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Conserved domains on  [gi|670451324|emb|CDO96635|]
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DNA Gyrase B Subunit, partial [Xanthomonas sp. BCC050]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
GyrB_insert pfam18053
DNA gyrase B subunit insert domain; This is the insert domain found in DNA gyrase B subunit ...
 20-186 5.32e-65

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: 198.13  E-value: 5.32e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670451324   20 AALIPATDEPPITGEALEKLLMLFTSANEAIARNAHRYDPALLTALIDLPPLDVEKLQAEGDHHPTLDALQAVLNRGTLG 99
Cdd:pfam18053   1 AALYPNEGAPPISGEALEELARQYRLAEAIIKRLSRRYDPAVLEALLYLPPLDAEDLDDEAAAEAWAAALEARLNQDGLG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670451324  100 TARYQLRFDPATENAPATLVAIRRHMGEEFTQVLPMGAFESGELRPLREVSLALHDLVREGAQIVRGNKSHPITNFAQAH 179
Cdd:pfam18053  81 GPRYRVSVEEDTERGKYLLRVTRRHHGNETVYVLDADFFESGDYRALAELGETLDGLIGEGAYIKRGEKEQPVESFKEAL 160


                  ....*..
gi 670451324  180 AWLL*EA 186
Cdd:pfam18053 161 DWLMEEA 167
DNA_gyraseB_C super family cl47616
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ...
 187-210 9.77e-12

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,.


The actual alignment was detected with superfamily member pfam00986:

Pssm-ID: 460016 [Multi-domain]  Cd Length: 63  Bit Score: 58.16  E-value: 9.77e-12
                          10        20
                  ....*....|....*....|....
gi 670451324  187 KKGRQVQRFKG*GEMNAEQLWETT 210
Cdd:pfam00986   1 KKKVEIQRYKGLGEMNPEQLWETT 24
 
Name Accession Description Interval E-value
GyrB_insert pfam18053
DNA gyrase B subunit insert domain; This is the insert domain found in DNA gyrase B subunit ...
 20-186 5.32e-65

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: 198.13  E-value: 5.32e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670451324   20 AALIPATDEPPITGEALEKLLMLFTSANEAIARNAHRYDPALLTALIDLPPLDVEKLQAEGDHHPTLDALQAVLNRGTLG 99
Cdd:pfam18053   1 AALYPNEGAPPISGEALEELARQYRLAEAIIKRLSRRYDPAVLEALLYLPPLDAEDLDDEAAAEAWAAALEARLNQDGLG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670451324  100 TARYQLRFDPATENAPATLVAIRRHMGEEFTQVLPMGAFESGELRPLREVSLALHDLVREGAQIVRGNKSHPITNFAQAH 179
Cdd:pfam18053  81 GPRYRVSVEEDTERGKYLLRVTRRHHGNETVYVLDADFFESGDYRALAELGETLDGLIGEGAYIKRGEKEQPVESFKEAL 160


                  ....*..
gi 670451324  180 AWLL*EA 186
Cdd:pfam18053 161 DWLMEEA 167
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-210 1.76e-47

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 165.65  E-value: 1.76e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670451324   1 YLKDDAALNAYLASNAVEGAALIPAtDEPPITGEALEKLLMLFTSANEAIARNAHRYDPALLTALIDLPPLDVEKLQAEG 80
Cdd:PRK14939 546 YLKDDEALDDYLIELALEGATLHLA-DGPAISGEALEKLVKEYRAVRKIIDRLERRYPRAVLEALIYAPALDLDDLADEA 624

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670451324  81 DhhptldalqavlnrgtlgtaryqlrfdpatenapatlvairrhmgeefTQVLPMGAFESGELRPLREVSLALHDLVREG 160
Cdd:PRK14939 625 A------------------------------------------------VAALDADFLTSAEYRRLVELAEKLRGLIEEG 656

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 670451324 161 AQIVRGNKSHPITNFAQAHAWLL*EAKKGRQVQRFKG*GEMNAEQLWETT 210
Cdd:PRK14939 657 AYLERGERKQPVSSFEEALDWLLAEARKGLSIQRYKGLGEMNPEQLWETT 706
DNA_gyraseB_C pfam00986
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ...
 187-210 9.77e-12

