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Conserved domains on  [gi|66474593|gb|AAY46866|]
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GyrB, partial [Aeromonas molluscorum]

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 66474593    1 HGVGVSVVNALSEKLLLTIRRNGHVYEQTYHMGEPQAPLKQIGDSNGTGTEVRFWPSATIFTDTLYHYDILAKRLRELSF 80
Cdd:PRK14939 118 HGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETDKTGTEVRFWPSPEIFENTEFDYDILAKRLRELAF 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   81 LNSGVSIRLEDERDGREVHFCYEGGIKAFVEYLNQNKTPIHQNVFHFSTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQR 160
Cdd:PRK14939 198 LNSGVRIRLKDERDGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQR 277

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593  161 DGGTHLVGFRTALTRTLNTYMDREDYSKKAKISAaSGDDVREDLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGE 240
Cdd:PRK14939 278 DGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSL-TGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNE 356

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593  241 KLGEFLLENPGDAKIVVNKIIDAARAREAARKAREMTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQG 320
Cdd:PRK14939 357 KLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQG 436

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|..
gi 66474593  321 RNRKNQAILPLKGKILNVERARFDRMISSQEVGTLITALGCGIGRDEYNPDK 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 66474593    1 HGVGVSVVNALSEKLLLTIRRNGHVYEQTYHMGEPQAPLKQIGDSNGTGTEVRFWPSATIFTDTLYHYDILAKRLRELSF 80
Cdd:PRK14939 118 HGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETDKTGTEVRFWPSPEIFENTEFDYDILAKRLRELAF 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   81 LNSGVSIRLEDERDGREVHFCYEGGIKAFVEYLNQNKTPIHQNVFHFSTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQR 160
Cdd:PRK14939 198 LNSGVRIRLKDERDGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQR 277

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593  161 DGGTHLVGFRTALTRTLNTYMDREDYSKKAKISAaSGDDVREDLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGE 240
Cdd:PRK14939 278 DGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSL-TGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNE 356

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593  241 KLGEFLLENPGDAKIVVNKIIDAARAREAARKAREMTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQG 320
Cdd:PRK14939 357 KLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQG 436

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|..
gi 66474593  321 RNRKNQAILPLKGKILNVERARFDRMISSQEVGTLITALGCGIGRDEYNPDK 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: 607.03  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   1 HGVGVSVVNALSEKLLLTIRRNGHVYEQTYHMGEPQAPLKQIGDSNGTGTEVRFWPSATIFTDTLYHYDILAKRLRELSF 80
Cdd:COG0187 116 HGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKTDRTGTTVRFKPDPEIFETTEFDYETLAERLRELAF 195

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593  81 LNSGVSIRLEDERDG--REVHFCYEGGIKAFVEYLNQNKTPIHQNVFHFSTEQDGIGVEVAMQWNDAYQEGVYCFTNNIP 158
Cdd:COG0187 196 LNKGLTITLTDEREEepKEETFHYEGGIKDFVEYLNEDKEPLHPEVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNNIN 275

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593 159 QRDGGTHLVGFRTALTRTLNTYMDREDYSKKaKISAASGDDVREDLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAM 238
Cdd:COG0187 276 TPEGGTHETGFRTALTRVINDYARKNGLLKE-KDKNLTGDDVREGLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVV 354

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593 239 GEKLGEFLLENPGDAKIVVNKIIDAARAREAARKAREMTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAK 318
Cdd:COG0187 355 SEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAK 434

                       330       340       350       360       370
                ....*....|....*....|....*....|....*....|....*....|....
gi 66474593 319 QGRNRKNQAILPLKGKILNVERARFDRMISSQEVGTLITALGCGIGrDEYNPDK 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: 601.65  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593     1 HGVGVSVVNALSEKLLLTIRRNGHVYEQTYHMGEPQAPLKQIGDSNGTGTEVRFWPSATIFTDTLYHYDILAKRLRELSF 80
Cdd:TIGR01059 111 HGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGTTVRFWPDPEIFETTEFDFDILAKRLRELAF 190

