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Conserved domains on  [gi|1005664698|gb|AMQ22855|]
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DNA gyrase subunit B, partial [Xanthomonas hortorum pv. hederae]

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
 1-293 0e+00

DNA gyrase subunit B; Provisional


The actual alignment was detected with superfamily member PRK14939:

Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 550.08  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698   1 SGGLHGVGVSVVNALSEHLWLDIWRDGFHYQQEYALGEPQYPLKQLEASTKRGTTLRFKPAVAIFSDVEFHYDILARRLR 80
Cdd:PRK14939  114 SGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETDKTGTEVRFWPSPEIFENTEFDYDILAKRLR 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698  81 ELSFLNSGVKIALIDERgEGRRDDFHYEGGIRSFVEHLAQLKSPLHPNVISVTGEHNGIVVDVALQWTDAYQETMYCFTN 160
Cdd:PRK14939  194 ELAFLNSGVRIRLKDER-DGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTN 272

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698 161 NIPQKDGGTHLAGFRAALTRVLSNYIEQNGIAKQAKVALTGDDMREGMIAVLSVKVPDPSFSSQTKEKLVSSDVRPAVEN 240
Cdd:PRK14939  273 NIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVES 352

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1005664698 241 AFGARLQEFLQENPNEAKAITGKIVDAARAREAARKARDLTRRKGALDIAGLP 293
Cdd:PRK14939  353 LVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLP 405
 
Name Accession Description Interval E-value
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-293 0e+00

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 550.08  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698   1 SGGLHGVGVSVVNALSEHLWLDIWRDGFHYQQEYALGEPQYPLKQLEASTKRGTTLRFKPAVAIFSDVEFHYDILARRLR 80
Cdd:PRK14939  114 SGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETDKTGTEVRFWPSPEIFENTEFDYDILAKRLR 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698  81 ELSFLNSGVKIALIDERgEGRRDDFHYEGGIRSFVEHLAQLKSPLHPNVISVTGEHNGIVVDVALQWTDAYQETMYCFTN 160
Cdd:PRK14939  194 ELAFLNSGVRIRLKDER-DGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTN 272

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698 161 NIPQKDGGTHLAGFRAALTRVLSNYIEQNGIAKQAKVALTGDDMREGMIAVLSVKVPDPSFSSQTKEKLVSSDVRPAVEN 240
Cdd:PRK14939  273 NIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVES 352

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1005664698 241 AFGARLQEFLQENPNEAKAITGKIVDAARAREAARKARDLTRRKGALDIAGLP 293
Cdd:PRK14939  353 LVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLP 405
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
1-293 3.48e-149

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


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 432.14  E-value: 3.48e-149
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698   1 SGGLHGVGVSVVNALSEHLWLDIWRDGFHYQQEYALGEPQYPLKQLEASTKRGTTLRFKPAVAIFSDVEFHYDILARRLR 80
Cdd:COG0187   112 SGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKTDRTGTTVRFKPDPEIFETTEFDYETLAERLR 191

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698  81 ELSFLNSGVKIALIDERGEG-RRDDFHYEGGIRSFVEHLAQLKSPLHPNVISVTGEHNGIVVDVALQWTDAYQETMYCFT 159
Cdd:COG0187   192 ELAFLNKGLTITLTDEREEEpKEETFHYEGGIKDFVEYLNEDKEPLHPEVIYFEGEKDGIEVEVALQWNDGYSENIHSFV 271

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698 160 NNIPQKDGGTHLAGFRAALTRVLSNYIEQNGIAKQAKVALTGDDMREGMIAVLSVKVPDPSFSSQTKEKLVSSDVRPAVE 239
Cdd:COG0187   272 NNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREGLTAVISVKLPEPQFEGQTKTKLGNSEARGIVE 351

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1005664698 240 NAFGARLQEFLQENPNEAKAITGKIVDAARAREAARKARDLTRRKGALDIAGLP 293
Cdd:COG0187   352 SVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALESSGLP 405
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-293 1.14e-102

