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Conserved domains on  [gi|66474597|gb|AAY46868|]
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GyrB, partial [Aeromonas veronii]

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
 1-372 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: 799.31  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597    1 HGVGVSVVNALSDTLKLTIRRQGHVYEQTYKLGEPQAPLKQIGDATTTGTEVRFWPSPTIFSDTLFHYETLAKRLRELSF 80
Cdd:PRK14939 118 HGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETDKTGTEVRFWPSPEIFENTEFDYDILAKRLRELAF 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   81 LNSGVSIVLSDERDGREINFCYEGGIKAFVEYLNQSKTPIHPKVFHFSTEHDGIGVEVAMQWNDGYQEGVYCFTNNIPQR 160
Cdd:PRK14939 198 LNSGVRIRLKDERDGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQR 277

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597  161 DGGTHLVGFRTALTRTLNTYMDKEDYSKKAKMSAaSGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGE 240
Cdd:PRK14939 278 DGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSL-TGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNE 356

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597  241 KMAEFLLENPSDAKIVVNKIIDAARAREAARKAREMTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQG 320
Cdd:PRK14939 357 KLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQG 436

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|..
gi 66474597  321 RNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGRDEYNPDK 372
Cdd:PRK14939 437 RDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIGRDEFNPDK 488
 
Name Accession Description Interval E-value
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-372 0e+00

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 799.31  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597    1 HGVGVSVVNALSDTLKLTIRRQGHVYEQTYKLGEPQAPLKQIGDATTTGTEVRFWPSPTIFSDTLFHYETLAKRLRELSF 80
Cdd:PRK14939 118 HGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETDKTGTEVRFWPSPEIFENTEFDYDILAKRLRELAF 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   81 LNSGVSIVLSDERDGREINFCYEGGIKAFVEYLNQSKTPIHPKVFHFSTEHDGIGVEVAMQWNDGYQEGVYCFTNNIPQR 160
Cdd:PRK14939 198 LNSGVRIRLKDERDGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQR 277

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597  161 DGGTHLVGFRTALTRTLNTYMDKEDYSKKAKMSAaSGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGE 240
Cdd:PRK14939 278 DGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSL-TGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNE 356

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597  241 KMAEFLLENPSDAKIVVNKIIDAARAREAARKAREMTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQG 320
Cdd:PRK14939 357 KLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQG 436

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|..
gi 66474597  321 RNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGRDEYNPDK 372
Cdd:PRK14939 437 RDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIGRDEFNPDK 488
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
1-372 0e+00

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


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 614.34  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   1 HGVGVSVVNALSDTLKLTIRRQGHVYEQTYKLGEPQAPLKQIGDATTTGTEVRFWPSPTIFSDTLFHYETLAKRLRELSF 80
Cdd:COG0187 116 HGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKTDRTGTTVRFKPDPEIFETTEFDYETLAERLRELAF 195

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597  81 LNSGVSIVLSDERDG--REINFCYEGGIKAFVEYLNQSKTPIHPKVFHFSTEHDGIGVEVAMQWNDGYQEGVYCFTNNIP 158
Cdd:COG0187 196 LNKGLTITLTDEREEepKEETFHYEGGIKDFVEYLNEDKEPLHPEVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNNIN 275

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597 159 QRDGGTHLVGFRTALTRTLNTYMDKEDYSKKaKMSAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAM 238
Cdd:COG0187 276 TPEGGTHETGFRTALTRVINDYARKNGLLKE-KDKNLTGDDVREGLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVV 354

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597 239 GEKMAEFLLENPSDAKIVVNKIIDAARAREAARKAREMTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAK 318
Cdd:COG0187 355 SEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAK 434

                       330       340       350       360       370
                ....*....|....*....|....*....|....*....|....*....|....
gi 66474597 319 QGRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGrDEYNPDK 372
Cdd:COG0187 435 QGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIG-DDFDLEK 487
gyrB TIGR01059
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ...
 1-372 0e+00

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: 605.89  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597     1 HGVGVSVVNALSDTLKLTIRRQGHVYEQTYKLGEPQAPLKQIGDATTTGTEVRFWPSPTIFSDTLFHYETLAKRLRELSF 80
Cdd:TIGR01059 111 HGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGTTVRFWPDPEIFETTEFDFDILAKRLRELAF 190

