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Conserved domains on  [gi|371560479|gb|AEX37021|]
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DNA gyrase B subunit, partial [Sphingomonas sp. 324]

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
 1-259 3.12e-156

DNA gyrase subunit B; Provisional


The actual alignment was detected with superfamily member PRK14939:

Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 452.63  E-value: 3.12e-156
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479   1 DNGRGIPTYIHEGDGVSAAAVIMFQLHAGGKFDQNSYKVSGGLHGVGVSVVKALSDWLKLVIYRNGKRLEMKFARGDTVE 80
Cdd:PRK14939  75 DNGRGIPTDIHPEEGVSAAEVIMTVLHAGGKFDQNSYKVSGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVA 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479  81 SLKFTGDApmsdnGKvlSGTEVTFYPSVTPFAHIDLDLKTLEHRLPELAFLNSGVVIKLQDHRGaEKfEEILHYEGGVEA 160
Cdd:PRK14939 155 PLKVVGET-----DK--TGTEVRFWPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRLKDERD-GK-EEEFHYEGGIKA 225

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479 161 FVRHLVKSKTPILKEVIVIRGKKEGIEIDLALWWNDTYHETMLCFTNNIPDKDGGTHLAAFRSALTPTLNNYTEKSGVLK 240
Cdd:PRK14939 226 FVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAK 305

                        250
                 ....*....|....*....
gi 371560479 241 KEKVTLTGDDMREGLTAIV 259
Cdd:PRK14939 306 KAKVSLTGDDAREGLTAVL 324
 
Name Accession Description Interval E-value
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-259 3.12e-156

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 452.63  E-value: 3.12e-156
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479   1 DNGRGIPTYIHEGDGVSAAAVIMFQLHAGGKFDQNSYKVSGGLHGVGVSVVKALSDWLKLVIYRNGKRLEMKFARGDTVE 80
Cdd:PRK14939  75 DNGRGIPTDIHPEEGVSAAEVIMTVLHAGGKFDQNSYKVSGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVA 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479  81 SLKFTGDApmsdnGKvlSGTEVTFYPSVTPFAHIDLDLKTLEHRLPELAFLNSGVVIKLQDHRGaEKfEEILHYEGGVEA 160
Cdd:PRK14939 155 PLKVVGET-----DK--TGTEVRFWPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRLKDERD-GK-EEEFHYEGGIKA 225

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479 161 FVRHLVKSKTPILKEVIVIRGKKEGIEIDLALWWNDTYHETMLCFTNNIPDKDGGTHLAAFRSALTPTLNNYTEKSGVLK 240
Cdd:PRK14939 226 FVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAK 305

                        250
                 ....*....|....*....
gi 371560479 241 KEKVTLTGDDMREGLTAIV 259
Cdd:PRK14939 306 KAKVSLTGDDAREGLTAVL 324
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
1-259 6.44e-118

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


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 350.48  E-value: 6.44e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479   1 DNGRGIPTYIHEGDGVSAAAVIMFQLHAGGKFDQNSYKVSGGLHGVGVSVVKALSDWLKLVIYRNGKRLEMKFARGDTVE 80
Cdd:COG0187   73 DNGRGIPVDIHPKEGKSALEVVLTVLHAGGKFDGGSYKVSGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVG 152

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479  81 SLKFTGDApmsdNGkvlSGTEVTFYPSVTPFAHIDLDLKTLEHRLPELAFLNSGVVIKLQDHRGAEKFEEILHYEGGVEA 160
Cdd:COG0187  153 PLEKIGKT----DR---TGTTVRFKPDPEIFETTEFDYETLAERLRELAFLNKGLTITLTDEREEEPKEETFHYEGGIKD 225

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479 161 FVRHLVKSKTPILKEVIVIRGKKEGIEIDLALWWNDTYHETMLCFTNNIPDKDGGTHLAAFRSALTPTLNNYTEKSGVLK 240
Cdd:COG0187  226 FVEYLNEDKEPLHPEVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLK 305

