|
Name |
Accession |
Description |
Interval |
E-value |
| topB |
TIGR01056 |
DNA topoisomerase III, bacteria and conjugative plasmid; This model describes topoisomerase ... |
2-655 |
0e+00 |
|
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: 990.11 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 2 NTLILCEKPSQAMDLSTVFAKKKKQNGYMEIsdeqlNVSGFLTWAVGHLVELKEPQEYDEKYKNFSTYPILLEKDDFQFK 81
Cdd:TIGR01056 1 MTLVLCEKPSQARDLATVLAKKKKGNGYLEI-----GVGGFVTWAVGHLVELAEPEEYDEKYKNWRTYDLPLEPEDWQLV 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 82 VSDKTKDQFNNIKKIFKENKIDEVIIATDPAREGENIAYKILNQLKVTDKVTIKRLWLTSKVESSIRKAFKNILPKEKTY 161
Cdd:TIGR01056 76 VSDKTKKQFNVIKRILKENKVDEVVIATDPDREGELIAREILDYLKVTDKVTIKRLWISSLVDSSIRKAFKNLRPKSETE 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 162 GFYKEGRARELSDWLVGINLSRHFTKISRELGNDGVIHIGRVSSPTLNMVYNRENNIKGFKGKKFYKVSATINKDEQEVK 241
Cdd:TIGR01056 156 GLYKSGVARARADWLVGINLTRAFTKLGREAGNDGVLSVGRVQTPTLAMVVKRENEIKNFVGKPFYEVSATINKDEQEFT 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 242 TELKN-KFDSEDELHEFLFENDITDLTQKG-LFTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEK- 318
Cdd:TIGR01056 236 TEWQPyKDEEERELHEFLAENVVTDLTQKPaLVTDIEKERKKTSAPLFYDLSALQEDANKRFGISAKRTLDIAQKLYETh 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 319 KLITYPRTDSRYITEDEKEMLLENIDYLKEITKINLN----NELTNNSLINPSKIEDHYAILITGNDFNKVDLKEEEINV 394
Cdd:TIGR01056 316 KLITYPRTDSRYLPEDEKEMLLEVLDALKVITPALLPikkrDELTNNRLWNDKKIEDHHAIIPTGNDFNLSDLSEEERNV 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 395 YKSILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKGKIIQDNGFKALLNKQKTSEE----TIPNFEKNEEVDIE-LDLLE 469
Cdd:TIGR01056 396 YKLIAQNYLMQFMPKEEYETTTIEIAIGKLMFEAKGKILQDNGWKALLGKQEEDEEtedtTLPAFQKGDELDVEtLELLE 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 470 KETTPPKRYTEKTLLKAMANPIETLEDEGLKSTLKEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLE 549
Cdd:TIGR01056 476 KQTKPPARYTEGTLLSAMTNPAAFVQDKGLKKTLKETKGLGTEATRADIIENLFKRGFIQKKKNKIYITKNGKLLCLLLP 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 550 gHLLSKPDLTGQWEKYLNGISKGEKDDDSFINTINEMIKKTINEEVKNKESIQKVAKEKVSTNNIAKCPACDNGYLIDRK 629
Cdd:TIGR01056 556 -ELLTKPDLTAQWEQYLNGISAGEKDDDDFINTINEMIKQTINEEKKNPETIQKVAKEPVSCGGIAKCPAKDNGRLIDCK 634
|
650 660
....*....|....*....|....*.
gi 581224777 630 GFYGCTEYNNGCEFTIPKKLLEKSIP 655
Cdd:TIGR01056 635 KFPECTEYGNGCEFTIPKKLREKSIP 660
|
|
| PRK07726 |
PRK07726 |
DNA topoisomerase 3; |
3-648 |
8.86e-172 |
|
DNA topoisomerase 3;
Pssm-ID: 236078 [Multi-domain] Cd Length: 658 Bit Score: 506.62 E-value: 8.86e-172
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 3 TLILCEKPSQAMDLSTVFAKKKKQNGYmeISDEQLNVsgflTWAVGHLVELKEPQEYDEKYK--NFSTYPILLEKddFQF 80
Cdd:PRK07726 2 RLFIAEKPSVGRDIADVLKPHKKGDGY--IEGNGYIV----TWAIGHLLELAEPEAYDERYKrwRLEDLPIIPEK--WKL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 81 KVSDKTKDQFNNIKKIFKEnkIDEVIIATDPAREGENIAYKILNQLKVTDKvtIKRLWLTSKVESSIRKAFKNILPKEKT 160
Cdd:PRK07726 74 VVKKKTAKQFNVVKKLLKQ--ATEIVIATDADREGELIAREILDYCGVRKP--IKRLWISSLTDKAIKRAFANLKPGKET 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 161 YGFYKEGRARELSDWLVGINLSRHFTKISRELGNDGVIHIGRVSSPTLNMVYNRENNIKGFKGKKFYKVSATInKDEQEV 240
Cdd:PRK07726 150 IPLYYSALARSRADWLVGINMTRAYTLLGRKAGYNGVLSVGRVQTPTLALVVRRDEEIENFVPKPYWEVEAHL-TPGERF 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 241 KTELKNKFDSEDE----LHEFLFENDITDLT-QKGLFTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTL 315
Cdd:PRK07726 229 TAKWQPSEPYQDEegrlLDRPLAEQVVARIQgQPAKVTEVETKRKKEYAPLLYDLSELQIDANKRFGLSAKETLDIAQSL 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 316 YEK-KLITYPRTDSRYITEDEKEML------LENID-YLKEITKInLNNELtNNSLINPSKIEDHYAILITGNDFNKVDL 387
Cdd:PRK07726 309 YEThKLITYPRTDSRYLPEDMVATLpevlnaISKVDpYLLLAPPV-LDPSI-RSRAWNDKKVTAHHAIIPTEQPPNLSKL 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 388 KEEEINVYKSILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKGKIIQDNGFKALLNKQKTSEE---TIPNFEKNEEVDIE 464
Cdd:PRK07726 387 SEDERKVYDLIARRYLAQFLPPAEYDKTTIELEIAGGTFIAKGKQVVEAGWKALLGKKEEDEEkeqPLPVLAKGDELKVE 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 465 -LDLLEKETTPPKRYTEKTLLKAMANPIETLEDEGLKSTLKEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGil 543
Cdd:PRK07726 467 kGEVKEGQTQPPKRFTEGTLLSAMENIARFVQDKELKKTLKETDGLGTEATRAGIIEKLFKRGYLEKKGKYIHATDKG-- 544
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 544 aCLLLE--GHLLSKPDLTGQWEKYLNGISKGEKDDDSFINTINEMIKKTInEEVKNkesiqkvAKEKVSTNNI--AKCPA 619
Cdd:PRK07726 545 -KQLIDalPEELTSPDMTAKWEQALDQISEGQLSYQDFMQPLKQWLKQLV-EQAKQ-------SSEKYKFDNLtgPKCPD 615
|
650 660 670
....*....|....*....|....*....|...
gi 581224777 620 CdNGYLIDRKG----FYGCTEYNNGCEFTIPKK 648
Cdd:PRK07726 616 C-GKPMLKVKGkngkMLVCQDRECGKRKNVSKK 647
|
|
| TopA |
COG0550 |
DNA topoisomerase IA [Replication, recombination and repair]; |
3-592 |
2.30e-132 |
|
DNA topoisomerase IA [Replication, recombination and repair];
Pssm-ID: 440316 [Multi-domain] Cd Length: 541 Bit Score: 401.40 E-value: 2.30e-132
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 3 TLILCEKPSQAMDLSTVFAKkkkqnGYMeisdeqlnvsgfLTWAVGHLVELKEPQ-EYDEKyKNFstypillekdDFQFK 81
Cdd:COG0550 2 KLVIVESPAKAKTIAKYLGK-----DYV------------VTASVGHLRDLPKPElDVDVE-NDF----------EPKYE 53
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 82 VSDKTKDQFNNIKKIFKenKIDEVIIATDPAREGENIAYKILNQLKvtDKVTIKRLWLTSKVESSIRKAFKNilPKEKTY 161
Cdd:COG0550 54 VIPGKKKQVKELKKLAK--KADEVILATDPDREGEAIAWHLLELLG--DKKPVKRVVFNEITKKAIKEAFKN--PRDIDM 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 162 GFYKEGRARELSDWLVGINLSRHFT-KISRELgndgviHIGRVSSPTLNMVYNRENNIKGFKGKKFYKVSATINKDEQEV 240
Cdd:COG0550 128 NLVDAQQARRILDRLVGYNLSPLLWkKVKRGL------SAGRVQSPALRLIVEREREIEAFVPEEYWTIEATFKTGGGEF 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 241 KTEL----KNKFDSEDELHEFLfeNDITDltQKGLFTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLY 316
Cdd:COG0550 202 TAKLvkidGKKILDEEEAEAIL--AALKG--KTFTVTSVEKKPKKRNPPPPFTTSTLQQEASRKLGFSAKKTMSIAQRLY 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 317 EKKLITYPRTDSRYITEDEKEMLLENI------DYLKEiTKINLNNeltnnsliNPSKIEDHYAILITGNDFNKVDLKEE 390
Cdd:COG0550 278 EVGLITYMRTDSVRLSEDAVAAAREYIealygkEYLPE-KPRVYKT--------SKNAQEAHEAIRPTGVTRTPESLSGD 348
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 391 EINVYKSILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKGKIIQDNGFKALLNKQKTSEE-----TIPNFEKNEEVDI-E 464
Cdd:COG0550 349 EFKLYDLIWKRFLASQMPPAEYETTTVTIEVGGEEFRASGKVIKFPGFLKVYGEGKDDEEeeeekRLPPLKEGEKLKLkK 428
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 465 LDLLEKETTPPKRYTEKTLLKAManpietledeglkstlkEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILA 544
Cdd:COG0550 429 IEPEQHFTKPPPRYTEASLVKAM-----------------EELGIGRPSTYASIIETLQDRGYVEREGKRLVPTELGFIV 491
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|
gi 581224777 545 CLLLEGHL--LSKPDLTGQWEKYLNGISKGEKDDDSFINTINEMIKKTIN 592
Cdd:COG0550 492 IDLLEEHFpdLVDYEFTAKMEEKLDEIAEGKLDWKDVLEEFYKPFKELVE 541
|
|
| TOP1Ac |
cd00186 |
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ... |
161-591 |
6.15e-107 |
|
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: 329.95 E-value: 6.15e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 161 YGFYKEGRARELSDWLVGINLSRHFTKIsreLGNDGVIHIGRVSSPTLNMVYNRENNIkgfkgkkfykvsatinkdeqev 240
Cdd:cd00186 1 ENLVNAQLARRILDRLVGFNLSRLLTKK---LRRKGVLSAGRVQSPTLGLIVEREREI---------------------- 55
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 241 ktelkNKFDSEDELHeflfenditdlTQKGLFTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEKKL 320
Cdd:cd00186 56 -----KAFVPEDYWE-----------IKEAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGL 119
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 321 ITYPRTDSRYITEDEKEMLLENIDYLKEITKINLNNELT-NNSLINPSKIEDHYAILITGNDF---NKVDLKEEEINVYK 396
Cdd:cd00186 120 ITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLGrRNPKRGKKEQGAHEAIRPTKVAPtpeLEANLSEDEFKLYE 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 397 SILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKGKIIQDNGFKALLNKQKTSEETI-PNFEKNEEVDI-ELDLLEKETTP 474
Cdd:cd00186 200 LIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEpPPLKEGDELKLeEVELEEKETQP 279
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 475 PKRYTEKTLLKAManpietledeglkstlkEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEGH--L 552
Cdd:cd00186 280 PPRYTEASLIKLM-----------------EKRGIGRPSTYASIIETLLDRGYVEKEKKKLIPTELGFAVIELLEKHfpE 342
|
410 420 430
....*....|....*....|....*....|....*....
