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Conserved domains on  [gi|16129235|ref|NP_415790|]
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DNA topoisomerase 1 [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

type I DNA topoisomerase (domain architecture ID 11482796)

DNA topoisomerase I is a type IA DNA topoisomerase that releases the supercoiling and torsional tension of DNA, which is introduced during DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
PRK07561 PRK07561
DNA topoisomerase I subunit omega; Validated
2-849 0e+00

DNA topoisomerase I subunit omega; Validated


:

Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 1547.45  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    2 GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADststktakkpkkderGALVNRMGVDPWHNWEA 81
Cdd:PRK07561   1 GKSLVIVESPAKAKTINKYLGSDYVVKASVGHIRDLPTSASSVPAKEK---------------GALWARMGVDPDHDFEA 65
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   82 HYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDR 161
Cdd:PRK07561  66 LYEVLPGKEKVVSELKKAAKDADELYLATDPDREGEAIAWHLLEVLGGDDVPVKRVVFNEITKNAIQEAFENPRELDINL 145
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  162 VNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQ 241
Cdd:PRK07561 146 VNAQQARRFLDRLVGYMVSPLLWKKIARGLSAGRVQSVAVRLIVEREREIEAFVPEEYWDIHADLTTPRGDAFEARLTHL 225
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  242 NDKPFRPV---NKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYIT 318
Cdd:PRK07561 226 DGKKFAPVdllNEAQAEAAVAALEGARYSVASVEDKPTTRKPSAPFTTSTLQQEASRKLGFSVKKTMRIAQRLYEAGYIT 305
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  319 YMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASK-ENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQ 397
Cdd:PRK07561 306 YMRTDSTNLSQEAINAARGYIGDNYGKKYLPEKPRQYSSKaKNAQEAHEAIRPSDVFRTPDQLKGLEGDAQRLYELIWKR 385
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  398 FVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKG---DEDRILPAVNKGDALTLVELTPAQHFTKPP 474
Cdd:PRK07561 386 FVASQMAPARYDSTTVTIAAGDAELRATGRVLRFDGFLKVYVEGRDDaldDEDRRLPALKVGDALTLEKLDPTQHFTKPP 465
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  475 ARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVA 554
Cdd:PRK07561 466 ARYSEASLVKELEKLGIGRPSTYASIISTIQDRGYVRLENRRFYPEKMGRIVTDRLEEFFPRLVDYDFTARMEEELDDIA 545
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  555 NHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQMVLTSIDCPTCGRKMGIRTASTGVFLGCSGYALppKERCKTTI 634
Cdd:PRK07561 546 NGEADWKPVLDDFYKDFSQQLEKAEELREEGGMRPNQMVITDRDCPTCGRGMGIRTGKTGVFLGCSGYAL--KERCKTTR 623
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  635 NLVPENEVLNVLEGEDAETNALRAKrrcPKCGTAM-------DSYLI----DPKRKLHVC-GNNPTCDGYEIEEGEFRIK 702
Cdd:PRK07561 624 NLTPEEETLNVLEGEDAETRALGAD---PECGTAMvlrsgrfGPYVQegegDKPRRLSLPkGNNPECVGLEIALGLLSLP 700
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  703 gydGPIVECEKCGSEMHLKMGRFGKYMAC--TNEECKNTRKILRNGEVAP---------PKEDPVPLPELPCEKSDAYFV 771
Cdd:PRK07561 701 ---RPVGEHPECGSEIQAKIGRFGPYVKCggTYASLKNTRKVLTIGLNRAvellaepkrPKEDPVPLPELGCPKSGAPFV 777
                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  772 LRDGAAGVFL----AANTFPKSRETRAPLVEELYRFRDRLPEKLRYLADAPQQDPEGNKTMVRFSRKTKQQYVSSEKDGK 847
Cdd:PRK07561 778 LRDGRYGPYVkhgkANATLPKGRETRAPTVEEALELLAEKPEKLRYLADAPAKDPAGKKAAVKFSRKTKQQYVASEKDGK 857

                 ..
gi 16129235  848 AT 849
Cdd:PRK07561 858 AT 859
 
Name Accession Description Interval E-value
PRK07561 PRK07561
DNA topoisomerase I subunit omega; Validated
2-849 0e+00

DNA topoisomerase I subunit omega; Validated


Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 1547.45  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    2 GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADststktakkpkkderGALVNRMGVDPWHNWEA 81
Cdd:PRK07561   1 GKSLVIVESPAKAKTINKYLGSDYVVKASVGHIRDLPTSASSVPAKEK---------------GALWARMGVDPDHDFEA 65
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   82 HYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDR 161
Cdd:PRK07561  66 LYEVLPGKEKVVSELKKAAKDADELYLATDPDREGEAIAWHLLEVLGGDDVPVKRVVFNEITKNAIQEAFENPRELDINL 145
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  162 VNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQ 241
Cdd:PRK07561 146 VNAQQARRFLDRLVGYMVSPLLWKKIARGLSAGRVQSVAVRLIVEREREIEAFVPEEYWDIHADLTTPRGDAFEARLTHL 225
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  242 NDKPFRPV---NKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYIT 318
Cdd:PRK07561 226 DGKKFAPVdllNEAQAEAAVAALEGARYSVASVEDKPTTRKPSAPFTTSTLQQEASRKLGFSVKKTMRIAQRLYEAGYIT 305
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  319 YMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASK-ENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQ 397
Cdd:PRK07561 306 YMRTDSTNLSQEAINAARGYIGDNYGKKYLPEKPRQYSSKaKNAQEAHEAIRPSDVFRTPDQLKGLEGDAQRLYELIWKR 385
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  398 FVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKG---DEDRILPAVNKGDALTLVELTPAQHFTKPP 474
Cdd:PRK07561 386 FVASQMAPARYDSTTVTIAAGDAELRATGRVLRFDGFLKVYVEGRDDaldDEDRRLPALKVGDALTLEKLDPTQHFTKPP 465
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  475 ARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVA 554
Cdd:PRK07561 466 ARYSEASLVKELEKLGIGRPSTYASIISTIQDRGYVRLENRRFYPEKMGRIVTDRLEEFFPRLVDYDFTARMEEELDDIA 545
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  555 NHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQMVLTSIDCPTCGRKMGIRTASTGVFLGCSGYALppKERCKTTI 634
Cdd:PRK07561 546 NGEADWKPVLDDFYKDFSQQLEKAEELREEGGMRPNQMVITDRDCPTCGRGMGIRTGKTGVFLGCSGYAL--KERCKTTR 623
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  635 NLVPENEVLNVLEGEDAETNALRAKrrcPKCGTAM-------DSYLI----DPKRKLHVC-GNNPTCDGYEIEEGEFRIK 702
Cdd:PRK07561 624 NLTPEEETLNVLEGEDAETRALGAD---PECGTAMvlrsgrfGPYVQegegDKPRRLSLPkGNNPECVGLEIALGLLSLP 700
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  703 gydGPIVECEKCGSEMHLKMGRFGKYMAC--TNEECKNTRKILRNGEVAP---------PKEDPVPLPELPCEKSDAYFV 771
Cdd:PRK07561 701 ---RPVGEHPECGSEIQAKIGRFGPYVKCggTYASLKNTRKVLTIGLNRAvellaepkrPKEDPVPLPELGCPKSGAPFV 777
                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  772 LRDGAAGVFL----AANTFPKSRETRAPLVEELYRFRDRLPEKLRYLADAPQQDPEGNKTMVRFSRKTKQQYVSSEKDGK 847
Cdd:PRK07561 778 LRDGRYGPYVkhgkANATLPKGRETRAPTVEEALELLAEKPEKLRYLADAPAKDPAGKKAAVKFSRKTKQQYVASEKDGK 857

                 ..
gi 16129235  848 AT 849
Cdd:PRK07561 858 AT 859
topA_bact TIGR01051
DNA topoisomerase I, bacterial; This model describes DNA topoisomerase I among the members of ...
5-637 0e+00

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: 948.74  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235     5 LVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSgsaakksadststktakkpkkdergalvnRMGVDPWHNWEAHYE 84
Cdd:TIGR01051   1 LVIVESPAKAKTIKKYLGDEYEVEASMGHIRDLPKS-----------------------------RLGVDIEKDFEPEYV 51
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    85 VLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNA 164
Cdd:TIGR01051  52 VSKGKKKVVKELKTLAKKADEVYLATDPDREGEAIAWHLAEVLKPKDPVYKRIVFNEITKKAIRAALKNPREIDMNLVNA 131
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   165 QQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTpSGEALALQVTHQNDK 244
Cdd:TIGR01051 132 QQARRILDRLVGYTLSPLLWKKVAKGLSAGRVQSVALRLIVDREREIKRFVPEEYWTIDATFQK-GEETFEALLTEVNGK 210
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   245 PFRPV---NKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEA------- 314
Cdd:TIGR01051 211 KLKAGsdlDEAEATALKEQLKGEELVVEEIEKKPKKSRPPPPFTTSTLQQEASRKLGFSAKKTMMIAQRLYEGvstgdgt 290
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   315 -GYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKE-NSQEAHEAIRPSDVNVMAESLKD-MEADAQKLY 391
Cdd:TIGR01051 291 iGLITYMRTDSTRLSNQAVNEARNLIDKNYGKEYLGPKPKRYKSKEkNAQEAHEAIRPTSVFRTPEELKDyLKRDEFRLY 370
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   392 QLIWRQFVACQMTPAKYDSTTLTVGA--GDFRLKARGRILRFDGWTKVMPALRKG---DEDRILPAVNKGDALTLVELTP 466
Cdd:TIGR01051 371 ELIWKRFVASQMADARYDSTSVRLTNedGEYVFKATGRKLIFDGYYKVYVEGSDDpleEKDRILPPLKEGDAVKLVEVKP 450
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   467 AQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQM 546
Cdd:TIGR01051 451 NQHFTQPPARYTEASLVKELEELGIGRPSTYASIISTIQDRGYVKKENKRLYPTELGFAVTDLLEKHFGDVVDYDFTAKM 530
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   547 ENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKdpeeggMRPNQMVLTSIDCPTCGRKMGIRTASTGVFLGCSGYalpp 626
Cdd:TIGR01051 531 EKDLDEIAEGKAEWKPVLKNFYTGFSSKVKKLRN------MRIIVDFKTSQDCPLCGRPMVVKLGKYGPFLACSNF---- 600
                         650
                  ....*....|.
gi 16129235   627 kERCKTTINLV 637
Cdd:TIGR01051 601 -PECKYTKSIV 610
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
3-593 0e+00

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 223624 [Multi-domain]  Cd Length: 570  Bit Score: 793.73  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   3 KALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAakksadststktakkpkkdergalvnRMGVDPWHN-WEA 81
Cdd:COG0550   1 KRLIIVESPSKAKTIAKYLGKGYVVTASVGHLRDLPFPEEY--------------------------KGWVDVDLPiFEP 54
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  82 HYEVLPG-KEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGD-DARYSRVVFNEITKNAIRQAFNKPGELNI 159
Cdd:COG0550  55 KYIIKPGkKKKVVKKLKKLAKKADEVYLATDPDREGEAIGWHILEVLKLKnPSKVKRVVFSEITKKAILSAFKNPREIDM 134
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 160 DRVNAQQARRFMDRVVGYMVSPLLWKKIARG-LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQV 238
Cdd:COG0550 135 NLVDAQLARRILDRLVGYNLSRLLWKKLKRGvLSAGRVQSPALRLVVEREREIEAFVPEEYWEIKAIFEKGGGEFSARLT 214
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 239 THQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEA-GYI 317
Cdd:COG0550 215 EIEGKKEGRLKDKDEAEEIVNKLKGKPAKVVSVEKKPKKRSPPPPFTTSTLQQEASRKLGFSAKKTMDIAQKLYEGhGLI 294
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 318 TYMRTDSTNLSQDAVNMVRGYISDN-FGKKYLPESPNQYASKE-NSQEAHEAIRPSDVNVmAESLKdmEADAQKLYQLIW 395
Cdd:COG0550 295 TYPRTDSTRLSEEALAEARLYILAIaYGKEYLPLKPRRYPSKGkKAQEAHEAIRPTDFET-PESLK--AYDELKLYDLIW 371
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 396 RQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPA 475
Cdd:COG0550 372 RRFLASQMPDAIYEKTTVTLEVAGEKFKASGKVLKFDGWLKVYGEDKDEEEDKELPELKEGDELKVEKLEVEEHFTKPPP 451
                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 476 RFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVAN 555
Cdd:COG0550 452 RYTEASLVKAMEKLGIGTPSTYASIIETLQKRGYVEKKGKRLVPTELGEAVIELLEEYFPELVDPDFTAKMEEKLDEIAE 531
                       570       580       590
                ....*....|....*....|....*....|....*...
gi 16129235 556 HEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQMV 593
Cdd:COG0550 532 GKLEWKDVLDEFKKKFSKLLEEAKKNIEEIKSELNKGL 569
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
159-575 1.86e-171