                        250
                 ....*....|....*....
gi 371560479 241 KEKVTLTGDDMREGLTAIV 259
Cdd:COG0187  306 EKDKNLTGDDVREGLTAVI 324
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-259 3.09e-80

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 252.48  E-value: 3.09e-80
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479     1 DNGRGIPTYIHEGDGVSAAAVIMFQLHAGGKFDQNSYKVSGGLHGVGVSVVKALSDWLKLVIYRNGKRLEMKFARGDT-V 79
Cdd:smart00433  39 DNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGGLHGVGASVVNALSTEFEVEVARDGKEYKQSFSNNGKpL 118

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479    80 ESLKFTGDAPmsdngkvLSGTEVTFYPSVTPFAHI-DLDLKTLEHRLPELAFLNSGVVIKLQDHRGAEkfEEILHYEGGV 158
Cdd:smart00433 119 SEPKIIGDTK-------KDGTKVTFKPDLEIFGMTtDDDFELLKRRLRELAFLNKGVKITLNDERSDE--EKTFLFEGGI 189

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479   159 EAFVRHLVKSKTPILKEVIVIRGKKEGIEIDLALWWNDTYHETMLCFTNNIPDKDGGTHLAAFRSALTPTLNNYTEKSGV 238
Cdd:smart00433 190 KDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKKK 269

                          250       260
                   ....*....|....*....|.
gi 371560479   239 LKKEKvtLTGDDMREGLTAIV 259
Cdd:smart00433 270 LKEKN--IKGEDVREGLTAFI 288
HATPase_GyrB-like cd16928
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ...
 1-147 5.72e-59

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: 185.05  E-value: 5.72e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479   1 DNGRGIPTYIHEGDGVSAAAVIMFQLHAGGKFDQNSYKVSGGLHGVGVSVVKALSDWLKLVIYRNGKRLEMKFARGDTVE 80
Cdd:cd16928   38 DNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGLHGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLT 117

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 371560479  81 SLKFTGDapmsdngKVLSGTEVTFYPSVTPFAHIDLDLKTLEHRLPELAFLNSGVVIKLQDHRGAEK 147
Cdd:cd16928  118 PLEVIGE-------TKKTGTTVRFWPDPEIFEKTEFDFDTLKRRLRELAFLNKGLKIVLEDERTGKE 177
parE_Gneg TIGR01055
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ...
 1-253 1.54e-43

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: 155.85  E-value: 1.54e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479    1 DNGRGIPTYIHEGDGVSAAAVIMFQLHAGGKFDQNSYKVSGGLHGVGVSVVKALSDWLKLVIYRNGKRLEMKFARGDTVE 80
Cdd:TIGR01055  68 DNGRGMPVDIHPKEGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVT 147

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479   81 SLKFTGDApmsdnGKVLSGTEVTFYPSVTPFAHIDLDLKTLEHRLPELAFLNSGVVIKLQDHrgAEKFEEILHYEGGVEA 160
Cdd:TIGR01055 148 DLISAGTC-----GKRLTGTSVHFTPDPEIFDSLHFSVSRLYHILRAKAVLCRGVEIEFEDE--VNNTKALWNYPDGLKD 220

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479  161 FVRHLVKSKTPILKEVIVIRGKKEGIEIDLAL-WWNDTYHETMLCFTNNIPDKDGGTHLAAFRSALTPTLNNYTEKSGVL 239
Cdd:TIGR01055 221 YLSEAVNGDNTLPPKPFSGNFEGDDEAVEWALlWLPEGGELFMESYVNLIPTPQGGTHVNGLRQGLLDALREFCEMRNNL 300

                         250
                  ....*....|....
gi 371560479  240 KKeKVTLTGDDMRE 253
Cdd:TIGR01055 301 PR-GVKLTAEDIWD 313
DNA_gyraseB pfam00204
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ...
 157-259 6.63e-37