gi 581224777 553 LSKPDLTGQWEKYLNGISKGEKDDDSFINTINEMIKKTI 591
Cdd:cd00186 343 LVDPEFTAKLEEKLDEIAEGKKDYQEVLEEFYEEFKKIV 381
|
|
| Topoisom_bac |
pfam01131 |
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ... |
164-581 |
5.05e-89 |
|
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: 284.52 E-value: 5.05e-89
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 164 YKEGRARELSDWLVGINLSRHFTKisrELGNDGVIHIGRVSSPTLNMVYNRENNIKGFKGKKFYKVSATINKDEQ--EVK 241
Cdd:pfam01131 7 VDAQLARRELDWLIGFNLSRLLTL---KLKGNKLLSAGRVQTPTLALIVEREREIENFVPEPYWTIEATLKDGGGvfANA 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 242 TELKNKFDSEDELHEFLfeNDItdLTQKGLFTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEK-KL 320
Cdd:pfam01131 84 KWKRGRIFDKEEAEAIL--EKL--KKGTAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQKLYEKhGL 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 321 ITYPRTDSRYITEDEK-----EMLLENIDYLKEITKINLnNELTNNSLINPSKIEDHYAILITGNDFNKVDLKEEEINVY 395
Cdd:pfam01131 160 ITYPRTDSTYLSDDATlkailEYLTKNYGKYLPYAPRLL-KKTKGKLTVGNAKVTAHEAIRPTGDIPVLPELSDDERKLY 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 396 KSILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKGKIIQDNGFKALLNKQKTSEE-TIPNFEKNEEVDIE-LDLLEKETT 473
Cdd:pfam01131 239 ELIVRRFLASQMPPAVYETTTVVLEVGGEEFRASGKVILEDGWLKVYPYEKKEDEeELPELKEGEELKVTqVEVEEKKTK 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 474 PPKRYTEKTLLKAManpietledeglkstlkEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEG-HL 552
Cdd:pfam01131 319 PPPRYTEASLIKAM-----------------EKAGIGTPATRATIIETLLERGYVERKKKSLVPTELGKALVEALEKfPD 381
|
410 420
....*....|....*....|....*....
gi 581224777 553 LSKPDLTGQWEKYLNGISKGEKDDDSFIN 581
Cdd:pfam01131 382 LVDPELTAELEEKLDEIAEGKLDWKDVLA 410
|
|
| TOP1Ac |
smart00437 |
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ... |
276-542 |
1.14e-77 |
|
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: 249.09 E-value: 1.14e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 276 EKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEKKLITYPRTDSRYITEDEKEMLLENIDYLKEITKINLN 355
Cdd:smart00437 1 EEKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGKEYLDLA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 356 NELTNNSL--INPSKIEDHYAILITGNDF---NKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKG 430
Cdd:smart00437 81 VVLLKPRKprKGKKAQGAHEAIRPTKPIFtpeLEKELSEDEFKLYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAKG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 431 KIIQDNGFKALLNKQ-KTSEETIPNFEKNEEVDI-ELDLLEKETTPPKRYTEKTLLKAManpietledeglkstlkEVKG 508
Cdd:smart00437 161 KTLLFDGWLKVYPEEkKEEEIELPTLKKGDELKVeEVEVEEKETKPPARYTEASLIKLM-----------------EKRG 223
|
250 260 270
....*....|....*....|....*....|....
gi 581224777 509 LGTPATRADIIENLKKNKYIQVQKNKIYITKNGI 542
Cdd:smart00437 224 IGRPSTYASIIETLLDRGYVTKKKKKLIPTELGI 257
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| topB |
TIGR01056 |
DNA topoisomerase III, bacteria and conjugative plasmid; This model describes topoisomerase ... |
2-655 |
0e+00 |
|
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: 990.11 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 2 NTLILCEKPSQAMDLSTVFAKKKKQNGYMEIsdeqlNVSGFLTWAVGHLVELKEPQEYDEKYKNFSTYPILLEKDDFQFK 81
Cdd:TIGR01056 1 MTLVLCEKPSQARDLATVLAKKKKGNGYLEI-----GVGGFVTWAVGHLVELAEPEEYDEKYKNWRTYDLPLEPEDWQLV 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 82 VSDKTKDQFNNIKKIFKENKIDEVIIATDPAREGENIAYKILNQLKVTDKVTIKRLWLTSKVESSIRKAFKNILPKEKTY 161
Cdd:TIGR01056 76 VSDKTKKQFNVIKRILKENKVDEVVIATDPDREGELIAREILDYLKVTDKVTIKRLWISSLVDSSIRKAFKNLRPKSETE 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 162 GFYKEGRARELSDWLVGINLSRHFTKISRELGNDGVIHIGRVSSPTLNMVYNRENNIKGFKGKKFYKVSATINKDEQEVK 241
Cdd:TIGR01056 156 GLYKSGVARARADWLVGINLTRAFTKLGREAGNDGVLSVGRVQTPTLAMVVKRENEIKNFVGKPFYEVSATINKDEQEFT 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 242 TELKN-KFDSEDELHEFLFENDITDLTQKG-LFTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEK- 318
Cdd:TIGR01056 236 TEWQPyKDEEERELHEFLAENVVTDLTQKPaLVTDIEKERKKTSAPLFYDLSALQEDANKRFGISAKRTLDIAQKLYETh 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 319 KLITYPRTDSRYITEDEKEMLLENIDYLKEITKINLN----NELTNNSLINPSKIEDHYAILITGNDFNKVDLKEEEINV 394
Cdd:TIGR01056 316 KLITYPRTDSRYLPEDEKEMLLEVLDALKVITPALLPikkrDELTNNRLWNDKKIEDHHAIIPTGNDFNLSDLSEEERNV 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 395 YKSILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKGKIIQDNGFKALLNKQKTSEE----TIPNFEKNEEVDIE-LDLLE 469
Cdd:TIGR01056 396 YKLIAQNYLMQFMPKEEYETTTIEIAIGKLMFEAKGKILQDNGWKALLGKQEEDEEtedtTLPAFQKGDELDVEtLELLE 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 470 KETTPPKRYTEKTLLKAMANPIETLEDEGLKSTLKEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLE 549
Cdd:TIGR01056 476 KQTKPPARYTEGTLLSAMTNPAAFVQDKGLKKTLKETKGLGTEATRADIIENLFKRGFIQKKKNKIYITKNGKLLCLLLP 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 550 gHLLSKPDLTGQWEKYLNGISKGEKDDDSFINTINEMIKKTINEEVKNKESIQKVAKEKVSTNNIAKCPACDNGYLIDRK 629
Cdd:TIGR01056 556 -ELLTKPDLTAQWEQYLNGISAGEKDDDDFINTINEMIKQTINEEKKNPETIQKVAKEPVSCGGIAKCPAKDNGRLIDCK 634
|
650 660
....*....|....*....|....*.
gi 581224777 630 GFYGCTEYNNGCEFTIPKKLLEKSIP 655
Cdd:TIGR01056 635 KFPECTEYGNGCEFTIPKKLREKSIP 660
|
|
| PRK07726 |
PRK07726 |
DNA topoisomerase 3; |
3-648 |
8.86e-172 |
|
DNA topoisomerase 3;
Pssm-ID: 236078 [Multi-domain] Cd Length: 658 Bit Score: 506.62 E-value: 8.86e-172
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 3 TLILCEKPSQAMDLSTVFAKKKKQNGYmeISDEQLNVsgflTWAVGHLVELKEPQEYDEKYK--NFSTYPILLEKddFQF 80
Cdd:PRK07726 2 RLFIAEKPSVGRDIADVLKPHKKGDGY--IEGNGYIV----TWAIGHLLELAEPEAYDERYKrwRLEDLPIIPEK--WKL 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 81 KVSDKTKDQFNNIKKIFKEnkIDEVIIATDPAREGENIAYKILNQLKVTDKvtIKRLWLTSKVESSIRKAFKNILPKEKT 160
Cdd:PRK07726 74 VVKKKTAKQFNVVKKLLKQ--ATEIVIATDADREGELIAREILDYCGVRKP--IKRLWISSLTDKAIKRAFANLKPGKET 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 161 YGFYKEGRARELSDWLVGINLSRHFTKISRELGNDGVIHIGRVSSPTLNMVYNRENNIKGFKGKKFYKVSATInKDEQEV 240
Cdd:PRK07726 150 IPLYYSALARSRADWLVGINMTRAYTLLGRKAGYNGVLSVGRVQTPTLALVVRRDEEIENFVPKPYWEVEAHL-TPGERF 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 241 KTELKNKFDSEDE----LHEFLFENDITDLT-QKGLFTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTL 315
Cdd:PRK07726 229 TAKWQPSEPYQDEegrlLDRPLAEQVVARIQgQPAKVTEVETKRKKEYAPLLYDLSELQIDANKRFGLSAKETLDIAQSL 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 316 YEK-KLITYPRTDSRYITEDEKEML------LENID-YLKEITKInLNNELtNNSLINPSKIEDHYAILITGNDFNKVDL 387
Cdd:PRK07726 309 YEThKLITYPRTDSRYLPEDMVATLpevlnaISKVDpYLLLAPPV-LDPSI-RSRAWNDKKVTAHHAIIPTEQPPNLSKL 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 388 KEEEINVYKSILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKGKIIQDNGFKALLNKQKTSEE---TIPNFEKNEEVDIE 464
Cdd:PRK07726 387 SEDERKVYDLIARRYLAQFLPPAEYDKTTIELEIAGGTFIAKGKQVVEAGWKALLGKKEEDEEkeqPLPVLAKGDELKVE 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 465 -LDLLEKETTPPKRYTEKTLLKAMANPIETLEDEGLKSTLKEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGil 543
Cdd:PRK07726 467 kGEVKEGQTQPPKRFTEGTLLSAMENIARFVQDKELKKTLKETDGLGTEATRAGIIEKLFKRGYLEKKGKYIHATDKG-- 544
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 544 aCLLLE--GHLLSKPDLTGQWEKYLNGISKGEKDDDSFINTINEMIKKTInEEVKNkesiqkvAKEKVSTNNI--AKCPA 619
Cdd:PRK07726 545 -KQLIDalPEELTSPDMTAKWEQALDQISEGQLSYQDFMQPLKQWLKQLV-EQAKQ-------SSEKYKFDNLtgPKCPD 615
|
650 660 670
....*....|....*....|....*....|...