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: 500.98  E-value: 1.86e-171
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 159 IDRVNAQQARRFMDRVVGYMVSPLLWKKIAR--GLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTttpsgealal 236
Cdd:cd00186   1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRkgVLSAGRVQSPTLGLIVEREREIKAFVPEDYWEIKEAV---------- 70
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 237 qvthqndkpfrpvnkeqtqaavsllekarysVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGY 316
Cdd:cd00186  71 -------------------------------VVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGL 119
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 317 ITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQ----YASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQ 392
Cdd:cd00186 120 ITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLgrrnPKRGKKEQGAHEAIRPTKVAPTPELEANLSEDEFKLYE 199
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 393 LIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDrILPAVNKGDALTLVELTPAQHFTK 472
Cdd:cd00186 200 LIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEE-EPPPLKEGDELKLEEVELEEKETQ 278
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 473 PPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQ 552
Cdd:cd00186 279 PPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKEKKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEKLDE 358
                       410       420
                ....*....|....*....|...
gi 16129235 553 VANHEAEWKAVLDHFFSDFTQQL 575
Cdd:cd00186 359 IAEGKKDYQEVLEEFYEEFKKIV 381
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
156-564 1.23e-159

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: 334397 [Multi-domain]  Cd Length: 409  Bit Score: 471.71  E-value: 1.23e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   156 ELNIDRVNAQQARRFMDRVVGYMVSPLLWKKI--ARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEA 233
Cdd:pfam01131   1 EIDDNLVDAQEARRELDWLIGINLSRALTLKKkgNKVLSAGRVQTPTLALIVEREREIENFVPEPYWTIEATLKDGGGPF 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   234 LalqvtHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYE 313
Cdd:pfam01131  81 V-----EAKKKRGRFFDKEEAEAILAKLKKGTAVVTSVEKKEKKEPPPLPFDTTTLQKEASRKLGFSAKKTMSIAQKLYE 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   314 -AGYITYMRTDSTNLSQDA-VNMVRGYISDNFGKKYLPESPNQYASK----ENSQ-EAHEAIRPSDVNVMAESLKDmeaD 386
Cdd:pfam01131 156 kHGLITYPRTDSTYLPEDAeLKAILEALAKNFGKEYLPFAEKLLKKTkgtvNNKKvTAHEAIRPTGNIPDLPELSD---D 232
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   387 AQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTP 466
Cdd:pfam01131 233 ERKLYELIVRRFLASQMPDAVYETTTVTLEVGGEEFKASGKRILEDGWKKVYPYGKKKDEEEILPELKEGEELDVKDVEL 312
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   467 AQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLeENFRELMNYDFTAQM 546
Cdd:pfam01131 313 EEKKTKPPKRYTEASLIKAMEKAGIGTPATRATIIETLVERGYVERKKKSLVPTELGKALVEAL-EKFPDLVSPELTAEL 391
                         410
                  ....*....|....*...
gi 16129235   547 ENSLDQVANHEAEWKAVL 564
Cdd:pfam01131 392 EEKLDEIAEGKLDWKDVL 409
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
272-526 7.15e-119

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: 360.79  E-value: 7.15e-119
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    272 EDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPE- 350
Cdd:smart00437   1 EEKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGKEYLDLa 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    351 ----SPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARG 426
Cdd:smart00437  81 vvllKPRKPRKGKKAQGAHEAIRPTKPIFTPELEKELSEDEFKLYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAKG 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    427 RILRFDGWTKVMPALRKgDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQD 506
Cdd:smart00437 161 KTLLFDGWLKVYPEEKK-EEEIELPTLKKGDELKVEEVEVEEKETKPPARYTEASLIKLMEKRGIGRPSTYASIIETLLD 239
                          250       260
                   ....*....|....*....|
gi 16129235    507 RGYVRVENRRFYAEKMGEIV 526
Cdd:smart00437 240 RGYVTKKKKKLIPTELGIAV 259
 
Name Accession Description Interval E-value
PRK07561 PRK07561
DNA topoisomerase I subunit omega; Validated
2-849 0e+00

DNA topoisomerase I subunit omega; Validated


Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 1547.45  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    2 GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADststktakkpkkderGALVNRMGVDPWHNWEA 81
Cdd:PRK07561   1 GKSLVIVESPAKAKTINKYLGSDYVVKASVGHIRDLPTSASSVPAKEK---------------GALWARMGVDPDHDFEA 65
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   82 HYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDR 161
Cdd:PRK07561  66 LYEVLPGKEKVVSELKKAAKDADELYLATDPDREGEAIAWHLLEVLGGDDVPVKRVVFNEITKNAIQEAFENPRELDINL 145
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  162 VNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQ 241
Cdd:PRK07561 146 VNAQQARRFLDRLVGYMVSPLLWKKIARGLSAGRVQSVAVRLIVEREREIEAFVPEEYWDIHADLTTPRGDAFEARLTHL 225
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  242 NDKPFRPV---NKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYIT 318
Cdd:PRK07561 226 DGKKFAPVdllNEAQAEAAVAALEGARYSVASVEDKPTTRKPSAPFTTSTLQQEASRKLGFSVKKTMRIAQRLYEAGYIT 305
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  319 YMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASK-ENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQ 397
Cdd:PRK07561 306 YMRTDSTNLSQEAINAARGYIGDNYGKKYLPEKPRQYSSKaKNAQEAHEAIRPSDVFRTPDQLKGLEGDAQRLYELIWKR 385
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  398 FVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKG---DEDRILPAVNKGDALTLVELTPAQHFTKPP 474
Cdd:PRK07561 386 FVASQMAPARYDSTTVTIAAGDAELRATGRVLRFDGFLKVYVEGRDDaldDEDRRLPALKVGDALTLEKLDPTQHFTKPP 465
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  475 ARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVA 554
Cdd:PRK07561 466 ARYSEASLVKELEKLGIGRPSTYASIISTIQDRGYVRLENRRFYPEKMGRIVTDRLEEFFPRLVDYDFTARMEEELDDIA 545
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  555 NHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQMVLTSIDCPTCGRKMGIRTASTGVFLGCSGYALppKERCKTTI 634
Cdd:PRK07561 546 NGEADWKPVLDDFYKDFSQQLEKAEELREEGGMRPNQMVITDRDCPTCGRGMGIRTGKTGVFLGCSGYAL--KERCKTTR 623
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  635 NLVPENEVLNVLEGEDAETNALRAKrrcPKCGTAM-------DSYLI----DPKRKLHVC-GNNPTCDGYEIEEGEFRIK 702
Cdd:PRK07561 624 NLTPEEETLNVLEGEDAETRALGAD---PECGTAMvlrsgrfGPYVQegegDKPRRLSLPkGNNPECVGLEIALGLLSLP 700
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  703 gydGPIVECEKCGSEMHLKMGRFGKYMAC--TNEECKNTRKILRNGEVAP---------PKEDPVPLPELPCEKSDAYFV 771
Cdd:PRK07561 701 ---RPVGEHPECGSEIQAKIGRFGPYVKCggTYASLKNTRKVLTIGLNRAvellaepkrPKEDPVPLPELGCPKSGAPFV 777
                        810       820       830       840       850       860       870       880
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  772 LRDGAAGVFL----AANTFPKSRETRAPLVEELYRFRDRLPEKLRYLADAPQQDPEGNKTMVRFSRKTKQQYVSSEKDGK 847
Cdd:PRK07561 778 LRDGRYGPYVkhgkANATLPKGRETRAPTVEEALELLAEKPEKLRYLADAPAKDPAGKKAAVKFSRKTKQQYVASEKDGK 857

                 ..
gi 16129235  848 AT 849
Cdd:PRK07561 858 AT 859
topA_bact TIGR01051
DNA topoisomerase I, bacterial; This model describes DNA topoisomerase I among the members of ...
5-637 0e+00

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: 948.74  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235     5 LVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSgsaakksadststktakkpkkdergalvnRMGVDPWHNWEAHYE 84
Cdd:TIGR01051   1 LVIVESPAKAKTIKKYLGDEYEVEASMGHIRDLPKS-----------------------------RLGVDIEKDFEPEYV 51
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    85 VLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNA 164
Cdd:TIGR01051  52 VSKGKKKVVKELKTLAKKADEVYLATDPDREGEAIAWHLAEVLKPKDPVYKRIVFNEITKKAIRAALKNPREIDMNLVNA 131
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   165 QQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTpSGEALALQVTHQNDK 244
Cdd:TIGR01051 132 QQARRILDRLVGYTLSPLLWKKVAKGLSAGRVQSVALRLIVDREREIKRFVPEEYWTIDATFQK-GEETFEALLTEVNGK 210
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   245 PFRPV---NKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEA------- 314
Cdd:TIGR01051 211 KLKAGsdlDEAEATALKEQLKGEELVVEEIEKKPKKSRPPPPFTTSTLQQEASRKLGFSAKKTMMIAQRLYEGvstgdgt 290
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   315 -GYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKE-NSQEAHEAIRPSDVNVMAESLKD-MEADAQKLY 391
Cdd:TIGR01051 291 iGLITYMRTDSTRLSNQAVNEARNLIDKNYGKEYLGPKPKRYKSKEkNAQEAHEAIRPTSVFRTPEELKDyLKRDEFRLY 370
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   392 QLIWRQFVACQMTPAKYDSTTLTVGA--GDFRLKARGRILRFDGWTKVMPALRKG---DEDRILPAVNKGDALTLVELTP 466
Cdd:TIGR01051 371 ELIWKRFVASQMADARYDSTSVRLTNedGEYVFKATGRKLIFDGYYKVYVEGSDDpleEKDRILPPLKEGDAVKLVEVKP 450
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   467 AQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQM 546
Cdd:TIGR01051 451 NQHFTQPPARYTEASLVKELEELGIGRPSTYASIISTIQDRGYVKKENKRLYPTELGFAVTDLLEKHFGDVVDYDFTAKM 530
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   547 ENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKdpeeggMRPNQMVLTSIDCPTCGRKMGIRTASTGVFLGCSGYalpp 626
Cdd:TIGR01051 531 EKDLDEIAEGKAEWKPVLKNFYTGFSSKVKKLRN------MRIIVDFKTSQDCPLCGRPMVVKLGKYGPFLACSNF---- 600
                         650
                  ....*....|.
gi 16129235   627 kERCKTTINLV 637
Cdd:TIGR01051 601 -PECKYTKSIV 610
PRK06599 PRK06599
DNA topoisomerase I; Validated
1-742 0e+00

