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Conserved domains on  [gi|7245299]
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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
4-599 0e+00

DNA topoisomerase I subunit omega; Validated


:

Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 1176.50  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     4 GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADststktakkpkkderGALVNRMGVDPWHNWEA 83
Cdd:PRK07561   1 GKSLVIVESPAKAKTINKYLGSDYVVKASVGHIRDLPTSASSVPAKEK---------------GALWARMGVDPDHDFEA 65
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    84 HYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDR 163
Cdd:PRK07561  66 LYEVLPGKEKVVSELKKAAKDADELYLATDPDREGEAIAWHLLEVLGGDDVPVKRVVFNEITKNAIQEAFENPRELDINL 145
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   164 VNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQ 243
Cdd:PRK07561 146 VNAQQARRFLDRLVGYMVSPLLWKKIARGLSAGRVQSVAVRLIVEREREIEAFVPEEYWDIHADLTTPRGDAFEARLTHL 225
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   244 NDKPFRPV---NKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYIT 320
Cdd:PRK07561 226 DGKKFAPVdllNEAQAEAAVAALEGARYSVASVEDKPTTRKPSAPFTTSTLQQEASRKLGFSVKKTMRIAQRLYEAGYIT 305
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   321 YMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASK-ENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQ 399
Cdd:PRK07561 306 YMRTDSTNLSQEAINAARGYIGDNYGKKYLPEKPRQYSSKaKNAQEAHEAIRPSDVFRTPDQLKGLEGDAQRLYELIWKR 385
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   400 FVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKG---DEDRILPAVNKGDALTLVELTPAQHFTKPP 476
Cdd:PRK07561 386 FVASQMAPARYDSTTVTIAAGDAELRATGRVLRFDGFLKVYVEGRDDaldDEDRRLPALKVGDALTLEKLDPTQHFTKPP 465
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   477 ARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVA 556
Cdd:PRK07561 466 ARYSEASLVKELEKLGIGRPSTYASIISTIQDRGYVRLENRRFYPEKMGRIVTDRLEEFFPRLVDYDFTARMEEELDDIA 545
                        570       580       590       600
                 ....*....|....*....|....*....|....*....|...
gi 7245299   557 NHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQMVLTSI 599
Cdd:PRK07561 546 NGEADWKPVLDDFYKDFSQQLEKAEELREEGGMRPNQMVITDR 588
 
Name Accession Description Interval E-value
PRK07561 PRK07561
DNA topoisomerase I subunit omega; Validated
4-599 0e+00

DNA topoisomerase I subunit omega; Validated


Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 1176.50  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     4 GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADststktakkpkkderGALVNRMGVDPWHNWEA 83
Cdd:PRK07561   1 GKSLVIVESPAKAKTINKYLGSDYVVKASVGHIRDLPTSASSVPAKEK---------------GALWARMGVDPDHDFEA 65
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    84 HYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDR 163
Cdd:PRK07561  66 LYEVLPGKEKVVSELKKAAKDADELYLATDPDREGEAIAWHLLEVLGGDDVPVKRVVFNEITKNAIQEAFENPRELDINL 145
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   164 VNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQ 243
Cdd:PRK07561 146 VNAQQARRFLDRLVGYMVSPLLWKKIARGLSAGRVQSVAVRLIVEREREIEAFVPEEYWDIHADLTTPRGDAFEARLTHL 225
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   244 NDKPFRPV---NKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYIT 320
Cdd:PRK07561 226 DGKKFAPVdllNEAQAEAAVAALEGARYSVASVEDKPTTRKPSAPFTTSTLQQEASRKLGFSVKKTMRIAQRLYEAGYIT 305
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   321 YMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASK-ENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQ 399
Cdd:PRK07561 306 YMRTDSTNLSQEAINAARGYIGDNYGKKYLPEKPRQYSSKaKNAQEAHEAIRPSDVFRTPDQLKGLEGDAQRLYELIWKR 385
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   400 FVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKG---DEDRILPAVNKGDALTLVELTPAQHFTKPP 476
Cdd:PRK07561 386 FVASQMAPARYDSTTVTIAAGDAELRATGRVLRFDGFLKVYVEGRDDaldDEDRRLPALKVGDALTLEKLDPTQHFTKPP 465
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   477 ARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVA 556
Cdd:PRK07561 466 ARYSEASLVKELEKLGIGRPSTYASIISTIQDRGYVRLENRRFYPEKMGRIVTDRLEEFFPRLVDYDFTARMEEELDDIA 545
                        570       580       590       600
                 ....*....|....*....|....*....|....*....|...
gi 7245299   557 NHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQMVLTSI 599
Cdd:PRK07561 546 NGEADWKPVLDDFYKDFSQQLEKAEELREEGGMRPNQMVITDR 588
topA_bact TIGR01051
DNA topoisomerase I, bacterial; This model describes DNA topoisomerase I among the members of ...
7-599 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: 898.67  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299      7 LVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSgsaakksadststktakkpkkdergalvnRMGVDPWHNWEAHYE 86
Cdd:TIGR01051   1 LVIVESPAKAKTIKKYLGDEYEVEASMGHIRDLPKS-----------------------------RLGVDIEKDFEPEYV 51
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     87 VLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNA 166
Cdd:TIGR01051  52 VSKGKKKVVKELKTLAKKADEVYLATDPDREGEAIAWHLAEVLKPKDPVYKRIVFNEITKKAIRAALKNPREIDMNLVNA 131
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    167 QQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTpSGEALALQVTHQNDK 246
Cdd:TIGR01051 132 QQARRILDRLVGYTLSPLLWKKVAKGLSAGRVQSVALRLIVDREREIKRFVPEEYWTIDATFQK-GEETFEALLTEVNGK 210
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    247 PFRPV---NKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEA------- 316
Cdd:TIGR01051 211 KLKAGsdlDEAEATALKEQLKGEELVVEEIEKKPKKSRPPPPFTTSTLQQEASRKLGFSAKKTMMIAQRLYEGvstgdgt 290
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    317 -GYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKE-NSQEAHEAIRPSDVNVMAESLKD-MEADAQKLY 393
Cdd:TIGR01051 291 iGLITYMRTDSTRLSNQAVNEARNLIDKNYGKEYLGPKPKRYKSKEkNAQEAHEAIRPTSVFRTPEELKDyLKRDEFRLY 370
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    394 QLIWRQFVACQMTPAKYDSTTLTVGA--GDFRLKARGRILRFDGWTKVMPALRKG---DEDRILPAVNKGDALTLVELTP 468
Cdd:TIGR01051 371 ELIWKRFVASQMADARYDSTSVRLTNedGEYVFKATGRKLIFDGYYKVYVEGSDDpleEKDRILPPLKEGDAVKLVEVKP 450
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    469 AQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQM 548
Cdd:TIGR01051 451 NQHFTQPPARYTEASLVKELEELGIGRPSTYASIISTIQDRGYVKKENKRLYPTELGFAVTDLLEKHFGDVVDYDFTAKM 530
                         570       580       590       600       610
                  ....*....|....*....|....*....|....*....|....*....|.
gi 7245299    549 ENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKdpeeggMRPNQMVLTSI 599
Cdd:TIGR01051 531 EKDLDEIAEGKAEWKPVLKNFYTGFSSKVKKLRN------MRIIVDFKTSQ 575
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
5-595 0e+00

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 223624 [Multi-domain]  Cd Length: 570  Bit Score: 786.41  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    5 KALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAakksadststktakkpkkdergalvnRMGVDPWHN-WEA 83
Cdd:COG0550   1 KRLIIVESPSKAKTIAKYLGKGYVVTASVGHLRDLPFPEEY--------------------------KGWVDVDLPiFEP 54
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   84 HYEVLPG-KEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGD-DARYSRVVFNEITKNAIRQAFNKPGELNI 161
Cdd:COG0550  55 KYIIKPGkKKKVVKKLKKLAKKADEVYLATDPDREGEAIGWHILEVLKLKnPSKVKRVVFSEITKKAILSAFKNPREIDM 134
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299  162 DRVNAQQARRFMDRVVGYMVSPLLWKKIARG-LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQV 240
Cdd:COG0550 135 NLVDAQLARRILDRLVGYNLSRLLWKKLKRGvLSAGRVQSPALRLVVEREREIEAFVPEEYWEIKAIFEKGGGEFSARLT 214
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299  241 THQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEA-GYI 319
Cdd:COG0550 215 EIEGKKEGRLKDKDEAEEIVNKLKGKPAKVVSVEKKPKKRSPPPPFTTSTLQQEASRKLGFSAKKTMDIAQKLYEGhGLI 294
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299  320 TYMRTDSTNLSQDAVNMVRGYISDN-FGKKYLPESPNQYASKE-NSQEAHEAIRPSDVNVmAESLKdmEADAQKLYQLIW 397
Cdd:COG0550 295 TYPRTDSTRLSEEALAEARLYILAIaYGKEYLPLKPRRYPSKGkKAQEAHEAIRPTDFET-PESLK--AYDELKLYDLIW 371
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299  398 RQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPA 477
Cdd:COG0550 372 RRFLASQMPDAIYEKTTVTLEVAGEKFKASGKVLKFDGWLKVYGEDKDEEEDKELPELKEGDELKVEKLEVEEHFTKPPP 451
                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299  478 RFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVAN 557
Cdd:COG0550 452 RYTEASLVKAMEKLGIGTPSTYASIIETLQKRGYVEKKGKRLVPTELGEAVIELLEEYFPELVDPDFTAKMEEKLDEIAE 531
                       570       580       590
                ....*....|....*....|....*....|....*...
gi 7245299  558 HEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQMV 595
Cdd:COG0550 532 GKLEWKDVLDEFKKKFSKLLEEAKKNIEEIKSELNKGL 569
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
161-577 1.43e-173

