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Conserved domains on  [gi|117956933|gb|ABK58982|]
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topoisomerase I, partial [Vibrio parahaemolyticus]

Protein Classification

type I DNA topoisomerase( domain architecture ID 1000362)

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

EC:  5.6.2.1
Gene Ontology:  GO:0003917|GO:0003677|GO:0006265|GO:0046872
PubMed:  19208647|17293019|9748482|7770916|12042765
SCOP:  4007652|4002819

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK07561 super family cl35595
DNA topoisomerase I subunit omega; Validated
 1-221 2.54e-150

DNA topoisomerase I subunit omega; Validated


The actual alignment was detected with superfamily member PRK07561:

Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 438.84  E-value: 2.54e-150
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   1 VFNEITKNAIQQAFQTPGELNMDGVNAQQARRFMDRVVGFMVSPLLWKKVARGLSAGRVQSVAVKLLVEREREINAFVPE 80
Cdd:PRK07561 122 VFNEITKNAIQEAFENPRELDINLVNAQQARRFLDRLVGYMVSPLLWKKIARGLSAGRVQSVAVRLIVEREREIEAFVPE 201

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933  81 EFWDIHANTKTKDKSDFKLLVAQKDGVAFKPV---NETETKAAISVLENASYEVCKREDRPTKSKPSAPYITSTLQQAAS 157
Cdd:PRK07561 202 EYWDIHADLTTPRGDAFEARLTHLDGKKFAPVdllNEAQAEAAVAALEGARYSVASVEDKPTTRKPSAPFTTSTLQQEAS 281

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 117956933 158 TRLGYGVKKTMMLAQRLYEAGYITYMRTDSTNLSAEAVDAVRDFIGSEFGDKYLPAKPLTYGSK 221
Cdd:PRK07561 282 RKLGFSVKKTMRIAQRLYEAGYITYMRTDSTNLSQEAINAARGYIGDNYGKKYLPEKPRQYSSK 345
 
Name Accession Description Interval E-value
PRK07561 PRK07561
DNA topoisomerase I subunit omega; Validated
 1-221 2.54e-150

DNA topoisomerase I subunit omega; Validated


Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 438.84  E-value: 2.54e-150
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   1 VFNEITKNAIQQAFQTPGELNMDGVNAQQARRFMDRVVGFMVSPLLWKKVARGLSAGRVQSVAVKLLVEREREINAFVPE 80
Cdd:PRK07561 122 VFNEITKNAIQEAFENPRELDINLVNAQQARRFLDRLVGYMVSPLLWKKIARGLSAGRVQSVAVRLIVEREREIEAFVPE 201

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933  81 EFWDIHANTKTKDKSDFKLLVAQKDGVAFKPV---NETETKAAISVLENASYEVCKREDRPTKSKPSAPYITSTLQQAAS 157
Cdd:PRK07561 202 EYWDIHADLTTPRGDAFEARLTHLDGKKFAPVdllNEAQAEAAVAALEGARYSVASVEDKPTTRKPSAPFTTSTLQQEAS 281

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 117956933 158 TRLGYGVKKTMMLAQRLYEAGYITYMRTDSTNLSAEAVDAVRDFIGSEFGDKYLPAKPLTYGSK 221
Cdd:PRK07561 282 RKLGFSVKKTMRIAQRLYEAGYITYMRTDSTNLSQEAINAARGYIGDNYGKKYLPEKPRQYSSK 345
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
1-222 4.78e-117

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 343.62  E-value: 4.78e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   1 VFNEITKNAIQQAFQTPGELNMDGVNAQQARRFMDRVVGFMVSPLLWKKVARGLSAGRVQSVAVKLLVEREREINAFVPE 80
Cdd:COG0550  106 VFNEITKKAIKEAFKNPRDIDMNLVDAQQARRILDRLVGYNLSPLLWKKVKRGLSAGRVQSPALRLIVEREREIEAFVPE 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933  81 EFWDIHANTKTKDKSdFKLLVAQKDGVAFKpvNETETKAAISVLENASYEVCKREDRPTKSKPSAPYITSTLQQAASTRL 160
Cdd:COG0550  186 EYWTIEATFKTGGGE-FTAKLVKIDGKKIL--DEEEAEAILAALKGKTFTVTSVEKKPKKRNPPPPFTTSTLQQEASRKL 262