gi 581224777 620 CdNGYLIDRKG----FYGCTEYNNGCEFTIPKK 648
Cdd:PRK07726 616 C-GKPMLKVKGkngkMLVCQDRECGKRKNVSKK 647
|
|
| TopA |
COG0550 |
DNA topoisomerase IA [Replication, recombination and repair]; |
3-592 |
2.30e-132 |
|
DNA topoisomerase IA [Replication, recombination and repair];
Pssm-ID: 440316 [Multi-domain] Cd Length: 541 Bit Score: 401.40 E-value: 2.30e-132
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 3 TLILCEKPSQAMDLSTVFAKkkkqnGYMeisdeqlnvsgfLTWAVGHLVELKEPQ-EYDEKyKNFstypillekdDFQFK 81
Cdd:COG0550 2 KLVIVESPAKAKTIAKYLGK-----DYV------------VTASVGHLRDLPKPElDVDVE-NDF----------EPKYE 53
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 82 VSDKTKDQFNNIKKIFKenKIDEVIIATDPAREGENIAYKILNQLKvtDKVTIKRLWLTSKVESSIRKAFKNilPKEKTY 161
Cdd:COG0550 54 VIPGKKKQVKELKKLAK--KADEVILATDPDREGEAIAWHLLELLG--DKKPVKRVVFNEITKKAIKEAFKN--PRDIDM 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 162 GFYKEGRARELSDWLVGINLSRHFT-KISRELgndgviHIGRVSSPTLNMVYNRENNIKGFKGKKFYKVSATINKDEQEV 240
Cdd:COG0550 128 NLVDAQQARRILDRLVGYNLSPLLWkKVKRGL------SAGRVQSPALRLIVEREREIEAFVPEEYWTIEATFKTGGGEF 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 241 KTEL----KNKFDSEDELHEFLfeNDITDltQKGLFTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLY 316
Cdd:COG0550 202 TAKLvkidGKKILDEEEAEAIL--AALKG--KTFTVTSVEKKPKKRNPPPPFTTSTLQQEASRKLGFSAKKTMSIAQRLY 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 317 EKKLITYPRTDSRYITEDEKEMLLENI------DYLKEiTKINLNNeltnnsliNPSKIEDHYAILITGNDFNKVDLKEE 390
Cdd:COG0550 278 EVGLITYMRTDSVRLSEDAVAAAREYIealygkEYLPE-KPRVYKT--------SKNAQEAHEAIRPTGVTRTPESLSGD 348
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 391 EINVYKSILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKGKIIQDNGFKALLNKQKTSEE-----TIPNFEKNEEVDI-E 464
Cdd:COG0550 349 EFKLYDLIWKRFLASQMPPAEYETTTVTIEVGGEEFRASGKVIKFPGFLKVYGEGKDDEEeeeekRLPPLKEGEKLKLkK 428
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 465 LDLLEKETTPPKRYTEKTLLKAManpietledeglkstlkEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILA 544
Cdd:COG0550 429 IEPEQHFTKPPPRYTEASLVKAM-----------------EELGIGRPSTYASIIETLQDRGYVEREGKRLVPTELGFIV 491
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|
gi 581224777 545 CLLLEGHL--LSKPDLTGQWEKYLNGISKGEKDDDSFINTINEMIKKTIN 592
Cdd:COG0550 492 IDLLEEHFpdLVDYEFTAKMEEKLDEIAEGKLDWKDVLEEFYKPFKELVE 541
|
|
| TOP1Ac |
cd00186 |
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ... |
161-591 |
6.15e-107 |
|
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: 329.95 E-value: 6.15e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 161 YGFYKEGRARELSDWLVGINLSRHFTKIsreLGNDGVIHIGRVSSPTLNMVYNRENNIkgfkgkkfykvsatinkdeqev 240
Cdd:cd00186 1 ENLVNAQLARRILDRLVGFNLSRLLTKK---LRRKGVLSAGRVQSPTLGLIVEREREI---------------------- 55
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 241 ktelkNKFDSEDELHeflfenditdlTQKGLFTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEKKL 320
Cdd:cd00186 56 -----KAFVPEDYWE-----------IKEAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGL 119
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 321 ITYPRTDSRYITEDEKEMLLENIDYLKEITKINLNNELT-NNSLINPSKIEDHYAILITGNDF---NKVDLKEEEINVYK 396
Cdd:cd00186 120 ITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLGrRNPKRGKKEQGAHEAIRPTKVAPtpeLEANLSEDEFKLYE 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 397 SILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKGKIIQDNGFKALLNKQKTSEETI-PNFEKNEEVDI-ELDLLEKETTP 474
Cdd:cd00186 200 LIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEpPPLKEGDELKLeEVELEEKETQP 279
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 475 PKRYTEKTLLKAManpietledeglkstlkEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEGH--L 552
Cdd:cd00186 280 PPRYTEASLIKLM-----------------EKRGIGRPSTYASIIETLLDRGYVEKEKKKLIPTELGFAVIELLEKHfpE 342
|
410 420 430
....*....|....*....|....*....|....*....
gi 581224777 553 LSKPDLTGQWEKYLNGISKGEKDDDSFINTINEMIKKTI 591
Cdd:cd00186 343 LVDPEFTAKLEEKLDEIAEGKKDYQEVLEEFYEEFKKIV 381
|
|
| PRK08173 |
PRK08173 |
DNA topoisomerase III; Validated |
3-647 |
2.99e-100 |
|
DNA topoisomerase III; Validated
Pssm-ID: 236172 [Multi-domain] Cd Length: 862 Bit Score: 327.01 E-value: 2.99e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 3 TLILCEKPSQAMDLSTVFAKKKKQNGYMEiSDEQLnvsgfLTWAVGHLVELKEPQEYDEKYK--NFSTYPILLEKddFQF 80
Cdd:PRK08173 4 ALIIAEKPSVANDIARALGGFTKHDEYFE-SDEYV-----LSSAVGHLLEIAAPEEYEVKRGkwSFAHLPVIPPH--FDL 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 81 KVSDKTKDQFNNIKKIFKENKIDEVIIATDPAREGENIAYKILNQLKVtdKVTIKRLWLTSKVESSIRKAFKNILPKEKT 160
Cdd:PRK08173 76 NPIAKTESRLKVLTKLIKRKDVTRLINACDAGREGELIFRLIAQHAKA--KKPVKRLWLQSMTPQAIRDGFANLRSDEDM 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 161 YGFYKEGRARELSDWLVGINLSRHFTKISRELGNDGVIHIGRVSSPTLNMVYNRENNIKGFkgkkfykvsatINKDEQEV 240
Cdd:PRK08173 154 QPLADAARCRSEADWLVGINGTRAMTAFNSKGGGFFLTTVGRVQTPTLSIVVEREEKIRRF-----------VPRDYWEV 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 241 KTEL-----------------KNKFDSEDElheflfENDITDLT-----------QKGLFTDIEKEiGYTMPPKFYDLSA 292
Cdd:PRK08173 223 RAEFvaaagfyegrwfdpkfkKDEFDPEKR------ASRLWSEAaaeaivaacrgKPGTVTEESKP-STQLSPLLFDLTS 295
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 293 LQEDMNDKYKISAKRTLEIAQTLYEK-KLITYPRTDSRYITED-------EKEMLLENIDYLKEITKINLNNELTNNSLI 364
Cdd:PRK08173 296 LQREANGRFGFSAKNTLGLAQALYEKhKVLTYPRTDSRALPEDylgtvkqTLEMLKESNNYLPHAKQILDKGWVKPNKRI 375
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 365 -NPSKIEDHYAILITGNdfNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKGKIIQDNGFKALLN 443
Cdd:PRK08173 376 fDNSKISDHFAIIPTLQ--APKSLSEPEQKLYDLVVKRFLAVFFPAAEFLVTTRITEVAGHHFKTEGKVLVNPGWLAVYG 453
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 444 KQKTSEE-TIPNFEKNEEV---DIELDLLekETTPPKRYTEKTLLKAMANPIETLEDEGLKSTLKEvKGLGTPATRADII 519
Cdd:PRK08173 454 KEAQGADaNLVPVQKGEKVktdKIEAVAL--TTKPPARYNEATLLSAMEGAGKLVEDDELREAMAE-KGLGTPATRAAII 530
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 520 ENLKKNKYIQVQKNKIYITKNGILACLLLEG---HLLSKPDLTGQWEKYLNGISKGEKDDDSFINTINEMiKKTINEEVK 596
Cdd:PRK08173 531 EGLLGEKYLVREGRELIPTAKAFQLMTLLRGlgvEELTSPELTGEWEYKLSQIERGKLSRDAFMQEIAQM-TQQIVKRAK 609
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....
gi 581224777 597 NKESiQKVAKEKVSTNniAKCPACdnGYLID---RKgfYGCTeynnGCEFTIPK 647
Cdd:PRK08173 610 EYDS-DTIPGDYATLQ--TPCPNC--GGVVKenyRR--FACT----KCDFSISK 652
|
|
| Topoisom_bac |
pfam01131 |
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ... |
164-581 |
5.05e-89 |
|
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: 284.52 E-value: 5.05e-89
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 164 YKEGRARELSDWLVGINLSRHFTKisrELGNDGVIHIGRVSSPTLNMVYNRENNIKGFKGKKFYKVSATINKDEQ--EVK 241
Cdd:pfam01131 7 VDAQLARRELDWLIGFNLSRLLTL---KLKGNKLLSAGRVQTPTLALIVEREREIENFVPEPYWTIEATLKDGGGvfANA 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 242 TELKNKFDSEDELHEFLfeNDItdLTQKGLFTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEK-KL 320
Cdd:pfam01131 84 KWKRGRIFDKEEAEAIL--EKL--KKGTAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQKLYEKhGL 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 321 ITYPRTDSRYITEDEK-----EMLLENIDYLKEITKINLnNELTNNSLINPSKIEDHYAILITGNDFNKVDLKEEEINVY 395
Cdd:pfam01131 160 ITYPRTDSTYLSDDATlkailEYLTKNYGKYLPYAPRLL-KKTKGKLTVGNAKVTAHEAIRPTGDIPVLPELSDDERKLY 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 396 KSILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKGKIIQDNGFKALLNKQKTSEE-TIPNFEKNEEVDIE-LDLLEKETT 473
Cdd:pfam01131 239 ELIVRRFLASQMPPAVYETTTVVLEVGGEEFRASGKVILEDGWLKVYPYEKKEDEeELPELKEGEELKVTqVEVEEKKTK 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 474 PPKRYTEKTLLKAManpietledeglkstlkEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEG-HL 552
Cdd:pfam01131 319 PPPRYTEASLIKAM-----------------EKAGIGTPATRATIIETLLERGYVERKKKSLVPTELGKALVEALEKfPD 381
|
410 420
....*....|....*....|....*....