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: 497.13  E-value: 1.43e-173
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299  161 IDRVNAQQARRFMDRVVGYMVSPLLWKKIAR--GLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTttpsgealal 238
Cdd:cd00186   1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRkgVLSAGRVQSPTLGLIVEREREIKAFVPEDYWEIKEAV---------- 70
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299  239 qvthqndkpfrpvnkeqtqaavsllekarysVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGY 318
Cdd:cd00186  71 -------------------------------VVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGL 119
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299  319 ITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQ----YASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQ 394
Cdd:cd00186 120 ITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLgrrnPKRGKKEQGAHEAIRPTKVAPTPELEANLSEDEFKLYE 199
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299  395 LIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDrILPAVNKGDALTLVELTPAQHFTK 474
Cdd:cd00186 200 LIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEE-EPPPLKEGDELKLEEVELEEKETQ 278
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299  475 PPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQ 554
Cdd:cd00186 279 PPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKEKKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEKLDE 358
                       410       420
                ....*....|....*....|...
gi 7245299  555 VANHEAEWKAVLDHFFSDFTQQL 577
Cdd:cd00186 359 IAEGKKDYQEVLEEFYEEFKKIV 381
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
158-566 8.44e-162

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: 468.25  E-value: 8.44e-162
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    158 ELNIDRVNAQQARRFMDRVVGYMVSPLLWKKI--ARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEA 235
Cdd:pfam01131   1 EIDDNLVDAQEARRELDWLIGINLSRALTLKKkgNKVLSAGRVQTPTLALIVEREREIENFVPEPYWTIEATLKDGGGPF 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    236 LalqvtHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYE 315
Cdd:pfam01131  81 V-----EAKKKRGRFFDKEEAEAILAKLKKGTAVVTSVEKKEKKEPPPLPFDTTTLQKEASRKLGFSAKKTMSIAQKLYE 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    316 -AGYITYMRTDSTNLSQDA-VNMVRGYISDNFGKKYLPESPNQYASK----ENSQ-EAHEAIRPSDVNVMAESLKDmeaD 388
Cdd:pfam01131 156 kHGLITYPRTDSTYLPEDAeLKAILEALAKNFGKEYLPFAEKLLKKTkgtvNNKKvTAHEAIRPTGNIPDLPELSD---D 232
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    389 AQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTP 468
Cdd:pfam01131 233 ERKLYELIVRRFLASQMPDAVYETTTVTLEVGGEEFKASGKRILEDGWKKVYPYGKKKDEEEILPELKEGEELDVKDVEL 312
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    469 AQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLeENFRELMNYDFTAQM 548
Cdd:pfam01131 313 EEKKTKPPKRYTEASLIKAMEKAGIGTPATRATIIETLVERGYVERKKKSLVPTELGKALVEAL-EKFPDLVSPELTAEL 391
                         410
                  ....*....|....*...
gi 7245299    549 ENSLDQVANHEAEWKAVL 566
Cdd:pfam01131 392 EEKLDEIAEGKLDWKDVL 409
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
274-528 1.33e-121

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: 359.64  E-value: 1.33e-121
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     274 EDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPE- 352
Cdd:smart00437   1 EEKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGKEYLDLa 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     353 ----SPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARG 428
Cdd:smart00437  81 vvllKPRKPRKGKKAQGAHEAIRPTKPIFTPELEKELSEDEFKLYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAKG 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     429 RILRFDGWTKVMPALRKgDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQD 508
Cdd:smart00437 161 KTLLFDGWLKVYPEEKK-EEEIELPTLKKGDELKVEEVEVEEKETKPPARYTEASLIKLMEKRGIGRPSTYASIIETLLD 239
                          250       260
                   ....*....|....*....|
gi 7245299     509 RGYVRVENRRFYAEKMGEIV 528
Cdd:smart00437 240 RGYVTKKKKKLIPTELGIAV 259
 
Name Accession Description Interval E-value
PRK07561 PRK07561
DNA topoisomerase I subunit omega; Validated
4-599 0e+00

DNA topoisomerase I subunit omega; Validated


Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 1176.50  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     4 GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADststktakkpkkderGALVNRMGVDPWHNWEA 83
Cdd:PRK07561   1 GKSLVIVESPAKAKTINKYLGSDYVVKASVGHIRDLPTSASSVPAKEK---------------GALWARMGVDPDHDFEA 65
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    84 HYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDR 163
Cdd:PRK07561  66 LYEVLPGKEKVVSELKKAAKDADELYLATDPDREGEAIAWHLLEVLGGDDVPVKRVVFNEITKNAIQEAFENPRELDINL 145
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   164 VNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQ 243
Cdd:PRK07561 146 VNAQQARRFLDRLVGYMVSPLLWKKIARGLSAGRVQSVAVRLIVEREREIEAFVPEEYWDIHADLTTPRGDAFEARLTHL 225
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   244 NDKPFRPV---NKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYIT 320
Cdd:PRK07561 226 DGKKFAPVdllNEAQAEAAVAALEGARYSVASVEDKPTTRKPSAPFTTSTLQQEASRKLGFSVKKTMRIAQRLYEAGYIT 305
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   321 YMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASK-ENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQ 399
Cdd:PRK07561 306 YMRTDSTNLSQEAINAARGYIGDNYGKKYLPEKPRQYSSKaKNAQEAHEAIRPSDVFRTPDQLKGLEGDAQRLYELIWKR 385
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   400 FVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKG---DEDRILPAVNKGDALTLVELTPAQHFTKPP 476
Cdd:PRK07561 386 FVASQMAPARYDSTTVTIAAGDAELRATGRVLRFDGFLKVYVEGRDDaldDEDRRLPALKVGDALTLEKLDPTQHFTKPP 465
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   477 ARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVA 556
Cdd:PRK07561 466 ARYSEASLVKELEKLGIGRPSTYASIISTIQDRGYVRLENRRFYPEKMGRIVTDRLEEFFPRLVDYDFTARMEEELDDIA 545
                        570       580       590       600
                 ....*....|....*....|....*....|....*....|...
gi 7245299   557 NHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQMVLTSI 599
Cdd:PRK07561 546 NGEADWKPVLDDFYKDFSQQLEKAEELREEGGMRPNQMVITDR 588
topA_bact TIGR01051
DNA topoisomerase I, bacterial; This model describes DNA topoisomerase I among the members of ...
7-599 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: 898.67  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299      7 LVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSgsaakksadststktakkpkkdergalvnRMGVDPWHNWEAHYE 86
Cdd:TIGR01051   1 LVIVESPAKAKTIKKYLGDEYEVEASMGHIRDLPKS-----------------------------RLGVDIEKDFEPEYV 51
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     87 VLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNA 166
Cdd:TIGR01051  52 VSKGKKKVVKELKTLAKKADEVYLATDPDREGEAIAWHLAEVLKPKDPVYKRIVFNEITKKAIRAALKNPREIDMNLVNA 131
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    167 QQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTpSGEALALQVTHQNDK 246
Cdd:TIGR01051 132 QQARRILDRLVGYTLSPLLWKKVAKGLSAGRVQSVALRLIVDREREIKRFVPEEYWTIDATFQK-GEETFEALLTEVNGK 210
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    247 PFRPV---NKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEA------- 316
Cdd:TIGR01051 211 KLKAGsdlDEAEATALKEQLKGEELVVEEIEKKPKKSRPPPPFTTSTLQQEASRKLGFSAKKTMMIAQRLYEGvstgdgt 290
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    317 -GYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKE-NSQEAHEAIRPSDVNVMAESLKD-MEADAQKLY 393
Cdd:TIGR01051 291 iGLITYMRTDSTRLSNQAVNEARNLIDKNYGKEYLGPKPKRYKSKEkNAQEAHEAIRPTSVFRTPEELKDyLKRDEFRLY 370
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    394 QLIWRQFVACQMTPAKYDSTTLTVGA--GDFRLKARGRILRFDGWTKVMPALRKG---DEDRILPAVNKGDALTLVELTP 468
Cdd:TIGR01051 371 ELIWKRFVASQMADARYDSTSVRLTNedGEYVFKATGRKLIFDGYYKVYVEGSDDpleEKDRILPPLKEGDAVKLVEVKP 450
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    469 AQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQM 548
Cdd:TIGR01051 451 NQHFTQPPARYTEASLVKELEELGIGRPSTYASIISTIQDRGYVKKENKRLYPTELGFAVTDLLEKHFGDVVDYDFTAKM 530
                         570       580       590       600       610
                  ....*....|....*....|....*....|....*....|....*....|.
gi 7245299    549 ENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKdpeeggMRPNQMVLTSI 599
Cdd:TIGR01051 531 EKDLDEIAEGKAEWKPVLKNFYTGFSSKVKKLRN------MRIIVDFKTSQ 575
PRK06599 PRK06599
DNA topoisomerase I; Validated
3-586 0e+00

DNA topoisomerase I; Validated


Pssm-ID: 235840 [Multi-domain]  Cd Length: 675  Bit Score: 833.74  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     3 MGKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPtsgsaakksadststktAKKpkkdergalvnrMGVDPWHNWE 82
Cdd:PRK06599   1 MAKKLVIVESPAKAKTIKKYLGKDYKVLASFGHVRDLP-----------------KKK------------GGVDPDNDFA 51
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    83 AHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIG---GDDARYSRVVFNEITKNAIRQAFNKPGEL 159
Cdd:PRK06599  52 PKYEIIEGKEKVVDALKKAAKKADAVYLATDPDREGEAIAWHIAEVLKeakLKDKNVKRVVFNEITKKAVQEAIENPRDI 131
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   160 NIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQ 239
Cdd:PRK06599 132 DMDLVDAQQARRALDYLVGFKLSPLLWKKVRRGLSAGRVQSVALRLICEREDEIEAFIPQEYWTIEADLATSNGEPFTAK 211
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   240 VTHQNDK---PFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEA 316
Cdd:PRK06599 212 LVEVNGKkleKFSITNEEQAKALVKALEGQAYTVDKIEKKERKRNPPPPFITSTLQQEASRKLGFSAKKTMRIAQKLYEG 291
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   317 --------GYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASK-ENSQEAHEAIRPSDVNVMAESLKD-ME 386
Cdd:PRK06599 292 idlgegtvGLITYMRTDSVRLSNEALDEARKYITKKYGKEYLPAKPRVYKKKsKNAQEAHEAIRPTSINRTPESLKPyLT 371
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   387 ADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGA--GDFRLKARGRILRFDGWTKVMPA---LRKGDEDRILPAVNKGDAL 461
Cdd:PRK06599 372 PDQFKLYELIWKRTVASQMAPAILDQTSVDIASenGKYVFRATGSVILFPGFLKVYGEskdDEEEDDEKLLPPLKEGEKL 451
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   462 TLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMN 541
Cdd:PRK06599 452 KLDELLPEQHFTEPPPRYSEASLVKKLEEYGIGRPSTYASIISTLQDREYVELEKKRFIPTDLGRIVNDFLVEHFPKYVD 531
                        570       580       590       600
                 ....*....|....*....|....*....|....*....|....*
gi 7245299   542 YDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEE 586
Cdd:PRK06599 532 YDFTAGLEDELDEIAEGKKDWKPVLREFWEPFISNLEKVEEDVRT 576
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
5-595 0e+00