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 311.80  E-value: 1.14e-102
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698    1 SGGLHGVGVSVVNALSEHLWLDIWRDGFHYQQEY-ALGEPQYPLKQLEASTKRGTTLRFKPAVAIFS-DVEFHYDILARR 78
Cdd:smart00433  78 SGGLHGVGASVVNALSTEFEVEVARDGKEYKQSFsNNGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGmTTDDDFELLKRR 157

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698   79 LRELSFLNSGVKIALIDERgEGRRDDFHYEGGIRSFVEHLAQLKSPLHPNVISVTGEHNGIVVDVALQWTDAYQETMYCF 158
Cdd:smart00433 158 LRELAFLNKGVKITLNDER-SDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSF 236

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698  159 TNNIPQKDGGTHLAGFRAALTRVLSNYIEQNGIAKQAKvaLTGDDMREGMIAVLSVKVPDPSFSSQTKEKLVSSDVRPAV 238
Cdd:smart00433 237 VNNIATTEGGTHENGFKDALTRVINEYAKKKKKLKEKN--IKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGV 314

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1005664698  239 ENAFGARLQEFLQENPNEAKAITGKIVDAARAREAARKARDLTRRKgALDIAGLP 293
Cdd:smart00433 315 EKIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKK-KLSSISLP 368
TopoII_Trans_DNA_gyrase cd00822
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ...
 109-266 7.37e-79

TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are heterodimers composed of two subunits. The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and eukaryotes. All type IIA topoisomerases are related to each other at amino acid sequence level, though their oligomeric organization sometimes differs. 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. TopoIIA enzymes also catenate/ decatenate duplex rings. E.coli DNA gyrase is a heterodimer composed of two subunits. E. coli DNA gyrase B subunit is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.


Pssm-ID: 238419 [Multi-domain]  Cd Length: 172  Bit Score: 236.69  E-value: 7.37e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698 109 GGIRSFVEHLAQLKSPLHPNVISVTGEHNGIVVDVALQWTDAYQETMYCFTNNIPQKDGGTHLAGFRAALTRVLSNYIEQ 188
Cdd:cd00822     1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1005664698 189 NGIAKQAKVALTGDDMREGMIAVLSVKVPDPSFSSQTKEKLVSSDVRPAVENAFGARLQEFLQENPNEAKAITGKIVD 266
Cdd:cd00822    81 NNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAIL 158
DNA_gyraseB pfam00204
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ...
 110-266 5.35e-67

DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal S5 domain 2-like fold. This family is structurally related to PF01119.


Pssm-ID: 425522 [Multi-domain]  Cd Length: 173  Bit Score: 206.70  E-value: 5.35e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698 110 GIRSFVEHLAQLKSPLHPNVISVTGEH--NGIVVDVALQWTDAYQETMYCFTNNIPQKDGGTHLAGFRAALTRVLSNYIE 187
Cdd:pfam00204   1 GLKDFVEELNKDKKPLHKEIIYFEGESpdNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1005664698 188 QNGIAKQAKVALTGDDMREGMIAVLSVKVPDPSFSSQTKEKLVSSDVRPAVENAFGARLQEFLQENPNEAKAITGKIVD 266
Cdd:pfam00204  81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQ 159
 
Name Accession Description Interval E-value
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-293 0e+00

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 550.08  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698   1 SGGLHGVGVSVVNALSEHLWLDIWRDGFHYQQEYALGEPQYPLKQLEASTKRGTTLRFKPAVAIFSDVEFHYDILARRLR 80
Cdd:PRK14939  114 SGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETDKTGTEVRFWPSPEIFENTEFDYDILAKRLR 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698  81 ELSFLNSGVKIALIDERgEGRRDDFHYEGGIRSFVEHLAQLKSPLHPNVISVTGEHNGIVVDVALQWTDAYQETMYCFTN 160
Cdd:PRK14939  194 ELAFLNSGVRIRLKDER-DGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTN 272