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597    81 LNSGVSIVLSDERD--GREINFCYEGGIKAFVEYLNQSKTPIHPKVFHFSTEHDGIGVEVAMQWNDGYQEGVYCFTNNIP 158
Cdd:TIGR01059 191 LNSGVKISLEDERDgkGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKEGIEVEVALQWNDGYSENILSFVNNIN 270

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   159 QRDGGTHLVGFRTALTRTLNTYMDKEDYSKKAKmSAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAM 238
Cdd:TIGR01059 271 TREGGTHLEGFRSALTRVINSYAKNNKLLKESK-PNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLV 349

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   239 GEKMAEFLLENPSDAKIVVNKIIDAARAREAARKAREMTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAK 318
Cdd:TIGR01059 350 YEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSELYIVEGDSAGGSAK 429

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....
gi 66474597   319 QGRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGRDeYNPDK 372
Cdd:TIGR01059 430 QGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKD-FDLEK 482
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-372 1.81e-160

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 462.80  E-value: 1.81e-160
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597      1 HGVGVSVVNALSDTLKLTIRRQGHVYEQTY-KLGEPQAPLKQIGDATTTGTEVRFWPSPTIFS-DTLFHYETLAKRLREL 78
Cdd:smart00433  82 HGVGASVVNALSTEFEVEVARDGKEYKQSFsNNGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGmTTDDDFELLKRRLREL 161

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597     79 SFLNSGVSIVLSDERDGREINFCYEGGIKAFVEYLNQSKTPIHPKVFHFSTEHDGIGVEVAMQWNDGYQEGVYCFTNNIP 158
Cdd:smart00433 162 AFLNKGVKITLNDERSDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVNNIA 241

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597    159 QRDGGTHLVGFRTALTRTLNTYMDKEDYSKKAKMsaaSGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAM 238
Cdd:smart00433 242 TTEGGTHENGFKDALTRVINEYAKKKKKLKEKNI---KGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIV 318

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597    239 GEKMAEFLLENPSDAKIVVNKIIDAARAREAARKAREMTRRKgALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAK 318
Cdd:smart00433 319 SECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKK-KLSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAK 397

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....
gi 66474597    319 QGRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGrDEYNPDK 372
Cdd:smart00433 398 SGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIG-KDFDIEK 450
TopoII_Trans_DNA_gyrase cd00822
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ...
 104-262 5.42e-82

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: 247.47  E-value: 5.42e-82
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597 104 GGIKAFVEYLNQSKTPIHPKVFHFSTEHDGIGVEVAMQWNDGYQEGVYCFTNNIPQRDGGTHLVGFRTALTRTLNTYMDK 183
Cdd:cd00822   1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 66474597 184 EDYSKKAKMSaASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKMAEFLLENPSDAKIVVNKIID 262
Cdd:cd00822  81 NNLLKKKDVK-LTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAIL 158
DNA_gyraseB pfam00204
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ...
 105-262 1.36e-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: 210.93  E-value: 1.36e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   105 GIKAFVEYLNQSKTPIHPKVFHFSTEH--DGIGVEVAMQWNDGYQEGVYCFTNNIPQRDGGTHLVGFRTALTRTLNTYMD 182
Cdd:pfam00204   1 GLKDFVEELNKDKKPLHKEIIYFEGESpdNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   183 KEDYSKKAKMsAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKMAEFLLENPSDAKIVVNKIID 262
Cdd:pfam00204  81 KKGLLKKKDE-KITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQ 159
 
Name Accession Description Interval E-value
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-372 0e+00

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 799.31  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597    1 HGVGVSVVNALSDTLKLTIRRQGHVYEQTYKLGEPQAPLKQIGDATTTGTEVRFWPSPTIFSDTLFHYETLAKRLRELSF 80
Cdd:PRK14939 118 HGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETDKTGTEVRFWPSPEIFENTEFDYDILAKRLRELAF 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   81 LNSGVSIVLSDERDGREINFCYEGGIKAFVEYLNQSKTPIHPKVFHFSTEHDGIGVEVAMQWNDGYQEGVYCFTNNIPQR 160
Cdd:PRK14939 198 LNSGVRIRLKDERDGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQR 277

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597  161 DGGTHLVGFRTALTRTLNTYMDKEDYSKKAKMSAaSGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGE 240
Cdd:PRK14939 278 DGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSL-TGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNE 356