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 117956933 161 GYGVKKTMMLAQRLYEAGYITYMRTDSTNLSAEAVDAVRDFIGSEFGDKYLPAKPLTYGSKE 222
Cdd:COG0550  263 GFSAKKTMSIAQRLYEVGLITYMRTDSVRLSEDAVAAAREYIEALYGKEYLPEKPRVYKTSK 324
topA_bact TIGR01051
DNA topoisomerase I, bacterial; This model describes DNA topoisomerase I among the members of ...
 1-222 1.60e-107

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: 321.64  E-value: 1.60e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933    1 VFNEITKNAIQQAFQTPGELNMDGVNAQQARRFMDRVVGFMVSPLLWKKVARGLSAGRVQSVAVKLLVEREREINAFVPE 80
Cdd:TIGR01051 105 VFNEITKKAIRAALKNPREIDMNLVNAQQARRILDRLVGYTLSPLLWKKVAKGLSAGRVQSVALRLIVDREREIKRFVPE 184

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   81 EFWDIHAnTKTKDKSDFKLLVAQKDG---VAFKPVNETETKAAISVLENASYEVCKREDRPTKSKPSAPYITSTLQQAAS 157
Cdd:TIGR01051 185 EYWTIDA-TFQKGEETFEALLTEVNGkklKAGSDLDEAEATALKEQLKGEELVVEEIEKKPKKSRPPPPFTTSTLQQEAS 263

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 117956933  158 TRLGYGVKKTMMLAQRLYEA--------GYITYMRTDSTNLSAEAVDAVRDFIGSEFGDKYLPAKPLTYGSKE 222
Cdd:TIGR01051 264 RKLGFSAKKTMMIAQRLYEGvstgdgtiGLITYMRTDSTRLSNQAVNEARNLIDKNYGKEYLGPKPKRYKSKE 336
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
 19-215 4.09e-69

DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA.


Pssm-ID: 426069 [Multi-domain]  Cd Length: 410  Bit Score: 217.11  E-value: 4.09e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   19 ELNMDGVNAQQARRFMDRVVGFMVSPLLWKKV--ARGLSAGRVQSVAVKLLVEREREINAFVPEEFWDIHANTKTKDKSd 96
Cdd:pfam01131   1 EIDENLVDAQLARRELDWLIGFNLSRLLTLKLkgNKLLSAGRVQTPTLALIVEREREIENFVPEPYWTIEATLKDGGGV- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   97 fkLLVAQKDGVAFKpvNETETKAAISVLENASYEVCKREDRPTKSKPSAPYITSTLQQAASTRLGYGVKKTMMLAQRLYE 176
Cdd:pfam01131  80 --FANAKWKRGRIF--DKEEAEAILEKLKKGTAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQKLYE 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 117956933  177 -AGYITYMRTDSTNLSAEA-VDAVRDFIGSEFGdKYLPAKP 215
Cdd:pfam01131 156 kHGLITYPRTDSTYLSDDAtLKAILEYLTKNYG-KYLPYAP 195
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 22-221 1.35e-65

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: 207.07  E-value: 1.35e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933  22 MDGVNAQQARRFMDRVVGFMVSPLLWKKVAR--GLSAGRVQSVAVKLLVEREREINAFVPEEFWDIHAntktkdksdfkl 99
Cdd:cd00186    1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRkgVLSAGRVQSPTLGLIVEREREIKAFVPEDYWEIKE------------ 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933 100 lvaqkdgvafkpvnetetkaaisvlenasYEVCKREDRPTKSKPSAPYITSTLQQAASTRLGYGVKKTMMLAQRLYEAGY 179
Cdd:cd00186   69 -----------------------------AVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGL 119

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 117956933 180 ITYMRTDSTNLSAEAVDAVRDFIGSEFGDKYLPAKPLTYGSK 221
Cdd:cd00186  120 ITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLGRRN 161
TOP1Bc smart00436
Bacterial DNA topoisomeraes I ATP-binding domain; Extension of TOPRIM in Bacterial DNA ...
 1-84 1.90e-41

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: 135.79  E-value: 1.90e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933     1 VFNEITKNAIQQAFQTPGELNMDGVNAQQARRFMDRVVGFMVSPLLWKKVAR-GLSAGRVQSVAVKLLVEREREINAFVP 79
Cdd:smart00436   5 EFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRNgVLSAGRVQTPTLGLIVEREREIKNFVP 84


                   ....*
gi 117956933    80 EEFWD 84
Cdd:smart00436  85 KPYWE 89
 
Name Accession Description Interval E-value
PRK07561 PRK07561
DNA topoisomerase I subunit omega; Validated
 1-221 2.54e-150