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 223624 [Multi-domain]  Cd Length: 570  Bit Score: 786.41  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    5 KALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAakksadststktakkpkkdergalvnRMGVDPWHN-WEA 83
Cdd:COG0550   1 KRLIIVESPSKAKTIAKYLGKGYVVTASVGHLRDLPFPEEY--------------------------KGWVDVDLPiFEP 54
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   84 HYEVLPG-KEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGD-DARYSRVVFNEITKNAIRQAFNKPGELNI 161
Cdd:COG0550  55 KYIIKPGkKKKVVKKLKKLAKKADEVYLATDPDREGEAIGWHILEVLKLKnPSKVKRVVFSEITKKAILSAFKNPREIDM 134
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299  162 DRVNAQQARRFMDRVVGYMVSPLLWKKIARG-LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQV 240
Cdd:COG0550 135 NLVDAQLARRILDRLVGYNLSRLLWKKLKRGvLSAGRVQSPALRLVVEREREIEAFVPEEYWEIKAIFEKGGGEFSARLT 214
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299  241 THQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEA-GYI 319
Cdd:COG0550 215 EIEGKKEGRLKDKDEAEEIVNKLKGKPAKVVSVEKKPKKRSPPPPFTTSTLQQEASRKLGFSAKKTMDIAQKLYEGhGLI 294
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299  320 TYMRTDSTNLSQDAVNMVRGYISDN-FGKKYLPESPNQYASKE-NSQEAHEAIRPSDVNVmAESLKdmEADAQKLYQLIW 397
Cdd:COG0550 295 TYPRTDSTRLSEEALAEARLYILAIaYGKEYLPLKPRRYPSKGkKAQEAHEAIRPTDFET-PESLK--AYDELKLYDLIW 371
                       410       420       430       440       450       460       470       480
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299  398 RQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPA 477
Cdd:COG0550 372 RRFLASQMPDAIYEKTTVTLEVAGEKFKASGKVLKFDGWLKVYGEDKDEEEDKELPELKEGDELKVEKLEVEEHFTKPPP 451
                       490       500       510       520       530       540       550       560
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299  478 RFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVAN 557
Cdd:COG0550 452 RYTEASLVKAMEKLGIGTPSTYASIIETLQKRGYVEKKGKRLVPTELGEAVIELLEEYFPELVDPDFTAKMEEKLDEIAE 531
                       570       580       590
                ....*....|....*....|....*....|....*...
gi 7245299  558 HEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQMV 595
Cdd:COG0550 532 GKLEWKDVLDEFKKKFSKLLEEAKKNIEEIKSELNKGL 569
PRK05582 PRK05582
DNA topoisomerase I; Validated
3-586 0e+00

DNA topoisomerase I; Validated


Pssm-ID: 235516 [Multi-domain]  Cd Length: 650  Bit Score: 773.22  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     3 MGKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGsaakksadststktakkpkkdergalvnrMGVDPWHNWE 82
Cdd:PRK05582   1 MMKKLVIVESPAKAKTIEKYLGKNYKVVASMGHIRDLPKSQ-----------------------------LGIDIENNFE 51
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    83 AHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNID 162
Cdd:PRK05582  52 PKYITIRGKGPVIKELKKAAKKAKKVYLATDPDREGEAIAWHLAHILGLDEKEKNRIVFNEITKDAIKNAFKNPRKIDMN 131
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   163 RVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDAsTTTPSGEALALQVTH 242
Cdd:PRK05582 132 LVDAQQARRILDRLVGYKLSPLLWKKVKKGLSAGRVQSVALKLIIDREKEIRAFVPEEYWTIDA-EFKKGKKKFEASFYG 210
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   243 QNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEA------ 316
Cdd:PRK05582 211 YKGKKIELKNEEDVKEILAELKKKDFKVSKVKKKERKRNPPPPFTTSTLQQEAARKLNFSTKKTMMIAQQLYEGidlgkq 290
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   317 ---GYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKENSQEAHEAIRPSDVNVMAESLKD-MEADAQKL 392
Cdd:PRK05582 291 gtvGLITYMRTDSTRISDTAQEEAREFIEEKYGKEYLPKKPKVYKKKSGAQDAHEAIRPTSVFLTPESAKKyLTKDQLKL 370
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   393 YQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPAlrKGDEDRILPAVNKGDALTLVELTPAQHF 472
Cdd:PRK05582 371 YKLIWNRFVASQMAPAVFDTVSVDLENNGVKFRASGSKVKFDGFMKVYVG--DEEKDKMLPELEEGEKVKLKKIEPEQHF 448
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   473 TKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSL 552
Cdd:PRK05582 449 TQPPARYTEASLIKTLEELGIGRPSTYAPTISTIQKRGYVKLEKKRLVPTELGEIVNELLEEFFPDIVDVEFTAEMEEKL 528
                        570       580       590
                 ....*....|....*....|....*....|....
gi 7245299   553 DQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEE 586
Cdd:PRK05582 529 DEIEEGKEDWKKVLDDFYKPFEKEIEKAEKEIEK 562
PRK06319 PRK06319
DNA topoisomerase I/SWI domain fusion protein; Validated
3-583 0e+00

DNA topoisomerase I/SWI domain fusion protein; Validated


Pssm-ID: 235778 [Multi-domain]  Cd Length: 860  Bit Score: 568.30  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     3 MGKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGsaakksadststktakkpkkdergalvnrMGVDPWHNWE 82
Cdd:PRK06319   1 MKKSLIIVESPAKIKTLQKLLGEGFIFASSLGHIVDLPAKE-----------------------------FGIDIENDFE 51
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    83 AHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGgDDARYSRVVFNEITKNAIRQAFNKPGELNID 162
Cdd:PRK06319  52 PDYQILPDKEEVINKICKLAKKCDVVYLSPDPDREGEAIAWHIANQLP-KNTKIQRISFNAITKGAVTEALKHPREIDMA 130
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   163 RVNAQQARRFMDRVVGYMVSPLLWKKIAR--GLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQV 240
Cdd:PRK06319 131 LVNAQQARRLLDRIVGYKISPILSRKLQRrsGVSAGRVQSVALKLVVDREKAIEAFVPVEYWNIRVHLKDPKTQKTFWAH 210
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   241 THQND-----------KPFRPV----NKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKK 305
Cdd:PRK06319 211 LYSVDgkkwekeipegKTEDEVllinSKEKADHIVELLESATYTVTRVESKEKRRNAYPPFITSTLQQEASRHFRFSSSR 290
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   306 TMMMAQRLYEA---------GYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKENSQEAHEAIRPSDVN 376
Cdd:PRK06319 291 TMNIAQTLYEGvdldsegatGLITYMRTDSVRTDPEALKQVRKYIEGTFGKEFLPSSPNVYTTKKMAQDAHEAIRPTDIT 370
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   377 VMAESLKDMEADAQ-KLYQLIWRQFVACQMTPAKYDSTTLTVGAG-DFRLKARGRILRFDGWTKVMPALR----KGDEDR 450
Cdd:PRK06319 371 LTPEKLRSKLTEDQyKLYSLIWKRFVASQMIPAIYDTLAIRITTNkGIDLRATGSLLKFKGFLAVYEEKRddegDEEENI 450
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   451 ILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTD 530
Cdd:PRK06319 451 HLPKLHEQDVLTKEELSAEQAFTKPLPRFTEASLVKELEKSGIGRPSTYATIMNKIQSREYTLKENQRLRPTELGKIISQ 530
                        570       580       590       600       610
                 ....*....|....*....|....*....|....*....|....*....|...
gi 7245299   531 RLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKD 583
Cdd:PRK06319 531 FLETNFPRIMDIGFTALMEDELELIADNKKPWKLLLQEFWELFLPVVVTAEKE 583
PRK08780 PRK08780
DNA topoisomerase I; Provisional
3-581 0e+00

DNA topoisomerase I; Provisional


Pssm-ID: 181555 [Multi-domain]  Cd Length: 780  Bit Score: 563.62  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     3 MGKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLptsgsaakksadststktakKPKKderGAlvnrmgVDPWHNWE 82
Cdd:PRK08780   1 MSKHLVIVESPAKAKTINKYLGKDFTVLASYGHVRDL--------------------VPKE---GA------VDPENGFA 51
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    83 AHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGG----DDARYSRVVFNEITKNAIRQAFNKPGE 158
Cdd:PRK08780  52 MRYDLIDKNEKHVEAIAKAAKSADDLYLATDPDREGEAISWHLAEILKErgllKDKPMQRVVFTEITPRAIKEAMAKPRD 131
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   159 LNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSgEALAL 238
Cdd:PRK08780 132 IASDLVDAQQARRALDYLVGFNLSPLLWRKIQRGLSAGRVQSPALRMIVEREEEIEAFIAREYWSIEADCAHPS-QPFNA 210
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   239 QVTH---QNDKPFRPVNKEQTQAAVSLLEKA---RYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQR 312
Cdd:PRK08780 211 KLIKldgQKFEQFTITDGDTAEAARLRIQQAaqgTLHVTDVESKERKRNPAPPFTTSTLQQEASRKLGFTTRRTMQVAQK 290
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   313 LYEA---------GYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASK-ENSQEAHEAIRPSDVNVMAESL 382
Cdd:PRK08780 291 LYEGvdlgdegsvGLITYMRTDSVNLSQDALAEIRDVIARDYGTASLPDQPNTYKTKsKNAQEAHEAVRPTSALRTPAQV 370
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   383 KD-MEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGD---FRlkARGRILRFDGWTKVMPALR------KGDEDRIL 452
Cdd:PRK08780 371 ARfLSDDQRRLYELIWKRAVACQMIPATLNTVSVDLAAGSehvFR--ATGSTVVVPGFLAVYEEGKddksaeDEDEGRKL 448
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   453 PAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRL 532
Cdd:PRK08780 449 PPMKEGDNVPLERIRAEQHFTEPPPRYTEASLVKALEEYGIGRPSTYASIISTLQFRKYVEMEGRRFRPTDVGRAVNKFL 528
                        570       580       590       600
                 ....*....|....*....|....*....|....*....|....*....
gi 7245299   533 EENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAE 581
Cdd:PRK08780 529 TGHFTRYVDYDFTARLEDDLDAVSRGEKEWIPLMEKFWGPFKELVEEKK 577
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
161-577 1.43e-173