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593    81 LNSGVSIRLEDERD--GREVHFCYEGGIKAFVEYLNQNKTPIHQNVFHFSTEQDGIGVEVAMQWNDAYQEGVYCFTNNIP 158
Cdd:TIGR01059 191 LNSGVKISLEDERDgkGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKEGIEVEVALQWNDGYSENILSFVNNIN 270

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   159 QRDGGTHLVGFRTALTRTLNTYMDREDYSKKAKiSAASGDDVREDLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAM 238
Cdd:TIGR01059 271 TREGGTHLEGFRSALTRVINSYAKNNKLLKESK-PNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLV 349

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   239 GEKLGEFLLENPGDAKIVVNKIIDAARAREAARKAREMTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAK 318
Cdd:TIGR01059 350 YEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSELYIVEGDSAGGSAK 429

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....
gi 66474593   319 QGRNRKNQAILPLKGKILNVERARFDRMISSQEVGTLITALGCGIGRDeYNPDK 372
Cdd:TIGR01059 430 QGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKD-FDLEK 482
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-372 1.20e-156

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 453.17  E-value: 1.20e-156
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593      1 HGVGVSVVNALSEKLLLTIRRNGHVYEQTYH-MGEPQAPLKQIGDSNGTGTEVRFWPSATIF-TDTLYHYDILAKRLREL 78
Cdd:smart00433  82 HGVGASVVNALSTEFEVEVARDGKEYKQSFSnNGKPLSEPKIIGDTKKDGTKVTFKPDLEIFgMTTDDDFELLKRRLREL 161

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593     79 SFLNSGVSIRLEDERDGREVHFCYEGGIKAFVEYLNQNKTPIHQNVFHFSTEQDGIGVEVAMQWNDAYQEGVYCFTNNIP 158
Cdd:smart00433 162 AFLNKGVKITLNDERSDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVNNIA 241

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593    159 QRDGGTHLVGFRTALTRTLNTYMDREDYSKKAKIsaaSGDDVREDLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAM 238
Cdd:smart00433 242 TTEGGTHENGFKDALTRVINEYAKKKKKLKEKNI---KGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIV 318

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593    239 GEKLGEFLLENPGDAKIVVNKIIDAARAREAARKAREMTRRKgALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAK 318
Cdd:smart00433 319 SECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKK-KLSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAK 397

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....
gi 66474593    319 QGRNRKNQAILPLKGKILNVERARFDRMISSQEVGTLITALGCGIGrDEYNPDK 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 1.21e-78

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: 239.00  E-value: 1.21e-78
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593 104 GGIKAFVEYLNQNKTPIHQNVFHFSTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRTALTRTLNTYMDR 183
Cdd:cd00822   1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 66474593 184 EDYSKKAKISaASGDDVREDLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENPGDAKIVVNKIID 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 1.29e-64

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: 203.23  E-value: 1.29e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   105 GIKAFVEYLNQNKTPIHQNVFHFSTE--QDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRTALTRTLNTYMD 182
Cdd:pfam00204   1 GLKDFVEELNKDKKPLHKEIIYFEGEspDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   183 REDYSKKAKIsAASGDDVREDLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENPGDAKIVVNKIID 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 66474593    1 HGVGVSVVNALSEKLLLTIRRNGHVYEQTYHMGEPQAPLKQIGDSNGTGTEVRFWPSATIFTDTLYHYDILAKRLRELSF 80
Cdd:PRK14939 118 HGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETDKTGTEVRFWPSPEIFENTEFDYDILAKRLRELAF 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   81 LNSGVSIRLEDERDGREVHFCYEGGIKAFVEYLNQNKTPIHQNVFHFSTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQR 160
Cdd:PRK14939 198 LNSGVRIRLKDERDGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQR 277

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593  161 DGGTHLVGFRTALTRTLNTYMDREDYSKKAKISAaSGDDVREDLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGE 240
Cdd:PRK14939 278 DGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSL-TGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNE 356

