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Conserved domains on  [gi|2234370088|gb|UPW37074|]
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GyrB, partial [Xanthomonas oryzae pv. oryzae]

Protein Classification

DNA gyrase subunit B family protein( domain architecture ID 999984)

DNA gyrase subunit B (GyrB) is the ATPase subunit of DNA gyrase, which is a type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state; may be partial

CATH:  3.30.230.10
EC:  5.6.2.2
Gene Ontology:  GO:0006265|GO:0005524|GO:0003677|GO:0003918
PubMed:  11395412|7980433|12596227
SCOP:  4000168

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
gyrB super family cl36442
DNA gyrase subunit B; Provisional
 1-292 1.24e-124

DNA gyrase subunit B; Provisional


The actual alignment was detected with superfamily member PRK14939:

Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 372.89  E-value: 1.24e-124
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088   1 DKLRYHRIILMTDADVDGSHIRTLLLTFFYRQMPELIERGYIYIGLPPLYKLKQGKSELYLKDDAALNAYLASNAVEGAA 80
Cdd:PRK14939  487 DKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDYLIELALEGAT 566

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088  81 LIPAtDEPPITGEALEKLLLLFTSANEAIARTAHRYDPALLTALIDLPPLDVETLQAEGNqhpaldalqavlnrgtlgta 160
Cdd:PRK14939  567 LHLA-DGPAISGEALEKLVKEYRAVRKIIDRLERRYPRAVLEALIYAPALDLDDLADEAA-------------------- 625

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088 161 ryqlrfdpatenapatlvairrhmgeefTQVLPMGAFESGELRPLREVSLALHDLVREGAQIVRGNKSHSITSFAQAHAW 240
Cdd:PRK14939  626 ----------------------------VAALDADFLTSAEYRRLVELAEKLRGLIEEGAYLERGERKQPVSSFEEALDW 677

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2234370088 241 LLDEAKKGRQVQRFKGLGEMNAEQLWETTVNPDPRRLLQVRIEDAVAADQIF 292
Cdd:PRK14939  678 LLAEARKGLSIQRYKGLGEMNPEQLWETTMDPENRRLLQVTIEDAIAADEIF 729
 
Name Accession Description Interval E-value
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-292 1.24e-124

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 372.89  E-value: 1.24e-124
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088   1 DKLRYHRIILMTDADVDGSHIRTLLLTFFYRQMPELIERGYIYIGLPPLYKLKQGKSELYLKDDAALNAYLASNAVEGAA 80
Cdd:PRK14939  487 DKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDYLIELALEGAT 566

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088  81 LIPAtDEPPITGEALEKLLLLFTSANEAIARTAHRYDPALLTALIDLPPLDVETLQAEGNqhpaldalqavlnrgtlgta 160
Cdd:PRK14939  567 LHLA-DGPAISGEALEKLVKEYRAVRKIIDRLERRYPRAVLEALIYAPALDLDDLADEAA-------------------- 625

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088 161 ryqlrfdpatenapatlvairrhmgeefTQVLPMGAFESGELRPLREVSLALHDLVREGAQIVRGNKSHSITSFAQAHAW 240
Cdd:PRK14939  626 ----------------------------VAALDADFLTSAEYRRLVELAEKLRGLIEEGAYLERGERKQPVSSFEEALDW 677

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2234370088 241 LLDEAKKGRQVQRFKGLGEMNAEQLWETTVNPDPRRLLQVRIEDAVAADQIF 292
Cdd:PRK14939  678 LLAEARKGLSIQRYKGLGEMNPEQLWETTMDPENRRLLQVTIEDAIAADEIF 729
GyrB_insert pfam18053
DNA gyrase B subunit insert domain; This is the insert domain found in DNA gyrase B subunit ...
 79-245 3.17e-64

DNA gyrase B subunit insert domain; This is the insert domain found in DNA gyrase B subunit proteins. Studies indicate that the insert has two functions, acting as a steric buttress to pre-configure the primary DNA-binding site, and serving as a relay that may help coordinate communication between different functional domains.