DNA topoisomerase I subunit omega; Validated


Pssm-ID: 236048 [Multi-domain]  Cd Length: 859  Bit Score: 438.84  E-value: 2.54e-150
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   1 VFNEITKNAIQQAFQTPGELNMDGVNAQQARRFMDRVVGFMVSPLLWKKVARGLSAGRVQSVAVKLLVEREREINAFVPE 80
Cdd:PRK07561 122 VFNEITKNAIQEAFENPRELDINLVNAQQARRFLDRLVGYMVSPLLWKKIARGLSAGRVQSVAVRLIVEREREIEAFVPE 201

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933  81 EFWDIHANTKTKDKSDFKLLVAQKDGVAFKPV---NETETKAAISVLENASYEVCKREDRPTKSKPSAPYITSTLQQAAS 157
Cdd:PRK07561 202 EYWDIHADLTTPRGDAFEARLTHLDGKKFAPVdllNEAQAEAAVAALEGARYSVASVEDKPTTRKPSAPFTTSTLQQEAS 281

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 117956933 158 TRLGYGVKKTMMLAQRLYEAGYITYMRTDSTNLSAEAVDAVRDFIGSEFGDKYLPAKPLTYGSK 221
Cdd:PRK07561 282 RKLGFSVKKTMRIAQRLYEAGYITYMRTDSTNLSQEAINAARGYIGDNYGKKYLPEKPRQYSSK 345
TopA COG0550
DNA topoisomerase IA [Replication, recombination and repair];
1-222 4.78e-117

DNA topoisomerase IA [Replication, recombination and repair];


Pssm-ID: 440316 [Multi-domain]  Cd Length: 541  Bit Score: 343.62  E-value: 4.78e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   1 VFNEITKNAIQQAFQTPGELNMDGVNAQQARRFMDRVVGFMVSPLLWKKVARGLSAGRVQSVAVKLLVEREREINAFVPE 80
Cdd:COG0550  106 VFNEITKKAIKEAFKNPRDIDMNLVDAQQARRILDRLVGYNLSPLLWKKVKRGLSAGRVQSPALRLIVEREREIEAFVPE 185

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933  81 EFWDIHANTKTKDKSdFKLLVAQKDGVAFKpvNETETKAAISVLENASYEVCKREDRPTKSKPSAPYITSTLQQAASTRL 160
Cdd:COG0550  186 EYWTIEATFKTGGGE-FTAKLVKIDGKKIL--DEEEAEAILAALKGKTFTVTSVEKKPKKRNPPPPFTTSTLQQEASRKL 262

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 117956933 161 GYGVKKTMMLAQRLYEAGYITYMRTDSTNLSAEAVDAVRDFIGSEFGDKYLPAKPLTYGSKE 222
Cdd:COG0550  263 GFSAKKTMSIAQRLYEVGLITYMRTDSVRLSEDAVAAAREYIEALYGKEYLPEKPRVYKTSK 324
PRK06599 PRK06599
DNA topoisomerase I; Validated
 1-221 3.24e-109

DNA topoisomerase I; Validated


Pssm-ID: 235840 [Multi-domain]  Cd Length: 675  Bit Score: 327.97  E-value: 3.24e-109
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   1 VFNEITKNAIQQAFQTPGELNMDGVNAQQARRFMDRVVGFMVSPLLWKKVARGLSAGRVQSVAVKLLVEREREINAFVPE 80
Cdd:PRK06599 112 VFNEITKKAVQEAIENPRDIDMDLVDAQQARRALDYLVGFKLSPLLWKKVRRGLSAGRVQSVALRLICEREDEIEAFIPQ 191

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933  81 EFWDIHANTKTKDKSDFKLLVAQKDG---VAFKPVNETETKAAISVLENASYEVCKREDRPTKSKPSAPYITSTLQQAAS 157
Cdd:PRK06599 192 EYWTIEADLATSNGEPFTAKLVEVNGkklEKFSITNEEQAKALVKALEGQAYTVDKIEKKERKRNPPPPFITSTLQQEAS 271

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 117956933 158 TRLGYGVKKTMMLAQRLYEA--------GYITYMRTDSTNLSAEAVDAVRDFIGSEFGDKYLPAKPLTYGSK 221
Cdd:PRK06599 272 RKLGFSAKKTMRIAQKLYEGidlgegtvGLITYMRTDSVRLSNEALDEARKYITKKYGKEYLPAKPRVYKKK 343
topA_bact TIGR01051
DNA topoisomerase I, bacterial; This model describes DNA topoisomerase I among the members of ...
 1-222 1.60e-107