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593  241 KLGEFLLENPGDAKIVVNKIIDAARAREAARKAREMTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQG 320
Cdd:PRK14939 357 KLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQG 436

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|..
gi 66474593  321 RNRKNQAILPLKGKILNVERARFDRMISSQEVGTLITALGCGIGRDEYNPDK 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: 607.03  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   1 HGVGVSVVNALSEKLLLTIRRNGHVYEQTYHMGEPQAPLKQIGDSNGTGTEVRFWPSATIFTDTLYHYDILAKRLRELSF 80
Cdd:COG0187 116 HGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKTDRTGTTVRFKPDPEIFETTEFDYETLAERLRELAF 195

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593  81 LNSGVSIRLEDERDG--REVHFCYEGGIKAFVEYLNQNKTPIHQNVFHFSTEQDGIGVEVAMQWNDAYQEGVYCFTNNIP 158
Cdd:COG0187 196 LNKGLTITLTDEREEepKEETFHYEGGIKDFVEYLNEDKEPLHPEVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNNIN 275

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593 159 QRDGGTHLVGFRTALTRTLNTYMDREDYSKKaKISAASGDDVREDLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAM 238
Cdd:COG0187 276 TPEGGTHETGFRTALTRVINDYARKNGLLKE-KDKNLTGDDVREGLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVV 354

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593 239 GEKLGEFLLENPGDAKIVVNKIIDAARAREAARKAREMTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAK 318
Cdd:COG0187 355 SEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAK 434

                       330       340       350       360       370
                ....*....|....*....|....*....|....*....|....*....|....
gi 66474593 319 QGRNRKNQAILPLKGKILNVERARFDRMISSQEVGTLITALGCGIGrDEYNPDK 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: 601.65  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593     1 HGVGVSVVNALSEKLLLTIRRNGHVYEQTYHMGEPQAPLKQIGDSNGTGTEVRFWPSATIFTDTLYHYDILAKRLRELSF 80
Cdd:TIGR01059 111 HGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGTTVRFWPDPEIFETTEFDFDILAKRLRELAF 190

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593    81 LNSGVSIRLEDERD--GREVHFCYEGGIKAFVEYLNQNKTPIHQNVFHFSTEQDGIGVEVAMQWNDAYQEGVYCFTNNIP 158
Cdd:TIGR01059 191 LNSGVKISLEDERDgkGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKEGIEVEVALQWNDGYSENILSFVNNIN 270

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   159 QRDGGTHLVGFRTALTRTLNTYMDREDYSKKAKiSAASGDDVREDLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAM 238
Cdd:TIGR01059 271 TREGGTHLEGFRSALTRVINSYAKNNKLLKESK-PNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLV 349

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   239 GEKLGEFLLENPGDAKIVVNKIIDAARAREAARKAREMTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAK 318
Cdd:TIGR01059 350 YEKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSELYIVEGDSAGGSAK 429

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....
gi 66474593   319 QGRNRKNQAILPLKGKILNVERARFDRMISSQEVGTLITALGCGIGRDeYNPDK 372
Cdd:TIGR01059 430 QGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKD-FDLEK 482
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: 598.62  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593    1 HGVGVSVVNALSEKLLLTIRRNGHVYEQTYHMGEPQAPLKQIGDSNGTGTEVRFWPSATIFTDTLYHYDILAKRLRELSF 80
Cdd:PRK05644 118 HGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIGETDETGTTVTFKPDPEIFETTEFDYDTLATRLRELAF 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   81 LNSGVSIRLEDERDG--REVHFCYEGGIKAFVEYLNQNKTPIHQNVFHFSTEQDGIGVEVAMQWNDAYQEGVYCFTNNIP 158
Cdd:PRK05644 198 LNKGLKITLTDEREGeeKEETFHYEGGIKEYVEYLNRNKEPLHEEPIYFEGEKDGIEVEVAMQYNDGYSENILSFANNIN 277

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593  159 QRDGGTHLVGFRTALTRTLNTYMDREDYSKKAKISAaSGDDVREDLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAM 238
Cdd:PRK05644 278 THEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNL-TGEDVREGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVV 356