Pssm-ID: 465629  Cd Length: 167  Bit Score: 199.29  E-value: 3.17e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088  79 AALIPATDEPPITGEALEKLLLLFTSANEAIARTAHRYDPALLTALIDLPPLDVETLQAEGNQHPALDALQAVLNRGTLG 158
Cdd:pfam18053   1 AALYPNEGAPPISGEALEELARQYRLAEAIIKRLSRRYDPAVLEALLYLPPLDAEDLDDEAAAEAWAAALEARLNQDGLG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088 159 TARYQLRFDPATENAPATLVAIRRHMGEEFTQVLPMGAFESGELRPLREVSLALHDLVREGAQIVRGNKSHSITSFAQAH 238
Cdd:pfam18053  81 GPRYRVSVEEDTERGKYLLRVTRRHHGNETVYVLDADFFESGDYRALAELGETLDGLIGEGAYIKRGEKEQPVESFKEAL 160


                  ....*..
gi 2234370088 239 AWLLDEA 245
Cdd:pfam18053 161 DWLMEEA 167
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
1-292 4.61e-53

DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 182.92  E-value: 4.61e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088   1 DKLRYHRIILMTDADVDGSHIRTLLLTFFYRQMPELIERGYIYIGLPPLYKLKQGKSELYLKDDAALNAYLAsnavegaa 80
Cdd:COG0187   486 EKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDELLK-------- 557

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088  81 lipatdeppitgealekllllftsaneaiartahrydpalltalidlppldvetlqaegnqhpaldalqavlnrgtlgta 160
Cdd:COG0187       --------------------------------------------------------------------------------

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088 161 ryqlrfdpatenapatlvairrhmgeeftqvlpmgafesgELRPlrevslalhdlvregaqivrgnkshsitsfaqahaw 240
Cdd:COG0187   558 ----------------------------------------ELKG------------------------------------ 561

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2234370088 241 lldeaKKGRQVQRFKGLGEMNAEQLWETTVNPDPRRLLQVRIEDAVAADQIF 292
Cdd:COG0187   562 -----KKKVEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIF 608
gyrB TIGR01059
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ...
 1-292 8.72e-52

DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. Proteins scoring above the noise cutoff for this model and below the trusted cutoff for topoisomerase IV models probably should be designated GyrB. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273421 [Multi-domain]  Cd Length: 654  Bit Score: 179.86  E-value: 8.72e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088   1 DKLRYHRIILMTDADVDGSHIRTLLLTFFYRQMPELIERGYIYIGLPPLYKLKQGKSELYLKDDaalnaylasnavegaa 80
Cdd:TIGR01059 481 EKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIKDD---------------- 544

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088  81 lipatDEPPITGEALEKLLLLFTSANEaiartahrydpalltalidlppldvetlqaegNQHPALDALQAVLNRgtlgta 160
Cdd:TIGR01059 545 -----KEKDLVGEALEDLKALYIYSDK--------------------------------EKEEAKTQIPVHLGR------ 581

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088 161 ryqlrfdpatenapatlvairrhmgeeftqvlpmgafesgelrplrevslalhdlvregaqivrgnkshsitsfaqahaw 240
Cdd:TIGR01059     --------------------------------------------------------------------------------

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2234370088 241 lldeakKGRQVQRFKGLGEMNAEQLWETTVNPDPRRLLQVRIEDAVAADQIF 292
Cdd:TIGR01059 582 ------KGIEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIF 627
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-292 9.85e-36

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 134.99  E-value: 9.85e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088    1 DKLRYHRIILMTDADVDGSHIRTLLLTFFYRQMPELIERGYIYIGLPPLYKLKQGKselylkddaalnaylasnavegaa 80
Cdd:smart00433 449 EKLRYGKIIIMTDADVDGSHIKGLLLTFFYRYMPPLIEAGFVYIAIPPLYKVTKGK------------------------ 504

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088   81 lipatdeppitgealekllllftsaneaiartahrydpalltalidlppldvetlqaegnqhpaldalqavlnrgtlgta 160
Cdd:smart00433     --------------------------------------------------------------------------------

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088  161 ryqlrfdpatenapatlvairrhmgeeftqvlpmgafesgelrplrevslalhdlvregaqivrGNKSHSITSFAQAHAW 240
Cdd:smart00433 505 ----------------------------------------------------------------KKYVYSFYSLDEYEKW 520

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2234370088  241 LLDEAKKGR--QVQRFKGLGEMNAEQLWETTVNPDPRRLLQVRIEDAVAADQIF 292
Cdd:smart00433 521 LEKTEGNKSkyEIQRYKGLGEMNADQLWETTMDPERRTLLFVTLDDADEADLIF 574
TOPRIM_TopoIIA_GyrB cd03366
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 1-47 2.99e-30

TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. DNA gyrase is more effective at relaxing supercoils than decatentating DNA. DNA gyrase in addition inserts negative supercoils in the presence of ATP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173786 [Multi-domain]  Cd Length: 114  Bit Score: 110.05  E-value: 2.99e-30
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2234370088   1 DKLRYHRIILMTDADVDGSHIRTLLLTFFYRQMPELIERGYIYIGLP 47
Cdd:cd03366    68 EKLRYHKIIIMTDADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
 
Name Accession Description Interval E-value
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-292 1.24e-124

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 372.89  E-value: 1.24e-124
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088   1 DKLRYHRIILMTDADVDGSHIRTLLLTFFYRQMPELIERGYIYIGLPPLYKLKQGKSELYLKDDAALNAYLASNAVEGAA 80
Cdd:PRK14939  487 DKLRYHKIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDYLIELALEGAT 566

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088  81 LIPAtDEPPITGEALEKLLLLFTSANEAIARTAHRYDPALLTALIDLPPLDVETLQAEGNqhpaldalqavlnrgtlgta 160
Cdd:PRK14939  567 LHLA-DGPAISGEALEKLVKEYRAVRKIIDRLERRYPRAVLEALIYAPALDLDDLADEAA-------------------- 625

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088 161 ryqlrfdpatenapatlvairrhmgeefTQVLPMGAFESGELRPLREVSLALHDLVREGAQIVRGNKSHSITSFAQAHAW 240
Cdd:PRK14939  626 ----------------------------VAALDADFLTSAEYRRLVELAEKLRGLIEEGAYLERGERKQPVSSFEEALDW 677

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2234370088 241 LLDEAKKGRQVQRFKGLGEMNAEQLWETTVNPDPRRLLQVRIEDAVAADQIF 292
Cdd:PRK14939  678 LLAEARKGLSIQRYKGLGEMNPEQLWETTMDPENRRLLQVTIEDAIAADEIF 729
GyrB_insert pfam18053
DNA gyrase B subunit insert domain; This is the insert domain found in DNA gyrase B subunit ...
 79-245 3.17e-64

DNA gyrase B subunit insert domain; This is the insert domain found in DNA gyrase B subunit proteins. Studies indicate that the insert has two functions, acting as a steric buttress to pre-configure the primary DNA-binding site, and serving as a relay that may help coordinate communication between different functional domains.


Pssm-ID: 465629  Cd Length: 167  Bit Score: 199.29  E-value: 3.17e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088  79 AALIPATDEPPITGEALEKLLLLFTSANEAIARTAHRYDPALLTALIDLPPLDVETLQAEGNQHPALDALQAVLNRGTLG 158
Cdd:pfam18053   1 AALYPNEGAPPISGEALEELARQYRLAEAIIKRLSRRYDPAVLEALLYLPPLDAEDLDDEAAAEAWAAALEARLNQDGLG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088 159 TARYQLRFDPATENAPATLVAIRRHMGEEFTQVLPMGAFESGELRPLREVSLALHDLVREGAQIVRGNKSHSITSFAQAH 238
Cdd:pfam18053  81 GPRYRVSVEEDTERGKYLLRVTRRHHGNETVYVLDADFFESGDYRALAELGETLDGLIGEGAYIKRGEKEQPVESFKEAL 160


                  ....*..
gi 2234370088 239 AWLLDEA 245
Cdd:pfam18053 161 DWLMEEA 167
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
1-292 4.61e-53

DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 182.92  E-value: 4.61e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088   1 DKLRYHRIILMTDADVDGSHIRTLLLTFFYRQMPELIERGYIYIGLPPLYKLKQGKSELYLKDDAALNAYLAsnavegaa 80
Cdd:COG0187   486 EKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDELLK-------- 557

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088  81 lipatdeppitgealekllllftsaneaiartahrydpalltalidlppldvetlqaegnqhpaldalqavlnrgtlgta 160
Cdd:COG0187       --------------------------------------------------------------------------------

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088 161 ryqlrfdpatenapatlvairrhmgeeftqvlpmgafesgELRPlrevslalhdlvregaqivrgnkshsitsfaqahaw 240
Cdd:COG0187   558 ----------------------------------------ELKG------------------------------------ 561

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2234370088 241 lldeaKKGRQVQRFKGLGEMNAEQLWETTVNPDPRRLLQVRIEDAVAADQIF 292
Cdd:COG0187   562 -----KKKVEIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIF 608
gyrB TIGR01059
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ...
 1-292 8.72e-52

DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. Proteins scoring above the noise cutoff for this model and below the trusted cutoff for topoisomerase IV models probably should be designated GyrB. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273421 [Multi-domain]  Cd Length: 654  Bit Score: 179.86  E-value: 8.72e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088   1 DKLRYHRIILMTDADVDGSHIRTLLLTFFYRQMPELIERGYIYIGLPPLYKLKQGKSELYLKDDaalnaylasnavegaa 80
Cdd:TIGR01059 481 EKLRYHKIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIKDD---------------- 544

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088  81 lipatDEPPITGEALEKLLLLFTSANEaiartahrydpalltalidlppldvetlqaegNQHPALDALQAVLNRgtlgta 160
Cdd:TIGR01059 545 -----KEKDLVGEALEDLKALYIYSDK--------------------------------EKEEAKTQIPVHLGR------ 581

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088 161 ryqlrfdpatenapatlvairrhmgeeftqvlpmgafesgelrplrevslalhdlvregaqivrgnkshsitsfaqahaw 240
Cdd:TIGR01059     --------------------------------------------------------------------------------

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2234370088 241 lldeakKGRQVQRFKGLGEMNAEQLWETTVNPDPRRLLQVRIEDAVAADQIF 292
Cdd:TIGR01059 582 ------KGIEIQRYKGLGEMNADQLWETTMDPESRTLLKVTIEDAVEADRIF 627
gyrB PRK05644
DNA gyrase subunit B; Validated
 1-292 1.90e-49

DNA gyrase subunit B; Validated


Pssm-ID: 235542 [Multi-domain]  Cd Length: 638  Bit Score: 172.97  E-value: 1.90e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088   1 DKLRYHRIILMTDADVDGSHIRTLLLTFFYRQMPELIERGYIYIGLPPLYKLKQGKSElYLKDDAALNAYLASnavegaa 80
Cdd:PRK05644  488 SKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLYKIKKGGKE-YAYSDEELDEILAE------- 559

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088  81 lipatdeppitgealekllllftsaneaiartahrydpalltalidlppldvetlqaegnqhpaldalqavlnrgtlgta 160
Cdd:PRK05644      --------------------------------------------------------------------------------

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088 161 ryqlrfdpatenapatlvairrhmgeeftqvlpmgafesgelrplrevslalhdlvregaqivrgnkshsitsfaqahaw 240
Cdd:PRK05644      --------------------------------------------------------------------------------

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2234370088 241 LLDEAKKGRQVQRFKGLGEMNAEQLWETTVNPDPRRLLQVRIEDAVAADQIF 292
Cdd:PRK05644  560 LKLKGNPKYGIQRYKGLGEMNPEQLWETTMDPETRTLLQVTIEDAAEADEIF 611
PRK05559 PRK05559
DNA topoisomerase IV subunit B; Reviewed
 1-292 1.24e-39

DNA topoisomerase IV subunit B; Reviewed


Pssm-ID: 235501 [Multi-domain]  Cd Length: 631  Bit Score: 146.01  E-value: 1.24e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088   1 DKLRYHRIILMTDADVDGSHIRTLLLTFFYRQMPELIERGYIYIGLPPLYKLKQGKSELYLKDDAALNaylasnavegaa 80
Cdd:PRK05559  483 EDLRYGKIIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRVDKGKKKIYALDEEEKE------------ 550

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088  81 lipatdeppitgEALEKLlllftsaneaiartahrydpalltalidlppldvetlqaegnqhpaldalqavlnrgtlgta 160
Cdd:PRK05559  551 ------------ELLKKL-------------------------------------------------------------- 556

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088 161 ryqlrfdpatenapatlvairrhmgeeftqvlpmgafesgelrplrevslalhdlvregaqivrGNKshsitsfaqahaw 240
Cdd:PRK05559  557 ----------------------------------------------------------------GKK------------- 559

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2234370088 241 lldeaKKGRQVQRFKGLGEMNAEQLWETTVNPDPRRLLQVRIEDAVAADQIF 292
Cdd:PRK05559  560 -----GGKPEIQRFKGLGEMNPDQLWETTMDPETRRLVRVTIDDAEETEKLV 606
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-292 9.85e-36

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 134.99  E-value: 9.85e-36
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088    1 DKLRYHRIILMTDADVDGSHIRTLLLTFFYRQMPELIERGYIYIGLPPLYKLKQGKselylkddaalnaylasnavegaa 80
Cdd:smart00433 449 EKLRYGKIIIMTDADVDGSHIKGLLLTFFYRYMPPLIEAGFVYIAIPPLYKVTKGK------------------------ 504