DNA topoisomerase I; Validated


Pssm-ID: 235840 [Multi-domain]  Cd Length: 675  Bit Score: 891.52  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    1 MGKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPtsgsaakksadststktAKKpkkdergalvnrMGVDPWHNWE 80
Cdd:PRK06599   1 MAKKLVIVESPAKAKTIKKYLGKDYKVLASFGHVRDLP-----------------KKK------------GGVDPDNDFA 51
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   81 AHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIG---GDDARYSRVVFNEITKNAIRQAFNKPGEL 157
Cdd:PRK06599  52 PKYEIIEGKEKVVDALKKAAKKADAVYLATDPDREGEAIAWHIAEVLKeakLKDKNVKRVVFNEITKKAVQEAIENPRDI 131
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  158 NIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQ 237
Cdd:PRK06599 132 DMDLVDAQQARRALDYLVGFKLSPLLWKKVRRGLSAGRVQSVALRLICEREDEIEAFIPQEYWTIEADLATSNGEPFTAK 211
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  238 VTHQNDK---PFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEA 314
Cdd:PRK06599 212 LVEVNGKkleKFSITNEEQAKALVKALEGQAYTVDKIEKKERKRNPPPPFITSTLQQEASRKLGFSAKKTMRIAQKLYEG 291
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  315 --------GYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASK-ENSQEAHEAIRPSDVNVMAESLKD-ME 384
Cdd:PRK06599 292 idlgegtvGLITYMRTDSVRLSNEALDEARKYITKKYGKEYLPAKPRVYKKKsKNAQEAHEAIRPTSINRTPESLKPyLT 371
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  385 ADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGA--GDFRLKARGRILRFDGWTKVMPA---LRKGDEDRILPAVNKGDAL 459
Cdd:PRK06599 372 PDQFKLYELIWKRTVASQMAPAILDQTSVDIASenGKYVFRATGSVILFPGFLKVYGEskdDEEEDDEKLLPPLKEGEKL 451
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  460 TLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMN 539
Cdd:PRK06599 452 KLDELLPEQHFTEPPPRYSEASLVKKLEEYGIGRPSTYASIISTLQDREYVELEKKRFIPTDLGRIVNDFLVEHFPKYVD 531
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  540 YDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQmvlTSIDCPTC-GRKMGIRTASTGVFLG 618
Cdd:PRK06599 532 YDFTAGLEDELDEIAEGKKDWKPVLREFWEPFISNLEKVEEDVRTEKVTQEE---TDETCPKCgGGPLVLKLGKNGKFLG 608
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  619 CSGYalpPKerCKTTINLVPENEvlnvlegEDAETNALRAKRRCPkcgtamdsylidpkrklhvcgnnptcdgyeieege 698
Cdd:PRK06599 609 CSGY---PE--CKYTKNITRDED-------EPIEEEEIVEEEKCP----------------------------------- 641
                        730       740       750       760
                 ....*....|....*....|....*....|....*....|....*
gi 16129235  699 frikgydgpiveceKCGSEMHLKMGRFGKYMACTN-EECKNTRKI 742
Cdd:PRK06599 642 --------------KCGGPLVLKKGRYGKFLACSGyPECKHIKPL 672
PRK05582 PRK05582
DNA topoisomerase I; Validated
1-690 0e+00

DNA topoisomerase I; Validated


Pssm-ID: 235516 [Multi-domain]  Cd Length: 650  Bit Score: 810.58  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    1 MGKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGsaakksadststktakkpkkdergalvnrMGVDPWHNWE 80
Cdd:PRK05582   1 MMKKLVIVESPAKAKTIEKYLGKNYKVVASMGHIRDLPKSQ-----------------------------LGIDIENNFE 51
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   81 AHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNID 160
Cdd:PRK05582  52 PKYITIRGKGPVIKELKKAAKKAKKVYLATDPDREGEAIAWHLAHILGLDEKEKNRIVFNEITKDAIKNAFKNPRKIDMN 131
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  161 RVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDAsTTTPSGEALALQVTH 240
Cdd:PRK05582 132 LVDAQQARRILDRLVGYKLSPLLWKKVKKGLSAGRVQSVALKLIIDREKEIRAFVPEEYWTIDA-EFKKGKKKFEASFYG 210
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  241 QNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEA------ 314
Cdd:PRK05582 211 YKGKKIELKNEEDVKEILAELKKKDFKVSKVKKKERKRNPPPPFTTSTLQQEAARKLNFSTKKTMMIAQQLYEGidlgkq 290
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  315 ---GYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKENSQEAHEAIRPSDVNVMAESLKD-MEADAQKL 390
Cdd:PRK05582 291 gtvGLITYMRTDSTRISDTAQEEAREFIEEKYGKEYLPKKPKVYKKKSGAQDAHEAIRPTSVFLTPESAKKyLTKDQLKL 370
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  391 YQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPAlrKGDEDRILPAVNKGDALTLVELTPAQHF 470
Cdd:PRK05582 371 YKLIWNRFVASQMAPAVFDTVSVDLENNGVKFRASGSKVKFDGFMKVYVG--DEEKDKMLPELEEGEKVKLKKIEPEQHF 448
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  471 TKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSL 550
Cdd:PRK05582 449 TQPPARYTEASLIKTLEELGIGRPSTYAPTISTIQKRGYVKLEKKRLVPTELGEIVNELLEEFFPDIVDVEFTAEMEEKL 528
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  551 DQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPnqmVLTSIDCPTCGRKMGIRTASTGVFLGCSGYalpPKerC 630
Cdd:PRK05582 529 DEIEEGKEDWKKVLDDFYKPFEKEIEKAEKEIEKIKIKD---EPAGEDCPKCGSPMVIKMGRYGKFIACSNF---PD--C 600
                        650       660       670       680       690       700
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  631 KTTINLVPENEVLnvlegedaetnalrakrrCPKCGTAMDSYLIDPKRKLHVCGNNPTCD 690
Cdd:PRK05582 601 RNTKPIVKEIGVK------------------CPKCGGQIVERKSKKGRKFYGCSRYPECD 642
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
3-593 0e+00

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 223624 [Multi-domain]  Cd Length: 570  Bit Score: 793.73  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   3 KALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAakksadststktakkpkkdergalvnRMGVDPWHN-WEA 81
Cdd:COG0550   1 KRLIIVESPSKAKTIAKYLGKGYVVTASVGHLRDLPFPEEY--------------------------KGWVDVDLPiFEP 54
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  82 HYEVLPG-KEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGD-DARYSRVVFNEITKNAIRQAFNKPGELNI 159
Cdd:COG0550  55 KYIIKPGkKKKVVKKLKKLAKKADEVYLATDPDREGEAIGWHILEVLKLKnPSKVKRVVFSEITKKAILSAFKNPREIDM 134
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 160 DRVNAQQARRFMDRVVGYMVSPLLWKKIARG-LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQV 238
Cdd:COG0550 135 NLVDAQLARRILDRLVGYNLSRLLWKKLKRGvLSAGRVQSPALRLVVEREREIEAFVPEEYWEIKAIFEKGGGEFSARLT 214
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 239 THQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEA-GYI 317
Cdd:COG0550 215 EIEGKKEGRLKDKDEAEEIVNKLKGKPAKVVSVEKKPKKRSPPPPFTTSTLQQEASRKLGFSAKKTMDIAQKLYEGhGLI 294
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 318 TYMRTDSTNLSQDAVNMVRGYISDN-FGKKYLPESPNQYASKE-NSQEAHEAIRPSDVNVmAESLKdmEADAQKLYQLIW 395
Cdd:COG0550 295 TYPRTDSTRLSEEALAEARLYILAIaYGKEYLPLKPRRYPSKGkKAQEAHEAIRPTDFET-PESLK--AYDELKLYDLIW 371
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 396 RQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPA 475
Cdd:COG0550 372 RRFLASQMPDAIYEKTTVTLEVAGEKFKASGKVLKFDGWLKVYGEDKDEEEDKELPELKEGDELKVEKLEVEEHFTKPPP 451
                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 476 RFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVAN 555
Cdd:COG0550 452 RYTEASLVKAMEKLGIGTPSTYASIIETLQKRGYVEKKGKRLVPTELGEAVIELLEEYFPELVDPDFTAKMEEKLDEIAE 531
                       570       580       590
                ....*....|....*....|....*....|....*...
gi 16129235 556 HEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQMV 593
Cdd:COG0550 532 GKLEWKDVLDEFKKKFSKLLEEAKKNIEEIKSELNKGL 569
PRK06319 PRK06319
DNA topoisomerase I/SWI domain fusion protein; Validated
1-763 0e+00

DNA topoisomerase I/SWI domain fusion protein; Validated


Pssm-ID: 235778 [Multi-domain]  Cd Length: 860  Bit Score: 605.28  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    1 MGKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGsaakksadststktakkpkkdergalvnrMGVDPWHNWE 80
Cdd:PRK06319   1 MKKSLIIVESPAKIKTLQKLLGEGFIFASSLGHIVDLPAKE-----------------------------FGIDIENDFE 51
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   81 AHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGgDDARYSRVVFNEITKNAIRQAFNKPGELNID 160
Cdd:PRK06319  52 PDYQILPDKEEVINKICKLAKKCDVVYLSPDPDREGEAIAWHIANQLP-KNTKIQRISFNAITKGAVTEALKHPREIDMA 130
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  161 RVNAQQARRFMDRVVGYMVSPLLWKKIAR--GLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQV 238
Cdd:PRK06319 131 LVNAQQARRLLDRIVGYKISPILSRKLQRrsGVSAGRVQSVALKLVVDREKAIEAFVPVEYWNIRVHLKDPKTQKTFWAH 210
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  239 THQND-----------KPFRPV----NKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKK 303
Cdd:PRK06319 211 LYSVDgkkwekeipegKTEDEVllinSKEKADHIVELLESATYTVTRVESKEKRRNAYPPFITSTLQQEASRHFRFSSSR 290
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  304 TMMMAQRLYEA---------GYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKENSQEAHEAIRPSDVN 374
Cdd:PRK06319 291 TMNIAQTLYEGvdldsegatGLITYMRTDSVRTDPEALKQVRKYIEGTFGKEFLPSSPNVYTTKKMAQDAHEAIRPTDIT 370
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  375 VMAESLKDMEADAQ-KLYQLIWRQFVACQMTPAKYDSTTLTVGAG-DFRLKARGRILRFDGWTKVMPALR----KGDEDR 448
Cdd:PRK06319 371 LTPEKLRSKLTEDQyKLYSLIWKRFVASQMIPAIYDTLAIRITTNkGIDLRATGSLLKFKGFLAVYEEKRddegDEEENI 450
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  449 ILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTD 528
Cdd:PRK06319 451 HLPKLHEQDVLTKEELSAEQAFTKPLPRFTEASLVKELEKSGIGRPSTYATIMNKIQSREYTLKENQRLRPTELGKIISQ 530
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  529 RLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDpeegGMRPNqmVLTSIDCPTC-GRKMG 607
Cdd:PRK06319 531 FLETNFPRIMDIGFTALMEDELELIADNKKPWKLLLQEFWELFLPVVVTAEKE----AFIPR--IVTEIDCPKChKGKLV 604
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  608 IRTASTGVFLGCSGYalppkerckttinlvpenevlnvlegedaetnalrakrrcpkcgtamdsylidpkrklhvcgnnP 687
Cdd:PRK06319 605 KIWAKNRYFYGCSEY----------------------------------------------------------------P 620
                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  688 TCDgYEIEEGE--FRIKGY------DGPiveCEKCGSEMHLKMGRFGKYMACTN-EECKNTRKILRNGEVAPPKEDPVPL 758
Cdd:PRK06319 621 ECD-YKTSEEEltFNKEDYaedtpwDSP---CPLCGGEMKVRHGRFGTFLGCENyPECRGIINIHKKGEEGIEPEETVPC 696

                 ....*
gi 16129235  759 PELPC 763
Cdd:PRK06319 697 PAIGC 701
PRK08780 PRK08780
DNA topoisomerase I; Provisional
1-616 0e+00