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597  241 KMAEFLLENPSDAKIVVNKIIDAARAREAARKAREMTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQG 320
Cdd:PRK14939 357 KLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQG 436

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|..
gi 66474597  321 RNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGRDEYNPDK 372
Cdd:PRK14939 437 RDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIGRDEFNPDK 488
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
1-372 0e+00

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


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 614.34  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   1 HGVGVSVVNALSDTLKLTIRRQGHVYEQTYKLGEPQAPLKQIGDATTTGTEVRFWPSPTIFSDTLFHYETLAKRLRELSF 80
Cdd:COG0187 116 HGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKTDRTGTTVRFKPDPEIFETTEFDYETLAERLRELAF 195

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597  81 LNSGVSIVLSDERDG--REINFCYEGGIKAFVEYLNQSKTPIHPKVFHFSTEHDGIGVEVAMQWNDGYQEGVYCFTNNIP 158
Cdd:COG0187 196 LNKGLTITLTDEREEepKEETFHYEGGIKDFVEYLNEDKEPLHPEVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNNIN 275

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597 159 QRDGGTHLVGFRTALTRTLNTYMDKEDYSKKaKMSAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAM 238
Cdd:COG0187 276 TPEGGTHETGFRTALTRVINDYARKNGLLKE-KDKNLTGDDVREGLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVV 354

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597 239 GEKMAEFLLENPSDAKIVVNKIIDAARAREAARKAREMTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAK 318
Cdd:COG0187 355 SEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAK 434

                       330       340       350       360       370
                ....*....|....*....|....*....|....*....|....*....|....
gi 66474597 319 QGRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGrDEYNPDK 372
Cdd:COG0187 435 QGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIG-DDFDLEK 487
gyrB PRK05644
DNA gyrase subunit B; Validated
 1-372 0e+00

DNA gyrase subunit B; Validated


Pssm-ID: 235542 [Multi-domain]  Cd Length: 638  Bit Score: 607.09  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597    1 HGVGVSVVNALSDTLKLTIRRQGHVYEQTYKLGEPQAPLKQIGDATTTGTEVRFWPSPTIFSDTLFHYETLAKRLRELSF 80
Cdd:PRK05644 118 HGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIGETDETGTTVTFKPDPEIFETTEFDYDTLATRLRELAF 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   81 LNSGVSIVLSDERDGREI--NFCYEGGIKAFVEYLNQSKTPIHPKVFHFSTEHDGIGVEVAMQWNDGYQEGVYCFTNNIP 158
Cdd:PRK05644 198 LNKGLKITLTDEREGEEKeeTFHYEGGIKEYVEYLNRNKEPLHEEPIYFEGEKDGIEVEVAMQYNDGYSENILSFANNIN 277

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597  159 QRDGGTHLVGFRTALTRTLNTYMDKEDYSKKAKMSAaSGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAM 238
Cdd:PRK05644 278 THEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNL-TGEDVREGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVV 356

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597  239 GEKMAEFLLENPSDAKIVVNKIIDAARAREAARKAREMTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAK 318
Cdd:PRK05644 357 SEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAK 436

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....
gi 66474597  319 QGRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGrDEYNPDK 372
Cdd:PRK05644 437 QGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIG-DDFDISK 489
gyrB TIGR01059
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ...
 1-372 0e+00

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: 605.89  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597     1 HGVGVSVVNALSDTLKLTIRRQGHVYEQTYKLGEPQAPLKQIGDATTTGTEVRFWPSPTIFSDTLFHYETLAKRLRELSF 80
Cdd:TIGR01059 111 HGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGTTVRFWPDPEIFETTEFDFDILAKRLRELAF 190

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597    81 LNSGVSIVLSDERD--GREINFCYEGGIKAFVEYLNQSKTPIHPKVFHFSTEHDGIGVEVAMQWNDGYQEGVYCFTNNIP 158
Cdd:TIGR01059 191 LNSGVKISLEDERDgkGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKEGIEVEVALQWNDGYSENILSFVNNIN 270

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   159 QRDGGTHLVGFRTALTRTLNTYMDKEDYSKKAKmSAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAM 238
Cdd:TIGR01059 271 TREGGTHLEGFRSALTRVINSYAKNNKLLKESK-PNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLV 349

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   239 GEKMAEFLLENPSDAKIVVNKIIDAARAREAARKAREMTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAK 318
Cdd:TIGR01059 350 YEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSELYIVEGDSAGGSAK 429