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: 497.13  E-value: 1.43e-173
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299  161 IDRVNAQQARRFMDRVVGYMVSPLLWKKIAR--GLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTttpsgealal 238
Cdd:cd00186   1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRkgVLSAGRVQSPTLGLIVEREREIKAFVPEDYWEIKEAV---------- 70
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299  239 qvthqndkpfrpvnkeqtqaavsllekarysVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGY 318
Cdd:cd00186  71 -------------------------------VVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGL 119
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299  319 ITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQ----YASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQ 394
Cdd:cd00186 120 ITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLgrrnPKRGKKEQGAHEAIRPTKVAPTPELEANLSEDEFKLYE 199
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299  395 LIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDrILPAVNKGDALTLVELTPAQHFTK 474
Cdd:cd00186 200 LIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEE-EPPPLKEGDELKLEEVELEEKETQ 278
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299  475 PPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQ 554
Cdd:cd00186 279 PPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKEKKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEKLDE 358
                       410       420
                ....*....|....*....|...
gi 7245299  555 VANHEAEWKAVLDHFFSDFTQQL 577
Cdd:cd00186 359 IAEGKKDYQEVLEEFYEEFKKIV 381
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
158-566 8.44e-162

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: 468.25  E-value: 8.44e-162
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    158 ELNIDRVNAQQARRFMDRVVGYMVSPLLWKKI--ARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEA 235
Cdd:pfam01131   1 EIDDNLVDAQEARRELDWLIGINLSRALTLKKkgNKVLSAGRVQTPTLALIVEREREIENFVPEPYWTIEATLKDGGGPF 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    236 LalqvtHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYE 315
Cdd:pfam01131  81 V-----EAKKKRGRFFDKEEAEAILAKLKKGTAVVTSVEKKEKKEPPPLPFDTTTLQKEASRKLGFSAKKTMSIAQKLYE 155
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    316 -AGYITYMRTDSTNLSQDA-VNMVRGYISDNFGKKYLPESPNQYASK----ENSQ-EAHEAIRPSDVNVMAESLKDmeaD 388
Cdd:pfam01131 156 kHGLITYPRTDSTYLPEDAeLKAILEALAKNFGKEYLPFAEKLLKKTkgtvNNKKvTAHEAIRPTGNIPDLPELSD---D 232
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    389 AQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTP 468
Cdd:pfam01131 233 ERKLYELIVRRFLASQMPDAVYETTTVTLEVGGEEFKASGKRILEDGWKKVYPYGKKKDEEEILPELKEGEELDVKDVEL 312
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    469 AQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLeENFRELMNYDFTAQM 548
Cdd:pfam01131 313 EEKKTKPPKRYTEASLIKAMEKAGIGTPATRATIIETLVERGYVERKKKSLVPTELGKALVEAL-EKFPDLVSPELTAEL 391
                         410
                  ....*....|....*...
gi 7245299    549 ENSLDQVANHEAEWKAVL 566
Cdd:pfam01131 392 EEKLDEIAEGKLDWKDVL 409
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
274-528 1.33e-121

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: 359.64  E-value: 1.33e-121
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     274 EDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPE- 352
Cdd:smart00437   1 EEKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGKEYLDLa 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     353 ----SPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARG 428
Cdd:smart00437  81 vvllKPRKPRKGKKAQGAHEAIRPTKPIFTPELEKELSEDEFKLYELIWRRFLASQMPDAKYEETKVTIKIGGEKFKAKG 160
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     429 RILRFDGWTKVMPALRKgDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQD 508
Cdd:smart00437 161 KTLLFDGWLKVYPEEKK-EEEIELPTLKKGDELKVEEVEVEEKETKPPARYTEASLIKLMEKRGIGRPSTYASIIETLLD 239
                          250       260
                   ....*....|....*....|
gi 7245299     509 RGYVRVENRRFYAEKMGEIV 528
Cdd:smart00437 240 RGYVTKKKKKLIPTELGIAV 259
PRK09401 PRK09401
reverse gyrase; Reviewed
6-572 2.40e-96

reverse gyrase; Reviewed


Pssm-ID: 236498 [Multi-domain]  Cd Length: 1176  Bit Score: 318.80  E-value: 2.40e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299      6 ALVIVESPAKAKTINKYLG-----------------SDYV--VKSSVGHIRDLPTsgsaakksadststktakkpKKDER 66
Cdd:PRK09401  603 TLLIVESPTKARTIANFFGrpsrrrigglvvyetvtGDRIltITASKGHVYDLTT--------------------EIGYY 662
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     67 GALVNRMGVDPWHN-----WEAHYEV--------------LPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLRE 127
Cdd:PRK09401  663 GVLVKDGGFVPVYDtikrcRDCGYQFtdesdkcprcgstnIEDKEEIIEALRELALEVDEVLIATDPDTEGEKIAWDLYL 742
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    128 VIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIA-RGLSAGRVQSVAVRLV 206
Cdd:PRK09401  743 LLSPYNSNIKRIEFHEVTRKAILEALRNPRDVNENLVKAQIVRRIEDRWIGFELSQKLQKKFGkRNLSAGRVQTPVLGWI 822
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    207 VEREREIKAFVPEEFWevdasTTTPSGEALALQVTHQNdkpfrpvnKEQTQAAVSLLEKARYSVLEREDKPttskPGAPF 286
Cdd:PRK09401  823 VERYKEYKKSKGYVLV-----IKLENGGGLELEGEFSE--------KEEAEKFYNNLIEVEKVEEKEEELN----PLPPY 885
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    287 ITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLpeSPNQYaSKENsqeA 366
Cdd:PRK09401  886 TTDTLLSDASRKLRLSAQETMRIAQDLFELGLITYHRTDSTRVSDVGISVAKEYLEKRGGEEYF--VPRSW-GEGG---A 959
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    367 HEAIRPsdVNVM-AESLKDMEADAQ------------KLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILR- 432
Cdd:PRK09401  960 HEAIRP--TRPLdAEELRQMIEEGIlklsegltknhlRLYDLIFRRFMASQMKPAKVRYQKVLIKADGKELELELVVEIl 1037
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    433 FDGWTKVMPAlrkgdedRILPAVNKGDALTLVELtpaqhFTKPPAR-FSEASLVKELEKRGIGRPSTYASIISTIQDRGY 511
Cdd:PRK09401 1038 EDGFNKVLPL-------KLYPLLEGKVKVKEKKT-----YKKSKVPlYTQGDLISEMKERGIGRPSTYAKIVETLLRRGY 1105
                         570       580       590       600       610       620
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 7245299    512 VrVENRRF---YAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSD 572
Cdd:PRK09401 1106 V-IESKGKkrlIPTKLGIKVYEYLSEKYKDLVSEERTRKLEEKMDKVEEGKEDYQEVLKELYEE 1168
rgy TIGR01054
reverse gyrase; This model describes reverse gyrase, found in both archaeal and bacterial ...
6-570 3.22e-87

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: 293.66  E-value: 3.22e-87
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299       6 ALVIVESPAKAKTINKYLG-----------------SDYV--VKSSVGHIRDLPTSG----------------SAAKKSA 50
Cdd:TIGR01054  603 ALLVVESPNKARTIARFFGkpsvrkiggsvvyevpvGDLIlmITASGGHVFDLVTDKgfhgvlvengryvpvyTSIKRCR 682
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299      51 DSTSTKTAKKPKKDERGAlvnrmgvdpwhnweahyEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIG 130
Cdd:TIGR01054  683 DCGYQFTEDRESCPKCGS-----------------ENIEDSKSIIEILRELAHEVDEVFIGTDPDTEGEKIGWDLALLLS 745
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     131 GDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIA-RGLSAGRVQSVAVRLVVER 209
Cdd:TIGR01054  746 PYNPNVKRAEFHEVTRRAILEALESPRSVDENLVKAQVVRRIEDRWIGFTLSQKLWEAFNkRWLSAGRVQTPVLGWIIDR 825
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     210 EREIKAFVPEEFwevdaSTTTPSGEALALQvtHQNDKPFRPVNKEQTQAAVSLLEkarysvlEREDKPTtskPGAPFITS 289
Cdd:TIGR01054  826 YRESREKRGYLL-----IFALESDFRLGLE--HDNRLEAKEFEKDLTWLDVEDIA-------EREEERN---PLPPYTTD 888
                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     290 TLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYlpespnQYASKENSQEAHEA 369
Cdd:TIGR01054  889 TMLEDANRKLGLSVKETMQIAQELFENGLITYHRTDSTRVSDVGMRVAKEYLASRLGGEY------FYPREWGEGGAHEC 962
                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     370 IRPS------DVNVMAES----LKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILR-FDGWTK 438
Cdd:TIGR01054  963 IRPTrpldvdDLQRLILEgvieLEGLTREHLRLYDLIFRRFMASQMRPAKVDTKEITLKADGKEAEEEGIVEIvERGFEL 1042
                          490       500       510       520       530       540       550       560
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     439 VMPALRKGDEDRILPAVNKGDALTLVELTPAqhftkpparFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRR 518
Cdd:TIGR01054 1043 VYPLWRKNELEKGSTFIVKDKELRSVPKVYP---------YTQGEIVQEMKERGIGRPSTYATIVEKLLRRGYVVESKGF 1113
                          570       580       590       600       610
                   ....*....|....*....|....*....|....*....|....*....|..
gi 7245299     519 FYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFF 570
Cdd:TIGR01054 1114 LIPTKLGIEVYNYLTNRYPKLVSEDRTRELEEAMDKIERGELDYLEVLESVY 1165
PRK07219 PRK07219
DNA topoisomerase I; Validated
89-567 4.24e-87