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: 128.12  E-value: 6.63e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479  157 GVEAFVRHLVKSKTPILKEVIVIRGK--KEGIEIDLALWWNDTYHETMLCFTNNIPDKDGGTHLAAFRSALTPTLNNYTE 234
Cdd:pfam00204   1 GLKDFVEELNKDKKPLHKEIIYFEGEspDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80

                          90       100
                  ....*....|....*....|....*
gi 371560479  235 KSGVLKKEKVTLTGDDMREGLTAIV 259
Cdd:pfam00204  81 KKGLLKKKDEKITGEDIREGLTAVV 105
 
Name Accession Description Interval E-value
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-259 3.12e-156

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 452.63  E-value: 3.12e-156
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479   1 DNGRGIPTYIHEGDGVSAAAVIMFQLHAGGKFDQNSYKVSGGLHGVGVSVVKALSDWLKLVIYRNGKRLEMKFARGDTVE 80
Cdd:PRK14939  75 DNGRGIPTDIHPEEGVSAAEVIMTVLHAGGKFDQNSYKVSGGLHGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVA 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479  81 SLKFTGDApmsdnGKvlSGTEVTFYPSVTPFAHIDLDLKTLEHRLPELAFLNSGVVIKLQDHRGaEKfEEILHYEGGVEA 160
Cdd:PRK14939 155 PLKVVGET-----DK--TGTEVRFWPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRLKDERD-GK-EEEFHYEGGIKA 225

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479 161 FVRHLVKSKTPILKEVIVIRGKKEGIEIDLALWWNDTYHETMLCFTNNIPDKDGGTHLAAFRSALTPTLNNYTEKSGVLK 240
Cdd:PRK14939 226 FVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAK 305

                        250
                 ....*....|....*....
gi 371560479 241 KEKVTLTGDDMREGLTAIV 259
Cdd:PRK14939 306 KAKVSLTGDDAREGLTAVL 324
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
1-259 6.44e-118

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


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 350.48  E-value: 6.44e-118
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479   1 DNGRGIPTYIHEGDGVSAAAVIMFQLHAGGKFDQNSYKVSGGLHGVGVSVVKALSDWLKLVIYRNGKRLEMKFARGDTVE 80
Cdd:COG0187   73 DNGRGIPVDIHPKEGKSALEVVLTVLHAGGKFDGGSYKVSGGLHGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVG 152

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479  81 SLKFTGDApmsdNGkvlSGTEVTFYPSVTPFAHIDLDLKTLEHRLPELAFLNSGVVIKLQDHRGAEKFEEILHYEGGVEA 160
Cdd:COG0187  153 PLEKIGKT----DR---TGTTVRFKPDPEIFETTEFDYETLAERLRELAFLNKGLTITLTDEREEEPKEETFHYEGGIKD 225

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479 161 FVRHLVKSKTPILKEVIVIRGKKEGIEIDLALWWNDTYHETMLCFTNNIPDKDGGTHLAAFRSALTPTLNNYTEKSGVLK 240
Cdd:COG0187  226 FVEYLNEDKEPLHPEVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLK 305

                        250
                 ....*....|....*....
gi 371560479 241 KEKVTLTGDDMREGLTAIV 259
Cdd:COG0187  306 EKDKNLTGDDVREGLTAVI 324
gyrB PRK05644
DNA gyrase subunit B; Validated
 1-259 1.59e-115