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....
gi 66474597   319 QGRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGRDeYNPDK 372
Cdd:TIGR01059 430 QGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKD-FDLEK 482
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-372 1.81e-160

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 462.80  E-value: 1.81e-160
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597      1 HGVGVSVVNALSDTLKLTIRRQGHVYEQTY-KLGEPQAPLKQIGDATTTGTEVRFWPSPTIFS-DTLFHYETLAKRLREL 78
Cdd:smart00433  82 HGVGASVVNALSTEFEVEVARDGKEYKQSFsNNGKPLSEPKIIGDTKKDGTKVTFKPDLEIFGmTTDDDFELLKRRLREL 161

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597     79 SFLNSGVSIVLSDERDGREINFCYEGGIKAFVEYLNQSKTPIHPKVFHFSTEHDGIGVEVAMQWNDGYQEGVYCFTNNIP 158
Cdd:smart00433 162 AFLNKGVKITLNDERSDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVNNIA 241

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597    159 QRDGGTHLVGFRTALTRTLNTYMDKEDYSKKAKMsaaSGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAM 238
Cdd:smart00433 242 TTEGGTHENGFKDALTRVINEYAKKKKKLKEKNI---KGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIV 318

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597    239 GEKMAEFLLENPSDAKIVVNKIIDAARAREAARKAREMTRRKgALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAK 318
Cdd:smart00433 319 SECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKK-KLSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAK 397

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....
gi 66474597    319 QGRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGrDEYNPDK 372
Cdd:smart00433 398 SGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIG-KDFDIEK 450
PRK05559 PRK05559
DNA topoisomerase IV subunit B; Reviewed
 1-367 1.03e-157

DNA topoisomerase IV subunit B; Reviewed


Pssm-ID: 235501 [Multi-domain]  Cd Length: 631  Bit Score: 456.87  E-value: 1.03e-157
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597    1 HGVGVSVVNALSDTLKLTIRRQGHVYEQTYKLGEPQAPLKQIGDATT--TGTEVRFWPSPTIFSDTLFHYETLAKRLREL 78
Cdd:PRK05559 118 HGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVGTAGKrkTGTRVRFWPDPKIFDSPKFSPERLKERLRSK 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   79 SFLNSGVSIVLSDERDGREinFCYEGGIKAFVEYLNQSKTPIHP-KVFHFSTEHDGIGVEVAMQWNDGYQEGVYCFTNNI 157
Cdd:PRK05559 198 AFLLPGLTITLNDERERQT--FHYENGLKDYLAELNEGKETLPEeFVGSFEGEAEGEAVEWALQWTDEGGENIESYVNLI 275

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597  158 PQRDGGTHLVGFRTALTRTLNTYMDKEDYSKKAKmsAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQA 237
Cdd:PRK05559 276 PTPQGGTHENGFREGLLKAVREFAEKRNLLPKGK--KLEGEDVREGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGV 353

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597  238 MGEKMAEFLLENPSDAKIVVNKIIDAARAREAARKARemTRRKGALDIAgLPGKLADCQEKDPALSELYIVEGDSAGGSA 317
Cdd:PRK05559 354 VKDAFDLWLNQNPELAEKLAEKAIKAAQARLRAAKKV--KRKKKTSGPA-LPGKLADCTSQDPERTELFLVEGDSAGGSA 430

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|
gi 66474597  318 KQGRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGRDE 367
Cdd:PRK05559 431 KQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAIGIGPGDSF 480
TopoII_Trans_DNA_gyrase cd00822
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ...
 104-262 5.42e-82

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: 247.47  E-value: 5.42e-82
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597 104 GGIKAFVEYLNQSKTPIHPKVFHFSTEHDGIGVEVAMQWNDGYQEGVYCFTNNIPQRDGGTHLVGFRTALTRTLNTYMDK 183
Cdd:cd00822   1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 66474597 184 EDYSKKAKMSaASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKMAEFLLENPSDAKIVVNKIID 262
Cdd:cd00822  81 NNLLKKKDVK-LTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAIL 158
PTZ00109 PTZ00109
DNA gyrase subunit b; Provisional
 1-366 1.91e-75