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: 321.64  E-value: 1.60e-107
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933    1 VFNEITKNAIQQAFQTPGELNMDGVNAQQARRFMDRVVGFMVSPLLWKKVARGLSAGRVQSVAVKLLVEREREINAFVPE 80
Cdd:TIGR01051 105 VFNEITKKAIRAALKNPREIDMNLVNAQQARRILDRLVGYTLSPLLWKKVAKGLSAGRVQSVALRLIVDREREIKRFVPE 184

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   81 EFWDIHAnTKTKDKSDFKLLVAQKDG---VAFKPVNETETKAAISVLENASYEVCKREDRPTKSKPSAPYITSTLQQAAS 157
Cdd:TIGR01051 185 EYWTIDA-TFQKGEETFEALLTEVNGkklKAGSDLDEAEATALKEQLKGEELVVEEIEKKPKKSRPPPPFTTSTLQQEAS 263

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 117956933  158 TRLGYGVKKTMMLAQRLYEA--------GYITYMRTDSTNLSAEAVDAVRDFIGSEFGDKYLPAKPLTYGSKE 222
Cdd:TIGR01051 264 RKLGFSAKKTMMIAQRLYEGvstgdgtiGLITYMRTDSTRLSNQAVNEARNLIDKNYGKEYLGPKPKRYKSKE 336
PRK08780 PRK08780
DNA topoisomerase I; Provisional
 1-221 2.94e-72

DNA topoisomerase I; Provisional


Pssm-ID: 181555 [Multi-domain]  Cd Length: 780  Bit Score: 233.89  E-value: 2.94e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   1 VFNEITKNAIQQAFQTPGELNMDGVNAQQARRFMDRVVGFMVSPLLWKKVARGLSAGRVQSVAVKLLVEREREINAFVPE 80
Cdd:PRK08780 113 VFTEITPRAIKEAMAKPRDIASDLVDAQQARRALDYLVGFNLSPLLWRKIQRGLSAGRVQSPALRMIVEREEEIEAFIAR 192

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933  81 EFWDIHANTKtKDKSDFKLLVAQKDGVAFKP---VNETETKAAISVLENAS---YEVCKREDRPTKSKPSAPYITSTLQQ 154
Cdd:PRK08780 193 EYWSIEADCA-HPSQPFNAKLIKLDGQKFEQftiTDGDTAEAARLRIQQAAqgtLHVTDVESKERKRNPAPPFTTSTLQQ 271

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 117956933 155 AASTRLGYGVKKTMMLAQRLYEA---------GYITYMRTDSTNLSAEAVDAVRDFIGSEFGDKYLPAKPLTYGSK 221
Cdd:PRK08780 272 EASRKLGFTTRRTMQVAQKLYEGvdlgdegsvGLITYMRTDSVNLSQDALAEIRDVIARDYGTASLPDQPNTYKTK 347
Topoisom_bac pfam01131
DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes ...
 19-215 4.09e-69

DNA topoisomerase; This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA.


Pssm-ID: 426069 [Multi-domain]  Cd Length: 410  Bit Score: 217.11  E-value: 4.09e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   19 ELNMDGVNAQQARRFMDRVVGFMVSPLLWKKV--ARGLSAGRVQSVAVKLLVEREREINAFVPEEFWDIHANTKTKDKSd 96
Cdd:pfam01131   1 EIDENLVDAQLARRELDWLIGFNLSRLLTLKLkgNKLLSAGRVQTPTLALIVEREREIENFVPEPYWTIEATLKDGGGV- 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   97 fkLLVAQKDGVAFKpvNETETKAAISVLENASYEVCKREDRPTKSKPSAPYITSTLQQAASTRLGYGVKKTMMLAQRLYE 176
Cdd:pfam01131  80 --FANAKWKRGRIF--DKEEAEAILEKLKKGTAVVTSVESKEKKKPPPLPFNTTTLQKEASRKLGFSAKKTMSIAQKLYE 155

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|.
gi 117956933  177 -AGYITYMRTDSTNLSAEA-VDAVRDFIGSEFGdKYLPAKP 215
Cdd:pfam01131 156 kHGLITYPRTDSTYLSDDAtLKAILEYLTKNYG-KYLPYAP 195
PRK06319 PRK06319
DNA topoisomerase I/SWI domain fusion protein; Validated
 2-222 9.26e-67