DNA topoisomerase I; Provisional


Pssm-ID: 181555 [Multi-domain]  Cd Length: 780  Bit Score: 569.39  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    1 MGKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLptsgsaakksadststktakKPKKderGAlvnrmgVDPWHNWE 80
Cdd:PRK08780   1 MSKHLVIVESPAKAKTINKYLGKDFTVLASYGHVRDL--------------------VPKE---GA------VDPENGFA 51
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   81 AHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGG----DDARYSRVVFNEITKNAIRQAFNKPGE 156
Cdd:PRK08780  52 MRYDLIDKNEKHVEAIAKAAKSADDLYLATDPDREGEAISWHLAEILKErgllKDKPMQRVVFTEITPRAIKEAMAKPRD 131
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  157 LNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSgEALAL 236
Cdd:PRK08780 132 IASDLVDAQQARRALDYLVGFNLSPLLWRKIQRGLSAGRVQSPALRMIVEREEEIEAFIAREYWSIEADCAHPS-QPFNA 210
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  237 QVTH---QNDKPFRPVNKEQTQAAVSLLEKA---RYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQR 310
Cdd:PRK08780 211 KLIKldgQKFEQFTITDGDTAEAARLRIQQAaqgTLHVTDVESKERKRNPAPPFTTSTLQQEASRKLGFTTRRTMQVAQK 290
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  311 LYEA---------GYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASK-ENSQEAHEAIRPSDVNVMAESL 380
Cdd:PRK08780 291 LYEGvdlgdegsvGLITYMRTDSVNLSQDALAEIRDVIARDYGTASLPDQPNTYKTKsKNAQEAHEAVRPTSALRTPAQV 370
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  381 KD-MEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGD---FRlkARGRILRFDGWTKVMPALR------KGDEDRIL 450
Cdd:PRK08780 371 ARfLSDDQRRLYELIWKRAVACQMIPATLNTVSVDLAAGSehvFR--ATGSTVVVPGFLAVYEEGKddksaeDEDEGRKL 448
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  451 PAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRL 530
Cdd:PRK08780 449 PPMKEGDNVPLERIRAEQHFTEPPPRYTEASLVKALEEYGIGRPSTYASIISTLQFRKYVEMEGRRFRPTDVGRAVNKFL 528
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  531 EENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEK--DPEEGGmrpnQMVLTSIDcPTCGRKMGI 608
Cdd:PRK08780 529 TGHFTRYVDYDFTARLEDDLDAVSRGEKEWIPLMEKFWGPFKELVEEKKDsvDRTEAG----QVRELGTD-PKSGKPVSV 603

                 ....*...
gi 16129235  609 RTASTGVF 616
Cdd:PRK08780 604 RIGRFGPM 611
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
159-575 1.86e-171

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: 500.98  E-value: 1.86e-171
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 159 IDRVNAQQARRFMDRVVGYMVSPLLWKKIAR--GLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTttpsgealal 236
Cdd:cd00186   1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRkgVLSAGRVQSPTLGLIVEREREIKAFVPEDYWEIKEAV---------- 70
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 237 qvthqndkpfrpvnkeqtqaavsllekarysVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGY 316
Cdd:cd00186  71 -------------------------------VVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGL 119
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 317 ITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQ----YASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQ 392
Cdd:cd00186 120 ITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLgrrnPKRGKKEQGAHEAIRPTKVAPTPELEANLSEDEFKLYE 199
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 393 LIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDrILPAVNKGDALTLVELTPAQHFTK 472
Cdd:cd00186 200 LIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEE-EPPPLKEGDELKLEEVELEEKETQ 278
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 473 PPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQ 552
Cdd:cd00186 279 PPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKEKKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEKLDE 358
                       410       420
                ....*....|....*....|...
gi 16129235 553 VANHEAEWKAVLDHFFSDFTQQL 575
Cdd:cd00186 359 IAEGKKDYQEVLEEFYEEFKKIV 381
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
156-564 1.23e-159

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: 334397 [Multi-domain]  Cd Length: 409  Bit Score: 471.71  E-value: 1.23e-159
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   156 ELNIDRVNAQQARRFMDRVVGYMVSPLLWKKI--ARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEA 233
Cdd:pfam01131   1 EIDDNLVDAQEARRELDWLIGINLSRALTLKKkgNKVLSAGRVQTPTLALIVEREREIENFVPEPYWTIEATLKDGGGPF 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   234 LalqvtHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYE 313
Cdd:pfam01131  81 V-----EAKKKRGRFFDKEEAEAILAKLKKGTAVVTSVEKKEKKEPPPLPFDTTTLQKEASRKLGFSAKKTMSIAQKLYE 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   314 -AGYITYMRTDSTNLSQDA-VNMVRGYISDNFGKKYLPESPNQYASK----ENSQ-EAHEAIRPSDVNVMAESLKDmeaD 386
Cdd:pfam01131 156 kHGLITYPRTDSTYLPEDAeLKAILEALAKNFGKEYLPFAEKLLKKTkgtvNNKKvTAHEAIRPTGNIPDLPELSD---D 232
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   387 AQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTP 466
Cdd:pfam01131 233 ERKLYELIVRRFLASQMPDAVYETTTVTLEVGGEEFKASGKRILEDGWKKVYPYGKKKDEEEILPELKEGEELDVKDVEL 312
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   467 AQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLeENFRELMNYDFTAQM 546
Cdd:pfam01131 313 EEKKTKPPKRYTEASLIKAMEKAGIGTPATRATIIETLVERGYVERKKKSLVPTELGKALVEAL-EKFPDLVSPELTAEL 391
                         410
                  ....*....|....*...
gi 16129235   547 ENSLDQVANHEAEWKAVL 564
Cdd:pfam01131 392 EEKLDEIAEGKLDWKDVL 409
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
272-526 7.15e-119

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: 360.79  E-value: 7.15e-119
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    272 EDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPE- 350
Cdd:smart00437   1 EEKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGKEYLDLa 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    351 ----SPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARG 426
Cdd:smart00437  81 vvllKPRKPRKGKKAQGAHEAIRPTKPIFTPELEKELSEDEFKLYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAKG 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    427 RILRFDGWTKVMPALRKgDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQD 506
Cdd:smart00437 161 KTLLFDGWLKVYPEEKK-EEEIELPTLKKGDELKVEEVEVEEKETKPPARYTEASLIKLMEKRGIGRPSTYASIIETLLD 239
                          250       260
                   ....*....|....*....|
gi 16129235    507 RGYVRVENRRFYAEKMGEIV 526
Cdd:smart00437 240 RGYVTKKKKKLIPTELGIAV 259
PRK07219 PRK07219
DNA topoisomerase I; Validated
87-793 3.29e-105

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 343.52  E-value: 3.29e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   87 PGKEKVVSELKQLAEKADHIYLATDLDREGEAI---AWHLREVIGGDDARysRVVFNEITKNAIRQAFNKPGELNIDRVN 163
Cdd:PRK07219  82 ITKQNYINALKKLAKDADEIIIATDYDREGELIgkeAYHILREVCQVPVK--RARFSSLTKKEIRKAFENPDEIDFNLAD 159
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  164 AQQARRFMDRVVGYMVSPLLW---KKIARG--LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDAS-TTTPSGEALALQ 237
Cdd:PRK07219 160 AGEARQIIDLYWGAALTRFLSlsvRQLGRWdfLSVGRVQTPTLAFIVDREREIRAFDPEDYWKIEALlDKEAQYFYRDLI 239
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  238 VTHQNDKPFrpvNKEQTQAAVSLLEKARYS-VLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGY 316
Cdd:PRK07219 240 GGHEAEKFW---DEEEAEEIYEKLKGAKEAtVSSVKKRERTISPPAPFNTTEFLREASKIFGISPKRAMEIAEKLYTAGY 316
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  317 ITYMRTDSTNLSQD-AVNMVRGYISDN--FGK--KYLPESPNQYAS--KENSQeAHEAIRPSDVnvmaESLKDMEADAQK 389
Cdd:PRK07219 317 ISYPRTDNTVYPDDlDPKELLKKLSKKkeYGPyaESILEQENIKPTegKKETT-DHPPIHPVDV----PKREELSDDEWK 391
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  390 LYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKgdEDRILPAVNKGDALTLVELTPAQH 469
Cdd:PRK07219 392 VYELIVRRFLATLADPAEWEYLKVELDVNGEIFKASGSRLVEEGWHEVYPYEKF--DEKELPDLEEGEKLKVNKIEIEAK 469
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  470 FTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVrVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENS 549
Cdd:PRK07219 470 ETQPPKRYTQSSLIKEMEKRGLGTKATRHDIIEKLYKRGYV-IEGDPPRPTDLGIAVIEALEKYAPEIVSEEMTAQLEAD 548
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  550 LDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEE------GGMRPNQMVLTSI-DCPTCGRKMGIRTASTGV-FLGCSG 621
Cdd:PRK07219 549 MQAIEDGKKKKEDVTEESREMLKEILSELKEKRKEigdhlaGSLKAENRSLKTIgKCPECGGDLIIIRTDKGSrFVGCSG 628
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  622 YalppkERCKTTINLvPENEVLNVLEgedaetnalrakRRCPKCGTAMDSYLIDPKRKLHVCgnnPTCDGYEIEEGEFRI 701
Cdd:PRK07219 629 Y-----PDCRNTFPL-PSTGRIKVLD------------EVCEKCGLPVIKILRGKQTFVVGC---PDCEAEKEEEDPDEV 687
                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  702 KGydgpivECEKCGSEMHLKMGRFGKYMACTN-EECKNTRKILRNGEVAPPKEDpvplpelpCEKSDAYFVLRDGAAGVF 780
Cdd:PRK07219 688 IG------PCPKCGGELAIKQLKYGSFLGCTNyPKCKYTLPLPRRGKITVTDEK--------CPECGLPLLRVKGGFGDE 753
                        730
                 ....*....|...
gi 16129235  781 LAANTFPKSRETR 793
Cdd:PRK07219 754 LGCCNNPKCNYTE 766
PRK09401 PRK09401
reverse gyrase; Reviewed
4-570 7.33e-94

reverse gyrase; Reviewed


Pssm-ID: 236498 [Multi-domain]  Cd Length: 1176  Bit Score: 319.95  E-value: 7.33e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235     4 ALVIVESPAKAKTINKYLG-----------------SDYV--VKSSVGHIRDLPTsgsaakksadststktakkpKKDER 64
Cdd:PRK09401  603 TLLIVESPTKARTIANFFGrpsrrrigglvvyetvtGDRIltITASKGHVYDLTT--------------------EIGYY 662
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    65 GALVNRMGVDPWHN-----WEAHYEV--------------LPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLRE 125
Cdd:PRK09401  663 GVLVKDGGFVPVYDtikrcRDCGYQFtdesdkcprcgstnIEDKEEIIEALRELALEVDEVLIATDPDTEGEKIAWDLYL 742
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   126 VIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIA-RGLSAGRVQSVAVRLV 204
Cdd:PRK09401  743 LLSPYNSNIKRIEFHEVTRKAILEALRNPRDVNENLVKAQIVRRIEDRWIGFELSQKLQKKFGkRNLSAGRVQTPVLGWI 822
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   205 VEREREIKAFVPEEFWevdasTTTPSGEALALQVTHQNdkpfrpvnKEQTQAAVSLLEKARYSVLEREDKPttskPGAPF 284
Cdd:PRK09401  823 VERYKEYKKSKGYVLV-----IKLENGGGLELEGEFSE--------KEEAEKFYNNLIEVEKVEEKEEELN----PLPPY 885
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   285 ITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLpeSPNQYaSKENsqeA 364
Cdd:PRK09401  886 TTDTLLSDASRKLRLSAQETMRIAQDLFELGLITYHRTDSTRVSDVGISVAKEYLEKRGGEEYF--VPRSW-GEGG---A 959
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   365 HEAIRPsdVNVM-AESLKDMEADAQ------------KLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILR- 430
Cdd:PRK09401  960 HEAIRP--TRPLdAEELRQMIEEGIlklsegltknhlRLYDLIFRRFMASQMKPAKVRYQKVLIKADGKELELELVVEIl 1037
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   431 FDGWTKVMPAlrkgdedRILPAVNKGDALTLVELtpaqhFTKPPAR-FSEASLVKELEKRGIGRPSTYASIISTIQDRGY 509
Cdd:PRK09401 1038 EDGFNKVLPL-------KLYPLLEGKVKVKEKKT-----YKKSKVPlYTQGDLISEMKERGIGRPSTYAKIVETLLRRGY 1105
                         570       580       590       600       610       620
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 16129235   510 VrVENRRF---YAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSD 570
Cdd:PRK09401 1106 V-IESKGKkrlIPTKLGIKVYEYLSEKYKDLVSEERTRKLEEKMDKVEEGKEDYQEVLKELYEE 1168
rgy TIGR01054
reverse gyrase; This model describes reverse gyrase, found in both archaeal and bacterial ...
4-568 1.06e-84