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698 161 NIPQKDGGTHLAGFRAALTRVLSNYIEQNGIAKQAKVALTGDDMREGMIAVLSVKVPDPSFSSQTKEKLVSSDVRPAVEN 240
Cdd:PRK14939  273 NIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVES 352

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1005664698 241 AFGARLQEFLQENPNEAKAITGKIVDAARAREAARKARDLTRRKGALDIAGLP 293
Cdd:PRK14939  353 LVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLP 405
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
1-293 3.48e-149

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


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 432.14  E-value: 3.48e-149
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698   1 SGGLHGVGVSVVNALSEHLWLDIWRDGFHYQQEYALGEPQYPLKQLEASTKRGTTLRFKPAVAIFSDVEFHYDILARRLR 80
Cdd:COG0187   112 SGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKTDRTGTTVRFKPDPEIFETTEFDYETLAERLR 191

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698  81 ELSFLNSGVKIALIDERGEG-RRDDFHYEGGIRSFVEHLAQLKSPLHPNVISVTGEHNGIVVDVALQWTDAYQETMYCFT 159
Cdd:COG0187   192 ELAFLNKGLTITLTDEREEEpKEETFHYEGGIKDFVEYLNEDKEPLHPEVIYFEGEKDGIEVEVALQWNDGYSENIHSFV 271

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698 160 NNIPQKDGGTHLAGFRAALTRVLSNYIEQNGIAKQAKVALTGDDMREGMIAVLSVKVPDPSFSSQTKEKLVSSDVRPAVE 239
Cdd:COG0187   272 NNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREGLTAVISVKLPEPQFEGQTKTKLGNSEARGIVE 351

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1005664698 240 NAFGARLQEFLQENPNEAKAITGKIVDAARAREAARKARDLTRRKGALDIAGLP 293
Cdd:COG0187   352 SVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALESSGLP 405
gyrB PRK05644
DNA gyrase subunit B; Validated
 1-293 9.67e-147

DNA gyrase subunit B; Validated


Pssm-ID: 235542 [Multi-domain]  Cd Length: 638  Bit Score: 426.05  E-value: 9.67e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698   1 SGGLHGVGVSVVNALSEHLWLDIWRDGFHYQQEYALGEPQYPLKQLEASTKRGTTLRFKPAVAIFSDVEFHYDILARRLR 80
Cdd:PRK05644  114 SGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIGETDETGTTVTFKPDPEIFETTEFDYDTLATRLR 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698  81 ELSFLNSGVKIALIDER-GEGRRDDFHYEGGIRSFVEHLAQLKSPLHPNVISVTGEHNGIVVDVALQWTDAYQETMYCFT 159
Cdd:PRK05644  194 ELAFLNKGLKITLTDEReGEEKEETFHYEGGIKEYVEYLNRNKEPLHEEPIYFEGEKDGIEVEVAMQYNDGYSENILSFA 273

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698 160 NNIPQKDGGTHLAGFRAALTRVLSNYIEQNGIAKQAKVALTGDDMREGMIAVLSVKVPDPSFSSQTKEKLVSSDVRPAVE 239
Cdd:PRK05644  274 NNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVREGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVD 353

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1005664698 240 NAFGARLQEFLQENPNEAKAITGKIVDAARAREAARKARDLTRRKGALDIAGLP 293
Cdd:PRK05644  354 SVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALESSSLP 407
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-293 1.14e-102

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 311.80  E-value: 1.14e-102
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698    1 SGGLHGVGVSVVNALSEHLWLDIWRDGFHYQQEY-ALGEPQYPLKQLEASTKRGTTLRFKPAVAIFS-DVEFHYDILARR 78
Cdd:smart00433  78 SGGLHGVGASVVNALSTEFEVEVARDGKEYKQSFsNNGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGmTTDDDFELLKRR 157

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698   79 LRELSFLNSGVKIALIDERgEGRRDDFHYEGGIRSFVEHLAQLKSPLHPNVISVTGEHNGIVVDVALQWTDAYQETMYCF 158
Cdd:smart00433 158 LRELAFLNKGVKITLNDER-SDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSF 236