gi 581224777 553 LSKPDLTGQWEKYLNGISKGEKDDDSFIN 581
Cdd:pfam01131 382 LVDPELTAELEEKLDEIAEGKLDWKDVLA 410
|
|
| PRK14724 |
PRK14724 |
DNA topoisomerase III; Provisional |
1-647 |
2.17e-87 |
|
DNA topoisomerase III; Provisional
Pssm-ID: 237803 [Multi-domain] Cd Length: 987 Bit Score: 294.94 E-value: 2.17e-87
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 1 MNTLILCEKPSQAMD----LSTVFAKKKKQNGYMEiSDEQLnvsgfLTWAVGHLVELKEPQEYDEKYK--NFSTYPILLE 74
Cdd:PRK14724 1 TKTLVIAEKPSVAQDivraLTPVAGKFEKHDEHFE-SDSYV-----VTSAVGHLVEIQAPEEFDVKRGkwSFANLPVIPP 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 75 KddFQFKVSDKTKDQFNNIKKIFKENKIDEVIIATDPAREGENIaYKILNQLKVTDKVT----IKRLWLTSKVESSIRKA 150
Cdd:PRK14724 75 Y--FDLKPVDKTKTRLNAVVKLAKRKDVTELVNACDAGREGELI-FRLIEQYAGGAKGGlgkpVKRLWLQSMTPQAIRDG 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 151 FKNILPKEKTYGFYKEGRARELSDWLVGINLSRHFTKISRELGNDGVIHIGRVSSPTLNMVYNRENNIKGFKGKKFYKVS 230
Cdd:PRK14724 152 FDNLRSDAQMQGLASAARSRSEADWLVGINGTRAMTAFNSRDGGFFLTTVGRVQTPTLSLVVEREEKIRKFVSRDYWEIH 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 231 ATINKDEQEVKTEL------KNKFDSE---DELHEFLFENDITDLTQKGLFTDIEKEIGYTM-PPKFYDLSALQEDMNDK 300
Cdd:PRK14724 232 AGFHAEAGEYLGKWfdpqwkKASDDPEaraDRVWSEREARAIADAVRGKAATVTEESKPTTQaSPLLFDLTSLQREANGK 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 301 YKISAKRTLEIAQTLYEK-KLITYPRTDSRYITEDEKEMLLENIDYLKE----------ITKINLNNELTNNSLINPSKI 369
Cdd:PRK14724 312 FGFSAKTTLALAQSLYERhKALTYPRTDSRALPEDYLPVAKQTFEMLATsgmrhlapfaQQALDGNYVRPSKRIFDNSKV 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 370 EDHYAILITGNdfNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKGKIIQDNGFKALLNKQKTSE 449
Cdd:PRK14724 392 SDHFAIIPTTQ--APSGLSEAEQKLYDLVVRRFMAVFFPSAEYQVTTRISQVVGHSFKTEGKVLVKPGWLAIYGKEAANE 469
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 450 ----------ETIPNFEKNEEVDIE-LDLLEKETTPPKRYTEKTLLKAMANPIETLEDEGLKSTLKEvKGLGTPATRADI 518
Cdd:PRK14724 470 vedakdgdkgQPLVPVKPGEMVRTEfAEAKGLKTKPPARYSEATLLGAMESAGKQIDDDELREAMQE-KGLGTPATRAAI 548
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 519 IENLKKNKYIQVQKNKIYITKNGILACLLLEG---HLLSKPDLTGQWEKYLNGISKGEKDDDSFINTINEMIKKTINeev 595
Cdd:PRK14724 549 IEGLLTEKYMLREGRELIPTAKAFQLMTLLRGlgvEELSRAELTGEWEYKLAQMEKGQLSREAFMQQIAAMTEKLVK--- 625
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*
gi 581224777 596 KNKESIQKVAKEKVSTNNiAKCPACdNGYLIDRKGFYGCTEYN---NGCEFTIPK 647
Cdd:PRK14724 626 KAKEYDRDTIPGDYATLS-TPCPNC-GGVVKENYRRYACTGANgagEGCGFSFTK 678
|
|
| PRK07219 |
PRK07219 |
DNA topoisomerase I; Validated |
2-664 |
6.25e-82 |
|
DNA topoisomerase I; Validated
Pssm-ID: 235971 [Multi-domain] Cd Length: 822 Bit Score: 276.88 E-value: 6.25e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 2 NTLILCEKPSQAMDLSTVF----AKKKKQNGYMEISDEQLNVSGFLTWAVGHLVELKEPqeydEKYKNFSTYPI--LLEK 75
Cdd:PRK07219 1 TELIIAEKNNAARRIADILsggkAKKKRVNGVPYYEFERKGEKWIVIGLSGHIVTVDFP----EEYGDWRDVDPaeLIDA 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 76 DDFQFKvsdKTKDQFNNIKKIFKenKIDEVIIATDPAREGENI---AYKILNQlkvTDKVTIKRLWLTSKVESSIRKAFK 152
Cdd:PRK07219 77 DPVKKI---TKQNYINALKKLAK--DADEIIIATDYDREGELIgkeAYHILRE---VCQVPVKRARFSSLTKKEIRKAFE 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 153 NilPKEKTYGFYKEGRARELSDWLVGINLSRHFTKISRELGNDGVIHIGRVSSPTLNMVYNRENNIKGFKGKKFYKVSAT 232
Cdd:PRK07219 149 N--PDEIDFNLADAGEARQIIDLYWGAALTRFLSLSVRQLGRWDFLSVGRVQTPTLAFIVDREREIRAFDPEDYWKIEAL 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 233 INKDEQ-----EVKTELKNKFDSEDELHEfLFEnDITDlTQKGLFTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKR 307
Cdd:PRK07219 227 LDKEAQyfyrdLIGGHEAEKFWDEEEAEE-IYE-KLKG-AKEATVSSVKKRERTISPPAPFNTTEFLREASKIFGISPKR 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 308 TLEIAQTLYEKKLITYPRTDS-RYITEDEKEMLLENI----DYLKEITKInLNNEltnnsLINPS--KIE--DHYAILIT 378
Cdd:PRK07219 304 AMEIAEKLYTAGYISYPRTDNtVYPDDLDPKELLKKLskkkEYGPYAESI-LEQE-----NIKPTegKKEttDHPPIHPV 377
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 379 GnDFNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKGKIIQDNGFKALLNKQKTSEETIPNFEKN 458
Cdd:PRK07219 378 D-VPKREELSDDEWKVYELIVRRFLATLADPAEWEYLKVELDVNGEIFKASGSRLVEEGWHEVYPYEKFDEKELPDLEEG 456
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 459 EEVDIE-LDLLEKETTPPKRYTEKTLLKAManpietledeglkstlkEVKGLGTPATRADIIENLKKNKYIqVQKNKIYI 537
Cdd:PRK07219 457 EKLKVNkIEIEAKETQPPKRYTQSSLIKEM-----------------EKRGLGTKATRHDIIEKLYKRGYV-IEGDPPRP 518
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 538 TKNGILACLLLEGH--LLSKPDLTGQWEKYLNGISKGEKDDDSFINTINEMIKKTINEEVKNKESI-----QKVAKEKVS 610
Cdd:PRK07219 519 TDLGIAVIEALEKYapEIVSEEMTAQLEADMQAIEDGKKKKEDVTEESREMLKEILSELKEKRKEIgdhlaGSLKAENRS 598
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*...
gi 581224777 611 TNNIAKCPACDNGYLIDRKG----FYGCTEYNNgCEFTIPkklLEKSIPPTVVKALCE 664
Cdd:PRK07219 599 LKTIGKCPECGGDLIIIRTDkgsrFVGCSGYPD-CRNTFP---LPSTGRIKVLDEVCE 652
|
|
| TOP1Ac |
smart00437 |
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ... |
276-542 |
1.14e-77 |
|
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: 249.09 E-value: 1.14e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 276 EKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEKKLITYPRTDSRYITEDEKEMLLENIDYLKEITKINLN 355
Cdd:smart00437 1 EEKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGKEYLDLA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 356 NELTNNSL--INPSKIEDHYAILITGNDF---NKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKG 430
Cdd:smart00437 81 VVLLKPRKprKGKKAQGAHEAIRPTKPIFtpeLEKELSEDEFKLYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAKG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 431 KIIQDNGFKALLNKQ-KTSEETIPNFEKNEEVDI-ELDLLEKETTPPKRYTEKTLLKAManpietledeglkstlkEVKG 508
Cdd:smart00437 161 KTLLFDGWLKVYPEEkKEEEIELPTLKKGDELKVeEVEVEEKETKPPARYTEASLIKLM-----------------EKRG 223
|
250 260 270
....*....|....*....|....*....|....
gi 581224777 509 LGTPATRADIIENLKKNKYIQVQKNKIYITKNGI 542
Cdd:smart00437 224 IGRPSTYASIIETLLDRGYVTKKKKKLIPTELGI 257
|
|
| PRK05776 |
PRK05776 |
DNA topoisomerase I; Provisional |
46-621 |
1.45e-60 |
|
DNA topoisomerase I; Provisional
Pssm-ID: 235602 [Multi-domain] Cd Length: 670 Bit Score: 215.24 E-value: 1.45e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 46 AVGHLVELKEPQEydekyknfsTYPILlekdDFQFK---VSDK----TKDQFNNIKKIFKenKIDEVIIATDPAREGENI 118
Cdd:PRK05776 49 AAGHLFGLHTKSK---------GFPVF----DYEWKplyEIDKgskyTKKYYELLSSLSK--YADEFINACDYDIEGSVI 113
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 119 AYKILNQLKVTDKVtiKRLWLTSKVESSIRKAFKNILPKEktYGFYKEGRARELSDWLVGINLSRHFTKISRELGNDGVI 198
Cdd:PRK05776 114 GYLIIKYLGDPKKA--KRMKFSALTKSDIRRAFRNLETLD--YEMINAGIARHELDWLWGINVSRALMSSVRDASGKRVI 189
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 199 -HIGRVSSPTLNMVYNRENNIKGFKGKKFYKVSATINKDEQEVKTELKNK-FDSEDELHEFLfeNDITDlTQKGLFTDIE 276
Cdd:PRK05776 190 lSAGRVQSPTLKYVVEREIERNLFVPLPYFSVSIIIEKNGYEFTLKYENKkFETKEEAKEIL--EEIKK-TGYLKVTKVE 266
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 277 KEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEKKLITYPRTDSRYI--TEDEKEML--LENIDYLKEITKI 352
Cdd:PRK05776 267 VKIEILEPPPPFNLGDLQVEAARIYGFSPYKTQSIAEDLYLDGLISYPRTNSQKLppTLNIRNILkgLSRSPQYRPLVNL 346
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 353 NLNneLTNNSLI-NPSKIED--HYAILITGNdfNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAVKK--LMFE 427
Cdd:PRK05776 347 LLK--ETKGVLKpVQGPKDDpaHPAIYPTGE--PPKNLSKDEFKLYDLIVRRFLASFAAPAVLSNTIVTLRVPGfpLVFS 422
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 428 VKGKIIQDNGFKALLNKQKTSEETIPNFEKNEEVDI-ELDLLEKETTPPKRYTEKTLLKAManpietledeglkstlkEV 506
Cdd:PRK05776 423 ASGQRIEERGWLKYYPFHKFDEEELPLLKKGERVKIvDVKVRKSYTKPPSRYSKASLLKWM-----------------ES 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 507 KGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEGHL--LSKPDLTGQWEKYLNGISKGEKDDDSFINTIN 584
Cdd:PRK05776 486 VGIGTEATRARIIETLFKRGYLTSNGKYIEVTPLGFGVAEVLEKYFpdIVSVELTRDFEEKLEMIRTGKATREEVIEEAK 565
|
570 580 590
....*....|....*....|....*....|....*...