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: 58.16  E-value: 9.77e-12
                          10        20
                  ....*....|....*....|....
gi 670451324  187 KKGRQVQRFKG*GEMNAEQLWETT 210
Cdd:pfam00986   1 KKKVEIQRYKGLGEMNPEQLWETT 24
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
155-210 1.04e-09

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


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 57.35  E-value: 1.04e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 670451324 155 DLVREG----AQ-----IVRGNKSHPITNFAQAHAWLL*-EAKKGRQVQRFKG*GEMNAEQLWETT 210
Cdd:COG0187  520 PLIEAGhvyiAQpplyrIKKGKKTYYAYSDAELDELLKElKGKKKVEIQRYKGLGEMNPEQLWETT 585
gyrB PRK05644
DNA gyrase subunit B; Validated
 182-210 2.46e-09

DNA gyrase subunit B; Validated


Pssm-ID: 235542 [Multi-domain]  Cd Length: 638  Bit Score: 56.26  E-value: 2.46e-09
                         10        20
                 ....*....|....*....|....*....
gi 670451324 182 LL*EAKKGRQVQRFKG*GEMNAEQLWETT 210
Cdd:PRK05644 560 LKLKGNPKYGIQRYKGLGEMNPEQLWETT 588
gyrB TIGR01059
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ...
 155-210 2.26e-08

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: 53.51  E-value: 2.26e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 670451324  155 DLVREGAQIVRGNKSHpitNFAQAHAWL----L*EAKKGRQVQRFKG*GEMNAEQLWETT 210
Cdd:TIGR01059 548 DLVGEALEDLKALYIY---SDKEKEEAKtqipVHLGRKGIEIQRYKGLGEMNADQLWETT 604
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 144-210 1.68e-07

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 50.63  E-value: 1.68e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 670451324   144 RPLRE---VSLALHDLVRegaqiVRGNKSHPITNFA---QAHAWLL*EAKKGR--QVQRFKG*GEMNAEQLWETT 210
Cdd:smart00433 482 PPLIEagfVYIAIPPLYK-----VTKGKKKYVYSFYsldEYEKWLEKTEGNKSkyEIQRYKGLGEMNADQLWETT 551
parE_Gneg TIGR01055
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ...
 183-210 2.17e-03

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: 38.36  E-value: 2.17e-03
                          10        20
                  ....*....|....*....|....*...
gi 670451324  183 L*EAKKGRQVQRFKG*GEMNAEQLWETT 210
Cdd:TIGR01055 550 LKKKKGKPNVQRFKGLGEMNPAQLRETT 577
 
Name Accession Description Interval E-value
GyrB_insert pfam18053
DNA gyrase B subunit insert domain; This is the insert domain found in DNA gyrase B subunit ...
 20-186 5.32e-65

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: 198.13  E-value: 5.32e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670451324   20 AALIPATDEPPITGEALEKLLMLFTSANEAIARNAHRYDPALLTALIDLPPLDVEKLQAEGDHHPTLDALQAVLNRGTLG 99
Cdd:pfam18053   1 AALYPNEGAPPISGEALEELARQYRLAEAIIKRLSRRYDPAVLEALLYLPPLDAEDLDDEAAAEAWAAALEARLNQDGLG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670451324  100 TARYQLRFDPATENAPATLVAIRRHMGEEFTQVLPMGAFESGELRPLREVSLALHDLVREGAQIVRGNKSHPITNFAQAH 179
Cdd:pfam18053  81 GPRYRVSVEEDTERGKYLLRVTRRHHGNETVYVLDADFFESGDYRALAELGETLDGLIGEGAYIKRGEKEQPVESFKEAL 160


                  ....*..
gi 670451324  180 AWLL*EA 186
Cdd:pfam18053 161 DWLMEEA 167
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-210 1.76e-47

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 165.65  E-value: 1.76e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670451324   1 YLKDDAALNAYLASNAVEGAALIPAtDEPPITGEALEKLLMLFTSANEAIARNAHRYDPALLTALIDLPPLDVEKLQAEG 80
Cdd:PRK14939 546 YLKDDEALDDYLIELALEGATLHLA-DGPAISGEALEKLVKEYRAVRKIIDRLERRYPRAVLEALIYAPALDLDDLADEA 624

