPTNIDTTGESL-SLSPPTRAVY 454
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 402 DEVVKRTMLMFMedyIYSET-KIVLCI-------ENVEFKLTGNVAKEQGWKllDSENKNSKEKL--------------- 458
Cdd:PTZ00407 455 DLVRRNTLAVFM---IPMKTeKIVATVkftsgsgEKLEFELQGKRVVEPGWT--RAFHKGDKGTTgpaeetdeditavee 529
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 459 ----LPNYKENEKLSLNLVPKELNTKPPKYLTE-------------ATLGGEGGLMencskfienEELKGNlkevhGIGT 521
Cdd:PTZ00407 530 gapvVPSLSQEEFKAIMNLRSQLGSGVQKGFFElrspqvrenrpvpPLPHSEGTLI---------EELKNN-----GVGR 595
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 488415014 522 PATRSSIVKSLIDRGYLETKKK-HLMITPKGTLLCSALENT--NLVSVEMTANWESTLKDISEKG 583
Cdd:PTZ00407 596 PSTYPMIVKTLLARGYIAVNPKgRCETTPVGRMLVETAKSTfpSIVDIGFTAAFEKKLDRIAKPG 660
|
|
| TOP1Bc |
smart00436 |
Bacterial DNA topoisomeraes I ATP-binding domain; Extension of TOPRIM in Bacterial DNA ... |
137-231 |
2.55e-25 |
|
Bacterial DNA topoisomeraes I ATP-binding domain; Extension of TOPRIM in Bacterial DNA topoisomeraes I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase beta subunit
Pssm-ID: 214662 [Multi-domain] Cd Length: 89 Bit Score: 99.96 E-value: 2.55e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 137 KRLWANTQEPEGLKLAFKNLKDADdtYRFYLEAEARSIADWLVGMNFTRYVTLEMKQlgideGVFSVGRVQTPTLYMVYK 216
Cdd:smart00436 2 KRIEFSEITKKAIREALKNPREID--ENLVNAQLARRILDRLIGFNLSRLLTKKLRN-----GVLSAGRVQTPTLGLIVE 74
|
90
....*....|....*
gi 488415014 217 RNNEIKNFESKTYYE 231
Cdd:smart00436 75 REREIKNFVPKPYWE 89
|
|
| Toprim_Crpt |
pfam13342 |
C-terminal repeat of topoisomerase; |
657-714 |
1.84e-18 |
|
C-terminal repeat of topoisomerase;
Pssm-ID: 463851 [Multi-domain] Cd Length: 60 Bit Score: 79.44 E-value: 1.84e-18
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 488415014 657 DCDFIIFGMISNKNITPQIVKEIIEKGKTKTIKGFTSKAGKKFNAKLKLTE-KGVEFDF 714
Cdd:pfam13342 1 GCGFSIGKTIAGKKLSEEQVKELLTKGKTGLIKGFKSKKGKKFDAYLVLDDdEKVEFDF 59
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
4-129 |
3.56e-10 |
|
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.
Pssm-ID: 396354 [Multi-domain] Cd Length: 93 Bit Score: 56.98 E-value: 3.56e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 4 LIIAEKPNQVKKYVEALGNSFNNkdgyieleselfdkkviVTWCVGHLIQLAHMEDydsnlkqwskdtlpfipedfifkv 83
Cdd:pfam01751 2 LIIVEGPSDAIALEKALGGGFQA-----------------VVAVLGHLLSLEKGPK------------------------ 40
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 488415014 84 sdygskqFKIIKELCENLNSDSEIIIATDPDREGEAIARYVLNKIP 129
Cdd:pfam01751 41 -------KKALKALKELALKAKEVILATDPDREGEAIALKLLELKE 79
|
|
| TOPRIM_TopoIA_TopoI |
cd03363 |
TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA ... |
4-135 |
1.22e-09 |
|
TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173783 [Multi-domain] Cd Length: 123 Bit Score: 56.42 E-value: 1.22e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 4 LIIAEKPNQVKKYVEALGNSFNnkdgyieleselfdkkviVTWCVGHLIQLAHMEDYDSnlkqwsKDTLPFIPEdfiFKV 83
Cdd:cd03363 3 LVIVESPAKAKTIKKYLGKEYE------------------VLASVGHIRDLPKKGLGVD------GEDDGFEPK---YVV 55
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|..