DNA gyrase subunit b; Provisional


Pssm-ID: 240272 [Multi-domain]  Cd Length: 903  Bit Score: 250.18  E-value: 1.91e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597    1 HGVGVSVVNALSDTLKLTIRRQGHVYEQTYKLGEPQAPLKQIGDATT-TGTEVRFWPS-PTIFSDTLFHYET-------- 70
Cdd:PTZ00109 250 HGVGLSVVNALSSFLKVDVFKGGKIYSIELSKGKVTKPLSVFSCPLKkRGTTIHFLPDyKHIFKTHHQHTETeeeegckn 329

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   71 ------LAKRLRELSFLNSGVSIVLSDERDGREINFC------YEGGIKAFVEYLNQSKTPIHP--KVFHFSTEHDGIGV 136
Cdd:PTZ00109 330 gfnldlIKNRIHELSYLNPGLTFYLVDERIANENNFYpyetikHEGGTREFLEELIKDKTPLYKdiNIISIRGVIKNVNV 409

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597  137 EVAMQWNDG-YQEGVYCFTNNIpQRDGGTHLVGFRTALTRTLNTYMDKEDYSKkAKMSAASGDDVREGLIAVISVKVPDP 215
Cdd:PTZ00109 410 EVSLSWSLEsYTALIKSFANNV-STTAGTHIDGFKYAITRCVNGNIKKNGYFK-GNFVNIPGEFIREGMTAIISVKLNGA 487

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597  216 KFSSQTKDKLVSSEVKTAVEQAMGEKMAEFLLENPSDAKIVVNKIIDAARAREAARKAREMTRRKGALDIA-GLPGKLAD 294
Cdd:PTZ00109 488 EFDGQTKTKLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYStILPGKLVD 567

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 66474597  295 CQEKDPALSELYIVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMI-SSQEVGTLITALGCGIGRD 366
Cdd:PTZ00109 568 CISDDIERNELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNKKVfENSEIKLLITSIGLSVNPV 640
parE_Gneg TIGR01055
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ...
 1-362 3.70e-75

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: 244.44  E-value: 3.70e-75
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597     1 HGVGVSVVNALSDTLKLTIRRQGHVYEQTYKLGEPQAPLKQIGDAT--TTGTEVRFWPSPTIFSDTLFHYETLAKRLREL 78
Cdd:TIGR01055 111 HGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCGkrLTGTSVHFTPDPEIFDSLHFSVSRLYHILRAK 190

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597    79 SFLNSGVSIVLSDERDGREINFCYEGGIKAFV-EYLNQSKTPIhPKVFHFSTEHDGIGVEVAMQW-NDGYQEGVYCFTNN 156
Cdd:TIGR01055 191 AVLCRGVEIEFEDEVNNTKALWNYPDGLKDYLsEAVNGDNTLP-PKPFSGNFEGDDEAVEWALLWlPEGGELFMESYVNL 269

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   157 IPQRDGGTHLVGFRTALTRTLNTYMD-KEDYSKKAKMSAasgDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVE 235
Cdd:TIGR01055 270 IPTPQGGTHVNGLRQGLLDALREFCEmRNNLPRGVKLTA---EDIWDRCSYVLSIKMQDPQFAGQTKERLSSRQVAKFVS 346

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   236 QAMGEKMAEFLLENPSDAKIVVNKIIDAARAREAARKAREmtrRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGG 315
Cdd:TIGR01055 347 GVIKDAFDLWLNQNVQLAEHLAEHAISSAQRRKRAAKKVV---RKKLTSGPALPGKLADCTRQDLEGTELFLVEGDSAGG 423

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 66474597   316 SAKQGRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCG 362
Cdd:TIGR01055 424 SAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALGID 470
DNA_gyraseB pfam00204
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ...
 105-262 1.36e-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: 210.93  E-value: 1.36e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   105 GIKAFVEYLNQSKTPIHPKVFHFSTEH--DGIGVEVAMQWNDGYQEGVYCFTNNIPQRDGGTHLVGFRTALTRTLNTYMD 182
Cdd:pfam00204   1 GLKDFVEELNKDKKPLHKEIIYFEGESpdNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   183 KEDYSKKAKMsAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKMAEFLLENPSDAKIVVNKIID 262
Cdd:pfam00204  81 KKGLLKKKDE-KITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQ 159
HATPase_GyrB-like cd16928
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ...
 1-100 3.29e-47

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: 158.47  E-value: 3.29e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   1 HGVGVSVVNALSDTLKLTIRRQGHVYEQTYKLGEPQAPLKQIGDATTTGTEVRFWPSPTIFSDTLFHYETLAKRLRELSF 80
Cdd:cd16928  81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIFEKTEFDFDTLKRRLRELAF 160