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593  239 GEKLGEFLLENPGDAKIVVNKIIDAARAREAARKAREMTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAK 318
Cdd:PRK05644 357 SEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAK 436

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....
gi 66474593  319 QGRNRKNQAILPLKGKILNVERARFDRMISSQEVGTLITALGCGIGrDEYNPDK 372
Cdd:PRK05644 437 QGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIG-DDFDISK 489
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-372 1.20e-156

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 453.17  E-value: 1.20e-156
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593      1 HGVGVSVVNALSEKLLLTIRRNGHVYEQTYH-MGEPQAPLKQIGDSNGTGTEVRFWPSATIF-TDTLYHYDILAKRLREL 78
Cdd:smart00433  82 HGVGASVVNALSTEFEVEVARDGKEYKQSFSnNGKPLSEPKIIGDTKKDGTKVTFKPDLEIFgMTTDDDFELLKRRLREL 161

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593     79 SFLNSGVSIRLEDERDGREVHFCYEGGIKAFVEYLNQNKTPIHQNVFHFSTEQDGIGVEVAMQWNDAYQEGVYCFTNNIP 158
Cdd:smart00433 162 AFLNKGVKITLNDERSDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVNNIA 241

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593    159 QRDGGTHLVGFRTALTRTLNTYMDREDYSKKAKIsaaSGDDVREDLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAM 238
Cdd:smart00433 242 TTEGGTHENGFKDALTRVINEYAKKKKKLKEKNI---KGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIV 318

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593    239 GEKLGEFLLENPGDAKIVVNKIIDAARAREAARKAREMTRRKgALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAK 318
Cdd:smart00433 319 SECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKK-KLSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAK 397

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....
gi 66474593    319 QGRNRKNQAILPLKGKILNVERARFDRMISSQEVGTLITALGCGIGrDEYNPDK 372
Cdd:smart00433 398 SGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIG-KDFDIEK 450
PRK05559 PRK05559
DNA topoisomerase IV subunit B; Reviewed
 1-367 5.56e-152

DNA topoisomerase IV subunit B; Reviewed


Pssm-ID: 235501 [Multi-domain]  Cd Length: 631  Bit Score: 442.23  E-value: 5.56e-152
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593    1 HGVGVSVVNALSEKLLLTIRRNGHVYEQTYHMGEPQAPLKQIGD--SNGTGTEVRFWPSATIFTDTLYHYDILAKRLREL 78
Cdd:PRK05559 118 HGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVGTagKRKTGTRVRFWPDPKIFDSPKFSPERLKERLRSK 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   79 SFLNSGVSIRLEDERDGREvhFCYEGGIKAFVEYLNQNKTPIH-QNVFHFSTEQDGIGVEVAMQWNDAYQEGVYCFTNNI 157
Cdd:PRK05559 198 AFLLPGLTITLNDERERQT--FHYENGLKDYLAELNEGKETLPeEFVGSFEGEAEGEAVEWALQWTDEGGENIESYVNLI 275

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593  158 PQRDGGTHLVGFRTALTRTLNTYMDREDYSKKAKisAASGDDVREDLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQA 237
Cdd:PRK05559 276 PTPQGGTHENGFREGLLKAVREFAEKRNLLPKGK--KLEGEDVREGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGV 353

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593  238 MGEKLGEFLLENPGDAKIVVNKIIDAARAREAARKARemTRRKGALDIAgLPGKLADCQEKDPALSELYIVEGDSAGGSA 317
Cdd:PRK05559 354 VKDAFDLWLNQNPELAEKLAEKAIKAAQARLRAAKKV--KRKKKTSGPA-LPGKLADCTSQDPERTELFLVEGDSAGGSA 430

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|
gi 66474593  318 KQGRNRKNQAILPLKGKILNVERARFDRMISSQEVGTLITALGCGIGRDE 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 1.21e-78