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 287.67  E-value: 4.24e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    89 PGKEKVVSELKQLAEKADHIYLATDLDREGEAI---AWHLREVIGGDDARysRVVFNEITKNAIRQAFNKPGELNIDRVN 165
Cdd:PRK07219  82 ITKQNYINALKKLAKDADEIIIATDYDREGELIgkeAYHILREVCQVPVK--RARFSSLTKKEIRKAFENPDEIDFNLAD 159
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   166 AQQARRFMDRVVGYMVSPLLW---KKIARG--LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDAS-TTTPSGEALALQ 239
Cdd:PRK07219 160 AGEARQIIDLYWGAALTRFLSlsvRQLGRWdfLSVGRVQTPTLAFIVDREREIRAFDPEDYWKIEALlDKEAQYFYRDLI 239
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   240 VTHQNDKPFrpvNKEQTQAAVSLLEKARYS-VLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGY 318
Cdd:PRK07219 240 GGHEAEKFW---DEEEAEEIYEKLKGAKEAtVSSVKKRERTISPPAPFNTTEFLREASKIFGISPKRAMEIAEKLYTAGY 316
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   319 ITYMRTDSTNLSQD-AVNMVRGYISDN--FGK--KYLPESPNQYAS--KENSQeAHEAIRPSDVnvmaESLKDMEADAQK 391
Cdd:PRK07219 317 ISYPRTDNTVYPDDlDPKELLKKLSKKkeYGPyaESILEQENIKPTegKKETT-DHPPIHPVDV----PKREELSDDEWK 391
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   392 LYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKgdEDRILPAVNKGDALTLVELTPAQH 471
Cdd:PRK07219 392 VYELIVRRFLATLADPAEWEYLKVELDVNGEIFKASGSRLVEEGWHEVYPYEKF--DEKELPDLEEGEKLKVNKIEIEAK 469
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   472 FTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVrVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENS 551
Cdd:PRK07219 470 ETQPPKRYTQSSLIKEMEKRGLGTKATRHDIIEKLYKRGYV-IEGDPPRPTDLGIAVIEALEKYAPEIVSEEMTAQLEAD 548
                        490
                 ....*....|....*.
gi 7245299   552 LDQVANHEAEWKAVLD 567
Cdd:PRK07219 549 MQAIEDGKKKKEDVTE 564
TopG2 COG1110
Reverse gyrase [Replication, recombination and repair];
6-573 1.16e-85

Reverse gyrase [Replication, recombination and repair];


Pssm-ID: 224035 [Multi-domain]  Cd Length: 1187  Bit Score: 289.67  E-value: 1.16e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     6 ALVIVESPAKAKTINKYLG-----------------SDYV--VKSSVGHIRDLPTsgsaakksadststktakkpKKDER 66
Cdd:COG1110  619 ALMIVESPNKARTIASFFGrpsvrrlgggvvyevaiGDLVltITASGGHVFDLVT--------------------EPGVH 678
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    67 GALVNRMGVDPWHN-----WEAHYEV--------------LPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLRE 127
Cdd:COG1110  679 GVLVKDGKYVPVYDtikrcRDCGEQFvdsedkcprcgsrnVEDKTETVEALRELALEVDEILIGTDPDTEGEKIAWDVFN 758
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   128 VIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIA-RGLSAGRVQSVAVRLV 206
Cdd:COG1110  759 YLRPYNPNVKRIEFHEVTRRAILEALKNPRDVDENLVKAQIVRRIEDRWIGFELSQKLWDVFNnKNLSAGRVQTPVLGWI 838
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   207 VEREREIKAFVPEEFWEVDasTTTPSgealalqvthQNDKPFRPVNKEQTQAAVSLLEKarysVLEREDKPttskPGAPF 286
Cdd:COG1110  839 VNRYEEYKEKRGYLVIQLD--LDLPS----------GNREEVENVKRKLKLIVVEVVDV----VEREEEKN----PLPPY 898
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   287 ITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLpespnqYASKENSQEA 366
Cdd:COG1110  899 TTDTMLRDASRRLRLSADETMQIAQDLFEGGLITYHRTDSTRVSDVGIRVAREYLRKEFGEEYF------RPRSWGEEGA 972
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   367 HEAIRPSDVNVmAESLKDM--EADAQ----------KLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARG--RILR 432
Cdd:COG1110  973 HEAIRPTRPID-VEELITLieEGVIQlpirltknhlRVYDLIFRRFMASQMRPAKVLKEKAEVKADGKDVELEAlvEILE 1051
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   433 fDGWTKVMPaLRKgdEDRILPAVNKGDALTLVELTPAQHFTkpparfsEASLVKELEKRGIGRPSTYASIISTIQDRGYV 512
Cdd:COG1110 1052 -DGFALVYP-TRV--LPELEKGTLKVTEVEIRKVSKVYLYT-------QGEVVEEMKERGIGRPSTYAKIVETLLRRGYV 1120
                        570       580       590       600       610       620
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 7245299   513 -RVENRRFYAE-KMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDF 573
Cdd:COG1110 1121 iESKGRKKLIPtKLGIEVYEYLSEKYKKLVSEERTRRLEEIMDKVEEGKADYQEVLKELYEEI 1183
PRK07726 PRK07726
DNA topoisomerase III; Provisional
85-579 2.62e-75

DNA topoisomerase III; Provisional


Pssm-ID: 236078 [Multi-domain]  Cd Length: 658  Bit Score: 252.39  E-value: 2.62e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    85 YEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAwhlREVIggDDARY----SRVVFNEITKNAIRQAFN--KPGE 158
Cdd:PRK07726  73 LVVKKKTAKQFNVVKKLLKQATEIVIATDADREGELIA---REIL--DYCGVrkpiKRLWISSLTDKAIKRAFAnlKPGK 147
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   159 LNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARG-----LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSG 233
Cdd:PRK07726 148 ETIPLYYSALARSRADWLVGINMTRAYTLLGRKAgyngvLSVGRVQTPTLALVVRRDEEIENFVPKPYWEVEAHLTPGER 227
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   234 EALALQVTHQ-NDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQR 312
Cdd:PRK07726 228 FTAKWQPSEPyQDEEGRLLDRPLAEQVVARIQGQPAKVTEVETKRKKEYAPLLYDLSELQIDANKRFGLSAKETLDIAQS 307
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   313 LYE-AGYITYMRTDSTNLSQDAVNMVRGYISD-NFGKKYLPESPNQYASKENSQ-------EAHEAIRPSDVNVMAESLK 383
Cdd:PRK07726 308 LYEtHKLITYPRTDSRYLPEDMVATLPEVLNAiSKVDPYLLLAPPVLDPSIRSRawndkkvTAHHAIIPTEQPPNLSKLS 387
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   384 DMEadaQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDE-DRILPAVNKGDALT 462
Cdd:PRK07726 388 EDE---RKVYDLIARRYLAQFLPPAEYDKTTIELEIAGGTFIAKGKQVVEAGWKALLGKKEEDEEkEQPLPVLAKGDELK 464
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   463 LVELTPAQHFTKPPARFSEASLV------------KELEKR-----GIGRPSTYASIISTIQDRGYVRVENRRFYAEKMG 525
Cdd:PRK07726 465 VEKGEVKEGQTQPPKRFTEGTLLsameniarfvqdKELKKTlketdGLGTEATRAGIIEKLFKRGYLEKKGKYIHATDKG 544
                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|....
gi 7245299   526 EIVTDRLEEnfrELMNYDFTAQMENSLDQVanheAEWKAVLDHFFSDFTQQLDK 579
Cdd:PRK07726 545 KQLIDALPE---ELTSPDMTAKWEQALDQI----SEGQLSYQDFMQPLKQWLKQ 591
PRK05776 PRK05776
DNA topoisomerase I; Provisional
4-553 6.18e-71

DNA topoisomerase I; Provisional


Pssm-ID: 235602 [Multi-domain]  Cd Length: 670  Bit Score: 241.05  E-value: 6.18e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     4 GKALVIVESPAKAKTIN--------------------KYLGSDYVVKSSVGHIRDLPTsgsaakksadststktakkpkk 63
Cdd:PRK05776   1 GYILVIAEKPKAARKIAealsekpircriygvpywivKRDGKKIVVAPAAGHLFGLHT---------------------- 58
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    64 DERGALVNRMgvdpwhNWEAHYEVLPGK---EKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGgDDARYSRVV 140
Cdd:PRK05776  59 KSKGFPVFDY------EWKPLYEIDKGSkytKKYYELLSSLSKYADEFINACDYDIEGSVIGYLIIKYLG-DPKKAKRMK 131
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   141 FNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWK--KIARG----LSAGRVQSVAVRLVVEREREIK 214
Cdd:PRK05776 132 FSALTKSDIRRAFRNLETLDYEMINAGIARHELDWLWGINVSRALMSsvRDASGkrviLSAGRVQSPTLKYVVEREIERN 211
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   215 AFVPEEFWEVDAsTTTPSGEALALQVThqnDKPFRpvNKEQTQAAVSLLEKARY-SVLEREDKPTTSKPGAPFITSTLQQ 293
Cdd:PRK05776 212 LFVPLPYFSVSI-IIEKNGYEFTLKYE---NKKFE--TKEEAKEILEEIKKTGYlKVTKVEVKIEILEPPPPFNLGDLQV 285
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   294 AASTRLGFGVKKTMMMAQRLYEAGYITYMRTDS-------------TNLSQdaVNMVRGYISD--NFGKKYLpeSPNQyA 358
Cdd:PRK05776 286 EAARIYGFSPYKTQSIAEDLYLDGLISYPRTNSqklpptlnirnilKGLSR--SPQYRPLVNLllKETKGVL--KPVQ-G 360
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   359 SKENSqeAHEAIRPSdvnvmAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDF--RLKARGRILRFDGW 436
Cdd:PRK05776 361 PKDDP--AHPAIYPT-----GEPPKNLSKDEFKLYDLIVRRFLASFAAPAVLSNTIVTLRVPGFplVFSASGQRIEERGW 433
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   437 TKVMPaLRKGDEDrILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVEN 516
Cdd:PRK05776 434 LKYYP-FHKFDEE-ELPLLKKGERVKIVDVKVRKSYTKPPSRYSKASLLKWMESVGIGTEATRARIIETLFKRGYLTSNG 511
                        570       580       590
                 ....*....|....*....|....*....|....*..
gi 7245299   517 RRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLD 553
Cdd:PRK05776 512 KYIEVTPLGFGVAEVLEKYFPDIVSVELTRDFEEKLE 548
topA_arch TIGR01057
DNA topoisomerase I, archaeal; This model describes topoisomerase I from archaea. These ...
81-588 4.07e-69