DNA topoisomerase I/SWI domain fusion protein; Validated


Pssm-ID: 235778 [Multi-domain]  Cd Length: 860  Bit Score: 220.08  E-value: 9.26e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   2 FNEITKNAIQQAFQTPGELNMDGVNAQQARRFMDRVVGFMVSPLLWKKVAR--GLSAGRVQSVAVKLLVEREREINAFVP 79
Cdd:PRK06319 109 FNAITKGAVTEALKHPREIDMALVNAQQARRLLDRIVGYKISPILSRKLQRrsGVSAGRVQSVALKLVVDREKAIEAFVP 188

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933  80 EEFWDIHANTKT-KDKSDFKLLVAQKDGVAFKPV--------------NETETKAAISVLENASYEVCKREDRPTKSKPS 144
Cdd:PRK06319 189 VEYWNIRVHLKDpKTQKTFWAHLYSVDGKKWEKEipegktedevllinSKEKADHIVELLESATYTVTRVESKEKRRNAY 268

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933 145 APYITSTLQQAASTRLGYGVKKTMMLAQRLYEA---------GYITYMRTDSTNLSAEAVDAVRDFIGSEFGDKYLPAKP 215
Cdd:PRK06319 269 PPFITSTLQQEASRHFRFSSSRTMNIAQTLYEGvdldsegatGLITYMRTDSVRTDPEALKQVRKYIEGTFGKEFLPSSP 348


                 ....*..
gi 117956933 216 LTYGSKE 222
Cdd:PRK06319 349 NVYTTKK 355
TOP1Ac cd00186
DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA ...
 22-221 1.35e-65

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: 207.07  E-value: 1.35e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933  22 MDGVNAQQARRFMDRVVGFMVSPLLWKKVAR--GLSAGRVQSVAVKLLVEREREINAFVPEEFWDIHAntktkdksdfkl 99
Cdd:cd00186    1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRkgVLSAGRVQSPTLGLIVEREREIKAFVPEDYWEIKE------------ 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933 100 lvaqkdgvafkpvnetetkaaisvlenasYEVCKREDRPTKSKPSAPYITSTLQQAASTRLGYGVKKTMMLAQRLYEAGY 179
Cdd:cd00186   69 -----------------------------AVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGL 119

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 117956933 180 ITYMRTDSTNLSAEAVDAVRDFIGSEFGDKYLPAKPLTYGSK 221
Cdd:cd00186  120 ITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLGRRN 161
TOP1Bc smart00436
Bacterial DNA topoisomeraes I ATP-binding domain; Extension of TOPRIM in Bacterial DNA ...
 1-84 1.90e-41

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: 135.79  E-value: 1.90e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933     1 VFNEITKNAIQQAFQTPGELNMDGVNAQQARRFMDRVVGFMVSPLLWKKVAR-GLSAGRVQSVAVKLLVEREREINAFVP 79
Cdd:smart00436   5 EFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRNgVLSAGRVQTPTLGLIVEREREIKNFVP 84


                   ....*
gi 117956933    80 EEFWD 84
Cdd:smart00436  85 KPYWE 89
TopG2 COG1110
Reverse gyrase [Replication, recombination and repair];
2-220 5.21e-40

Reverse gyrase [Replication, recombination and repair];


Pssm-ID: 440727 [Multi-domain]  Cd Length: 1219  Bit Score: 145.50  E-value: 5.21e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933    2 FNEITKNAIQQAFQTPGELNMDGVNAQQARRFMDRVVGFMVSPLLWKKVARG-LSAGRVQSVAVKLLVEREreinafvpE 80
Cdd:COG1110   787 FHEVTRKAILEALKNPREIDENLVEAQIVRRIEDRWIGFTLSQKLWKVFGNRnLSAGRVQTPVLGWIIERY--------E 858

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   81 EFwdihantkTKDKSDFKLLVAQKDGVAFKPVNETETKAAISVLENASY-EVCKREDRPTKSKPSAPYITSTLQQAASTR 159
Cdd:COG1110   859 ES--------RKSKKYLIILTLENGRLELSIEDLKEAEEVRKALEKEVKvKVKKVEEEEEELNPLPPYTTDTLLRDASRR 930

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 117956933  160 LGYGVKKTMMLAQRLYEAGYITYMRTDSTNLSAEAVDAVRDFIGSEFGDKYLpaKPLTYGS 220
Cdd:COG1110   931 LGLSAEETMRLAQDLFESGLITYHRTDSTRVSDAGIAVAKEYISERFGEEYF--KPRRWGE 989
rgy TIGR01054
reverse gyrase; This model describes reverse gyrase, found in both archaeal and bacterial ...
 2-219 1.42e-36