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088   81 lipatdeppitgealekllllftsaneaiartahrydpalltalidlppldvetlqaegnqhpaldalqavlnrgtlgta 160
Cdd:smart00433     --------------------------------------------------------------------------------

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088  161 ryqlrfdpatenapatlvairrhmgeeftqvlpmgafesgelrplrevslalhdlvregaqivrGNKSHSITSFAQAHAW 240
Cdd:smart00433 505 ----------------------------------------------------------------KKYVYSFYSLDEYEKW 520

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2234370088  241 LLDEAKKGR--QVQRFKGLGEMNAEQLWETTVNPDPRRLLQVRIEDAVAADQIF 292
Cdd:smart00433 521 LEKTEGNKSkyEIQRYKGLGEMNADQLWETTMDPERRTLLFVTLDDADEADLIF 574
TOPRIM_TopoIIA_GyrB cd03366
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 1-47 2.99e-30

TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. DNA gyrase is more effective at relaxing supercoils than decatentating DNA. DNA gyrase in addition inserts negative supercoils in the presence of ATP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173786 [Multi-domain]  Cd Length: 114  Bit Score: 110.05  E-value: 2.99e-30
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2234370088   1 DKLRYHRIILMTDADVDGSHIRTLLLTFFYRQMPELIERGYIYIGLP 47
Cdd:cd03366    68 EKLRYHKIIIMTDADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
DNA_gyraseB_C pfam00986
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ...
 246-292 8.96e-28

DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA topoisomerase II are similar, but they have a different carboxyl terminus. The amino-terminal portion of the DNA gyrase B protein is thought to catalyze the ATP-dependent super-coiling of DNA. See pfam00204. The carboxyl-terminal end supports the complexation with the DNA gyrase A protein and the ATP-independent relaxation. This family also contains Topoisomerase IV. This is a bacterial enzyme that is closely related to DNA gyrase,.


Pssm-ID: 460016 [Multi-domain]  Cd Length: 63  Bit Score: 102.07  E-value: 8.96e-28
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2234370088 246 KKGRQVQRFKGLGEMNAEQLWETTVNPDPRRLLQVRIEDAVAADQIF 292
Cdd:pfam00986   1 KKKVEIQRYKGLGEMNPEQLWETTMDPETRRLLQVTIEDAAEADEIF 47
TOPRIM_TopoIIA_like cd01030
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 1-47 1.85e-27

TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173780 [Multi-domain]  Cd Length: 115  Bit Score: 102.97  E-value: 1.85e-27
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2234370088   1 DKLRYHRIILMTDADVDGSHIRTLLLTFFYRQMPELIERGYIYIGLP 47
Cdd:cd01030    69 DKLRYGKIIIMTDADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
PTZ00109 PTZ00109
DNA gyrase subunit b; Provisional
 2-291 4.27e-27

DNA gyrase subunit b; Provisional


Pssm-ID: 240272 [Multi-domain]  Cd Length: 903  Bit Score: 110.74  E-value: 4.27e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088   2 KLRYHRIILMTDADVDGSHIRTLLLTFFYRQMPELIERGYIYIGLPPLYKLKQGKSELYlkddaalnaylASNAVEGAAL 81
Cdd:PTZ00109  677 PLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRITNNRMKQF-----------NVSTKNSKKY 745

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088  82 IPATDEppitgEALEKLLLLFTSANEAIARTAHRYDPAlltaliDLPPLDVET-LQAEGNQHPALDALQAVLNRGTLGTA 160
Cdd:PTZ00109  746 IYTWSD-----EELNVLIKLLNKDYSSKETTRSVEEKG------NAPDLDNEYeDEKLDNKNMRENNVDEVELKTELGTN 814

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088 161 RYQlrfdpaTENAPatlvairrhmgeeftqvlpmgafesgelrplrevslalhdlvregaqIVRGNKSHSITSfaqahaw 240
Cdd:PTZ00109  815 VAD------TEQTD-----------------------------------------------ELDINKAFFKFS------- 834

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2234370088 241 lldeakKGRQVQRFKGLGEMNAEQLWETTVNPDPRRLLQVRIEDAVAADQI 291
Cdd:PTZ00109  835 ------KHYEIQRFKGLGEMMADQLWETTMDPKKRILIRITVSDAMRASEL 879
parE_Gneg TIGR01055
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ...
 1-284 4.89e-15

DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason. This protein is active as an alpha(2)beta(2) heterotetramer. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 130127 [Multi-domain]  Cd Length: 625  Bit Score: 74.96  E-value: 4.89e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088   1 DKLRYHRIILMTDADVDGSHIRTLLLTFFYRQMPELIERGYIYIGLPPLYKLKQGKSELYlkddaalnaylasnavegaa 80
Cdd:TIGR01055 477 SQLRYGKICILADADSDGLHIATLLCALFFLHFPKLVEEGHVYVAKPPLYRIDLSKEVYY-------------------- 536

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088  81 lipATDEppitgEALEKLLllftsaneaiartahrydpalltalidlppldvetlqaegnqhpaldalqavlnrgtlgta 160
Cdd:TIGR01055 537 ---ALDE-----EEKEKLL------------------------------------------------------------- 547

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2234370088 161 rYQLRfdpatenapatlvairrhmgeeftqvlpmgafesgelrplrevslalhdlvregaqivrgnkshsitsfaqahaw 240
Cdd:TIGR01055 548 -YKLK--------------------------------------------------------------------------- 551

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....*
gi 2234370088 241 lldeAKKGR-QVQRFKGLGEMNAEQLWETTVNPDPRRLLQVRIED 284
Cdd:TIGR01055 552 ----KKKGKpNVQRFKGLGEMNPAQLRETTMDPNTRRLVQLTLDD 592
TOPRIM_TopoIIA cd03365
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 1-39 3.31e-08

TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. The TOPRIM 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 strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173785 [Multi-domain]  Cd Length: 120  Bit Score: 51.15  E-value: 3.31e-08
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 2234370088   1 DKLRYHRIILMTDADVDGSHIRTLLLTFFYRQMPELIER 39
Cdd:cd03365    73 KSLRYGRLMIMTDQDHDGSHIKGLLINFIHSFWPSLLKI 111
39 PHA02569
DNA topoisomerase II large subunit; Provisional
 1-58 3.74e-08

DNA topoisomerase II large subunit; Provisional


Pssm-ID: 177398 [Multi-domain]  Cd Length: 602  Bit Score: 54.37  E-value: 3.74e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2234370088   1 DKLRYHRIILMTDADVDG-SHIRTLLLTFFYRqMPELIERGYIYIGLPPLYKLKQGKSE 58
Cdd:PHA02569  471 ENMNYKNIAIMTDADVDGkGSIYPLLLAFFSR-WPELFEQGRIRFVKTPVIIAQVGKET 528
PTZ00108 PTZ00108
DNA topoisomerase 2-like protein; Provisional
 1-59 1.13e-07

DNA topoisomerase 2-like protein; Provisional


Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 53.13  E-value: 1.13e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2234370088    1 DKLRYHRIILMTDADVDGSHIRTLLLTFFYRQMPELIE-RGYIYIGLPPLYKL-KQGKSEL 59
Cdd:PTZ00108   507 KGLRYGSLMIMTDQDHDGSHIKGLLINMIHHFWPSLLKnPGFLKEFITPIVKAtKKGNQVI 567
PLN03128 PLN03128
DNA topoisomerase 2; Provisional
 2-56 2.43e-07

DNA topoisomerase 2; Provisional


Pssm-ID: 215593 [Multi-domain]  Cd Length: 1135  Bit Score: 52.02  E-value: 2.43e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2234370088    2 KLRYHRIILMTDADVDGSHIRTLLLTFFYRQMPELIER-GYIYIGLPPLYKLKQGK 56
Cdd:PLN03128   500 SLRYGHLMIMTDQDHDGSHIKGLIINFFHSFWPSLLKIpGFLVEFITPIVKATKGG 555
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 2-29 1.99e-05

Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.


Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 42.34  E-value: 1.99e-05
                          10        20
                  ....*....|....*....|....*...
gi 2234370088   2 KLRYHRIILMTDADVDGSHIRTLLLTFF 29
Cdd:pfam01751  51 ALKAKEVILATDPDREGEAIALKLLELK 78
PLN03237 PLN03237
DNA topoisomerase 2; Provisional
 3-38 3.88e-05

DNA topoisomerase 2; Provisional


Pssm-ID: 215641 [Multi-domain]  Cd Length: 1465  Bit Score: 45.24  E-value: 3.88e-05
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 2234370088    3 LRYHRIILMTDADVDGSHIRTLLLTFFYRQMPELIE 38
Cdd:PLN03237   525 LRYGHLMIMTDQDHDGSHIKGLLINFIHSFWPSLLK 560
 
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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