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698  159 TNNIPQKDGGTHLAGFRAALTRVLSNYIEQNGIAKQAKvaLTGDDMREGMIAVLSVKVPDPSFSSQTKEKLVSSDVRPAV 238
Cdd:smart00433 237 VNNIATTEGGTHENGFKDALTRVINEYAKKKKKLKEKN--IKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGV 314

                          250       260       270       280       290
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1005664698  239 ENAFGARLQEFLQENPNEAKAITGKIVDAARAREAARKARDLTRRKgALDIAGLP 293
Cdd:smart00433 315 EKIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKK-KLSSISLP 368
PRK05559 PRK05559
DNA topoisomerase IV subunit B; Reviewed
 1-266 4.57e-102

DNA topoisomerase IV subunit B; Reviewed


Pssm-ID: 235501 [Multi-domain]  Cd Length: 631  Bit Score: 311.26  E-value: 4.57e-102
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698   1 SGGLHGVGVSVVNALSEHLWLDIWRDGFHYQQEYALGEPQYPLKQLEASTKR--GTTLRFKPAVAIFSDVEFHYDILARR 78
Cdd:PRK05559  114 SGGLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVGTAGKRktGTRVRFWPDPKIFDSPKFSPERLKER 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698  79 LRELSFLNSGVKIALIDERGEGRrddFHYEGGIRSFVEHLAQLKSPLHPN-VISVTGEHNGIVVDVALQWTDAYQETMYC 157
Cdd:PRK05559  194 LRSKAFLLPGLTITLNDERERQT---FHYENGLKDYLAELNEGKETLPEEfVGSFEGEAEGEAVEWALQWTDEGGENIES 270

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698 158 FTNNIPQKDGGTHLAGFRAALTRVLSNYIEQNGIAKQAKvALTGDDMREGMIAVLSVKVPDPSFSSQTKEKLVSSDVRPA 237
Cdd:PRK05559  271 YVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLPKGK-KLEGEDVREGLAAVLSVKIPEPQFEGQTKEKLGSREARRF 349

                         250       260
                  ....*....|....*....|....*....
gi 1005664698 238 VENAFGARLQEFLQENPNEAKAITGKIVD 266
Cdd:PRK05559  350 VSGVVKDAFDLWLNQNPELAEKLAEKAIK 378
TopoII_Trans_DNA_gyrase cd00822
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ...
 109-266 7.37e-79

TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are heterodimers composed of two subunits. The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and eukaryotes. All type IIA topoisomerases are related to each other at amino acid sequence level, though their oligomeric organization sometimes differs. 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. TopoIIA enzymes also catenate/ decatenate duplex rings. E.coli DNA gyrase is a heterodimer composed of two subunits. E. coli DNA gyrase B subunit is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.


Pssm-ID: 238419 [Multi-domain]  Cd Length: 172  Bit Score: 236.69  E-value: 7.37e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698 109 GGIRSFVEHLAQLKSPLHPNVISVTGEHNGIVVDVALQWTDAYQETMYCFTNNIPQKDGGTHLAGFRAALTRVLSNYIEQ 188
Cdd:cd00822     1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1005664698 189 NGIAKQAKVALTGDDMREGMIAVLSVKVPDPSFSSQTKEKLVSSDVRPAVENAFGARLQEFLQENPNEAKAITGKIVD 266
Cdd:cd00822    81 NNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAIL 158
DNA_gyraseB pfam00204
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ...
 110-266 5.35e-67

DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal S5 domain 2-like fold. This family is structurally related to PF01119.