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: 135.73  E-value: 1.42e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933     2 FNEITKNAIQQAFQTPGELNMDGVNAQQARRFMDRVVGFMVSPLLWKKVA-RGLSAGRVQSVAVKLLVEREREINAFVPE 80
Cdd:TIGR01054  756 FHEVTRRAILEALESPRSVDENLVKAQVVRRIEDRWIGFTLSQKLWEAFNkRWLSAGRVQTPVLGWIIDRYRESREKRGY 835

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933    81 EFwdIHANtktkdKSDFKLLVAQKDGVAFKPVNETETKAAISVLENasyevcKREDRPtkskPSAPYITSTLQQAASTRL 160
Cdd:TIGR01054  836 LL--IFAL-----ESDFRLGLEHDNRLEAKEFEKDLTWLDVEDIAE------REEERN----PLPPYTTDTMLEDANRKL 898

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 117956933   161 GYGVKKTMMLAQRLYEAGYITYMRTDSTNLSAEAVDAVRDFIGSEFGDKYLpaKPLTYG 219
Cdd:TIGR01054  899 GLSVKETMQIAQELFENGLITYHRTDSTRVSDVGMRVAKEYLASRLGGEYF--YPREWG 955
PRK07219 PRK07219
DNA topoisomerase I; Validated
 2-188 3.26e-35

DNA topoisomerase I; Validated


Pssm-ID: 235971 [Multi-domain]  Cd Length: 822  Bit Score: 131.66  E-value: 3.26e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   2 FNEITKNAIQQAFQTPGELNMDGVNAQQARRFMDRVVG------FMVSPllwKKVARG--LSAGRVQSVAVKLLVERERE 73
Cdd:PRK07219 135 FSSLTKKEIRKAFENPDEIDFNLADAGEARQIIDLYWGaaltrfLSLSV---RQLGRWdfLSVGRVQTPTLAFIVDRERE 211

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933  74 INAFVPEEFWDIHANTKTKdksdfkllvAQKDGVAFKPVNETE-------TKAAISVLENA-SYEVCKREDRPTKSKPSA 145
Cdd:PRK07219 212 IRAFDPEDYWKIEALLDKE---------AQYFYRDLIGGHEAEkfwdeeeAEEIYEKLKGAkEATVSSVKKRERTISPPA 282

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 117956933 146 PYITSTLQQAASTRLGYGVKKTMMLAQRLYEAGYITYMRTDST 188
Cdd:PRK07219 283 PFNTTEFLREASKIFGISPKRAMEIAEKLYTAGYISYPRTDNT 325
TOP1Ac smart00437
Bacterial DNA topoisomerase I DNA-binding domain; Bacterial DNA topoisomerase I and III, ...
 135-212 1.10e-31

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: 116.19  E-value: 1.10e-31
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 117956933   135 EDRPTKSKPSAPYITSTLQQAASTRLGYGVKKTMMLAQRLYEAGYITYMRTDSTNLSAEAVDAVRDFIGSEFGDKYLP 212
Cdd:smart00437   1 EEKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYIQKLYGKEYLD 78
PRK07220 PRK07220
DNA topoisomerase I; Validated
 2-222 5.28e-27

DNA topoisomerase I; Validated


Pssm-ID: 180892 [Multi-domain]  Cd Length: 740  Bit Score: 107.92  E-value: 5.28e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   2 FNEITKNAIQQAFQTPGELNMDGVNAQQARRFMDRVVGFMVSPLLWKKVAR-G---LSAGRVQSVAVKLLVEREREINAF 77
Cdd:PRK07220 136 YSAITKKEIERAFSNPVEVDFNLADAGHSRQVIDLVWGAALTRYISLAAGRlGkmfLSVGRVQSPTLALIVDREKEREAF 215

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933  78 VPEEFWDIHAnTKTKDKSDFkllVAQKDGVAFKpvnetETKAAISVLENAS--YEVCKREDRPTKSKPSAPYITSTLQQA 155
Cdd:PRK07220 216 VPTPYWEIYA-TLENNGETF---VAQHSTRRFW-----EKEEADRVFEKLGktAEVTEVEKGTKTDKPPTPFNTTEFISA 286

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 117956933 156 ASTrLGYGVKKTMMLAQRLYEAGYITYMRTDSTnLSAEAVDaVRDFIG-------SEFGDKYLPAKPL--TYGSKE 222
Cdd:PRK07220 287 ANS-IGFSAANAMRIAESLYTNGYISYPRTDNT-VYPESLD-LREQIEifaegpfGEYAQKLLEKGELvpTRGKKE 359
PRK07726 PRK07726
DNA topoisomerase 3;
54-200 6.99e-26