DNA gyrase subunit B; Validated


Pssm-ID: 235542 [Multi-domain]  Cd Length: 638  Bit Score: 344.38  E-value: 1.59e-115
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479   1 DNGRGIPTYIHEGDGVSAAAVIMFQLHAGGKFDQNSYKVSGGLHGVGVSVVKALSDWLKLVIYRNGKRLEMKFARGDTVE 80
Cdd:PRK05644  75 DNGRGIPVDIHPKTGKPAVEVVLTVLHAGGKFGGGGYKVSGGLHGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVT 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479  81 SLKFTGDAPmsdngkvLSGTEVTFYPSVTPFAHIDLDLKTLEHRLPELAFLNSGVVIKLQDHRGAEKFEEILHYEGGVEA 160
Cdd:PRK05644 155 PLEVIGETD-------ETGTTVTFKPDPEIFETTEFDYDTLATRLRELAFLNKGLKITLTDEREGEEKEETFHYEGGIKE 227

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479 161 FVRHLVKSKTPILKEVIVIRGKKEGIEIDLALWWNDTYHETMLCFTNNIPDKDGGTHLAAFRSALTPTLNNYTEKSGVLK 240
Cdd:PRK05644 228 YVEYLNRNKEPLHEEPIYFEGEKDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLK 307

                        250
                 ....*....|....*....
gi 371560479 241 KEKVTLTGDDMREGLTAIV 259
Cdd:PRK05644 308 EKDDNLTGEDVREGLTAVI 326
PRK05559 PRK05559
DNA topoisomerase IV subunit B; Reviewed
 1-259 3.00e-88

DNA topoisomerase IV subunit B; Reviewed


Pssm-ID: 235501 [Multi-domain]  Cd Length: 631  Bit Score: 273.90  E-value: 3.00e-88
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479   1 DNGRGIPTYIHEGDGVSAAAVIMFQLHAGGKFDQNSYKVSGGLHGVGVSVVKALSDWLKLVIYRNGKRLEMKFARGDTVE 80
Cdd:PRK05559  75 DNGRGIPVGIHPEEGKSGVEVILTKLHAGGKFSNKAYKFSGGLHGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVG 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479  81 SLKFTGDAPMSDNgkvlsGTEVTFYPSVTPFAHIDLDLKTLEHRLPELAFLNSGVVIKLQDHRGAEKFeeilHYEGGVEA 160
Cdd:PRK05559 155 PLEVVGTAGKRKT-----GTRVRFWPDPKIFDSPKFSPERLKERLRSKAFLLPGLTITLNDERERQTF----HYENGLKD 225

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479 161 FVRHLVKSKTPILKE-VIVIRGKKEGIEIDLALWWNDTYHETMLCFTNNIPDKDGGTHLAAFRSALTPTLNNYTEKSGVL 239
Cdd:PRK05559 226 YLAELNEGKETLPEEfVGSFEGEAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLL 305

                        250       260
                 ....*....|....*....|
gi 371560479 240 KKEKvTLTGDDMREGLTAIV 259
Cdd:PRK05559 306 PKGK-KLEGEDVREGLAAVL 324
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-259 3.09e-80

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 252.48  E-value: 3.09e-80
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479     1 DNGRGIPTYIHEGDGVSAAAVIMFQLHAGGKFDQNSYKVSGGLHGVGVSVVKALSDWLKLVIYRNGKRLEMKFARGDT-V 79
Cdd:smart00433  39 DNGRGIPVEIHPKEKKYAPEVIFTVLHAGGKFDDDAYKVSGGLHGVGASVVNALSTEFEVEVARDGKEYKQSFSNNGKpL 118

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479    80 ESLKFTGDAPmsdngkvLSGTEVTFYPSVTPFAHI-DLDLKTLEHRLPELAFLNSGVVIKLQDHRGAEkfEEILHYEGGV 158
Cdd:smart00433 119 SEPKIIGDTK-------KDGTKVTFKPDLEIFGMTtDDDFELLKRRLRELAFLNKGVKITLNDERSDE--EKTFLFEGGI 189

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479   159 EAFVRHLVKSKTPILKEVIVIRGKKEGIEIDLALWWNDTYHETMLCFTNNIPDKDGGTHLAAFRSALTPTLNNYTEKSGV 238
Cdd:smart00433 190 KDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKKK 269