gi 488415014 84 SdygSKQFKIIKELCENLNSDSEIIIATDPDREGEAIARYVLNKIPCTKNLK 135
Cdd:cd03363 56 I---PGKKKVVKELKKLAKKADEIYLATDPDREGEAIAWHLAEVLKLKKNVK 104
|
|
| TOPRIM |
smart00493 |
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins; |
4-129 |
5.93e-09 |
|
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
Pssm-ID: 214695 [Multi-domain] Cd Length: 75 Bit Score: 53.03 E-value: 5.93e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 4 LIIAEKPNQVKKYVEALGNSFNnkdgyieleselfdkkviVTWCVGHLIQLahmedydsnlkqwskdtlpfipedfifkv 83
Cdd:smart00493 3 LIIVEGPADAIALEKAGGKRGN------------------VVALGGHLLSK----------------------------- 35
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 488415014 84 sdygsKQFKIIKELCENlnsdSEIIIATDPDREGEAIARYVLNKIP 129
Cdd:smart00493 36 -----EQIKLLKKLAKK----AEVILATDPDREGEAIAWELAELLK 72
|
|
| YrdD |
COG0551 |
DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination ... |
55-661 |
1.20e-06 |
|
DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination and repair];
Pssm-ID: 440317 [Multi-domain] Cd Length: 695 Bit Score: 51.79 E-value: 1.20e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 55 AHMEDYDSNLKQWSKDTLPFIPEDFIFKVSDYGSKQFKIIKELCENLNSDSEIIIATDPDREGEAIARYVLNKIPC---- 130
Cdd:COG0551 38 LGLKKKLVDLLLKEKLKKLVENEKLIAELDIKDLKKLKKDKKKKAKALAAALAAADDDAIEAAAAADEEEALKAAEalea 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 131 TKNLKLKRLWANTQEPEGLKLAFKNLKDADDTYRFYLEAEARSIADWLVGMNFTRYVTLEMKQLGIDEGVFSVGRVQTPT 210
Cdd:COG0551 118 IRKAVVEEVKSRARKRAARAPADVAAAAAAAALARLLLLAAASRALRLLLLLAAGRLRLLSAVAAGLLELEELLKEFEEE 197
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 211 LYMVYKRNNEIKNFESKTYYEMVAKDKENENAVFKSEHKFDSIDEFEQFLNENNLNCECEGEIKEISISEKRKVAPNLFK 290
Cdd:COG0551 198 EEEEAAEEEEEEEEAKKKKEEDKKKKKKKKKKDKEEETKAIKKKKKAAEAVLAAKKAAKEAKAKKELPTTTTDALPEALA 277
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 291 LGGIQKVANQKWGYTLDKTLSIVQSLYDKGYLSYPRTDCSLITHSEFEYLKDNFSSYckllnIEIEQKNIEPRTQYVNDS 370
Cdd:COG0551 278 TTSLTAAAAASALAAALLEEEGELLYTGGYIRYTRTPKSSEADALAALEALKKIAEE-----PPDERAKKKKKKAKKKKA 352
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 371 KVLEHYAIIPTKQIPENDVYNNFSDDEKKIYDEVVKRTMLMFMEDYIYSETKIVLCIENVEFKLTGNVAKEQGWKLLDSE 450
Cdd:COG0551 353 SEAKETTDHPPIPPTTAAALLELLEDRKLLLELLVRRRFAAAADLAKVEELTKVEEADEEELVEAEGGLLEVLGEEEEDD 432
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 451 NKNSKEKLLPNYKENEKLSLNLVPKELNTKPPKYlteatlggegglmencskfIENEELKGNLKEVHGIGTPATRSSIVK 530
Cdd:COG0551 433 EDEEEELLLPPLEEGEPLLLEELLLEKQTTTPPP-------------------RYTTELLLKKLEEEGGGGRGTTATIII 493
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 531 SLIDRGYLETKKKHLMITPKGTLLCSALENTNLVSVEMTANWESTLKDISEKGHRIRQNEFIDSIKQYIKqminsDNKLL 610
Cdd:COG0551 494 LILKRRYVVLEEKKTTPTELLVEVVLLLLLPFPKLEDTTETAEEEEALLDKEEGKEDKVVEIREEEYPFF-----KKLLE 568
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*...