DNA topoisomerase 3;


Pssm-ID: 236078 [Multi-domain]  Cd Length: 658  Bit Score: 104.86  E-value: 6.99e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933  54 LSAGRVQSVAVKLLVEREREINAFVPEEFWDIHAntKTKDKSDFKLLVAQKDGVAFKP---VNETETKAAISVLENASYE 130
Cdd:PRK07726 187 LSVGRVQTPTLALVVRRDEEIENFVPKPYWEVEA--HLTPGERFTAKWQPSEPYQDEEgrlLDRPLAEQVVARIQGQPAK 264

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 117956933 131 VCKREDRPTKSKPSAPYITSTLQQAASTRLGYGVKKTMMLAQRLYE-AGYITYMRTDSTNLSAEAVDAVRD 200
Cdd:PRK07726 265 VTEVETKRKKEYAPLLYDLSELQIDANKRFGLSAKETLDIAQSLYEtHKLITYPRTDSRYLPEDMVATLPE 335
PRK14973 PRK14973
DNA topoisomerase I; Provisional
 2-188 1.52e-25

DNA topoisomerase I; Provisional


Pssm-ID: 184936 [Multi-domain]  Cd Length: 936  Bit Score: 103.77  E-value: 1.52e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   2 FNEITKNAIQQAFQTPGELNMDGVNAQQARRFMDRVVGFMVSPLLWKKVARG----LSAGRVQSVAVKLLVEREREINAF 77
Cdd:PRK14973 135 FSAITKEEIVTAFAEPTDLDFALAAAGEARQIIDLIWGASLTRFISLAAHRGgdniLSVGRVQSPTLAMIVDREKEIEAF 214

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933  78 VPEEFWDI--------------HANTKTKDKsdfKLLVAQKDGVAfKPVNETETKAAisvlenasyevcKREDR-PTksk 142
Cdd:PRK14973 215 VPEKYWMLslatekdgegiearHTHGRFTDS---AAAEAAYDATK-EPLVVTEVKEG------------HKVDRaPT--- 275

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 117956933 143 psaPYITSTLQQAAStRLGYGVKKTMMLAQRLYEAGYITYMRTDST 188
Cdd:PRK14973 276 ---PFDTTTFIVAAS-RLGFSAANAMRIAEDLYMNGYISYPRTDNT 317
PRK05776 PRK05776
DNA topoisomerase I; Provisional
 2-190 1.20e-24

DNA topoisomerase I; Provisional


Pssm-ID: 235602 [Multi-domain]  Cd Length: 670  Bit Score: 101.22  E-value: 1.20e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   2 FNEITKNAIQQAFQTPGELNMDGVNAQQARRFMDRVVGFMVSPLLWK--KVARG----LSAGRVQSVAVKLLVEREREIN 75
Cdd:PRK05776 132 FSALTKSDIRRAFRNLETLDYEMINAGIARHELDWLWGINVSRALMSsvRDASGkrviLSAGRVQSPTLKYVVEREIERN 211

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933  76 AFVPEEFWDIHANTKTKDKSdFKLLVAQKdgvafKPVNETETKAAISVLENASY-EVCKREDRPTKSKPSAPYITSTLQQ 154
Cdd:PRK05776 212 LFVPLPYFSVSIIIEKNGYE-FTLKYENK-----KFETKEEAKEILEEIKKTGYlKVTKVEVKIEILEPPPPFNLGDLQV 285

                        170       180       190
                 ....*....|....*....|....*....|....*.
gi 117956933 155 AASTRLGYGVKKTMMLAQRLYEAGYITYMRTDSTNL 190
Cdd:PRK05776 286 EAARIYGFSPYKTQSIAEDLYLDGLISYPRTNSQKL 321
topB TIGR01056
DNA topoisomerase III, bacteria and conjugative plasmid; This model describes topoisomerase ...
 3-202 2.60e-18

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: 82.97  E-value: 2.60e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933    3 NEITKNAIQQAFQT--PGELNMDGVNAQQARRFMDRVVGFMVSPLLWKKVARG-----LSAGRVQSVAVKLLVEREREIN 75
Cdd:TIGR01056 134 SSLVDSSIRKAFKNlrPKSETEGLYKSGVARARADWLVGINLTRAFTKLGREAgndgvLSVGRVQTPTLAMVVKRENEIK 213

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   76 AFVPEEFWDIHAnTKTKDKSDFKL-LVAQKD--------GVAFKPVNETETKAAIsvlenasyeVCKREDRPTKSKPSAP 146
Cdd:TIGR01056 214 NFVGKPFYEVSA-TINKDEQEFTTeWQPYKDeeerelheFLAENVVTDLTQKPAL---------VTDIEKERKKTSAPLF 283