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: 294.05  E-value: 1.06e-84
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235      4 ALVIVESPAKAKTINKYLG-----------------SDYV--VKSSVGHIRDLPTSG----------------SAAKKSA 48
Cdd:TIGR01054  603 ALLVVESPNKARTIARFFGkpsvrkiggsvvyevpvGDLIlmITASGGHVFDLVTDKgfhgvlvengryvpvyTSIKRCR 682
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235     49 DSTSTKTAKKPKKDERGAlvnrmgvdpwhnweahyEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIG 128
Cdd:TIGR01054  683 DCGYQFTEDRESCPKCGS-----------------ENIEDSKSIIEILRELAHEVDEVFIGTDPDTEGEKIGWDLALLLS 745
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    129 GDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIA-RGLSAGRVQSVAVRLVVER 207
Cdd:TIGR01054  746 PYNPNVKRAEFHEVTRRAILEALESPRSVDENLVKAQVVRRIEDRWIGFTLSQKLWEAFNkRWLSAGRVQTPVLGWIIDR 825
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    208 EREIKAFVPEEFwevdaSTTTPSGEALALQvtHQNDKPFRPVNKEQTQAAVSLLEkarysvlEREDKPTtskPGAPFITS 287
Cdd:TIGR01054  826 YRESREKRGYLL-----IFALESDFRLGLE--HDNRLEAKEFEKDLTWLDVEDIA-------EREEERN---PLPPYTTD 888
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    288 TLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYlpespnQYASKENSQEAHEA 367
Cdd:TIGR01054  889 TMLEDANRKLGLSVKETMQIAQELFENGLITYHRTDSTRVSDVGMRVAKEYLASRLGGEY------FYPREWGEGGAHEC 962
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    368 IRPS------DVNVMAES----LKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILR-FDGWTK 436
Cdd:TIGR01054  963 IRPTrpldvdDLQRLILEgvieLEGLTREHLRLYDLIFRRFMASQMRPAKVDTKEITLKADGKEAEEEGIVEIvERGFEL 1042
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    437 VMPALRKGDEDRILPAVNKGDALTLVELTPAqhftkpparFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRR 516
Cdd:TIGR01054 1043 VYPLWRKNELEKGSTFIVKDKELRSVPKVYP---------YTQGEIVQEMKERGIGRPSTYATIVEKLLRRGYVVESKGF 1113
                          570       580       590       600       610
                   ....*....|....*....|....*....|....*....|....*....|..
gi 16129235    517 FYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFF 568
Cdd:TIGR01054 1114 LIPTKLGIEVYNYLTNRYPKLVSEDRTRELEEAMDKIERGELDYLEVLESVY 1165
TopG2 COG1110
Reverse gyrase [Replication, recombination and repair];
4-571 2.03e-83

Reverse gyrase [Replication, recombination and repair];


Pssm-ID: 224035 [Multi-domain]  Cd Length: 1187  Bit Score: 290.83  E-value: 2.03e-83
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    4 ALVIVESPAKAKTINKYLG-----------------SDYV--VKSSVGHIRDLPTsgsaakksadststktakkpKKDER 64
Cdd:COG1110  619 ALMIVESPNKARTIASFFGrpsvrrlgggvvyevaiGDLVltITASGGHVFDLVT--------------------EPGVH 678
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   65 GALVNRMGVDPWHN-----WEAHYEV--------------LPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLRE 125
Cdd:COG1110  679 GVLVKDGKYVPVYDtikrcRDCGEQFvdsedkcprcgsrnVEDKTETVEALRELALEVDEILIGTDPDTEGEKIAWDVFN 758
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  126 VIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIA-RGLSAGRVQSVAVRLV 204
Cdd:COG1110  759 YLRPYNPNVKRIEFHEVTRRAILEALKNPRDVDENLVKAQIVRRIEDRWIGFELSQKLWDVFNnKNLSAGRVQTPVLGWI 838
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  205 VEREREIKAFVPEEFWEVDasTTTPSgealalqvthQNDKPFRPVNKEQTQAAVSLLEKarysVLEREDKPttskPGAPF 284
Cdd:COG1110  839 VNRYEEYKEKRGYLVIQLD--LDLPS----------GNREEVENVKRKLKLIVVEVVDV----VEREEEKN----PLPPY 898
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  285 ITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLpespnqYASKENSQEA 364
Cdd:COG1110  899 TTDTMLRDASRRLRLSADETMQIAQDLFEGGLITYHRTDSTRVSDVGIRVAREYLRKEFGEEYF------RPRSWGEEGA 972
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  365 HEAIRPSDVNVmAESLKDM--EADAQ----------KLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARG--RILR 430
Cdd:COG1110  973 HEAIRPTRPID-VEELITLieEGVIQlpirltknhlRVYDLIFRRFMASQMRPAKVLKEKAEVKADGKDVELEAlvEILE 1051
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  431 fDGWTKVMPaLRKgdEDRILPAVNKGDALTLVELTPAQHFTkpparfsEASLVKELEKRGIGRPSTYASIISTIQDRGYV 510
Cdd:COG1110 1052 -DGFALVYP-TRV--LPELEKGTLKVTEVEIRKVSKVYLYT-------QGEVVEEMKERGIGRPSTYAKIVETLLRRGYV 1120
                        570       580       590       600       610       620
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16129235  511 -RVENRRFYAE-KMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDF 571
Cdd:COG1110 1121 iESKGRKKLIPtKLGIEVYEYLSEKYKKLVSEERTRRLEEIMDKVEEGKADYQEVLKELYEEI 1183
PRK07726 PRK07726
DNA topoisomerase III; Provisional
83-622 7.26e-82

DNA topoisomerase III; Provisional


Pssm-ID: 236078 [Multi-domain]  Cd Length: 658  Bit Score: 276.66  E-value: 7.26e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   83 YEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAwhlREVIggDDARY----SRVVFNEITKNAIRQAFN--KPGE 156
Cdd:PRK07726  73 LVVKKKTAKQFNVVKKLLKQATEIVIATDADREGELIA---REIL--DYCGVrkpiKRLWISSLTDKAIKRAFAnlKPGK 147
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  157 LNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARG-----LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSG 231
Cdd:PRK07726 148 ETIPLYYSALARSRADWLVGINMTRAYTLLGRKAgyngvLSVGRVQTPTLALVVRRDEEIENFVPKPYWEVEAHLTPGER 227
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  232 EALALQVTHQ-NDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQR 310
Cdd:PRK07726 228 FTAKWQPSEPyQDEEGRLLDRPLAEQVVARIQGQPAKVTEVETKRKKEYAPLLYDLSELQIDANKRFGLSAKETLDIAQS 307
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  311 LYE-AGYITYMRTDSTNLSQDAVNMVRGYISD-NFGKKYLPESPNQYASKENSQ-------EAHEAIRPSDVNVMAESLK 381
Cdd:PRK07726 308 LYEtHKLITYPRTDSRYLPEDMVATLPEVLNAiSKVDPYLLLAPPVLDPSIRSRawndkkvTAHHAIIPTEQPPNLSKLS 387
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  382 DMEadaQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDE-DRILPAVNKGDALT 460
Cdd:PRK07726 388 EDE---RKVYDLIARRYLAQFLPPAEYDKTTIELEIAGGTFIAKGKQVVEAGWKALLGKKEEDEEkEQPLPVLAKGDELK 464
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  461 LVELTPAQHFTKPPARFSEASLV------------KELEKR-----GIGRPSTYASIISTIQDRGYVRVENRRFYAEKMG 523
Cdd:PRK07726 465 VEKGEVKEGQTQPPKRFTEGTLLsameniarfvqdKELKKTlketdGLGTEATRAGIIEKLFKRGYLEKKGKYIHATDKG 544
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  524 EIVTDRLEEnfrELMNYDFTAQMENSLDQVanheAEWKAVLDHFFSDFTQQLDKAekdPEEGGMRPNQMVLTSID---CP 600
Cdd:PRK07726 545 KQLIDALPE---ELTSPDMTAKWEQALDQI----SEGQLSYQDFMQPLKQWLKQL---VEQAKQSSEKYKFDNLTgpkCP 614
                        570       580
                 ....*....|....*....|..
gi 16129235  601 TCGRKMGIRTASTGVFLGCSGY 622
Cdd:PRK07726 615 DCGKPMLKVKGKNGKMLVCQDR 636
PRK07220 PRK07220
DNA topoisomerase I; Validated
43-665 1.17e-73

DNA topoisomerase I; Validated


Pssm-ID: 180892 [Multi-domain]  Cd Length: 740  Bit Score: 256.22  E-value: 1.17e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   43 AAKKSADSTSTKTAKKPK------------KDER------GALVNRMGVDPWHNWE---------AHYEVLPGKEKVVSE 95
Cdd:PRK07220  11 AARRIAQILAPKKPKKTRvsgvdvyryednGDDTvvvglsGHIVNIDFPKEYNNWQkvdardlidAEIITTPTQKKIVTA 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   96 LKQLAEKADHIYLATDLDREGEAIAWHLREVIGG--DDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDR 173
Cdd:PRK07220  91 LKKLGKEADRVTIATDYDREGELIGVEALNIIKKvnPDIKFDRVRYSAITKKEIERAFSNPVEVDFNLADAGHSRQVIDL 170
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  174 VVGYMVSPllWKKIARG------LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDAsTTTPSGEALALQvtHQNDkpfR 247
Cdd:PRK07220 171 VWGAALTR--YISLAAGrlgkmfLSVGRVQSPTLALIVDREKEREAFVPTPYWEIYA-TLENNGETFVAQ--HSTR---R 242
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  248 PVNKEQTQAAVSLL-EKARYSVLEREDKptTSKPGAPFITSTLQQAASTrLGFGVKKTMMMAQRLYEAGYITYMRTDSTN 326
Cdd:PRK07220 243 FWEKEEADRVFEKLgKTAEVTEVEKGTK--TDKPPTPFNTTEFISAANS-IGFSAANAMRIAESLYTNGYISYPRTDNTV 319
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  327 L--SQDAVNMVRGYISDNFGK--KYLPESPNQYASKENSQEA-HEAIRPsdVNVMAESlkDMEADAQKLYQLIWRQFVAC 401
Cdd:PRK07220 320 YpeSLDLREQIEIFAEGPFGEyaQKLLEKGELVPTRGKKETTdHPPIYP--ASLAKKS--ELKEDEWKVYELVVRRFFAT 395
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  402 QMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKgdEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEAS 481
Cdd:PRK07220 396 FAGPAEWETMKLRFDIGGEEFRANGSRLTEPGWRWYYPYNAP--EDRLLPELSEGEELKVKKKEMLDKETQPPGRYGQGR 473
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  482 LVKELEKRGIGRPSTYASIISTIQDRGYVR----VENRRFYAekmgeiVTDRLEENFRELMNYDFTAQMENSLDQVANHE 557
Cdd:PRK07220 474 LIKLMEDLGLGTKATRHEIISKLYSRAYIHgnpiQPTNTAFA------VVDALEKYAPTITKPDMTSRLEEDMDKIAEGK 547
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  558 AEWKAVLDH---FFSDFTQQLDKAEKDPEE---GGMRPNQMVLTsidCPTCGRKMGIRTASTGV-FLGCSGYAlppkeRC 630
Cdd:PRK07220 548 IKEDAVLEEsreMLEQVFDELDKNREKIREslrEGLREDKIIGK---CPLCGSDLMVRRSKRGSrFIGCEGYP-----EC 619
                        650       660       670       680
                 ....*....|....*....|....*....|....*....|....*.
gi 16129235  631 KTTINLVPENEVlnVLEGEDAETNAL-------RAKRR----CPKC 665
Cdd:PRK07220 620 TFSLPLPKSGQI--IVTDKVCEAHGLnhiriinGGKRPwdlgCPQC 663
topA_arch TIGR01057
DNA topoisomerase I, archaeal; This model describes topoisomerase I from archaea. These ...
79-622 2.29e-73