gi 581224777 585 EMIKKTINEEVKNKESI-QKVAKEKVSTNNIAKCPACD 621
Cdd:PRK05776 566 ETLNKLLEEFKKNKDEIgEELAKALGLIKPVGKCKICG 603
|
|
| PRK07220 |
PRK07220 |
DNA topoisomerase I; Validated |
4-664 |
5.38e-49 |
|
DNA topoisomerase I; Validated
Pssm-ID: 180892 [Multi-domain] Cd Length: 740 Bit Score: 183.81 E-value: 5.38e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 4 LILCEKPSQAMDLSTVFA----KKKKQNG----YMEISDEQLNVSGFltwaVGHLVELKEPQEYDEKYKNFSTYPIllek 75
Cdd:PRK07220 3 LIITEKNIAARRIAQILApkkpKKTRVSGvdvyRYEDNGDDTVVVGL----SGHIVNIDFPKEYNNWQKVDARDLI---- 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 76 dDFQFKVSDKTKDQFNNIKKIFKEnkIDEVIIATDPAREGENIAYKILNQLK-VTDKVTIKRLWLTSKVESSIRKAFKNi 154
Cdd:PRK07220 75 -DAEIITTPTQKKIVTALKKLGKE--ADRVTIATDYDREGELIGVEALNIIKkVNPDIKFDRVRYSAITKKEIERAFSN- 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 155 lPKEKTYGFYKEGRARELSDWLVGINLSRHFTKISRELGNDgVIHIGRVSSPTLNMVYNRENNIKGFKGKKFYKVSATIN 234
Cdd:PRK07220 151 -PVEVDFNLADAGHSRQVIDLVWGAALTRYISLAAGRLGKM-FLSVGRVQSPTLALIVDREKEREAFVPTPYWEIYATLE 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 235 KDEQEVKTELK-NKFDSEDELhEFLFENditdLTQKGLFTDIEKEIGYTMPPKFYDLSALQEDMNDkYKISAKRTLEIAQ 313
Cdd:PRK07220 229 NNGETFVAQHStRRFWEKEEA-DRVFEK----LGKTAEVTEVEKGTKTDKPPTPFNTTEFISAANS-IGFSAANAMRIAE 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 314 TLYEKKLITYPRTDSRYITEDEKemLLENIDYLKEITKINLNNELTNNSLINPSK----IEDHYAILITGNDfNKVDLKE 389
Cdd:PRK07220 303 SLYTNGYISYPRTDNTVYPESLD--LREQIEIFAEGPFGEYAQKLLEKGELVPTRgkkeTTDHPPIYPASLA-KKSELKE 379
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 390 EEINVYKSILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKGKIIQDNGFKALLNKQKTSEETIPNFEKNEEVD-IELDLL 468
Cdd:PRK07220 380 DEWKVYELVVRRFFATFAGPAEWETMKLRFDIGGEEFRANGSRLTEPGWRWYYPYNAPEDRLLPELSEGEELKvKKKEML 459
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 469 EKETTPPKRYTEKTLLKAManpietledeglkstlkEVKGLGTPATRADIIENLKKNKYIqvQKNKIYITKNGILACLLL 548
Cdd:PRK07220 460 DKETQPPGRYGQGRLIKLM-----------------EDLGLGTKATRHEIISKLYSRAYI--HGNPIQPTNTAFAVVDAL 520
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 549 EGH--LLSKPDLTGQWEKYLNGISKGEKDDDSFINTINEMIKKTINEEVKNKESIQKVAKEKVSTNN-IAKCPACDNGYL 625
Cdd:PRK07220 521 EKYapTITKPDMTSRLEEDMDKIAEGKIKEDAVLEESREMLEQVFDELDKNREKIRESLREGLREDKiIGKCPLCGSDLM 600
|
650 660 670 680
....*....|....*....|....*....|....*....|...
gi 581224777 626 I--DRKG--FYGCTEYNNgCEFTIPkklLEKSIPPTVVKALCE 664
Cdd:PRK07220 601 VrrSKRGsrFIGCEGYPE-CTFSLP---LPKSGQIIVTDKVCE 639
|
|
| topA_bact |
TIGR01051 |
DNA topoisomerase I, bacterial; This model describes DNA topoisomerase I among the members of ... |
76-646 |
2.26e-46 |
|
DNA topoisomerase I, bacterial; This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273416 [Multi-domain] Cd Length: 610 Bit Score: 174.11 E-value: 2.26e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 76 DDFQ--FKVSDKTKDQFNNIKKIFKenKIDEVIIATDPAREGENIAYKILNQLKVTDKVtIKRLWLTSKVESSIRKAFKN 153
Cdd:TIGR01051 44 KDFEpeYVVSKGKKKVVKELKTLAK--KADEVYLATDPDREGEAIAWHLAEVLKPKDPV-YKRIVFNEITKKAIRAALKN 120
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 154 ilPKEKTYGFYKEGRARELSDWLVGINLSR-HFTKISRELGndgvihIGRVSSPTLNMVYNRENNIKGFKGKKFYKVSAT 232
Cdd:TIGR01051 121 --PREIDMNLVNAQQARRILDRLVGYTLSPlLWKKVAKGLS------AGRVQSVALRLIVDREREIKRFVPEEYWTIDAT 192
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 233 INKDEQEVKTELKNKFDSEDELHEFLFENDITDLT-----QKGLFTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKR 307
Cdd:TIGR01051 193 FQKGEETFEALLTEVNGKKLKAGSDLDEAEATALKeqlkgEELVVEEIEKKPKKSRPPPPFTTSTLQQEASRKLGFSAKK 272
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 308 TLEIAQTLYEKK--------LITYPRTDSRYITEDEKEMLLENID------YLKEITKINLNNEltNNSLinpskiEDHY 373
Cdd:TIGR01051 273 TMMIAQRLYEGVstgdgtigLITYMRTDSTRLSNQAVNEARNLIDknygkeYLGPKPKRYKSKE--KNAQ------EAHE 344
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 374 AI-----LITGNDFnKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAVKK--LMFEVKGKIIQDNGF----KALL 442
Cdd:TIGR01051 345 AIrptsvFRTPEEL-KDYLKRDEFRLYELIWKRFVASQMADARYDSTSVRLTNEDgeYVFKATGRKLIFDGYykvyVEGS 423
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 443 NKQKTSEETI-PNFEKNEEVDI-ELDLLEKETTPPKRYTEKTLLKAManpietledeglkstlkEVKGLGTPATRADIIE 520
Cdd:TIGR01051 424 DDPLEEKDRIlPPLKEGDAVKLvEVKPNQHFTQPPARYTEASLVKEL-----------------EELGIGRPSTYASIIS 486
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 521 NLKKNKYIQVQKNKIYITKNGILACLLLEGHL--LSKPDLTGQWEKYLNGISKGEKDDDSFINTI----NEMIKKTINEE 594
Cdd:TIGR01051 487 TIQDRGYVKKENKRLYPTELGFAVTDLLEKHFgdVVDYDFTAKMEKDLDEIAEGKAEWKPVLKNFytgfSSKVKKLRNMR 566
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*
gi 581224777 595 VKNKESIQKVakekvstnniakCPACDN--GYLIDRKGFY-GCTEYNNgCEFTIP 646
Cdd:TIGR01051 567 IIVDFKTSQD------------CPLCGRpmVVKLGKYGPFlACSNFPE-CKYTKS 608
|
|
| TOPRIM_TopoIA_TopoIII |
cd03362 |
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type ... |
2-153 |
1.48e-45 |
|
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: 159.32 E-value: 1.48e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 2 NTLILCEKPSQAMDLSTVFAKKKKQNGYMEISDEQLNVSGFL-TWAVGHLVELKEPQEYDEKYKNFSTYPILLeKDDFQF 80
Cdd:cd03362 1 MVLIIAEKPSVAKAIAKILGGGSKKKGKGRYYEFYGEGGGYVvTWASGHLLELDFPEEYDPWDKVWPLEDPLF-PAPFKL 79
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 581224777 81 KVSDKTKDQFNNIKKIFKENkiDEVIIATDPAREGENIAYKILNQLKVTDKVTIKRLWLTSKVESSIRKAFKN 153
Cdd:cd03362 80 KVDKGKKKQFKVLKKLAKRA--DEIVIATDADREGELIGREILEYAKCVKRKPVKRAWFSSLTPKAIRRAFKN 150
|
|
| PRK06599 |
PRK06599 |
DNA topoisomerase I; Validated |
76-646 |
1.48e-42 |
|
DNA topoisomerase I; Validated
Pssm-ID: 235840 [Multi-domain] Cd Length: 675 Bit Score: 164.26 E-value: 1.48e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 76 DDF--QFKVSDKTKDQFNNIKKIFKenKIDEVIIATDPAREGENIAYKILNQLK--VTDKVTIKRLWLTSKVESSIRKAF 151
Cdd:PRK06599 48 NDFapKYEIIEGKEKVVDALKKAAK--KADAVYLATDPDREGEAIAWHIAEVLKeaKLKDKNVKRVVFNEITKKAVQEAI 125
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 152 KNilPKEKTYGFYKEGRARELSDWLVGINLSRH-FTKISRELGndgvihIGRVSSPTLNMVYNRENNIKGFKGKKFYKVS 230
Cdd:PRK06599 126 EN--PRDIDMDLVDAQQARRALDYLVGFKLSPLlWKKVRRGLS------AGRVQSVALRLICEREDEIEAFIPQEYWTIE 197
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 231 ATINKDEQE-VKTELKnKFDSEDeLHEFLFEN-----DITDLTQKGLFT--DIEKEIGYTMPPKFYDLSALQEDMNDKYK 302
Cdd:PRK06599 198 ADLATSNGEpFTAKLV-EVNGKK-LEKFSITNeeqakALVKALEGQAYTvdKIEKKERKRNPPPPFITSTLQQEASRKLG 275
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 303 ISAKRTLEIAQTLYE--------KKLITYPRTDSRYITEDEKEMLLENI------DYLKEITKInlnneltnnsLINPSK 368
Cdd:PRK06599 276 FSAKKTMRIAQKLYEgidlgegtVGLITYMRTDSVRLSNEALDEARKYItkkygkEYLPAKPRV----------YKKKSK 345
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 369 --IEDHYAILITGNDFNKVDLKE----EEINVYKSILQNVAMNFMDKEQYETTTIEIAV--KKLMFEVKGKIIQDNGFKA 440
Cdd:PRK06599 346 naQEAHEAIRPTSINRTPESLKPyltpDQFKLYELIWKRTVASQMAPAILDQTSVDIASenGKYVFRATGSVILFPGFLK 425
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 441 LLNKQKTSEE-----TIPNFEKNEEVDieLDLLEKE---TTPPKRYTEKTLLKAManpietledeglkstlkEVKGLGTP 512
Cdd:PRK06599 426 VYGESKDDEEeddekLLPPLKEGEKLK--LDELLPEqhfTEPPPRYSEASLVKKL-----------------EEYGIGRP 486
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 513 ATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEGHLlskPDL-----TGQWEKYLNGISKGEKD--------DDSF 579
Cdd:PRK06599 487 STYASIISTLQDREYVELEKKRFIPTDLGRIVNDFLVEHF---PKYvdydfTAGLEDELDEIAEGKKDwkpvlrefWEPF 563