DNA topoisomerase I, archaeal; This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273420 [Multi-domain]  Cd Length: 618  Bit Score: 235.11  E-value: 4.07e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     81 WEAHYEVLPGKE---KVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDaRYSRVVFNEITKNAIRQAFNKPG 157
Cdd:TIGR01057  67 WVPIFEFDKGKGyvsKYIKALSKLAKGADEYINACDYDIEGEVIGFKALKYFCGVE-RAKRMKFSTLTKQDIRRAYANPE 145
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    158 ELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARG------LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTP 231
Cdd:TIGR01057 146 EIDYGMVDAGMARHILDWYWGINLSRALMEAIRAAagrwviLSAGRVQGPTLAFLVEREREINLFVPKPYWVIKATLEKG 225
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    232 SGEALAlqvTHQNDKPFrpvNKEQTQAAVSLLEKARY-SVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMA 310
Cdd:TIGR01057 226 GGVFDA---RPEKWKIW---SEEEAKSIKEELKKSPWaAVEEVRSERSILKPPPPFDLGTLQREAYRIFGFSPKKTQSIA 299
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    311 QRLYEAGYITYMRTDSTNLSQDavnmvRGY--ISDNFGK-----------KYLPESPNQYASKENsqEAHEAIRPsdvnV 377
Cdd:TIGR01057 300 QELYEEALISYPRTSSQKLPPS-----INYraILDNLAKgplyreaaerlLETGVLKPVEGKKED--PAHPAIHP----T 368
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    378 MAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDriLPAVNK 457
Cdd:TIGR01057 369 GEIPSQELSKDEKKVYDLIVRRFLAAFSEEAIREKSKVLLRIGQEKFRLSGLRVVKLGWLEYYHYSKFEEKE--LPPLDR 446
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    458 GDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVrVENRRFYAEKMGEIVTDRLEENFR 537
Cdd:TIGR01057 447 GDKIKVVRVDVRVKETQPPARYDKASLIREMESRGLGTKATRARIIETLYKRGYI-EGKKSIKVTPLGEAVIETLQRYCP 525
                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|.
gi 7245299    538 ELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGG 588
Cdd:TIGR01057 526 EIISEELTRRFESKLEDIMSGRITKDEVIDEAKKRLRKILEEFKKRLDDIG 576
PRK07220 PRK07220
DNA topoisomerase I; Validated
45-586 8.07e-68

DNA topoisomerase I; Validated


Pssm-ID: 180892 [Multi-domain]  Cd Length: 740  Bit Score: 234.27  E-value: 8.07e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    45 AAKKSADSTSTKTAKKPK------------KDER------GALVNRMGVDPWHNWE---------AHYEVLPGKEKVVSE 97
Cdd:PRK07220  11 AARRIAQILAPKKPKKTRvsgvdvyryednGDDTvvvglsGHIVNIDFPKEYNNWQkvdardlidAEIITTPTQKKIVTA 90
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    98 LKQLAEKADHIYLATDLDREGEAIAWHLREVIGG--DDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDR 175
Cdd:PRK07220  91 LKKLGKEADRVTIATDYDREGELIGVEALNIIKKvnPDIKFDRVRYSAITKKEIERAFSNPVEVDFNLADAGHSRQVIDL 170
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   176 VVGYMVSPllWKKIARG------LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDAsTTTPSGEALALQvtHQNDkpfR 249
Cdd:PRK07220 171 VWGAALTR--YISLAAGrlgkmfLSVGRVQSPTLALIVDREKEREAFVPTPYWEIYA-TLENNGETFVAQ--HSTR---R 242
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   250 PVNKEQTQAAVSLL-EKARYSVLEREDKptTSKPGAPFITSTLQQAASTrLGFGVKKTMMMAQRLYEAGYITYMRTDSTN 328
Cdd:PRK07220 243 FWEKEEADRVFEKLgKTAEVTEVEKGTK--TDKPPTPFNTTEFISAANS-IGFSAANAMRIAESLYTNGYISYPRTDNTV 319
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   329 L--SQDAVNMVRGYISDNFGK--KYLPESPNQYASKENSQEA-HEAIRPsdVNVMAESlkDMEADAQKLYQLIWRQFVAC 403
Cdd:PRK07220 320 YpeSLDLREQIEIFAEGPFGEyaQKLLEKGELVPTRGKKETTdHPPIYP--ASLAKKS--ELKEDEWKVYELVVRRFFAT 395
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   404 QMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKgdEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEAS 483
Cdd:PRK07220 396 FAGPAEWETMKLRFDIGGEEFRANGSRLTEPGWRWYYPYNAP--EDRLLPELSEGEELKVKKKEMLDKETQPPGRYGQGR 473
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   484 LVKELEKRGIGRPSTYASIISTIQDRGYVR----VENRRFYAekmgeiVTDRLEENFRELMNYDFTAQMENSLDQVANHE 559
Cdd:PRK07220 474 LIKLMEDLGLGTKATRHEIISKLYSRAYIHgnpiQPTNTAFA------VVDALEKYAPTITKPDMTSRLEEDMDKIAEGK 547
                        570       580
                 ....*....|....*....|....*..
gi 7245299   560 AEWKAVLDHFFSDFTQQLDKAEKDPEE 586
Cdd:PRK07220 548 IKEDAVLEESREMLEQVFDELDKNREK 574
topB TIGR01056
DNA topoisomerase III, bacteria and conjugative plasmid; This model describes topoisomerase ...
99-585 2.87e-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: 220.10  E-value: 2.87e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     99 KQLAE-KADHIYLATDLDREGEAIA-WHLREVIGGDDARYSRVVFNEITKNAIRQAFNK--PGELNIDRVNAQQARRFMD 174
Cdd:TIGR01056  89 RILKEnKVDEVVIATDPDREGELIArEILDYLKVTDKVTIKRLWISSLVDSSIRKAFKNlrPKSETEGLYKSGVARARAD 168
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    175 RVVGYMVSPLLWKK-----IARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPsGEALALQVTHQNDKPFR 249
Cdd:TIGR01056 169 WLVGINLTRAFTKLgreagNDGVLSVGRVQTPTLAMVVKRENEIKNFVGKPFYEVSATINKD-EQEFTTEWQPYKDEEER 247
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    250 PVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAG-YITYMRTDSTN 328
Cdd:TIGR01056 248 ELHEFLAENVVTDLTQKPALVTDIEKERKKTSAPLFYDLSALQEDANKRFGISAKRTLDIAQKLYETHkLITYPRTDSRY 327
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    329 LSQDAVNMVRGYIS-------DNFGKKYLPESPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEAdaqKLYQLIWRQFV 401
Cdd:TIGR01056 328 LPEDEKEMLLEVLDalkvitpALLPIKKRDELTNNRLWNDKKIEDHHAIIPTGNDFNLSDLSEEER---NVYKLIAQNYL 404
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    402 ACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDE--DRILPAVNKGDALTLVELTPAQHFTKPPARF 479
Cdd:TIGR01056 405 MQFMPKEEYETTTIEIAIGKLMFEAKGKILQDNGWKALLGKQEEDEEteDTTLPAFQKGDELDVETLELLEKQTKPPARY 484
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    480 SEASLVKEL-----------------EKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEEnfrELMNY 542
Cdd:TIGR01056 485 TEGTLLSAMtnpaafvqdkglkktlkETKGLGTEATRADIIENLFKRGFIQKKKNKIYITKNGKLLCLLLPE---LLTKP 561
                         490       500       510       520
                  ....*....|....*....|....*....|....*....|....*..
gi 7245299    543 DFTAQMENSLDQVanheAEWKAVLDHFFSDFT----QQLDKAEKDPE 585
Cdd:TIGR01056 562 DLTAQWEQYLNGI----SAGEKDDDDFINTINemikQTINEEKKNPE 604
TOPRIM_TopoIA_TopoI cd03363
TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA ...
5-156 8.89e-61

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: 197.40  E-value: 8.89e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    5 KALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGsaakksadststktakkpkkdergalvnrMGVDPWHN-WEA 83
Cdd:cd03363   1 KKLVIVESPAKAKTIKKYLGKEYEVLASVGHIRDLPKKG-----------------------------LGVDGEDDgFEP 51
                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 7245299   84 HYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIgGDDARYSRVVFNEITKNAIRQAFNKP 156
Cdd:cd03363  52 KYVVIPGKKKVVKELKKLAKKADEIYLATDPDREGEAIAWHLAEVL-KLKKNVKRVVFNEITKEAIKEALKNP 123
PRK14973 PRK14973
DNA topoisomerase I; Provisional
89-588 4.14e-57