gi 488415014 611 KLESNDKNIEKAIEQSTICNCPKCS------NGRikkllsknKKLFYACSNK-DCDFI 661
Cdd:COG0551 569 IAEEEGEEELSEEDEVLGEKCPKCGkplvikKGR--------YGKFLGCSNYpECKYT 618
|
|
| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
92-140 |
4.18e-06 |
|
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173773 [Multi-domain] Cd Length: 83 Bit Score: 45.11 E-value: 4.18e-06
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 488415014 92 KIIKELCENLNSDSEIIIATDPDREGEAIARYVLNKIPCtKNLKLKRLW 140
Cdd:cd00188 35 KTRELLKRLLGEAKEVIIATDADREGEAIALRLLELLKS-LGKKVRRLL 82
|
|
| TOPRIM_TopoIA_RevGyr |
cd03361 |
TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA ... |
2-135 |
5.72e-06 |
|
TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Pssm-ID: 173781 [Multi-domain] Cd Length: 170 Bit Score: 47.31 E-value: 5.72e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488415014 2 TILIIAEKPNQVKKYVEALGN-SFNNKDGYIELESELFDKKVIVTWCVGHLIQLAHMEDYDSNLKqwskDTLPFIP-EDF 79
Cdd:cd03361 1 TALMIVESPNKARTIANFFGRpSVRRLGGLVVYEVSTGDGVLMITASGGHVYDLVTKEGGHGVVE----DDGRYVPvYDS 76
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488415014 80 IFKVSDyGSKQFKIIKELCENLNSDS-------------------EIIIATDPDREGEAIARYVLNKI-PCTKNLK 135
Cdd:cd03361 77 IKRCRD-CGYQFTEDSDKCPRCGSENiddkletlealrelalevdEVLIATDPDTEGEKIAWDVYLALrPYNKNIK 151
|
|
| RnmV |
COG1658 |
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure ... |
87-138 |
5.38e-05 |
|
5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure and biogenesis];
Pssm-ID: 441264 [Multi-domain] Cd Length: 184 Bit Score: 44.63 E-value: 5.38e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|..
gi 488415014 87 GSKQFKIIKELCENLNSDSEIIIATDPDREGEAIARYVLNKIPCTKNLKLKR 138
Cdd:COG1658 35 GSAISEETLELIKVAAEKRGVIILTDPDRAGERIRKRISEHLPGAKHAFIDR 86
|
|
| Toprim_4 |
pfam13662 |
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ... |
99-127 |
2.20e-03 |
|
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation.
Pssm-ID: 433387 [Multi-domain] Cd Length: 85 Bit Score: 37.65 E-value: 2.20e-03
10 20
....*....|....*....|....*....
gi 488415014 99 ENLNSDSEIIIATDPDREGEAIARYVLNK 127
Cdd:pfam13662 45 DSLGGIKEVILALDGDVAGEKTALYLAEA 73
|
|
| TOPRIM_recR |
cd01025 |
TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
90-139 |
3.00e-03 |
|
TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a single-stranded DNA molecule coated with RecA to allow invasion of a homologous molecule. The RecFOR system directs the loading of RecA onto gapped DNA coated with SSB protein. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). In RecR sequences this glutamate in the first turn of the TOPRIM domain is semiconserved, the DXD motif is not conserved.
Pssm-ID: 173775 Cd Length: 112 Bit Score: 37.88 E-value: 3.00e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|
gi 488415014 90 QFKIIKELCENLNSdSEIIIATDPDREGEAIARYVLNKIPcTKNLKLKRL 139
Cdd:cd01025 44 NIDKLLERIAKGQV-KEVILATNPTVEGEATALYIAKLLK-DFGVKVTRL 91
|
|
| |