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: 252.44  E-value: 2.29e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    79 WEAHYEVLPGKE---KVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDaRYSRVVFNEITKNAIRQAFNKPG 155
Cdd:TIGR01057  67 WVPIFEFDKGKGyvsKYIKALSKLAKGADEYINACDYDIEGEVIGFKALKYFCGVE-RAKRMKFSTLTKQDIRRAYANPE 145
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   156 ELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARG------LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTP 229
Cdd:TIGR01057 146 EIDYGMVDAGMARHILDWYWGINLSRALMEAIRAAagrwviLSAGRVQGPTLAFLVEREREINLFVPKPYWVIKATLEKG 225
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   230 SGEALAlqvTHQNDKPFrpvNKEQTQAAVSLLEKARY-SVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMA 308
Cdd:TIGR01057 226 GGVFDA---RPEKWKIW---SEEEAKSIKEELKKSPWaAVEEVRSERSILKPPPPFDLGTLQREAYRIFGFSPKKTQSIA 299
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   309 QRLYEAGYITYMRTDSTNLSQDavnmvRGY--ISDNFGK-----------KYLPESPNQYASKENsqEAHEAIRPsdvnV 375
Cdd:TIGR01057 300 QELYEEALISYPRTSSQKLPPS-----INYraILDNLAKgplyreaaerlLETGVLKPVEGKKED--PAHPAIHP----T 368
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   376 MAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDriLPAVNK 455
Cdd:TIGR01057 369 GEIPSQELSKDEKKVYDLIVRRFLAAFSEEAIREKSKVLLRIGQEKFRLSGLRVVKLGWLEYYHYSKFEEKE--LPPLDR 446
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   456 GDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVrVENRRFYAEKMGEIVTDRLEENFR 535
Cdd:TIGR01057 447 GDKIKVVRVDVRVKETQPPARYDKASLIREMESRGLGTKATRARIIETLYKRGYI-EGKKSIKVTPLGEAVIETLQRYCP 525
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   536 ELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGM---RPNQMVLTSIDCPTCGRKMGIRTAS 612
Cdd:TIGR01057 526 EIISEELTRRFESKLEDIMSGRITKDEVIDEAKKRLRKILEEFKKRLDDIGIelgKSLGSVEVVGKCPKCGGKLVSKYAK 605
                         570
                  ....*....|
gi 16129235   613 TGVFLGCSGY 622
Cdd:TIGR01057 606 KGRFVGCSNY 615
PRK05776 PRK05776
DNA topoisomerase I; Provisional
2-605 1.01e-68

DNA topoisomerase I; Provisional


Pssm-ID: 235602 [Multi-domain]  Cd Length: 670  Bit Score: 240.66  E-value: 1.01e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    2 GKALVIVESPAKAKTIN--------------------KYLGSDYVVKSSVGHIRDLPTsgsaakksadststktakkpkk 61
Cdd:PRK05776   1 GYILVIAEKPKAARKIAealsekpircriygvpywivKRDGKKIVVAPAAGHLFGLHT---------------------- 58
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   62 DERGALVNRMgvdpwhNWEAHYEVLPGK---EKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGgDDARYSRVV 138
Cdd:PRK05776  59 KSKGFPVFDY------EWKPLYEIDKGSkytKKYYELLSSLSKYADEFINACDYDIEGSVIGYLIIKYLG-DPKKAKRMK 131
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  139 FNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWK--KIARG----LSAGRVQSVAVRLVVEREREIK 212
Cdd:PRK05776 132 FSALTKSDIRRAFRNLETLDYEMINAGIARHELDWLWGINVSRALMSsvRDASGkrviLSAGRVQSPTLKYVVEREIERN 211
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  213 AFVPEEFWEVDAsTTTPSGEALALQVThqnDKPFRpvNKEQTQAAVSLLEKARY-SVLEREDKPTTSKPGAPFITSTLQQ 291
Cdd:PRK05776 212 LFVPLPYFSVSI-IIEKNGYEFTLKYE---NKKFE--TKEEAKEILEEIKKTGYlKVTKVEVKIEILEPPPPFNLGDLQV 285
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  292 AASTRLGFGVKKTMMMAQRLYEAGYITYMRTDS-------------TNLSQdaVNMVRGYISD--NFGKKYLpeSPNQyA 356
Cdd:PRK05776 286 EAARIYGFSPYKTQSIAEDLYLDGLISYPRTNSqklpptlnirnilKGLSR--SPQYRPLVNLllKETKGVL--KPVQ-G 360
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  357 SKENSqeAHEAIRPSdvnvmAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDF--RLKARGRILRFDGW 434
Cdd:PRK05776 361 PKDDP--AHPAIYPT-----GEPPKNLSKDEFKLYDLIVRRFLASFAAPAVLSNTIVTLRVPGFplVFSASGQRIEERGW 433
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  435 TKVMPaLRKGDEDrILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVEN 514
Cdd:PRK05776 434 LKYYP-FHKFDEE-ELPLLKKGERVKIVDVKVRKSYTKPPSRYSKASLLKWMESVGIGTEATRARIIETLFKRGYLTSNG 511
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  515 RRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEA-------EWKAVLDHFFSDFTQQLDKAEKDPEE--G 585
Cdd:PRK05776 512 KYIEVTPLGFGVAEVLEKYFPDIVSVELTRDFEEKLEMIRTGKAtreevieEAKETLNKLLEEFKKNKDEIGEELAKalG 591
                        650       660
                 ....*....|....*....|
gi 16129235  586 GMRPNQmvltsiDCPTCGRK 605
Cdd:PRK05776 592 LIKPVG------KCKICGRE 605
topB TIGR01056
DNA topoisomerase III, bacteria and conjugative plasmid; This model describes topoisomerase ...
97-622 1.84e-63

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: 225.88  E-value: 1.84e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    97 KQLAE-KADHIYLATDLDREGEAIA-WHLREVIGGDDARYSRVVFNEITKNAIRQAFNK--PGELNIDRVNAQQARRFMD 172
Cdd:TIGR01056  89 RILKEnKVDEVVIATDPDREGELIArEILDYLKVTDKVTIKRLWISSLVDSSIRKAFKNlrPKSETEGLYKSGVARARAD 168
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   173 RVVGYMVSPLLWKK-----IARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPsGEALALQVTHQNDKPFR 247
Cdd:TIGR01056 169 WLVGINLTRAFTKLgreagNDGVLSVGRVQTPTLAMVVKRENEIKNFVGKPFYEVSATINKD-EQEFTTEWQPYKDEEER 247
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   248 PVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAG-YITYMRTDSTN 326
Cdd:TIGR01056 248 ELHEFLAENVVTDLTQKPALVTDIEKERKKTSAPLFYDLSALQEDANKRFGISAKRTLDIAQKLYETHkLITYPRTDSRY 327
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   327 LSQDAVNMVRGYIS-------DNFGKKYLPESPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEAdaqKLYQLIWRQFV 399
Cdd:TIGR01056 328 LPEDEKEMLLEVLDalkvitpALLPIKKRDELTNNRLWNDKKIEDHHAIIPTGNDFNLSDLSEEER---NVYKLIAQNYL 404
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   400 ACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDED--RILPAVNKGDALTLVELTPAQHFTKPPARF 477
Cdd:TIGR01056 405 MQFMPKEEYETTTIEIAIGKLMFEAKGKILQDNGWKALLGKQEEDEETedTTLPAFQKGDELDVETLELLEKQTKPPARY 484
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   478 SEASLVKEL-----------------EKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEEnfrELMNY 540
Cdd:TIGR01056 485 TEGTLLSAMtnpaafvqdkglkktlkETKGLGTEATRADIIENLFKRGFIQKKKNKIYITKNGKLLCLLLPE---LLTKP 561
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   541 DFTAQMENSLDQVanheAEWKAVLDHFFSDFTQ---QLDKAEKDPEEGGMRPNqmvltSIDCPTCGRKMgIRTASTGVFL 617
Cdd:TIGR01056 562 DLTAQWEQYLNGI----SAGEKDDDDFINTINEmikQTINEEKKNPETIQKVA-----KEPVSCGGIAK-CPAKDNGRLI 631

                  ....*
gi 16129235   618 GCSGY 622
Cdd:TIGR01056 632 DCKKF 636
PRK14973 PRK14973
DNA topoisomerase I; Provisional
87-634 4.45e-63

DNA topoisomerase I; Provisional


Pssm-ID: 184936 [Multi-domain]  Cd Length: 936  Bit Score: 229.35  E-value: 4.45e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   87 PGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGG--DDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNA 164
Cdd:PRK14973  81 PTEKKIVGLIQKLAKKADRVTIATDFDTEGELIGKEAYELVRAvnPKVPIDRARFSAITKEEIVTAFAEPTDLDFALAAA 160
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  165 QQARRFMDRVVGYMVSPLLWKKIARG----LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVdASTTTPSGEALALQVTH 240
Cdd:PRK14973 161 GEARQIIDLIWGASLTRFISLAAHRGgdniLSVGRVQSPTLAMIVDREKEIEAFVPEKYWML-SLATEKDGEGIEARHTH 239
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  241 Q--NDKPFRPVNKEQTQAAVSLLEKARYSVLERedKPTtskpgaPFITSTLQQAAStRLGFGVKKTMMMAQRLYEAGYIT 318
Cdd:PRK14973 240 GrfTDSAAAEAAYDATKEPLVVTEVKEGHKVDR--APT------PFDTTTFIVAAS-RLGFSAANAMRIAEDLYMNGYIS 310
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  319 YMRTDST------NLSQDAVNMVRGYISDNFG--KKYLPESPNQyaSKENSQEaHEAIRPSDVnVMAESLKDmeaDAQKL 390
Cdd:PRK14973 311 YPRTDNTiypkslDLNGVLATLAKGAFSKDVAwvKDNRRPVPTR--GKKSSTD-HPPIHPTGV-ATREELGD---DRWKL 383
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  391 YQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKgdEDRILPAVNKGDALTLVELTPAQHF 470
Cdd:PRK14973 384 YELVVRRFLATLSPDAEWATMKVNFDAGGEPYTATGGRLLEAGWRTVYPYSEA--KENILPAFALGEKLPILAVNLEEKE 461
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  471 TKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYvrVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSL 550
Cdd:PRK14973 462 TQPPARYSQSRLIQRMEELGLGTKSTRHEVIGKLVSRKY--IEGNPLRPTLVGRAVTESLEEHAGTITEPDMTQTLEEHM 539
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  551 DQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGG---MRPNQMVLTSIDCPTCGRKMGIRTASTGVFLGCSGYalpPK 627
Cdd:PRK14973 540 QQIKERKRTRDDVVTESRKMLHRAFDELEANEAVIGrdiMERTAEELTIGPCPVCGKDLRIKHIGSSQFIGCSGY---PD 616