Pssm-ID: 425522 [Multi-domain]  Cd Length: 173  Bit Score: 206.70  E-value: 5.35e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698 110 GIRSFVEHLAQLKSPLHPNVISVTGEH--NGIVVDVALQWTDAYQETMYCFTNNIPQKDGGTHLAGFRAALTRVLSNYIE 187
Cdd:pfam00204   1 GLKDFVEELNKDKKPLHKEIIYFEGESpdNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1005664698 188 QNGIAKQAKVALTGDDMREGMIAVLSVKVPDPSFSSQTKEKLVSSDVRPAVENAFGARLQEFLQENPNEAKAITGKIVD 266
Cdd:pfam00204  81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQ 159
PTZ00109 PTZ00109
DNA gyrase subunit b; Provisional
 1-286 2.78e-57

DNA gyrase subunit b; Provisional


Pssm-ID: 240272 [Multi-domain]  Cd Length: 903  Bit Score: 197.41  E-value: 2.78e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698   1 SGGLHGVGVSVVNALSEHLWLDIWRDGFHYQQEYALGEPQYPLKQL-EASTKRGTTLRFKPAVA-IF------------- 65
Cdd:PTZ00109  246 SSGLHGVGLSVVNALSSFLKVDVFKGGKIYSIELSKGKVTKPLSVFsCPLKKRGTTIHFLPDYKhIFkthhqhteteeee 325

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698  66 -SDVEFHYDILARRLRELSFLNSGVKIALIDERGEGRRDDFHYE-----GGIRSFVEHLAQLKSPLHP--NVISVTGEHN 137
Cdd:PTZ00109  326 gCKNGFNLDLIKNRIHELSYLNPGLTFYLVDERIANENNFYPYEtikheGGTREFLEELIKDKTPLYKdiNIISIRGVIK 405

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698 138 GIVVDVALQWT-DAYQETMYCFTNNIpQKDGGTHLAGFRAALTRVLSNYIEQNGIAKQAKVALTGDDMREGMIAVLSVKV 216
Cdd:PTZ00109  406 NVNVEVSLSWSlESYTALIKSFANNV-STTAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISVKL 484

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698 217 PDPSFSSQTKEKLVSSDVRPAVENAFGARLQEFLQENPNEAKAITGKIVDAARAREAARKARDLTRRKGA 286
Cdd:PTZ00109  485 NGAEFDGQTKTKLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNN 554
HATPase_GyrB-like cd16928
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ...
 1-105 1.46e-45

Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes histidine kinase-like ATPase domain of the B subunit of DNA gyrase. Bacterial DNA gyrase is a type II topoisomerase (type II as it transiently cleaves both strands of DNA) which catalyzes the introduction of negative supercoils into DNA, possibly by a mechanism in which one segment of the double-stranded DNA substrate is passed through a transient break in a second segment. It consists of GyrA and GyrB subunits in an A2B2 stoichiometry; GyrA subunits catalyze strand-breakage and reunion reactions, and GyrB subunits hydrolyze ATP. DNA gyrase is found in bacteria, plants and archaea, but as it is absent in humans it is a possible drug target for the treatment of bacterial and parasite infections.


Pssm-ID: 340405 [Multi-domain]  Cd Length: 180  Bit Score: 151.92  E-value: 1.46e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698   1 SGGLHGVGVSVVNALSEHLWLDIWRDGFHYQQEYALGEPQYPLKQLEASTKRGTTLRFKPAVAIFSDVEFHYDILARRLR 80
Cdd:cd16928    77 SGGLHGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIFEKTEFDFDTLKRRLR 156

                          90       100
                  ....*....|....*....|....*
gi 1005664698  81 ELSFLNSGVKIALIDERgEGRRDDF 105
Cdd:cd16928   157 ELAFLNKGLKIVLEDER-TGKEEVF 180
TopoII_MutL_Trans cd00329
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ...
 111-229 1.19e-21

MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2. MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch repair (MMR). Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families.