DNA topoisomerase I; Provisional


Pssm-ID: 184936 [Multi-domain]  Cd Length: 936  Bit Score: 206.62  E-value: 4.14e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    89 PGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGG--DDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNA 166
Cdd:PRK14973  81 PTEKKIVGLIQKLAKKADRVTIATDFDTEGELIGKEAYELVRAvnPKVPIDRARFSAITKEEIVTAFAEPTDLDFALAAA 160
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   167 QQARRFMDRVVGYMVSPLLWKKIARG----LSAGRVQSVAVRLVVEREREIKAFVPEEFWEVdASTTTPSGEALALQVTH 242
Cdd:PRK14973 161 GEARQIIDLIWGASLTRFISLAAHRGgdniLSVGRVQSPTLAMIVDREKEIEAFVPEKYWML-SLATEKDGEGIEARHTH 239
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   243 Q--NDKPFRPVNKEQTQAAVSLLEKARYSVLERedKPTtskpgaPFITSTLQQAAStRLGFGVKKTMMMAQRLYEAGYIT 320
Cdd:PRK14973 240 GrfTDSAAAEAAYDATKEPLVVTEVKEGHKVDR--APT------PFDTTTFIVAAS-RLGFSAANAMRIAEDLYMNGYIS 310
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   321 YMRTDST------NLSQDAVNMVRGYISDNFG--KKYLPESPNQyaSKENSQEaHEAIRPSDVnVMAESLKDmeaDAQKL 392
Cdd:PRK14973 311 YPRTDNTiypkslDLNGVLATLAKGAFSKDVAwvKDNRRPVPTR--GKKSSTD-HPPIHPTGV-ATREELGD---DRWKL 383
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   393 YQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKgdEDRILPAVNKGDALTLVELTPAQHF 472
Cdd:PRK14973 384 YELVVRRFLATLSPDAEWATMKVNFDAGGEPYTATGGRLLEAGWRTVYPYSEA--KENILPAFALGEKLPILAVNLEEKE 461
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   473 TKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYvrVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSL 552
Cdd:PRK14973 462 TQPPARYSQSRLIQRMEELGLGTKSTRHEVIGKLVSRKY--IEGNPLRPTLVGRAVTESLEEHAGTITEPDMTQTLEEHM 539
                        490       500       510
                 ....*....|....*....|....*....|....*.
gi 7245299   553 DQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGG 588
Cdd:PRK14973 540 QQIKERKRTRDDVVTESRKMLHRAFDELEANEAVIG 575
PTZ00407 PTZ00407
DNA topoisomerase IA; Provisional
7-556 8.62e-50

DNA topoisomerase IA; Provisional


Pssm-ID: 173597 [Multi-domain]  Cd Length: 805  Bit Score: 184.76  E-value: 8.62e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     7 LVIVESPAKAKTINKYLGSDYVVKS---SVGHIRDLPTSGSAAKKSADS------------------TSTKTAKKPKKDE 65
Cdd:PTZ00407  12 LVIVESPNKVIKVEGLLSDPKVIPDwsfKQSHLRRIGTGAEKAVAMATTghfmalkeitwspqasspASVVGAGDEPFPS 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    66 RGALVNrmgvdpwhnWEAHYEVLPGK---EKVVSELKQLAEKADHIYLATDLDREGEAIAWH----LREVIGGDDARYSR 138
Cdd:PTZ00407  92 NGTLAE---------YTLEWELLPGRriqETLERYIEEKADNVTEIILATDPDREGELIAVHalqtIKRLYPKLKVPFSR 162
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   139 VVFNEITKNAIRQAFNK--PGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAF 216
Cdd:PTZ00407 163 AYMHSITEDGIRKAMRErhVEACDYDLANAAETRHAMDRIFGFLGSSVVRAANSQMRSIGRVQTPALILINEREDKIKAF 242
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   217 VPEE--FWEVDAST--TTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYS-----VLEREDKPTTSK--PGAP 285
Cdd:PTZ00407 243 LESNksTFEVQAMCqfPSPHGTTFSQVVTITPDRKGGASHWATEAEARRCLEQWKLNnctgfSVPLEPKPQPSVvpPPQP 322
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   286 FITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYL--------------- 350
Cdd:PTZ00407 323 FTMATAIAKANRQLKYSSEMVSGCLQDLFQLGHITYPRTDSTRIDESALPDIYAAVKKEFGKEFLyrledrtvsaqegkg 402
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   351 ---PESPNQYASKENS-------QEAHEAIRPSDVNVMAESLKdMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTV--- 417
Cdd:PTZ00407 403 skkTGKKRSTKQKKGAdtpvgnvEDAHEAIRPTNIDTTGESLS-LSPPTRAVYDLVRRNTLAVFMIPMKTEKIVATVkft 481
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   418 -GAGD-FRLKARGRILRFDGWTKvmpALRKGDEDRILPAV----------------------------------NKGDAL 461
Cdd:PTZ00407 482 sGSGEkLEFELQGKRVVEPGWTR---AFHKGDKGTTGPAEetdeditaveegapvvpslsqeefkaimnlrsqlGSGVQK 558
                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   462 TLVELTPAQ---HFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENR-RFYAEKMGEIVTDRLEENFR 537
Cdd:PTZ00407 559 GFFELRSPQvreNRPVPPLPHSEGTLIEELKNNGVGRPSTYPMIVKTLLARGYIAVNPKgRCETTPVGRMLVETAKSTFP 638
                        650
                 ....*....|....*....
gi 7245299   538 ELMNYDFTAQMENSLDQVA 556
Cdd:PTZ00407 639 SIVDIGFTAAFEKKLDRIA 657
PRK08173 PRK08173
DNA topoisomerase III; Validated
3-517 3.81e-47

DNA topoisomerase III; Validated


Pssm-ID: 236172 [Multi-domain]  Cd Length: 862  Bit Score: 177.55  E-value: 3.81e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     3 MGKALVIVESPAKAKTINKYLG----------SD-YVVKSSVGHIRDLptsgsAAKKSADststktakkPKkdeRGAlvn 71
Cdd:PRK08173   1 MSKALIIAEKPSVANDIARALGgftkhdeyfeSDeYVLSSAVGHLLEI-----AAPEEYE---------VK---RGK--- 60
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    72 rmgvdpwhnWE-AHYEVLPGK------EKVVSELKQLAEKA-----DHIYLATDLDREGEAIAWHLREVIGGDDArYSRV 139
Cdd:PRK08173  61 ---------WSfAHLPVIPPHfdlnpiAKTESRLKVLTKLIkrkdvTRLINACDAGREGELIFRLIAQHAKAKKP-VKRL 130
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   140 VFNEITKNAIRQAFNK--PGELNIDRVNAQQARRFMDRVVGYMVSpllwkkiaRGLSA-------------GRVQSVAVR 204
Cdd:PRK08173 131 WLQSMTPQAIRDGFANlrSDEDMQPLADAARCRSEADWLVGINGT--------RAMTAfnskgggfflttvGRVQTPTLS 202
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   205 LVVEREREIKAFVPEEFWEVDASTTTPSG--------EALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLErEDK 276
Cdd:PRK08173 203 IVVEREEKIRRFVPRDYWEVRAEFVAAAGfyegrwfdPKFKKDEFDPEKRASRLWSEAAAEAIVAACRGKPGTVTE-ESK 281
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   277 PTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEA-GYITYMRTDSTNLSQDAVNMVRgyisDNFGKkyLPESPN 355
Cdd:PRK08173 282 PSTQLSPLLFDLTSLQREANGRFGFSAKNTLGLAQALYEKhKVLTYPRTDSRALPEDYLGTVK----QTLEM--LKESNN 355
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   356 --QYASK--------------ENSQEA-HEAIRPSdvNVMAESLKDMEadaQKLYQLIWRQFVACQMTPAKYDSTTLTVG 418
Cdd:PRK08173 356 ylPHAKQildkgwvkpnkrifDNSKISdHFAIIPT--LQAPKSLSEPE---QKLYDLVVKRFLAVFFPAAEFLVTTRITE 430
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   419 AGDFRLKARGRILRFDGWtKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELE--------- 489
Cdd:PRK08173 431 VAGHHFKTEGKVLVNPGW-LAVYGKEAQGADANLVPVQKGEKVKTDKIEAVALTTKPPARYNEATLLSAMEgagklvedd 509
                        570       580       590
                 ....*....|....*....|....*....|....*
gi 7245299   490 -------KRGIGRPSTYASIISTIQDRGYVRVENR 517
Cdd:PRK08173 510 elreamaEKGLGTPATRAAIIEGLLGEKYLVREGR 544
TOPRIM_TopoIA cd01028
TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
5-156 5.84e-43

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: 150.45  E-value: 5.84e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    5 KALVIVESPAKAKTINKYLGS------------DYVVKSSVGHIRDLPTsgsaakksadststktakkpkkDERGALVNR 72
Cdd:cd01028   1 KVLIIAEKPSKAKTIAKILGKgskkkgfygeggGYVVTASVGHLLELPF----------------------PEEYVDWDK 58
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   73 MGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQA 152
Cdd:cd01028  59 DWPLELFPFEPKYVVIPDKKKQLKALKKLAKKADEIVLATDPDREGELIAWEILEVLKCDNKPVKRAWFSEITPKAIREA 138

                ....
gi 7245299  153 FNKP 156
Cdd:cd01028 139 FKNL 142
TOP1Bc smart00436
Bacterial DNA topoisomeraes I ATP-binding domain; Extension of TOPRIM in Bacterial DNA ...
136-223 6.81e-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: 148.50  E-value: 6.81e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     136 YSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIAR-GLSAGRVQSVAVRLVVEREREIK 214
Cdd:smart00436   1 IKRIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRNgVLSAGRVQTPTLGLIVEREREIK 80

                   ....*....
gi 7245299     215 AFVPEEFWE 223
Cdd:smart00436  81 NFVPKPYWE 89
PRK14724 PRK14724
DNA topoisomerase III; Provisional
5-555 5.64e-36