                 ....*..
gi 16129235  628 ERCKTTI 634
Cdd:PRK14973 617 CTFNIGL 623
TOPRIM_TopoIA_TopoI cd03363
TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA ...
3-154 6.43e-60

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: 198.94  E-value: 6.43e-60
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   3 KALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGsaakksadststktakkpkkdergalvnrMGVDPWHN-WEA 81
Cdd:cd03363   1 KKLVIVESPAKAKTIKKYLGKEYEVLASVGHIRDLPKKG-----------------------------LGVDGEDDgFEP 51
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16129235  82 HYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIgGDDARYSRVVFNEITKNAIRQAFNKP 154
Cdd:cd03363  52 KYVVIPGKKKVVKELKKLAKKADEIYLATDPDREGEAIAWHLAEVL-KLKKNVKRVVFNEITKEAIKEALKNP 123
PTZ00407 PTZ00407
DNA topoisomerase IA; Provisional
5-554 3.16e-49

DNA topoisomerase IA; Provisional


Pssm-ID: 173597 [Multi-domain]  Cd Length: 805  Bit Score: 187.07  E-value: 3.16e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    5 LVIVESPAKAKTINKYLGSDYVVKS---SVGHIRDLPTSGSAAKKSADS------------------TSTKTAKKPKKDE 63
Cdd:PTZ00407  12 LVIVESPNKVIKVEGLLSDPKVIPDwsfKQSHLRRIGTGAEKAVAMATTghfmalkeitwspqasspASVVGAGDEPFPS 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   64 RGALVNrmgvdpwhnWEAHYEVLPGK---EKVVSELKQLAEKADHIYLATDLDREGEAIAWH----LREVIGGDDARYSR 136
Cdd:PTZ00407  92 NGTLAE---------YTLEWELLPGRriqETLERYIEEKADNVTEIILATDPDREGELIAVHalqtIKRLYPKLKVPFSR 162
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  137 VVFNEITKNAIRQAFNK--PGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAF 214
Cdd:PTZ00407 163 AYMHSITEDGIRKAMRErhVEACDYDLANAAETRHAMDRIFGFLGSSVVRAANSQMRSIGRVQTPALILINEREDKIKAF 242
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  215 VPEE--FWEVDAST--TTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYS-----VLEREDKPTTSK--PGAP 283
Cdd:PTZ00407 243 LESNksTFEVQAMCqfPSPHGTTFSQVVTITPDRKGGASHWATEAEARRCLEQWKLNnctgfSVPLEPKPQPSVvpPPQP 322
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  284 FITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYL--------------- 348
Cdd:PTZ00407 323 FTMATAIAKANRQLKYSSEMVSGCLQDLFQLGHITYPRTDSTRIDESALPDIYAAVKKEFGKEFLyrledrtvsaqegkg 402
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  349 ---PESPNQYASKENS-------QEAHEAIRPSDVNVMAESLKdMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTV--- 415
Cdd:PTZ00407 403 skkTGKKRSTKQKKGAdtpvgnvEDAHEAIRPTNIDTTGESLS-LSPPTRAVYDLVRRNTLAVFMIPMKTEKIVATVkft 481
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  416 -GAGD-FRLKARGRILRFDGWTKvmpALRKGDEDRILPAV----------------------------------NKGDAL 459
Cdd:PTZ00407 482 sGSGEkLEFELQGKRVVEPGWTR---AFHKGDKGTTGPAEetdeditaveegapvvpslsqeefkaimnlrsqlGSGVQK 558
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  460 TLVELTPAQ---HFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENR-RFYAEKMGEIVTDRLEENFR 535
Cdd:PTZ00407 559 GFFELRSPQvreNRPVPPLPHSEGTLIEELKNNGVGRPSTYPMIVKTLLARGYIAVNPKgRCETTPVGRMLVETAKSTFP 638
                        650
                 ....*....|....*....
gi 16129235  536 ELMNYDFTAQMENSLDQVA 554
Cdd:PTZ00407 639 SIVDIGFTAAFEKKLDRIA 657
PRK08173 PRK08173
DNA topoisomerase III; Validated
1-515 5.97e-46

DNA topoisomerase III; Validated


Pssm-ID: 236172 [Multi-domain]  Cd Length: 862  Bit Score: 177.55  E-value: 5.97e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    1 MGKALVIVESPAKAKTINKYLG----------SD-YVVKSSVGHIRDLptsgsAAKKSADststktakkPKkdeRGAlvn 69
Cdd:PRK08173   1 MSKALIIAEKPSVANDIARALGgftkhdeyfeSDeYVLSSAVGHLLEI-----AAPEEYE---------VK---RGK--- 60
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   70 rmgvdpwhnWE-AHYEVLPGK------EKVVSELKQLAEKA-----DHIYLATDLDREGEAIAWHLREVIGGDDArYSRV 137
Cdd:PRK08173  61 ---------WSfAHLPVIPPHfdlnpiAKTESRLKVLTKLIkrkdvTRLINACDAGREGELIFRLIAQHAKAKKP-VKRL 130
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  138 VFNEITKNAIRQAFNK--PGELNIDRVNAQQARRFMDRVVGYMVSpllwkkiaRGLSA-------------GRVQSVAVR 202
Cdd:PRK08173 131 WLQSMTPQAIRDGFANlrSDEDMQPLADAARCRSEADWLVGINGT--------RAMTAfnskgggfflttvGRVQTPTLS 202
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  203 LVVEREREIKAFVPEEFWEVDASTTTPSG--------EALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLErEDK 274
Cdd:PRK08173 203 IVVEREEKIRRFVPRDYWEVRAEFVAAAGfyegrwfdPKFKKDEFDPEKRASRLWSEAAAEAIVAACRGKPGTVTE-ESK 281
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  275 PTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEA-GYITYMRTDSTNLSQDAVNMVRgyisDNFGKkyLPESPN 353
Cdd:PRK08173 282 PSTQLSPLLFDLTSLQREANGRFGFSAKNTLGLAQALYEKhKVLTYPRTDSRALPEDYLGTVK----QTLEM--LKESNN 355
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  354 --QYASK--------------ENSQEA-HEAIRPSdvNVMAESLKDMEadaQKLYQLIWRQFVACQMTPAKYDSTTLTVG 416
Cdd:PRK08173 356 ylPHAKQildkgwvkpnkrifDNSKISdHFAIIPT--LQAPKSLSEPE---QKLYDLVVKRFLAVFFPAAEFLVTTRITE 430
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  417 AGDFRLKARGRILRFDGWtKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELE--------- 487
Cdd:PRK08173 431 VAGHHFKTEGKVLVNPGW-LAVYGKEAQGADANLVPVQKGEKVKTDKIEAVALTTKPPARYNEATLLSAMEgagklvedd 509
                        570       580       590
                 ....*....|....*....|....*....|....*
gi 16129235  488 -------KRGIGRPSTYASIISTIQDRGYVRVENR 515
Cdd:PRK08173 510 elreamaEKGLGTPATRAAIIEGLLGEKYLVREGR 544
TOP1Bc smart00436
Bacterial DNA topoisomeraes I ATP-binding domain; Extension of TOPRIM in Bacterial DNA ...
134-221 7.05e-43

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: 150.04  E-value: 7.05e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    134 YSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIAR-GLSAGRVQSVAVRLVVEREREIK 212
Cdd:smart00436   1 IKRIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRNgVLSAGRVQTPTLGLIVEREREIK 80

                   ....*....
gi 16129235    213 AFVPEEFWE 221
Cdd:smart00436  81 NFVPKPYWE 89
TOPRIM_TopoIA cd01028
TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
3-154 2.45e-42

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: 150.84  E-value: 2.45e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   3 KALVIVESPAKAKTINKYLGS------------DYVVKSSVGHIRDLPTsgsaakksadststktakkpkkDERGALVNR 70
Cdd:cd01028   1 KVLIIAEKPSKAKTIAKILGKgskkkgfygeggGYVVTASVGHLLELPF----------------------PEEYVDWDK 58
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  71 MGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQA 150
Cdd:cd01028  59 DWPLELFPFEPKYVVIPDKKKQLKALKKLAKKADEIVLATDPDREGELIAWEILEVLKCDNKPVKRAWFSEITPKAIREA 138

                ....
gi 16129235 151 FNKP 154
Cdd:cd01028 139 FKNL 142
PRK14724 PRK14724
DNA topoisomerase III; Provisional
3-603 2.49e-37

DNA topoisomerase III; Provisional


Pssm-ID: 237803 [Multi-domain]  Cd Length: 987  Bit Score: 151.26  E-value: 2.49e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    3 KALVIVESPAKAKTI--------------NKYLGSD-YVVKSSVGHIRDLptsgsaakKSADSTSTKTAKkpkkderGAL 67
Cdd:PRK14724   2 KTLVIAEKPSVAQDIvraltpvagkfekhDEHFESDsYVVTSAVGHLVEI--------QAPEEFDVKRGK-------WSF 66
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   68 VNRMGVDPwhnweaHYEVLPgKEKVVSELK---QLAEKADHIYL--ATDLDREGEAIAWHLREVIGGDDARYSRVV---- 138
Cdd:PRK14724  67 ANLPVIPP------YFDLKP-VDKTKTRLNavvKLAKRKDVTELvnACDAGREGELIFRLIEQYAGGAKGGLGKPVkrlw 139
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  139 FNEITKNAIRQAFN--KPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARG-----LSAGRVQSVAVRLVVEREREI 211
Cdd:PRK14724 140 LQSMTPQAIRDGFDnlRSDAQMQGLASAARSRSEADWLVGINGTRAMTAFNSRDggfflTTVGRVQTPTLSLVVEREEKI 219
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  212 KAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPF--------RPVNKEQTQAAVSLLEKARYSVLErEDKPTTSKPGAP 283
Cdd:PRK14724 220 RKFVSRDYWEIHAGFHAEAGEYLGKWFDPQWKKASddpearadRVWSEREARAIADAVRGKAATVTE-ESKPTTQASPLL 298
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  284 FITSTLQQAASTRLGFGVKKTMMMAQRLYEA-GYITYMRTDSTNLSQDAVNMVR---GYISDN-------FGKKYLPES- 351
Cdd:PRK14724 299 FDLTSLQREANGKFGFSAKTTLALAQSLYERhKALTYPRTDSRALPEDYLPVAKqtfEMLATSgmrhlapFAQQALDGNy 378
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  352 --PNQYASKENSQEAHEAIRPSdvnVMAES-LKDMEadaQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRI 428
Cdd:PRK14724 379 vrPSKRIFDNSKVSDHFAIIPT---TQAPSgLSEAE---QKLYDLVVRRFMAVFFPSAEYQVTTRISQVVGHSFKTEGKV 452
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  429 LRFDGWTKV--------MPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELE------------- 487
Cdd:PRK14724 453 LVKPGWLAIygkeaaneVEDAKDGDKGQPLVPVKPGEMVRTEFAEAKGLKTKPPARYSEATLLGAMEsagkqidddelre 532
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  488 ---KRGIGRPSTYASIISTIQDRGYVRVENRRFY-AEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAV 563
Cdd:PRK14724 533 amqEKGLGTPATRAAIIEGLLTEKYMLREGRELIpTAKAFQLMTLLRGLGVEELSRAELTGEWEYKLAQMEKGQLSREAF 612
                        650       660       670       680
                 ....*....|....*....|....*....|....*....|
gi 16129235  564 LDHfFSDFTQQLDKAEKDPEEGGMrPNQMVLTSIDCPTCG 603
Cdd:PRK14724 613 MQQ-IAAMTEKLVKKAKEYDRDTI-PGDYATLSTPCPNCG 650
PRK14701 PRK14701
reverse gyrase; Provisional
4-315 1.87e-31