Pssm-ID: 238202 [Multi-domain]  Cd Length: 107  Bit Score: 87.32  E-value: 1.19e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698 111 IRSFVEHLaqLKSPLHPNVISVTGEHNGIVVDVALQWTD---AYQETMYCFTNNIPQKDGGTHLAGFRAALTRVLSnyie 187
Cdd:cd00329     1 LKDRLAEI--LGDKVADKLIYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---- 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1005664698 188 qngiakqakvaltGDDMREGMIAVLSVKVPD--PSFS-SQTKEKL 229
Cdd:cd00329    75 -------------GDDVRRYPVAVLSLKIPPslVDVNvHPTKEEV 106
PTZ00108 PTZ00108
DNA topoisomerase 2-like protein; Provisional
 58-237 1.71e-05

DNA topoisomerase 2-like protein; Provisional


Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 46.19  E-value: 1.71e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698   58 FKPAVAIFSDVEF---HYDILARRLRELSFLNSGVKIALIDERGegrrddfhyegGIRSFVEHlAQLKSPLHPNVISVTG 134
Cdd:PTZ00108   200 FYPDYAKFGMTEFdddMLRLLKKRVYDLAGCFGKLKVYLNGERI-----------AIKSFKDY-VDLYLPDGEEGKKPPY 267

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698  135 EHNGIVV----DVALQWTDAyQETMYCFTNNIPQKDGGTHLAgfraALTRVLSNYIEQNGIAKQAKvaltGDDMREGMIA 210
Cdd:PTZ00108   268 PFVYTSVngrwEVVVSLSDG-QFQQVSFVNSICTTKGGTHVN----YILDQLISKLQEKAKKKKKK----GKEIKPNQIK 338

                          170       180       190
                   ....*....|....*....|....*....|...
gi 1005664698  211 ------VLSVKVpDPSFSSQTKEKLVSSDVRPA 237
Cdd:PTZ00108   339 nhlwvfVNCLIV-NPSFDSQTKETLTTKPSKFG 370
PLN03128 PLN03128
DNA topoisomerase 2; Provisional
 1-250 4.14e-05

DNA topoisomerase 2; Provisional


Pssm-ID: 215593 [Multi-domain]  Cd Length: 1135  Bit Score: 45.08  E-value: 4.14e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698    1 SGGLHGVGVSVVNALSEHLWLDIW--RDGFHYQQEY-----ALGEPQypLKQLEASTKRgTTLRFKPAVAIFSDVEFHYD 73
Cdd:PLN03128   131 TGGRNGYGAKLANIFSTEFTVETAdgNRGKKYKQVFtnnmsVKSEPK--ITSCKASENW-TKITFKPDLAKFNMTRLDED 207

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698   74 I---LARRLRELS-FLNSGVKIALIDERGEgrrddfhyeggIRSFVEHLA-QLKSPLHPNVISVTGEHNGIVVDVALQWT 148
Cdd:PLN03128   208 VvalMSKRVYDIAgCLGKKLKVELNGKKLP-----------VKSFQDYVGlYLGPNSREDPLPRIYEKVNDRWEVCVSLS 276

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698  149 DAyQETMYCFTNNIPQKDGGTHLAgfraALTRVLSNYIeQNGIAKQAK--VALTGDDMREGMIAVLSVKVPDPSFSSQTK 226
Cdd:PLN03128   277 DG-SFQQVSFVNSIATIKGGTHVD----YVADQIVKHI-QEKVKKKNKnaTHVKPFQIKNHLWVFVNCLIENPTFDSQTK 350

                          250       260
                   ....*....|....*....|....*..
gi 1005664698  227 EKLVSSdvrpavENAFGARLQ---EFL 250
Cdd:PLN03128   351 ETLTTR------PSSFGSKCElseEFL 371
39 PHA02569
DNA topoisomerase II large subunit; Provisional
 158-236 5.39e-05

DNA topoisomerase II large subunit; Provisional


Pssm-ID: 177398 [Multi-domain]  Cd Length: 602  Bit Score: 44.36  E-value: 5.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005664698 158 FTNNIPQKDGGTHLAGFRAALTRVLsnyieQNGIAKQAKVALTGDDMREGMIAVLSVK-VPDPSFSSQTKEKLVSS--DV 234
Cdd:PHA02569  264 FVNGLHTKNGGHHVDCVMDDICEEL-----IPMIKKKHKIEVTKARVKECLTIVLFVRnMSNPRFDSQTKERLTSPfgEI 338


                  ..
gi 1005664698 235 RP 236
Cdd:PHA02569  339 RN 340
 
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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