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 581224777 580 INTInemikktinEEVKNKESIQKVAKEKVStnniAKCPACDNGYLIDRKG----FYGCTEYNNgCEFTIP 646
Cdd:PRK06599 564 ISNL---------EKVEEDVRTEKVTQEETD----ETCPKCGGGPLVLKLGkngkFLGCSGYPE-CKYTKN 620
|
|
| PRK14973 |
PRK14973 |
DNA topoisomerase I; Provisional |
4-657 |
2.83e-39 |
|
DNA topoisomerase I; Provisional
Pssm-ID: 184936 [Multi-domain] Cd Length: 936 Bit Score: 155.78 E-value: 2.83e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 4 LILCEKPSQAMDLSTVFAKKKKqngYMEISDEQLNVSGFLTWAV----GHLVELkepqEYDEKYKNF--STYPILLEKDD 77
Cdd:PRK14973 3 LIIAEKNIAANRIAQILAGKTK---VQVKKDGGVSTYSFDDTVVvglrGHVVEV----DFEPGYTNWrsEEHTPRSLIDA 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 78 FQFKVSDKtKDQFNNIKKIFKenKIDEVIIATDPAREGENI---AYKILNqlKVTDKVTIKRLWLTSKVESSIRKAFKNi 154
Cdd:PRK14973 76 DTIKKPTE-KKIVGLIQKLAK--KADRVTIATDFDTEGELIgkeAYELVR--AVNPKVPIDRARFSAITKEEIVTAFAE- 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 155 lPKEKTYGFYKEGRARELSDWLVGINLSRhFTKISRELGNDGVIHIGRVSSPTLNMVYNRENNIKGFKGKKFYKVSATIN 234
Cdd:PRK14973 150 -PTDLDFALAAAGEARQIIDLIWGASLTR-FISLAAHRGGDNILSVGRVQSPTLAMIVDREKEIEAFVPEKYWMLSLATE 227
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 235 KDEQEVKTELKNKFDSEDELHEFLFENDITDLtqkgLFTDIEKEIGYTMPPKFYDLSALQEDMNdKYKISAKRTLEIAQT 314
Cdd:PRK14973 228 KDGEGIEARHTHGRFTDSAAAEAAYDATKEPL----VVTEVKEGHKVDRAPTPFDTTTFIVAAS-RLGFSAANAMRIAED 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 315 LYEKKLITYPRTDS----RYITEDEKEMLLENIDYLKEI--TKINLNNELTNNSlinpSKIEDHYAILITGNDfNKVDLK 388
Cdd:PRK14973 303 LYMNGYISYPRTDNtiypKSLDLNGVLATLAKGAFSKDVawVKDNRRPVPTRGK----KSSTDHPPIHPTGVA-TREELG 377
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 389 EEEINVYKSILQNVAMNFMDKEQYETTTIEIAVKKLMFEVKGKIIQDNGFKALLNKQKTSEETIPNFEKNEEVDIE-LDL 467
Cdd:PRK14973 378 DDRWKLYELVVRRFLATLSPDAEWATMKVNFDAGGEPYTATGGRLLEAGWRTVYPYSEAKENILPAFALGEKLPILaVNL 457
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 468 LEKETTPPKRYTEKTLLKAManpietledeglkstlkEVKGLGTPATRADIIENLKKNKYIqvQKNKIYITKNGILACLL 547
Cdd:PRK14973 458 EEKETQPPARYSQSRLIQRM-----------------EELGLGTKSTRHEVIGKLVSRKYI--EGNPLRPTLVGRAVTES 518
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 548 LEGH--LLSKPDLTGQWEKYLNGISKGEKDDDSFINTINEMIKKTINEEVKNKESI-QKVAKEKVSTNNIAKCPACDNGY 624
Cdd:PRK14973 519 LEEHagTITEPDMTQTLEEHMQQIKERKRTRDDVVTESRKMLHRAFDELEANEAVIgRDIMERTAEELTIGPCPVCGKDL 598
|
650 660 670
....*....|....*....|....*....|....*.
gi 581224777 625 LIDRKG---FYGCTEYNNgCEFTIpkkllekSIPPT 657
Cdd:PRK14973 599 RIKHIGssqFIGCSGYPD-CTFNI-------GLPGT 626
|
|
| TOPRIM_TopoIA |
cd01028 |
TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
2-153 |
1.65e-36 |
|
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: 133.89 E-value: 1.65e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 2 NTLILCEKPSQAMDLSTVFAKKKKQNGYMEISDEQLnvsgfLTWAVGHLVELKEPQEYDEKYKNFSTYPILlekDDFQFK 81
Cdd:cd01028 1 KVLIIAEKPSKAKTIAKILGKGSKKKGFYGEGGGYV-----VTASVGHLLELPFPEEYVDWDKDWPLELFP---FEPKYV 72
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 581224777 82 VSDKTKDQFNNIKKIFKENkiDEVIIATDPAREGENIAYKILNQLKVTDKvTIKRLWLTSKVESSIRKAFKN 153
Cdd:cd01028 73 VIPDKKKQLKALKKLAKKA--DEIVLATDPDREGELIAWEILEVLKCDNK-PVKRAWFSEITPKAIREAFKN 141
|
|
| PRK08780 |
PRK08780 |
DNA topoisomerase I; Provisional |
79-575 |
1.24e-34 |
|
DNA topoisomerase I; Provisional
Pssm-ID: 181555 [Multi-domain] Cd Length: 780 Bit Score: 141.05 E-value: 1.24e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 79 QFKVSDKTKDQFNNIKKIFKenKIDEVIIATDPAREGENIAYKILNQLK---VTDKVTIKRLWLTSKVESSIRKAFKNil 155
Cdd:PRK08780 53 RYDLIDKNEKHVEAIAKAAK--SADDLYLATDPDREGEAISWHLAEILKergLLKDKPMQRVVFTEITPRAIKEAMAK-- 128
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 156 PKEKTYGFYKEGRARELSDWLVGINLSR-HFTKISRELGndgvihIGRVSSPTLNMVYNRENNIKGFKGKKFYKVSATIN 234
Cdd:PRK08780 129 PRDIASDLVDAQQARRALDYLVGFNLSPlLWRKIQRGLS------AGRVQSPALRMIVEREEEIEAFIAREYWSIEADCA 202
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 235 KDEQEVKTELK-------NKFDSEDELHEFLFENDITDLTQKGL-FTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAK 306
Cdd:PRK08780 203 HPSQPFNAKLIkldgqkfEQFTITDGDTAEAARLRIQQAAQGTLhVTDVESKERKRNPAPPFTTSTLQQEASRKLGFTTR 282
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 307 RTLEIAQTLYEK---------KLITYPRTDSRYITEDEkemllenidyLKEITKInLNNELTNNSLINPSKI-------- 369
Cdd:PRK08780 283 RTMQVAQKLYEGvdlgdegsvGLITYMRTDSVNLSQDA----------LAEIRDV-IARDYGTASLPDQPNTyktkskna 351
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 370 -EDHYAILITGN----DFNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAV-KKLMFEVKGKIIQDNGFKALL- 442
Cdd:PRK08780 352 qEAHEAVRPTSAlrtpAQVARFLSDDQRRLYELIWKRAVACQMIPATLNTVSVDLAAgSEHVFRATGSTVVVPGFLAVYe 431
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 443 ----NKQKTSEET---IPNFEKNEEVDIELDLLEKE-TTPPKRYTEKTLLKAManpietledeglkstlkEVKGLGTPAT 514
Cdd:PRK08780 432 egkdDKSAEDEDEgrkLPPMKEGDNVPLERIRAEQHfTEPPPRYTEASLVKAL-----------------EEYGIGRPST 494
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 581224777 515 RADIIENLKKNKYIQVQKNKIYITKNGILACLLLEGHL--LSKPDLTGQWEKYLNGISKGEKD 575
Cdd:PRK08780 495 YASIISTLQFRKYVEMEGRRFRPTDVGRAVNKFLTGHFtrYVDYDFTARLEDDLDAVSRGEKE 557
|
|
| PRK07561 |
PRK07561 |
DNA topoisomerase I subunit omega; Validated |
83-646 |
6.33e-34 |
|
DNA topoisomerase I subunit omega; Validated
Pssm-ID: 236048 [Multi-domain] Cd Length: 859 Bit Score: 139.16 E-value: 6.33e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 83 SDKTKdQFNNIKKIFKenKIDEVIIATDPAREGENIAYKILNQLKvTDKVTIKRLwltskV-----ESSIRKAFKNilpk 157
Cdd:PRK07561 71 PGKEK-VVSELKKAAK--DADELYLATDPDREGEAIAWHLLEVLG-GDDVPVKRV-----VfneitKNAIQEAFEN---- 137
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 158 ektygfykegrARELS-------------DWLVGINLS----RhftKISRELGndgvihIGRVSSPTLNMVYNRENNIKG 220
Cdd:PRK07561 138 -----------PRELDinlvnaqqarrflDRLVGYMVSpllwK---KIARGLS------AGRVQSVAVRLIVEREREIEA 197
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 221 FKGKKFYKVSA---TINKDEQEVK-TELKNK-FDSEDELHEflfE--NDITDLTQKGLFT--DIEKEIGYTMPPKFYDLS 291
Cdd:PRK07561 198 FVPEEYWDIHAdltTPRGDAFEARlTHLDGKkFAPVDLLNE---AqaEAAVAALEGARYSvaSVEDKPTTRKPSAPFTTS 274
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 292 ALQEDMNDKYKISAKRTLEIAQTLYEKKLITYPRTDSRYITEDEKEMLLENI------DYLKEitkinlnneltnnsliN 365
Cdd:PRK07561 275 TLQQEASRKLGFSVKKTMRIAQRLYEAGYITYMRTDSTNLSQEAINAARGYIgdnygkKYLPE----------------K 338
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 366 P----SKIED----HYAILITgnDFNKV-----DLKEEEINVYKSI-LQNVAMNFMDkEQYETTTIEIAVKKLMFEVKGK 431
Cdd:PRK07561 339 PrqysSKAKNaqeaHEAIRPS--DVFRTpdqlkGLEGDAQRLYELIwKRFVASQMAP-ARYDSTTVTIAAGDAELRATGR 415
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 432 IIQDNGFKALLNKQKTSEE-----TIPNFEKNEEVDIE-LDLLEKETTPPKRYTEKTLLKAManpietledeglkstlkE 505
Cdd:PRK07561 416 VLRFDGFLKVYVEGRDDALddedrRLPALKVGDALTLEkLDPTQHFTKPPARYSEASLVKEL-----------------E 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 506 VKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEGHL--LSKPDLTGQWEKYLNGISKGEKD----DDSF 579
Cdd:PRK07561 479 KLGIGRPSTYASIISTIQDRGYVRLENRRFYPEKMGRIVTDRLEEFFprLVDYDFTARMEEELDDIANGEADwkpvLDDF 558
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 581224777 580 INTINEMIKKTinEEVKNKESIQkvAKEKVSTNNIakCPACDNGYLIdRKG----FYGCTEYNNG--CEFTIP 646
Cdd:PRK07561 559 YKDFSQQLEKA--EELREEGGMR--PNQMVITDRD--CPTCGRGMGI-RTGktgvFLGCSGYALKerCKTTRN 624