reverse gyrase; Provisional


Pssm-ID: 237791 [Multi-domain]  Cd Length: 1638  Bit Score: 133.09  E-value: 1.87e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235     4 ALVIVESPAKAKTINKYLGSDYVVK-------------------SSVGHIRDLPTSG----------------SAAKKSA 48
Cdd:PRK14701  582 ALMIVESPNKARTIANFFGQPSVRKigdlvayevsigdhmliitASGGHVFDLVTNEgfhgvlinnnlfipiyDSIKRCR 661
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    49 DSTSTKTAKKPKKD-ERGALVNrmgvdpwhnweahyeVLPGKEKVVSeLKQLAEKADHIYLATDLDREGEAIAWHLREVI 127
Cdd:PRK14701  662 DCGHQFTDWEDKGVcPRCGSKN---------------VDDAKENIKA-MRELAHEVDEILIGTDPDTEGEKIAWDIRNVL 725
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   128 GGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKI-ARGLSAGRVQSVAVRLVVE 206
Cdd:PRK14701  726 APYGPNIKRIEFHEVTRRAILKAIKEARDIDENRVKAQIVRRIEDRWIGFELSQKLWEVFeDRNLSAGRVQTPVLGWIIQ 805
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   207 REREIKAFvpeefwEVDASTTTPSGEalaLQVTHQNDkpfrpvnKEQTQAAVSLLEkarysvLEREDKPttskPGAPFIT 286
Cdd:PRK14701  806 RYKEFTES------KVPFLGIILEND---LTVTIEDS-------KDEVEVEVELVE------EEEKERN----PLPPYTT 859
                         330       340
                  ....*....|....*....|....*....
gi 16129235   287 STLQQAASTRLGFGVKKTMMMAQRLYEAG 315
Cdd:PRK14701  860 DTMLRDASAFLKLSAKETMKLAQDLFEAG 888
PRK14701 PRK14701
reverse gyrase; Provisional
318-570 4.88e-29

reverse gyrase; Provisional


Pssm-ID: 237791 [Multi-domain]  Cd Length: 1638  Bit Score: 125.39  E-value: 4.88e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   318 TYMRTDSTNLSQDAVNMVRGYISDNFGKKYLpeSPNQYASkensQEAHEAIRPS---DVNVMAESLKD-------MEADA 387
Cdd:PRK14701 1382 TYHRTDSTRVSNTGIRVAREYLTQENGEDYF--KPRDWFM----EGAHECIRPTrpiDTDRLIQLIREgiiqvpgLTRNH 1455
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   388 QKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRI-LRFDGWTKVM-PALRKgdedriLPAVNKGDaltlVELT 465
Cdd:PRK14701 1456 LRLYDLIFRRFMASQMKPAKVLYEKALIRYDGKDVEVEGYVeIEGDGWSRLYsLPLRV------LPKLEKGK----LKVL 1525
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   466 PAQHFTKPPAR-FSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRR--FYAEKMGEIVTDRLEENFRELMNYDF 542
Cdd:PRK14701 1526 EAKIRKAPKVPlYTQGDIVALMKERGIGRPSTYAKIVDTLLMRGYVIETKGRkkLIPTKKGIKVYNYLISNYGDLVSEER 1605
                         250       260
                  ....*....|....*....|....*...
gi 16129235   543 TAQMENSLDQVANHEAEWKAVLDHFFSD 570
Cdd:PRK14701 1606 TRELEEIMDAVEEGELDYIKVLQELYEE 1633
YrdD COG0551
ssDNA-binding Zn-finger and Zn-ribbon domains of topoisomerase 1 [Replication, recombination ...
636-750 9.51e-22

ssDNA-binding Zn-finger and Zn-ribbon domains of topoisomerase 1 [Replication, recombination and repair];


Pssm-ID: 223625 [Multi-domain]  Cd Length: 140  Bit Score: 91.85  E-value: 9.51e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 636 LVPENEVLNVLegedaetNALRAKRRCPKCGTAMDSYLIDPKrKLHVCGNNPTCDGYEIEEgefriKGYDGPIVECEKCG 715
Cdd:COG0551   1 LIAEEEVKVVL-------KDLKTGQICPKCGKNMVKKFGKYG-IFLGCSNYPKCDYYEPEK-----AIAEKTGVKCPKCG 67
                        90       100       110
                ....*....|....*....|....*....|....*...
gi 16129235 716 -SEMHLKMGRFGK--YMACTNEECKNTRKILRNGEVAP 750
Cdd:COG0551  68 kGLLVLKKGRFGKnfLGCSNYPKCRFTEKPKPKEKKCP 105
Topo_Zn_Ribbon pfam08272
Topoisomerase I zinc-ribbon-like; Some Proteobacteria topoisomerase I contain two ...
824-862 3.27e-20

Topoisomerase I zinc-ribbon-like; Some Proteobacteria topoisomerase I contain two zinc-ribbon-like domains at the C-terminus that structurally homologous to pfam01396. However, this domain no longer bind zinc. Indeed, only one of the four cysteine residues remains.


Pssm-ID: 336979  Cd Length: 39  Bit Score: 83.82  E-value: 3.27e-20
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 16129235   824 GNKTMVRFSRKTKQQYVSSEKDGKATGWSAFYVDGKWVE 862
Cdd:pfam08272   1 GNPALVRFSRKTKEQYVLSEKDGKATGWLAAYIDGKWRE 39
TOPRIM_TopoIA_TopoIII cd03362
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type ...
3-154 4.36e-19

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: 84.59  E-value: 4.36e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   3 KALVIVESPAKAKTI------------------NKYLGSDYVVKSSVGHIRDLptsgsaakksadststktakkpkkDER 64
Cdd:cd03362   1 MVLIIAEKPSVAKAIakilgggskkkgkgryyeFYGEGGGYVVTWASGHLLEL------------------------DFP 56
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  65 GALVNRMGVDPWHN----WEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIG-GDDARYSRVVF 139
Cdd:cd03362  57 EEYDPWDKVWPLEDplfpAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKcVKRKPVKRAWF 136
                       170
                ....*....|....*
gi 16129235 140 NEITKNAIRQAFNKP 154
Cdd:cd03362 137 SSLTPKAIRRAFKNL 151
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
4-142 6.56e-19

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: 334664 [Multi-domain]  Cd Length: 90  Bit Score: 81.98  E-value: 6.56e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235     4 ALVIVESPAKAKTINKYLGSDY-VVKSSVGHIRDLPtsgsaakksadststktakkpkkdergalvnrmgvdpwhnweah 82
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGFqAVVAVLGHLLSLA-------------------------------------------- 36
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235    83 yevlpgKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEI 142
Cdd:pfam01751  37 ------TKDKLKALKELALKAKEVILATDPDREGEAIALKLLTLKELLEAAGGRVKISEL 90
TOPRIM_TopoIA_RevGyr cd03361
TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA ...
4-154 2.62e-17

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: 80.05  E-value: 2.62e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   4 ALVIVESPAKAKTINKYLG-----------------SDYV--VKSSVGHIRDLPTSG----------------SAAKKSA 48
Cdd:cd03361   2 ALMIVESPNKARTIANFFGrpsvrrlgglvvyevstGDGVlmITASGGHVYDLVTKEgghgvveddgryvpvyDSIKRCR 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235  49 DSTSTKTAKKPKKDERGAlvnrmgvdpwhnweahyEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIG 128
Cdd:cd03361  82 DCGYQFTEDSDKCPRCGS-----------------ENIDDKLETLEALRELALEVDEVLIATDPDTEGEKIAWDVYLALR 144
                       170       180
                ....*....|....*....|....*.
gi 16129235 129 GDDARYSRVVFNEITKNAIRQAFNKP 154
Cdd:cd03361 145 PYNKNIKRAEFHEVTRRAILEALRNP 170
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
3-131 8.89e-15

topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 69.60  E-value: 8.89e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235      3 KALVIVESPAKAKTINKYLGSDYVVKSSVGHIRdlptsgsaakksadststktakkpkkdergalvnrmgvdpwhnweah 82
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALGGHLL----------------------------------------------- 33
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 16129235     83 yevlpgKEKVVSELKQLAEKAdHIYLATDLDREGEAIAWHLREVIGGDD 131
Cdd:smart00493  34 ------SKEQIKLLKKLAKKA-EVILATDPDREGEAIAWELAELLKPAG 75
YrdD COG0551
ssDNA-binding Zn-finger and Zn-ribbon domains of topoisomerase 1 [Replication, recombination ...
708-858 1.06e-14

ssDNA-binding Zn-finger and Zn-ribbon domains of topoisomerase 1 [Replication, recombination and repair];


Pssm-ID: 223625 [Multi-domain]  Cd Length: 140  Bit Score: 71.82  E-value: 1.06e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235 708 IVECEKCGSEMHLKMGRFGKYMACTNEECKntrkilrngEVAPPKEDPVPLPELPCEKSDAYF-VLRDGAAG-VFLAANT 785
Cdd:COG0551  17 GQICPKCGKNMVKKFGKYGIFLGCSNYPKC---------DYYEPEKAIAEKTGVKCPKCGKGLlVLKKGRFGkNFLGCSN 87
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 16129235 786 FPKSRETRAPLVEELyrfrdrlpeklrylaDAPQQdpeGNKTMVRfsRKTKQQYVSSEKDGKATGWSAFYVDG 858
Cdd:COG0551  88 YPKCRFTEKPKPKEK---------------KCPKC---GSRKLVE--KKEKKKGVFLECSNKPCCLKVENLKN 140
zf-C4_Topoisom pfam01396
Topoisomerase DNA binding C4 zinc finger;
708-745 6.03e-13

Topoisomerase DNA binding C4 zinc finger;


Pssm-ID: 307520 [Multi-domain]  Cd Length: 39  Bit Score: 63.43  E-value: 6.03e-13
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 16129235   708 IVECEKCGSEMHLKMGRFGKYMACTNE-ECKNTRKILRN 745
Cdd:pfam01396   1 GGKCPKCGGDLVLKRGRFGKFVGCSNYpECRFTRPLKKN 39
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
3-139 1.74e-10

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: 57.82  E-value: 1.74e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16129235   3 KALVIVESPAKAKTINKYLGSDYVVKSSVGHIRdlptsgsaakksadststktakkpkkdergalvnrmgvdpwhnweah 82
Cdd:cd00188   1 KKLIIVEGPSDALALAQAGGYGGAVVALGGHAL----------------------------------------------- 33
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 16129235  83 yevlpgkEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVF 139
Cdd:cd00188  34 -------NKTRELLKRLLGEAKEVIIATDADREGEAIALRLLELLKSLGKKVRRLLL 83
Topo_Zn_Ribbon pfam08272
Topoisomerase I zinc-ribbon-like; Some Proteobacteria topoisomerase I contain two ...
757-791 2.11e-07

Topoisomerase I zinc-ribbon-like; Some Proteobacteria topoisomerase I contain two zinc-ribbon-like domains at the C-terminus that structurally homologous to pfam01396. However, this domain no longer bind zinc. Indeed, only one of the four cysteine residues remains.


Pssm-ID: 336979  Cd Length: 39  Bit Score: 47.61  E-value: 2.11e-07
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 16129235   757 PLPELP--CEKSDAYFVLR--DGAAGVFLAANTFPKSRE 791
Cdd:pfam08272   1 GNPALVrfSRKTKEQYVLSekDGKATGWLAAYIDGKWRE 39
zf-C4_Topoisom pfam01396
Topoisomerase DNA binding C4 zinc finger;
597-638 6.61e-05

Topoisomerase DNA binding C4 zinc finger;


Pssm-ID: 307520 [Multi-domain]  Cd Length: 39  Bit Score: 40.70  E-value: 6.61e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 16129235   597 IDCPTCGRKMGIRTASTGVFLGCSGYalpPKerCKTTINLVP 638
Cdd:pfam01396   2 GKCPKCGGDLVLKRGRFGKFVGCSNY---PE--CRFTRPLKK 38
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.17
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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