                          250       260
                   ....*....|....*....|.
gi 371560479   239 LKKEKvtLTGDDMREGLTAIV 259
Cdd:smart00433 270 LKEKN--IKGEDVREGLTAFI 288
HATPase_GyrB-like cd16928
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ...
 1-147 5.72e-59

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: 185.05  E-value: 5.72e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479   1 DNGRGIPTYIHEGDGVSAAAVIMFQLHAGGKFDQNSYKVSGGLHGVGVSVVKALSDWLKLVIYRNGKRLEMKFARGDTVE 80
Cdd:cd16928   38 DNGRGIPVDIHPKTGKSAVEVVLTVLHAGGKFDGGSYKVSGGLHGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLT 117

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 371560479  81 SLKFTGDapmsdngKVLSGTEVTFYPSVTPFAHIDLDLKTLEHRLPELAFLNSGVVIKLQDHRGAEK 147
Cdd:cd16928  118 PLEVIGE-------TKKTGTTVRFWPDPEIFEKTEFDFDTLKRRLRELAFLNKGLKIVLEDERTGKE 177
PTZ00109 PTZ00109
DNA gyrase subunit b; Provisional
 1-259 2.42e-48

DNA gyrase subunit b; Provisional


Pssm-ID: 240272 [Multi-domain]  Cd Length: 903  Bit Score: 170.83  E-value: 2.42e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479   1 DNGRGIPTYIHEGDGVSAAAVIMFQLHAGGKF--------------DQNS--------------------------YKVS 40
Cdd:PTZ00109 167 DNGRGIPCDVSEKTGKSGLETVLTVLHSGGKFqdtfpknsrsdkseDKNDtksskkgksshvkgpkeakekessqmYEYS 246

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479  41 GGLHGVGVSVVKALSDWLKLVIYRNGKRLEMKFARGDTVESLKFTgDAPMSDngkvlSGTEVTFYPSVTPF--AHID--- 115
Cdd:PTZ00109 247 SGLHGVGLSVVNALSSFLKVDVFKGGKIYSIELSKGKVTKPLSVF-SCPLKK-----RGTTIHFLPDYKHIfkTHHQhte 320

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479 116 ----------LDLKTLEHRLPELAFLNSGVVIKLQDHRGAEK----FEEILHYEGGVEAFVRHLVKSKTPILKE--VIVI 179
Cdd:PTZ00109 321 teeeegckngFNLDLIKNRIHELSYLNPGLTFYLVDERIANEnnfyPYETIKHEGGTREFLEELIKDKTPLYKDinIISI 400

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479 180 RGKKEGIEIDLALWWN-DTYHETMLCFTNNIpDKDGGTHLAAFRSALTPTLNNYTEKSGVLKKEKVTLTGDDMREGLTAI 258
Cdd:PTZ00109 401 RGVIKNVNVEVSLSWSlESYTALIKSFANNV-STTAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAI 479


                 .
gi 371560479 259 V 259
Cdd:PTZ00109 480 I 480
TopoII_Trans_DNA_gyrase cd00822
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ...
 156-259 8.92e-46

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: 151.17  E-value: 8.92e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479 156 GGVEAFVRHLVKSKTPILKEVIVIRGKKEGIEIDLALWWNDTYHETMLCFTNNIPDKDGGTHLAAFRSALTPTLNNYTEK 235
Cdd:cd00822    1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80

                         90       100
                 ....*....|....*....|....
gi 371560479 236 SGVLKKEKVTLTGDDMREGLTAIV 259
Cdd:cd00822   81 NNLLKKKDVKLTGDDIREGLTAVI 104
parE_Gneg TIGR01055
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ...
 1-253 1.54e-43