|
|
| PRK06319 |
PRK06319 |
DNA topoisomerase I/SWI domain fusion protein; Validated |
46-650 |
1.57e-31 |
|
DNA topoisomerase I/SWI domain fusion protein; Validated
Pssm-ID: 235778 [Multi-domain] Cd Length: 860 Bit Score: 131.48 E-value: 1.57e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 46 AVGHLVELKEpqeydekyKNFStypILLEKD-DFQFKVSDKTKDQFNNIKKIFKenKIDEVIIATDPAREGENIAYKILN 124
Cdd:PRK06319 30 SLGHIVDLPA--------KEFG---IDIENDfEPDYQILPDKEEVINKICKLAK--KCDVVYLSPDPDREGEAIAWHIAN 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 125 QLKvtDKVTIKRLWLTSKVESSIRKAFKNilPKEKTYGFYKEGRARELSDWLVGINLSrhfTKISRELGNDGVIHIGRVS 204
Cdd:PRK06319 97 QLP--KNTKIQRISFNAITKGAVTEALKH--PREIDMALVNAQQARRLLDRIVGYKIS---PILSRKLQRRSGVSAGRVQ 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 205 SPTLNMVYNRENNIKGFKGKKFYKVSATInKDEQEVKTELKNKFDS-----EDELHEFLFENDIT------------DLT 267
Cdd:PRK06319 170 SVALKLVVDREKAIEAFVPVEYWNIRVHL-KDPKTQKTFWAHLYSVdgkkwEKEIPEGKTEDEVLlinskekadhivELL 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 268 QKGLF--TDIE-KEIGYTMPPKFYDlSALQEDMNDKYKISAKRTLEIAQTLYE---------KKLITYPRTDSRYItedE 335
Cdd:PRK06319 249 ESATYtvTRVEsKEKRRNAYPPFIT-STLQQEASRHFRFSSSRTMNIAQTLYEgvdldsegaTGLITYMRTDSVRT---D 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 336 KEMLLENIDYLKEITKINLNNELTNNSLINPSKIEDHYAILIT----GNDFNKVDLKEEEINVYKSILQNVAMNFMDKEQ 411
Cdd:PRK06319 325 PEALKQVRKYIEGTFGKEFLPSSPNVYTTKKMAQDAHEAIRPTditlTPEKLRSKLTEDQYKLYSLIWKRFVASQMIPAI 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 412 YETTTIEIAV-KKLMFEVKGKIIQDNGFKALLNKQKTSEET------IPNFEKNEEVDI-ELDLLEKETTPPKRYTEKTL 483
Cdd:PRK06319 405 YDTLAIRITTnKGIDLRATGSLLKFKGFLAVYEEKRDDEGDeeenihLPKLHEQDVLTKeELSAEQAFTKPLPRFTEASL 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 484 LKAManpietledeglkstlkEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEGHLLSKPDL--TGQ 561
Cdd:PRK06319 485 VKEL-----------------EKSGIGRPSTYATIMNKIQSREYTLKENQRLRPTELGKIISQFLETNFPRIMDIgfTAL 547
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 562 WEKYLNGISKGEKDDDSFINTINEMIKKTINEEVKNKeSIQKVAKEkvstnniAKCPACDNGYLID----RKGFYGCTEY 637
Cdd:PRK06319 548 MEDELELIADNKKPWKLLLQEFWELFLPVVVTAEKEA-FIPRIVTE-------IDCPKCHKGKLVKiwakNRYFYGCSEY 619
|
650
....*....|...
gi 581224777 638 NNgCEFTIPKKLL 650
Cdd:PRK06319 620 PE-CDYKTSEEEL 631
|
|
| rgy |
TIGR01054 |
reverse gyrase; This model describes reverse gyrase, found in both archaeal and bacterial ... |
3-588 |
5.77e-26 |
|
reverse gyrase; This model describes reverse gyrase, found in both archaeal and bacterial thermophiles. This enzyme, a fusion of a type I topoisomerase domain and a helicase domain, introduces positive supercoiling to increase the melting temperature of DNA double strands. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273418 [Multi-domain] Cd Length: 1171 Bit Score: 114.54 E-value: 5.77e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 3 TLILCEKPSQAMDLSTVFAK--KKKQNG--YMEISDEQLNVsgFLTWAVGHLVEL-KEPQEYDEKYKNFSTYPI------ 71
Cdd:TIGR01054 603 ALLVVESPNKARTIARFFGKpsVRKIGGsvVYEVPVGDLIL--MITASGGHVFDLvTDKGFHGVLVENGRYVPVytsikr 680
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 72 -------LLEKDDFQFKV-SDKTKDQFNNIKKIFK-ENKIDEVIIATDPAREGENIAYKILNQLKVTDKvTIKRLWLTSK 142
Cdd:TIGR01054 681 crdcgyqFTEDRESCPKCgSENIEDSKSIIEILRElAHEVDEVFIGTDPDTEGEKIGWDLALLLSPYNP-NVKRAEFHEV 759
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 143 VESSIRKAFKNilPKEKTYGFYKEGRARELSDWLVGINLSRH----FTKisRELGNdgvihiGRVSSPTLNMVYNRENni 218
Cdd:TIGR01054 760 TRRAILEALES--PRSVDENLVKAQVVRRIEDRWIGFTLSQKlweaFNK--RWLSA------GRVQTPVLGWIIDRYR-- 827
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 219 kgFKGKKFYKVSATINKDEQEVKTELKNKFDSEdELHEFLFENDITDLTQKglftdiEKEIGytmPPKFYDLSALQEDMN 298
Cdd:TIGR01054 828 --ESREKRGYLLIFALESDFRLGLEHDNRLEAK-EFEKDLTWLDVEDIAER------EEERN---PLPPYTTDTMLEDAN 895
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 299 DKYKISAKRTLEIAQTLYEKKLITYPRTDSRYITEDEKEMLLEnidYLKEitkiNLNNELTNN---------SLINPSK- 368
Cdd:TIGR01054 896 RKLGLSVKETMQIAQELFENGLITYHRTDSTRVSDVGMRVAKE---YLAS----RLGGEYFYPrewgeggahECIRPTRp 968
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 369 IE-DHYAILITGNDFNKVDLKEEEINVYKSILQnvamNFMDKEQYETT--TIEIAVKKLMFEVKGKIIQD---NGFkALL 442
Cdd:TIGR01054 969 LDvDDLQRLILEGVIELEGLTREHLRLYDLIFR----RFMASQMRPAKvdTKEITLKADGKEAEEEGIVEiveRGF-ELV 1043
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 443 NKQKTSEEtIPNFEKNEEVDIELDLLEKetTPPkrYTEKTLLKAManpietledeglkstlKEvKGLGTPATRADIIENL 522
Cdd:TIGR01054 1044 YPLWRKNE-LEKGSTFIVKDKELRSVPK--VYP--YTQGEIVQEM----------------KE-RGIGRPSTYATIVEKL 1101
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 581224777 523 KKNKYIQVQKNKIYITKNGILACLLLEGHL--LSKPDLTGQWEKYLNGISKGEKDDDSFINTINEMIK 588
Cdd:TIGR01054 1102 LRRGYVVESKGFLIPTKLGIEVYNYLTNRYpkLVSEDRTRELEEAMDKIERGELDYLEVLESVYREIK 1169
|
|
| TOP1Bc |
smart00436 |
Bacterial DNA topoisomeraes I ATP-binding domain; Extension of TOPRIM in Bacterial DNA ... |
134-218 |
6.82e-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: 98.81 E-value: 6.82e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 134 IKRLWLTSKVESSIRKAFKNilPKEKTYGFYKEGRARELSDWLVGINLSRHFTKISRElgndGVIHIGRVSSPTLNMVYN 213
Cdd:smart00436 1 IKRIEFSEITKKAIREALKN--PREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRN----GVLSAGRVQTPTLGLIVE 74
|
....*
gi 581224777 214 RENNI 218
Cdd:smart00436 75 REREI 79
|
|
| TopG2 |
COG1110 |
Reverse gyrase [Replication, recombination and repair]; |
83-595 |
1.18e-17 |
|
Reverse gyrase [Replication, recombination and repair];
Pssm-ID: 440727 [Multi-domain] Cd Length: 1219 Bit Score: 87.72 E-value: 1.18e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 83 SDKTKDQFNNIK---KIFKEnkIDEVIIATDPAREGENIAYKILNQLKVTDKvTIKRLWLTSKVESSIRKAFKNilPKEK 159
Cdd:COG1110 731 SPNIVDSLEIVEalrELATE--VDEVLIGTDPDTEGEKIGWDVYNLLRPYAK-NIKRIEFHEVTRKAILEALKN--PREI 805
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 160 TYGFYKEGRARELSDWLVGINLSRHFTKI--SRELGndgvihIGRVSSPTLNMVYNRENNikgFKGKKFYKVSATINKDE 237
Cdd:COG1110 806 DENLVEAQIVRRIEDRWIGFTLSQKLWKVfgNRNLS------AGRVQTPVLGWIIERYEE---SRKSKKYLIILTLENGR 876
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 238 QEVKtelknkFDSEDELHEFLFENDITDltqKGLFTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYE 317
Cdd:COG1110 877 LELS------IEDLKEAEEVRKALEKEV---KVKVKKVEEEEEELNPLPPYTTDTLLRDASRRLGLSAEETMRLAQDLFE 947
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 318 KKLITYPRTDSRYITED----EKEMLLENI--DYLK-----------------EITKINLNNELTNNSLINPSKI-EDHY 373
Cdd:COG1110 948 SGLITYHRTDSTRVSDAgiavAKEYISERFgeEYFKprrwgeggaheairptrPLDAEDLRRLIEEGVIELPIPLtRRHL 1027
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 374 AI--LItgndFNK--------VDLKEEEINVykSILQNvamnfmdkeqYETTTIEIAVKklmfevkgkiIQDNGFKALLn 443
Cdd:COG1110 1028 RLydLI----FRRfmasqmrpAKVEKVKLRV--SLELP----------GGEIEEERIVE----------IIEDGFLLIY- 1080
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 444 kqktseetiPNFEKNEEV-DIELDLLEKE-----TTPPkrYTEKTLLKAManpietledeglkstlKEvKGLGTPATRAD 517
Cdd:COG1110 1081 ---------PPIKVEPELkEGEYKVTEVKirkvpKVPL--YTQGDLVREM----------------KE-RGIGRPSTYAK 1132
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 518 IIENLKKNKYIQVQK--NKIYITKNGILA--CLLLE-GHLLSKpDLTGQWEKYLNGISKGEKDDDSFINTI-NEMIKKTI 591
Cdd:COG1110 1133 IVETLLRRGYVVESKkgKKLVPTKLGIEVynYLSENfPDLVSE-ERTRELEEKMDEIEEGEADYQDVLEELyNELRELVL 1211
|
....