                        90       100
                ....*....|....*....|
gi 66474597  81 LNSGVSIVLSDERDGREINF 100
Cdd:cd16928 161 LNKGLKIVLEDERTGKEEVF 180
TopoII_MutL_Trans cd00329
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ...
 106-225 1.54e-22

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: 91.17  E-value: 1.54e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597 106 IKAFVEYLNQSKTpiHPKVFHFSTEHDGIGVEVAMQWND---GYQEGVYCFTNNIPQRDGGTHLVGFRTALTRTLNtymd 182
Cdd:cd00329   1 LKDRLAEILGDKV--ADKLIYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---- 74

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 66474597 183 kedyskkakmsaasGDDVREGLIAVISVKVPD--PKFS-SQTKDKL 225
Cdd:cd00329  75 --------------GDDVRRYPVAVLSLKIPPslVDVNvHPTKEEV 106
PTZ00108 PTZ00108
DNA topoisomerase 2-like protein; Provisional
 1-371 6.88e-18

DNA topoisomerase 2-like protein; Provisional


Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 85.48  E-value: 6.88e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597     1 HGVGVSVVNALSDTLKLTIR--RQGHVYEQTYK--LGEPQAP-LKQIGDATTTgTEVRFWPSPTIFSDTLF---HYETLA 72
Cdd:PTZ00108  143 NGFGAKLTNIFSTKFTVECVdsKSGKKFKMTWTdnMSKKSEPrITSYDGKKDY-TKVTFYPDYAKFGMTEFdddMLRLLK 221

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597    73 KRLRELSFLNSGVSIVLSDERdgreInfcyegGIKAFVEYLN---QSKTPIHPKVFHFSTEHDGIGVEVAMQWNDGYQEG 149
Cdd:PTZ00108  222 KRVYDLAGCFGKLKVYLNGER----I------AIKSFKDYVDlylPDGEEGKKPPYPFVYTSVNGRWEVVVSLSDGQFQQ 291

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   150 VyCFTNNIPQRDGGTHLvgfrTALTRTLNTYMDKEDYSKKAKMSAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSE 229
Cdd:PTZ00108  292 V-SFVNSICTTKGGTHV----NYILDQLISKLQEKAKKKKKKGKEIKPNQIKNHLWVFVNCLIVNPSFDSQTKETLTTKP 366

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   230 VKTAVEQAMGEKMAEFLLENPsdakiVVNKIIDAARAREAARKAREM--TRRKGaldIAGLPgKLADCQEKDPALSE--- 304
Cdd:PTZ00108  367 SKFGSTCELSEKLIKYVLKSP-----ILENIVEWAQAKLAAELNKKMkaGKKSR---ILGIP-KLDDANDAGGKNSEect 437

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   305 LYIVEGDSAGGSAKQG---RNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGRDEYNPD 371
Cdd:PTZ00108  438 LILTEGDSAKALALAGlsvVGRDYYGVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYEDPK 507
39 PHA02569
DNA topoisomerase II large subunit; Provisional
 153-370 1.06e-11

DNA topoisomerase II large subunit; Provisional


Pssm-ID: 177398 [Multi-domain]  Cd Length: 602  Bit Score: 66.32  E-value: 1.06e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597  153 FTNNIPQRDGGTHLVGFRTALTRTLNTyMDKEDYskKAKMSAASgddVREGLIAVISVK-VPDPKFSSQTKDKLVSS--E 229
Cdd:PHA02569 264 FVNGLHTKNGGHHVDCVMDDICEELIP-MIKKKH--KIEVTKAR---VKECLTIVLFVRnMSNPRFDSQTKERLTSPfgE 337

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597  230 VKTAVeQAMGEKMAEFLLENPSdakiVVNKIIDAARAREAARKAREMTR-RKGALDI-------AGLPGKLADcqekdpa 301
Cdd:PHA02569 338 IRNHI-DLDYKKIAKQILKTEA----IIMPIIEAALARKLAAEKAAETKaAKKAKKAkvakhikANLIGKDAE------- 405

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 66474597  302 lSELYIVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGRDEYNP 370
Cdd:PHA02569 406 -TTLFLTEGDSAIGYLIEVRDEELHGGYPLRGKVLNTWGMSYADILKNKELFDICAITGLVLGEKAENM 473
PLN03128 PLN03128
DNA topoisomerase 2; Provisional
 44-371 2.18e-11