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: 155.85  E-value: 1.54e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479    1 DNGRGIPTYIHEGDGVSAAAVIMFQLHAGGKFDQNSYKVSGGLHGVGVSVVKALSDWLKLVIYRNGKRLEMKFARGDTVE 80
Cdd:TIGR01055  68 DNGRGMPVDIHPKEGVSAVEVILTTLHAGGKFSNKNYHFSGGLHGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVT 147

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479   81 SLKFTGDApmsdnGKVLSGTEVTFYPSVTPFAHIDLDLKTLEHRLPELAFLNSGVVIKLQDHrgAEKFEEILHYEGGVEA 160
Cdd:TIGR01055 148 DLISAGTC-----GKRLTGTSVHFTPDPEIFDSLHFSVSRLYHILRAKAVLCRGVEIEFEDE--VNNTKALWNYPDGLKD 220

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479  161 FVRHLVKSKTPILKEVIVIRGKKEGIEIDLAL-WWNDTYHETMLCFTNNIPDKDGGTHLAAFRSALTPTLNNYTEKSGVL 239
Cdd:TIGR01055 221 YLSEAVNGDNTLPPKPFSGNFEGDDEAVEWALlWLPEGGELFMESYVNLIPTPQGGTHVNGLRQGLLDALREFCEMRNNL 300

                         250
                  ....*....|....
gi 371560479  240 KKeKVTLTGDDMRE 253
Cdd:TIGR01055 301 PR-GVKLTAEDIWD 313
DNA_gyraseB pfam00204
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ...
 157-259 6.63e-37

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: 128.12  E-value: 6.63e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479  157 GVEAFVRHLVKSKTPILKEVIVIRGK--KEGIEIDLALWWNDTYHETMLCFTNNIPDKDGGTHLAAFRSALTPTLNNYTE 234
Cdd:pfam00204   1 GLKDFVEELNKDKKPLHKEIIYFEGEspDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80

                          90       100
                  ....*....|....*....|....*
gi 371560479  235 KSGVLKKEKVTLTGDDMREGLTAIV 259
Cdd:pfam00204  81 KKGLLKKKDEKITGEDIREGLTAVV 105
TopoII_MutL_Trans cd00329
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ...
 158-259 3.80e-10

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: 55.73  E-value: 3.80e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479 158 VEAFVRHLVKSKTPilKEVIVIRGKKEGIEIDLALWWND---TYHETMLCFTNNIPDKDGGTHLAAFRSALTPTLNnyte 234
Cdd:cd00329    1 LKDRLAEILGDKVA--DKLIYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---- 74

                         90       100
                 ....*....|....*....|....*
gi 371560479 235 ksgvlkkekvtltGDDMREGLTAIV 259
Cdd:cd00329   75 -------------GDDVRRYPVAVL 86
HATPase_TopII-like cd16930
Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the ...
 1-106 4.35e-05

Histidine kinase-like ATPase domain of eukaryotic topoisomerase II; This family includes the histidine kinase-like ATPase (HATpase) domains of human topoisomerase IIA (TopIIA) and TopIIB, Saccharomyces cerevisae TOP2p, and related proteins. These proteins catalyze the passage of DNA double strands through a transient double-strand break in the presence of ATP.


Pssm-ID: 340407 [Multi-domain]  Cd Length: 147  Bit Score: 42.33  E-value: 4.35e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479   1 DNGRGIPTYIHEGDGVSAAAVIMFQLHAGGKFDQNSYKVSGGLHGVGVSVVKALSdwLKLVI----YRNGKRLEMKFArg 76
Cdd:cd16930   44 NNGKGIPVVIHKEEKIYVPEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFS--TEFTVetadSESKKKFKQTWT-- 119

                         90       100       110
                 ....*....|....*....|....*....|
gi 371560479  77 dtvESLKFTGDAPMSDNGKVLSGTEVTFYP 106
Cdd:cd16930  120 ---NNMGKASEPKITPYEKGKDYTKVTFKP 146
39 PHA02569
DNA topoisomerase II large subunit; Provisional
 1-259 1.01e-04