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 117956933  147 YITSTLQQAASTRLGYGVKKTMMLAQRLYEAG-YITYMRTDSTNLSAEAVDAVRDFI 202
Cdd:TIGR01056 284 YDLSALQEDANKRFGISAKRTLDIAQKLYETHkLITYPRTDSRYLPEDEKEMLLEVL 340
PRK08173 PRK08173
DNA topoisomerase III; Validated
 57-200 4.14e-15

DNA topoisomerase III; Validated


Pssm-ID: 236172 [Multi-domain]  Cd Length: 862  Bit Score: 73.55  E-value: 4.14e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933  57 GRVQSVAVKLLVEREREINAFVPEEFWDIHANtktkdksdFKLLVAQKDGVAFKP---VNETETKAAISVL-ENASYE-- 130
Cdd:PRK08173 194 GRVQTPTLSIVVEREEKIRRFVPRDYWEVRAE--------FVAAAGFYEGRWFDPkfkKDEFDPEKRASRLwSEAAAEai 265

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933 131 VCKREDRP----TKSKPS---AP--YITSTLQQAASTRLGYGVKKTMMLAQRLYEA-GYITYMRTDSTNLSAEAVDAVRD 200
Cdd:PRK08173 266 VAACRGKPgtvtEESKPStqlSPllFDLTSLQREANGRFGFSAKNTLGLAQALYEKhKVLTYPRTDSRALPEDYLGTVKQ 345
PRK14724 PRK14724
DNA topoisomerase III; Provisional
 55-200 4.31e-14

DNA topoisomerase III; Provisional


Pssm-ID: 237803 [Multi-domain]  Cd Length: 987  Bit Score: 70.75  E-value: 4.31e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933  55 SAGRVQSVAVKLLVEREREINAFVPEEFWDIHANTKTKD--------KSDFKLLVAQKDGVAFKPVNETETKAAISVLEN 126
Cdd:PRK14724 200 TVGRVQTPTLSLVVEREEKIRKFVSRDYWEIHAGFHAEAgeylgkwfDPQWKKASDDPEARADRVWSEREARAIADAVRG 279

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 117956933 127 ASYEVCKrEDRPTKSKPSAPYITSTLQQAASTRLGYGVKKTMMLAQRLYEA-GYITYMRTDSTNLSAEAVDAVRD 200
Cdd:PRK14724 280 KAATVTE-ESKPTTQASPLLFDLTSLQREANGKFGFSAKTTLALAQSLYERhKALTYPRTDSRALPEDYLPVAKQ 353
PTZ00407 PTZ00407
DNA topoisomerase IA; Provisional
 5-211 5.15e-14

DNA topoisomerase IA; Provisional


Pssm-ID: 173597 [Multi-domain]  Cd Length: 805  Bit Score: 70.35  E-value: 5.15e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933   5 ITKNAIQQAFQ--TPGELNMDGVNAQQARRFMDRVVGFMVSPLLWKKVARGLSAGRVQSVAVKLLVEREREINAFVpeef 82
Cdd:PTZ00407 168 ITEDGIRKAMRerHVEACDYDLANAAETRHAMDRIFGFLGSSVVRAANSQMRSIGRVQTPALILINEREDKIKAFL---- 243

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117956933  83 wDIHANT---------KTKDKSDFKLLV---AQKDGVAFKPVNETETKAAIS--VLENASYEVCKREDRPTKSK--PSAP 146
Cdd:PTZ00407 244 -ESNKSTfevqamcqfPSPHGTTFSQVVtitPDRKGGASHWATEAEARRCLEqwKLNNCTGFSVPLEPKPQPSVvpPPQP 322

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 117956933 147 YITSTLQQAASTRLGYGVKKTMMLAQRLYEAGYITYMRTDSTNLSAEAVDAVRDFIGSEFGDKYL 211
Cdd:PTZ00407 323 FTMATAIAKANRQLKYSSEMVSGCLQDLFQLGHITYPRTDSTRIDESALPDIYAAVKKEFGKEFL 387
TOPRIM_TopoIA_TopoI cd03363
TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA ...
 1-17 4.47e-03

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: 36.00  E-value: 4.47e-03
                         10
                 ....*....|....*..
gi 117956933   1 VFNEITKNAIQQAFQTP 17
Cdd:cd03363  107 VFNEITKEAIKEALKNP 123
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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