DNA topoisomerase III; Provisional


Pssm-ID: 237803 [Multi-domain]  Cd Length: 987  Bit Score: 144.33  E-value: 5.64e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     5 KALVIVESPAKAKTI--------------NKYLGSD-YVVKSSVGHIRDLptsgsaakKSADSTSTKTAKkpkkderGAL 69
Cdd:PRK14724   2 KTLVIAEKPSVAQDIvraltpvagkfekhDEHFESDsYVVTSAVGHLVEI--------QAPEEFDVKRGK-------WSF 66
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    70 VNRMGVDPwhnweaHYEVLPgKEKVVSELK---QLAEKADHIYL--ATDLDREGEAIAWHLREVIGGDDARYSRVV---- 140
Cdd:PRK14724  67 ANLPVIPP------YFDLKP-VDKTKTRLNavvKLAKRKDVTELvnACDAGREGELIFRLIEQYAGGAKGGLGKPVkrlw 139
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   141 FNEITKNAIRQAFN--KPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARG-----LSAGRVQSVAVRLVVEREREI 213
Cdd:PRK14724 140 LQSMTPQAIRDGFDnlRSDAQMQGLASAARSRSEADWLVGINGTRAMTAFNSRDggfflTTVGRVQTPTLSLVVEREEKI 219
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   214 KAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPF--------RPVNKEQTQAAVSLLEKARYSVLErEDKPTTSKPGAP 285
Cdd:PRK14724 220 RKFVSRDYWEIHAGFHAEAGEYLGKWFDPQWKKASddpearadRVWSEREARAIADAVRGKAATVTE-ESKPTTQASPLL 298
                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   286 FITSTLQQAASTRLGFGVKKTMMMAQRLYEA-GYITYMRTDSTNLSQDAVNMVR---GYISDN-------FGKKYLPES- 353
Cdd:PRK14724 299 FDLTSLQREANGKFGFSAKTTLALAQSLYERhKALTYPRTDSRALPEDYLPVAKqtfEMLATSgmrhlapFAQQALDGNy 378
                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   354 --PNQYASKENSQEAHEAIRPSdvnVMAES-LKDMEadaQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRI 430
Cdd:PRK14724 379 vrPSKRIFDNSKVSDHFAIIPT---TQAPSgLSEAE---QKLYDLVVRRFMAVFFPSAEYQVTTRISQVVGHSFKTEGKV 452
                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   431 LRFDGWTKV--------MPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELE------------- 489
Cdd:PRK14724 453 LVKPGWLAIygkeaaneVEDAKDGDKGQPLVPVKPGEMVRTEFAEAKGLKTKPPARYSEATLLGAMEsagkqidddelre 532
                        570       580       590       600       610       620       630
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   490 ---KRGIGRPSTYASIISTIQDRGYVRVENRRFY-AEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQV 555
Cdd:PRK14724 533 amqEKGLGTPATRAAIIEGLLTEKYMLREGRELIpTAKAFQLMTLLRGLGVEELSRAELTGEWEYKLAQM 602
PRK14701 PRK14701
reverse gyrase; Provisional
6-317 4.46e-32

reverse gyrase; Provisional


Pssm-ID: 237791 [Multi-domain]  Cd Length: 1638  Bit Score: 132.71  E-value: 4.46e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299      6 ALVIVESPAKAKTINKYLGSDYVVK-------------------SSVGHIRDLPTSG----------------SAAKKSA 50
Cdd:PRK14701  582 ALMIVESPNKARTIANFFGQPSVRKigdlvayevsigdhmliitASGGHVFDLVTNEgfhgvlinnnlfipiyDSIKRCR 661
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     51 DSTSTKTAKKPKKD-ERGALVNrmgvdpwhnweahyeVLPGKEKVVSeLKQLAEKADHIYLATDLDREGEAIAWHLREVI 129
Cdd:PRK14701  662 DCGHQFTDWEDKGVcPRCGSKN---------------VDDAKENIKA-MRELAHEVDEILIGTDPDTEGEKIAWDIRNVL 725
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    130 GGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKI-ARGLSAGRVQSVAVRLVVE 208
Cdd:PRK14701  726 APYGPNIKRIEFHEVTRRAILKAIKEARDIDENRVKAQIVRRIEDRWIGFELSQKLWEVFeDRNLSAGRVQTPVLGWIIQ 805
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    209 REREIKAFvpeefwEVDASTTTPSGEalaLQVTHQNDkpfrpvnKEQTQAAVSLLEkarysvLEREDKPttskPGAPFIT 288
Cdd:PRK14701  806 RYKEFTES------KVPFLGIILEND---LTVTIEDS-------KDEVEVEVELVE------EEEKERN----PLPPYTT 859
                         330       340
                  ....*....|....*....|....*....
gi 7245299    289 STLQQAASTRLGFGVKKTMMMAQRLYEAG 317
Cdd:PRK14701  860 DTMLRDASAFLKLSAKETMKLAQDLFEAG 888
PRK14701 PRK14701
reverse gyrase; Provisional
320-572 1.30e-29

reverse gyrase; Provisional


Pssm-ID: 237791 [Multi-domain]  Cd Length: 1638  Bit Score: 125.00  E-value: 1.30e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    320 TYMRTDSTNLSQDAVNMVRGYISDNFGKKYLpeSPNQYASkensQEAHEAIRPS---DVNVMAESLKD-------MEADA 389
Cdd:PRK14701 1382 TYHRTDSTRVSNTGIRVAREYLTQENGEDYF--KPRDWFM----EGAHECIRPTrpiDTDRLIQLIREgiiqvpgLTRNH 1455
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    390 QKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRI-LRFDGWTKVM-PALRKgdedriLPAVNKGDaltlVELT 467
Cdd:PRK14701 1456 LRLYDLIFRRFMASQMKPAKVLYEKALIRYDGKDVEVEGYVeIEGDGWSRLYsLPLRV------LPKLEKGK----LKVL 1525
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    468 PAQHFTKPPAR-FSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRR--FYAEKMGEIVTDRLEENFRELMNYDF 544
Cdd:PRK14701 1526 EAKIRKAPKVPlYTQGDIVALMKERGIGRPSTYAKIVDTLLMRGYVIETKGRkkLIPTKKGIKVYNYLISNYGDLVSEER 1605
                         250       260
                  ....*....|....*....|....*...
gi 7245299    545 TAQMENSLDQVANHEAEWKAVLDHFFSD 572
Cdd:PRK14701 1606 TRELEEIMDAVEEGELDYIKVLQELYEE 1633
TOPRIM_TopoIA_TopoIII cd03362
TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type ...
5-156 2.47e-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: 2.47e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    5 KALVIVESPAKAKTI------------------NKYLGSDYVVKSSVGHIRDLptsgsaakksadststktakkpkkDER 66
Cdd:cd03362   1 MVLIIAEKPSVAKAIakilgggskkkgkgryyeFYGEGGGYVVTWASGHLLEL------------------------DFP 56
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   67 GALVNRMGVDPWHN----WEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIG-GDDARYSRVVF 141
Cdd:cd03362  57 EEYDPWDKVWPLEDplfpAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKcVKRKPVKRAWF 136
                       170
                ....*....|....*
gi 7245299  142 NEITKNAIRQAFNKP 156
Cdd:cd03362 137 SSLTPKAIRRAFKNL 151
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
6-144 1.46e-18

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: 80.44  E-value: 1.46e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299      6 ALVIVESPAKAKTINKYLGSDY-VVKSSVGHIRDLPtsgsaakksadststktakkpkkdergalvnrmgvdpwhnweah 84
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGFqAVVAVLGHLLSLA-------------------------------------------- 36
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299     85 yevlpgKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEI 144
Cdd:pfam01751  37 ------TKDKLKALKELALKAKEVILATDPDREGEAIALKLLTLKELLEAAGGRVKISEL 90
TOPRIM_TopoIA_RevGyr cd03361
TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA ...
6-156 1.09e-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: 80.44  E-value: 1.09e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    6 ALVIVESPAKAKTINKYLG-----------------SDYV--VKSSVGHIRDLPTSG----------------SAAKKSA 50
Cdd:cd03361   2 ALMIVESPNKARTIANFFGrpsvrrlgglvvyevstGDGVlmITASGGHVYDLVTKEgghgvveddgryvpvyDSIKRCR 81
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299   51 DSTSTKTAKKPKKDERGAlvnrmgvdpwhnweahyEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIG 130
Cdd:cd03361  82 DCGYQFTEDSDKCPRCGS-----------------ENIDDKLETLEALRELALEVDEVLIATDPDTEGEKIAWDVYLALR 144
                       170       180
                ....*....|....*....|....*.
gi 7245299  131 GDDARYSRVVFNEITKNAIRQAFNKP 156
Cdd:cd03361 145 PYNKNIKRAEFHEVTRRAILEALRNP 170
TOPRIM smart00493
topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins;
5-133 1.37e-14

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


Pssm-ID: 214695 [Multi-domain]  Cd Length: 75  Bit Score: 68.83  E-value: 1.37e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299       5 KALVIVESPAKAKTINKYLGSDYVVKSSVGHIRdlptsgsaakksadststktakkpkkdergalvnrmgvdpwhnweah 84
Cdd:smart00493   1 KVLIIVEGPADAIALEKAGGKRGNVVALGGHLL----------------------------------------------- 33
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 7245299      85 yevlpgKEKVVSELKQLAEKAdHIYLATDLDREGEAIAWHLREVIGGDD 133
Cdd:smart00493  34 ------SKEQIKLLKKLAKKA-EVILATDPDREGEAIAWELAELLKPAG 75
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
5-141 2.21e-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: 57.05  E-value: 2.21e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7245299    5 KALVIVESPAKAKTINKYLGSDYVVKSSVGHIRdlptsgsaakksadststktakkpkkdergalvnrmgvdpwhnweah 84
Cdd:cd00188   1 KKLIIVEGPSDALALAQAGGYGGAVVALGGHAL----------------------------------------------- 33
                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 7245299   85 yevlpgkEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVF 141
Cdd:cd00188  34 -------NKTRELLKRLLGEAKEVIIATDADREGEAIALRLLELLKSLGKKVRRLLL 83
 
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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