gi 581224777 592 NEEV 595
Cdd:COG1110 1212 SPES 1215
|
|
| PTZ00407 |
PTZ00407 |
DNA topoisomerase IA; Provisional |
98-571 |
6.32e-13 |
|
DNA topoisomerase IA; Provisional
Pssm-ID: 173597 [Multi-domain] Cd Length: 805 Bit Score: 72.28 E-value: 6.32e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 98 KENKIDEVIIATDPAREGENIAYKILNQLK---VTDKVTIKRLWLTSKVESSIRKAFKNILPKEKTYGFYKEGRARELSD 174
Cdd:PTZ00407 121 KADNVTEIILATDPDREGELIAVHALQTIKrlyPKLKVPFSRAYMHSITEDGIRKAMRERHVEACDYDLANAAETRHAMD 200
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 175 WLVGINLSrhftKISReLGNDGVIHIGRVSSPTLNMVYNRENNIKG--FKGKKFYKVSA----------------TINKD 236
Cdd:PTZ00407 201 RIFGFLGS----SVVR-AANSQMRSIGRVQTPALILINEREDKIKAflESNKSTFEVQAmcqfpsphgttfsqvvTITPD 275
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 237 EQEVKTELKNKFDSEDELHEFLFENditdLTQKGLFTDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLY 316
Cdd:PTZ00407 276 RKGGASHWATEAEARRCLEQWKLNN----CTGFSVPLEPKPQPSVVPPPQPFTMATAIAKANRQLKYSSEMVSGCLQDLF 351
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 317 EKKLITYPRTDSRYITEDE-------------KEMLLENIDYL---------KEITKINLNNElTNNSLINPSKIED-HY 373
Cdd:PTZ00407 352 QLGHITYPRTDSTRIDESAlpdiyaavkkefgKEFLYRLEDRTvsaqegkgsKKTGKKRSTKQ-KKGADTPVGNVEDaHE 430
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 374 AILITG--NDFNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAVK-----KLMFEVKGKIIQDNGFKALLNK-- 444
Cdd:PTZ00407 431 AIRPTNidTTGESLSLSPPTRAVYDLVRRNTLAVFMIPMKTEKIVATVKFTsgsgeKLEFELQGKRVVEPGWTRAFHKgd 510
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 445 -------QKTSEE---------TIPNFEKNEEVDIeLDLLEKETTPPK----RYTEKTLLKAMANPIETLEDEGLKSTLK 504
Cdd:PTZ00407 511 kgttgpaEETDEDitaveegapVVPSLSQEEFKAI-MNLRSQLGSGVQkgffELRSPQVRENRPVPPLPHSEGTLIEELK 589
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 505 EvKGLGTPATRADIIENLKKNKYIQVQ-KNKIYITKNGILACLLLEGHLLSKPDL--TGQWEKYLNGISK 571
Cdd:PTZ00407 590 N-NGVGRPSTYPMIVKTLLARGYIAVNpKGRCETTPVGRMLVETAKSTFPSIVDIgfTAAFEKKLDRIAK 658
|
|
| YrdD |
COG0551 |
DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination ... |
44-653 |
7.89e-11 |
|
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: 65.27 E-value: 7.89e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 44 TWAVGHLVELKEPQEYDEKYKNFSTYPILLEKDDFQFKVSDKTKDQFNNIKKIFKENKIDEVIIATDPAREGENIAYKIL 123
Cdd:COG0551 11 AAKEAVKLVKKKKKKKKEGKKKGLAGALGLKKKLVDLLLKEKLKKLVENEKLIAELDIKDLKKLKKDKKKKAKALAAALA 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 124 NQLKVTDKVTIKRLWLTSKVESSIRKAFKNILPKEKTYGFYKE-----------GRARELSDWLVGINLSRHFTKISREL 192
Cdd:COG0551 91 AADDDAIEAAAAADEEEALKAAEALEAIRKAVVEEVKSRARKRaarapadvaaaAAAAALARLLLLAAASRALRLLLLLA 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 193 GNDGVIHIGRVSSPTLNMVYNRENNIKGFKGKKFYKVSATINKDEQEVKTELKNKFDSEDELHEFLFENDITDLTQKGLF 272
Cdd:COG0551 171 AGRLRLLSAVAAGLLELEELLKEFEEEEEEEAAEEEEEEEEAKKKKEEDKKKKKKKKKKDKEEETKAIKKKKKAAEAVLA 250
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 273 TDIEKEIGYTMPPKFYDLSALQEDMNDKYKISAKRTLEIAQTLYEKK-------LITYPRTDSRYITEDEKEMLLENIDY 345
Cdd:COG0551 251 AKKAAKEAKAKKELPTTTTDALPEALATTSLTAAAAASALAAALLEEegellytGGYIRYTRTPKSSEADALAALEALKK 330
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 346 LKEITKINLNNELTNNSLINPSKIEDHYAILITGNDFNKVDLKEEEINVYKSILQNVAMNFMDKEQYETTTIEIAVKKLM 425
Cdd:COG0551 331 IAEEPPDERAKKKKKKAKKKKASEAKETTDHPPIPPTTAAALLELLEDRKLLLELLVRRRFAAAADLAKVEELTKVEEAD 410
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 426 FEVKGKIIQDNGFKALLNKQKTSEETIPNF-----EKNEEVDIELDLLEKETTPPKRYTEKTLLKAManpietledeglk 500
Cdd:COG0551 411 EEELVEAEGGLLEVLGEEEEDDEDEEEELLlppleEGEPLLLEELLLEKQTTTPPPRYTTELLLKKL------------- 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 501 stlkEVKGLGTPATRADIIENLKKNKYIQVQKNKIYITKNGILACLLLEGHLLSKPDLTGQWEKYLNGISKGEKDDDSfI 580
Cdd:COG0551 478 ----EEEGGGGRGTTATIIILILKRRYVVLEEKKTTPTELLVEVVLLLLLPFPKLEDTTETAEEEEALLDKEEGKEDK-V 552
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 581224777 581 NTINEMIKKTINEEVKNKESIQKVAKEKVSTNNIAKCPACdNGYLIDRKG----FYGCTEYNNgCEFTIPKKLLEKS 653
Cdd:COG0551 553 VEIREEEYPFFKKLLEIAEEEGEEELSEEDEVLGEKCPKC-GKPLVIKKGrygkFLGCSNYPE-CKYTKPLPKPEVT 627
|
|
| TOPRIM_TopoIA_TopoI |
cd03363 |
TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA ... |
3-153 |
2.75e-10 |
|
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: 58.34 E-value: 2.75e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 3 TLILCEKPsqamdlstvfAKKKKQNGYMEisdeqlnvSGFLTWA-VGHLVELKEPQEY-DEKYKNFS-TYPILLEKddfq 79
Cdd:cd03363 2 KLVIVESP----------AKAKTIKKYLG--------KEYEVLAsVGHIRDLPKKGLGvDGEDDGFEpKYVVIPGK---- 59
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 581224777 80 fkvsdktKDQFNNIKKIFKenKIDEVIIATDPAREGENIAYKILNQLKvtDKVTIKRLWLTSKVESSIRKAFKN 153
Cdd:cd03363 60 -------KKVVKELKKLAK--KADEIYLATDPDREGEAIAWHLAEVLK--LKKNVKRVVFNEITKEAIKEALKN 122
|
|
| TOPRIM |
smart00493 |
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins; |
86-127 |
4.86e-07 |
|
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
Pssm-ID: 214695 [Multi-domain] Cd Length: 75 Bit Score: 47.64 E-value: 4.86e-07
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 581224777 86 TKDQFNNIKKIFKENkidEVIIATDPAREGENIAYKILNQLK 127
Cdd:smart00493 34 SKEQIKLLKKLAKKA---EVILATDPDREGEAIAWELAELLK 72
|
|
| Toprim |
pfam01751 |
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ... |
3-140 |
8.91e-07 |
|
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: 47.35 E-value: 8.91e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 581224777 3 TLILCEKPSQAMDLSTVFAKKKKQngymeisdeqlnvsgfLTWAVGHLVELKEpqeydekyknfstypillekddfqfkv 82
Cdd:pfam01751 1 ELIIVEGPSDAIALEKALGGGFQA----------------VVAVLGHLLSLEK--------------------------- 37
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 581224777 83 sDKTKDQFNNIKKIFKenKIDEVIIATDPAREGENIAYKILNQLKVTDKVtIKRLWLT 140
Cdd:pfam01751 38 -GPKKKALKALKELAL--KAKEVILATDPDREGEAIALKLLELKELLENA-GGRVEFS 91
|
|
| TOPRIM |
cd00188 |
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ... |
88-139 |
4.65e-05 |
|
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: 42.41 E-value: 4.65e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|..
gi 581224777 88 DQFNNIKKIFKEnkIDEVIIATDPAREGENIAYKILNQLKVTDKvTIKRLWL 139
Cdd:cd00188 35 KTRELLKRLLGE--AKEVIIATDADREGEAIALRLLELLKSLGK-KVRRLLL 83
|
|
| TOPRIM_TopoIA_RevGyr |
cd03361 |
TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA ... |
103-154 |
5.65e-04 |
|
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: 41.15 E-value: 5.65e-04
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|..
gi 581224777 103 DEVIIATDPAREGENIAYKILNQLKVTDKvTIKRLWLTSKVESSIRKAFKNI 154
Cdd:cd03361 120 DEVLIATDPDTEGEKIAWDVYLALRPYNK-NIKRAEFHEVTRRAILEALRNP 170
|
|
| Toprim_4 |
pfam13662 |
Toprim domain; The toprim domain is found in a wide variety of enzymes involved in nucleic ... |
94-137 |
6.61e-04 |
|
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: 39.19 E-value: 6.61e-04
10 20 30 40
....*....|....*....|....*....|....*....|....
gi 581224777 94 KKIFKENKIDEVIIATDPAREGENIAYKILNQLKVTDkVTIKRL 137
Cdd:pfam13662 42 LNIDSLGGIKEVILALDGDVAGEKTALYLAEALLEEG-VKVSRL 84
|
|
| TOPRIM_recR |
cd01025 |
TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ... |
92-137 |
1.55e-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: 38.65 E-value: 1.55e-03
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 581224777 92 NIKKIFK---ENKIDEVIIATDPAREGENIAYKILNQLKVTDkVTIKRL 137
Cdd:cd01025 44 NIDKLLEriaKGQVKEVILATNPTVEGEATALYIAKLLKDFG-VKVTRL 91
|
|
| |