DNA topoisomerase II large subunit; Provisional


Pssm-ID: 177398 [Multi-domain]  Cd Length: 602  Bit Score: 43.20  E-value: 1.01e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479   1 DNGRGIPTYI---HEGDGVSAAAVIMFQLHAGGKFDqNSYKVSGGLHGVGVSVVKALSDWLkLVIYRNGKRlEMKFARGD 77
Cdd:PHA02569  85 DNGRGIPQAMvttPEGEEIPGPVAAWTRTKAGSNFD-DTNRVTGGMNGVGSSLTNFFSVLF-IGETCDGKN-EVTVNCSN 161

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479  78 TVESLKFTgdapmSDNGKvLSGTEVTFYPSVTPFAHIDLDLKTLE---HRLPELAFLNSGVVIKLQDHRGAEKFEEILHY 154
Cdd:PHA02569 162 GAENISWS-----TKPGK-GKGTSVTFIPDFSHFEVNGLDQQYLDiilDRLQTLAVVFPDIKFTFNGKKVSGKFKKYAKQ 235

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479 155 EGgveafvrhlvksktpilKEVIVIRGKKEGIEIDLAlwwNDTYHEtmLCFTNNIPDKDGGTHLAAFRSALTPTLnnyte 234
Cdd:PHA02569 236 FG-----------------DDTIVQENDNVSIALAPS---PDGFRQ--LSFVNGLHTKNGGHHVDCVMDDICEEL----- 288

                        250       260
                 ....*....|....*....|....*
gi 371560479 235 KSGVLKKEKVTLTGDDMREGLTAIV 259
Cdd:PHA02569 289 IPMIKKKHKIEVTKARVKECLTIVL 313
PLN03128 PLN03128
DNA topoisomerase 2; Provisional
 1-111 2.14e-04

DNA topoisomerase 2; Provisional


Pssm-ID: 215593 [Multi-domain]  Cd Length: 1135  Bit Score: 42.39  E-value: 2.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 371560479    1 DNGRGIPTYIHEGDGVSAAAVIMFQLHAGGKFDQNSYKVSGGLHGVGVSVVKALSDWLKLVIY--RNGKRLEMKFARGDT 78
Cdd:PLN03128   92 NNGKGIPVEIHKEEGVYVPELIFGHLLTSSNFDDNEKKTTGGRNGYGAKLANIFSTEFTVETAdgNRGKKYKQVFTNNMS 171

                          90       100       110
                  ....*....|....*....|....*....|...
gi 371560479   79 VESLKFTGDAPMSDNgkvlsGTEVTFYPSVTPF 111
Cdd:PLN03128  172 VKSEPKITSCKASEN-----WTKITFKPDLAKF 199
HATPase_c smart00387
Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.
 1-67 3.87e-04

Histidine kinase-like ATPases; Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases.


Pssm-ID: 214643 [Multi-domain]  Cd Length: 111  Bit Score: 39.17  E-value: 3.87e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 371560479     1 DNGRGIPtyihegdgvsaAAVIMFQLHAGGKFDQNSYKVSGglHGVGVSVVKALSDWLKLVIYRNGK 67
Cdd:smart00387  44 DNGPGIP-----------PEDLEKIFEPFFRTDKRSRKIGG--TGLGLSIVKKLVELHGGEISVESE 97
HATPase_c pfam02518
Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the ...
 1-58 8.33e-03

Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase; This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.


Pssm-ID: 460579 [Multi-domain]  Cd Length: 109  Bit Score: 35.04  E-value: 8.33e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 371560479    1 DNGRGIPTYIHEgdgvsaaavimfqlHAGGKFDQnSYKVSGGLHGVGVSVVKALSDWL 58
Cdd:pfam02518  43 DNGIGIPPEDLP--------------RIFEPFST-ADKRGGGGTGLGLSIVRKLVELL 85
 
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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