DNA topoisomerase 2; Provisional


Pssm-ID: 215593 [Multi-domain]  Cd Length: 1135  Bit Score: 65.50  E-value: 2.18e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597    44 DATTTGTEVRFWPSPTIFSDTLFHYET---LAKRLRELS-FLNSGVSIVLSDERDGreinfcyeggIKAFVEYLN----- 114
Cdd:PLN03128  182 KASENWTKITFKPDLAKFNMTRLDEDVvalMSKRVYDIAgCLGKKLKVELNGKKLP----------VKSFQDYVGlylgp 251

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   115 QSKTPIHPKVFHFSTEhdgiGVEVAMQWNDGYQEGVyCFTNNIPQRDGGTHLvgfrTALTRTLNTYMdKEDYSKKAKMSA 194
Cdd:PLN03128  252 NSREDPLPRIYEKVND----RWEVCVSLSDGSFQQV-SFVNSIATIKGGTHV----DYVADQIVKHI-QEKVKKKNKNAT 321

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   195 A-SGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEqamGEKMAEFL--LENPSdakiVVNKIIDAARAREAAR 271
Cdd:PLN03128  322 HvKPFQIKNHLWVFVNCLIENPTFDSQTKETLTTRPSSFGSK---CELSEEFLkkVEKCG----VVENILSWAQFKQQKE 394

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   272 KAREMTRRKGALdiAGLPgKLADCQEKDPALSE---LYIVEGDSAGGSAKQGR---NRKNQAILPLKGKILNVEKARFDK 345
Cdd:PLN03128  395 LKKKDGAKRQRL--TGIP-KLDDANDAGGKKSKdctLILTEGDSAKALAMSGLsvvGRDHYGVFPLRGKLLNVREASHKQ 471

                         330       340
                  ....*....|....*....|....*.
gi 66474597   346 MISSQEVGTLITALGCGIGRdEYNPD 371
Cdd:PLN03128  472 IMKNAEITNIKQILGLQFGK-TYDEE 496
TOPRIM_TopoIIA cd03365
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 305-369 1.80e-09

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: 55.00  E-value: 1.80e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 66474597 305 LYIVEGDSAGGSAKQGRN---RKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGRDEYN 369
Cdd:cd03365   3 LILTEGDSAKALAVAGLSvvgRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGKSDYE 70
PLN03237 PLN03237
DNA topoisomerase 2; Provisional
 106-360 1.03e-07

DNA topoisomerase 2; Provisional


Pssm-ID: 215641 [Multi-domain]  Cd Length: 1465  Bit Score: 54.10  E-value: 1.03e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   106 IKAFVEYLN---QSKTPIHPKVFHFSTEHDGIGVEVAMQWNDGYQEGVyCFTNNIPQRDGGTHLvgfrTALTRTLNTYMd 182
Cdd:PLN03237  263 VKSFSDYVDlylESANKSRPENLPRIYEKVNDRWEVCVSLSEGQFQQV-SFVNSIATIKGGTHV----DYVTNQIANHV- 336

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   183 KEDYSKKAKMSAASGDDVREGLIAVISVKVPDPKFSSQTKDKLvssevkTAVEQAMGEKmaeFLLENPSDAKIVVNKIID 262
Cdd:PLN03237  337 MEAVNKKNKNANIKAHNVKNHLWVFVNALIDNPAFDSQTKETL------TLRQSSFGSK---CELSEDFLKKVMKSGIVE 407

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474597   263 AARAREAARKAREMTRRKGA--LDIAGLPgKLADCQE---KDPALSELYIVEGDSAGGSAKQGRN---RKNQAILPLKGK 334
Cdd:PLN03237  408 NLLSWADFKQSKELKKTDGAktTRVTGIP-KLEDANEaggKNSEKCTLILTEGDSAKALAVAGLSvvgRNYYGVFPLRGK 486

                         250       260
                  ....*....|....*....|....*.
gi 66474597   335 ILNVEKARFDKMISSQEVGTLITALG 360
Cdd:PLN03237  487 LLNVREASHKQIMNNAEIENIKQILG 512
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 304-348 5.07e-07

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: 47.35  E-value: 5.07e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 66474597   304 ELYIVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMIS 348
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKALK 45
 
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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