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 670451324  81 DhhptldalqavlnrgtlgtaryqlrfdpatenapatlvairrhmgeefTQVLPMGAFESGELRPLREVSLALHDLVREG 160
Cdd:PRK14939 625 A------------------------------------------------VAALDADFLTSAEYRRLVELAEKLRGLIEEG 656

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 670451324 161 AQIVRGNKSHPITNFAQAHAWLL*EAKKGRQVQRFKG*GEMNAEQLWETT 210
Cdd:PRK14939 657 AYLERGERKQPVSSFEEALDWLLAEARKGLSIQRYKGLGEMNPEQLWETT 706
DNA_gyraseB_C pfam00986
DNA gyrase B subunit, carboxyl terminus; The amino terminus of eukaryotic and prokaryotic DNA ...
 187-210 9.77e-12

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: 58.16  E-value: 9.77e-12
                          10        20
                  ....*....|....*....|....
gi 670451324  187 KKGRQVQRFKG*GEMNAEQLWETT 210
Cdd:pfam00986   1 KKKVEIQRYKGLGEMNPEQLWETT 24
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
155-210 1.04e-09

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


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 57.35  E-value: 1.04e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 670451324 155 DLVREG----AQ-----IVRGNKSHPITNFAQAHAWLL*-EAKKGRQVQRFKG*GEMNAEQLWETT 210
Cdd:COG0187  520 PLIEAGhvyiAQpplyrIKKGKKTYYAYSDAELDELLKElKGKKKVEIQRYKGLGEMNPEQLWETT 585
gyrB PRK05644
DNA gyrase subunit B; Validated
 182-210 2.46e-09

DNA gyrase subunit B; Validated


Pssm-ID: 235542 [Multi-domain]  Cd Length: 638  Bit Score: 56.26  E-value: 2.46e-09
                         10        20
                 ....*....|....*....|....*....
gi 670451324 182 LL*EAKKGRQVQRFKG*GEMNAEQLWETT 210
Cdd:PRK05644 560 LKLKGNPKYGIQRYKGLGEMNPEQLWETT 588
PRK05559 PRK05559
DNA topoisomerase IV subunit B; Reviewed
 183-210 5.41e-09

DNA topoisomerase IV subunit B; Reviewed


Pssm-ID: 235501 [Multi-domain]  Cd Length: 631  Bit Score: 55.11  E-value: 5.41e-09
                         10        20
                 ....*....|....*....|....*...
gi 670451324 183 L*EAKKGRQVQRFKG*GEMNAEQLWETT 210
Cdd:PRK05559 556 LGKKGGKPEIQRFKGLGEMNPDQLWETT 583
gyrB TIGR01059
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ...
 155-210 2.26e-08

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: 53.51  E-value: 2.26e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 670451324  155 DLVREGAQIVRGNKSHpitNFAQAHAWL----L*EAKKGRQVQRFKG*GEMNAEQLWETT 210
Cdd:TIGR01059 548 DLVGEALEDLKALYIY---SDKEKEEAKtqipVHLGRKGIEIQRYKGLGEMNADQLWETT 604
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 144-210 1.68e-07

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 50.63  E-value: 1.68e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 670451324   144 RPLRE---VSLALHDLVRegaqiVRGNKSHPITNFA---QAHAWLL*EAKKGR--QVQRFKG*GEMNAEQLWETT 210
Cdd:smart00433 482 PPLIEagfVYIAIPPLYK-----VTKGKKKYVYSFYsldEYEKWLEKTEGNKSkyEIQRYKGLGEMNADQLWETT 551
PTZ00109 PTZ00109
DNA gyrase subunit b; Provisional
 188-210 1.11e-05

DNA gyrase subunit b; Provisional


Pssm-ID: 240272 [Multi-domain]  Cd Length: 903  Bit Score: 45.64  E-value: 1.11e-05
                         10        20
                 ....*....|....*....|...
gi 670451324 188 KGRQVQRFKG*GEMNAEQLWETT 210
Cdd:PTZ00109 835 KHYEIQRFKGLGEMMADQLWETT 857
parE_Gneg TIGR01055
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ...
 183-210 2.17e-03

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: 38.36  E-value: 2.17e-03
                          10        20
                  ....*....|....*....|....*...
gi 670451324  183 L*EAKKGRQVQRFKG*GEMNAEQLWETT 210
Cdd:TIGR01055 550 LKKKKGKPNVQRFKGLGEMNPAQLRETT 577
 
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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