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: 239.00  E-value: 1.21e-78
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593 104 GGIKAFVEYLNQNKTPIHQNVFHFSTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRTALTRTLNTYMDR 183
Cdd:cd00822   1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 66474593 184 EDYSKKAKISaASGDDVREDLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENPGDAKIVVNKIID 262
Cdd:cd00822  81 NNLLKKKDVK-LTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAIL 158
PTZ00109 PTZ00109
DNA gyrase subunit b; Provisional
 1-366 9.22e-74

DNA gyrase subunit b; Provisional


Pssm-ID: 240272 [Multi-domain]  Cd Length: 903  Bit Score: 245.95  E-value: 9.22e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593    1 HGVGVSVVNALSEKLLLTIRRNGHVYEQTYHMGEPQAPLKQIGDS-NGTGTEVRFWPSA-TIFTDTLYHY---------- 68
Cdd:PTZ00109 250 HGVGLSVVNALSSFLKVDVFKGGKIYSIELSKGKVTKPLSVFSCPlKKRGTTIHFLPDYkHIFKTHHQHTeteeeegckn 329

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   69 ----DILAKRLRELSFLNSGVSIRLEDERDGREVHFC------YEGGIKAFVEYLNQNKTPIHQ--NVFHFSTEQDGIGV 136
Cdd:PTZ00109 330 gfnlDLIKNRIHELSYLNPGLTFYLVDERIANENNFYpyetikHEGGTREFLEELIKDKTPLYKdiNIISIRGVIKNVNV 409

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593  137 EVAMQWN-DAYQEGVYCFTNNIpQRDGGTHLVGFRTALTRTLNTYMDREDYSKkAKISAASGDDVREDLIAVISVKVPDP 215
Cdd:PTZ00109 410 EVSLSWSlESYTALIKSFANNV-STTAGTHIDGFKYAITRCVNGNIKKNGYFK-GNFVNIPGEFIREGMTAIISVKLNGA 487

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593  216 KFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENPGDAKIVVNKIIDAARAREAARKAREMTRRKGALDIA-GLPGKLAD 294
Cdd:PTZ00109 488 EFDGQTKTKLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYStILPGKLVD 567

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 66474593  295 CQEKDPALSELYIVEGDSAGGSAKQGRNRKNQAILPLKGKILNVERARFD-RMISSQEVGTLITALGCGIGRD 366
Cdd:PTZ00109 568 CISDDIERNELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkKVFENSEIKLLITSIGLSVNPV 640
parE_Gneg TIGR01055
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ...
 1-362 6.96e-71

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: 232.89  E-value: 6.96e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593     1 HGVGVSVVNALSEKLLLTIRRNGHVYEQTYHMGEPQAPLKQIGDSNG--TGTEVRFWPSATIFTDTLYHYDILAKRLREL 78
Cdd:TIGR01055 111 HGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCGKrlTGTSVHFTPDPEIFDSLHFSVSRLYHILRAK 190

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593    79 SFLNSGVSIRLEDERDGREVHFCYEGGIKAFV-EYLNQNKTPIhQNVFHFSTEQDGIGVEVAMQWNDAYQEGV---YCft 154
Cdd:TIGR01055 191 AVLCRGVEIEFEDEVNNTKALWNYPDGLKDYLsEAVNGDNTLP-PKPFSGNFEGDDEAVEWALLWLPEGGELFmesYV-- 267

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   155 NNIPQRDGGTHLVGFRTALTRTLNTYMD-REDYSKKAKISAasgDDVREDLIAVISVKVPDPKFSSQTKDKLVSSEVKTA 233
Cdd:TIGR01055 268 NLIPTPQGGTHVNGLRQGLLDALREFCEmRNNLPRGVKLTA---EDIWDRCSYVLSIKMQDPQFAGQTKERLSSRQVAKF 344

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   234 VEQAMGEKLGEFLLENPGDAKIVVNKIIDAARAREAARKAREmtrRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSA 313
Cdd:TIGR01055 345 VSGVIKDAFDLWLNQNVQLAEHLAEHAISSAQRRKRAAKKVV---RKKLTSGPALPGKLADCTRQDLEGTELFLVEGDSA 421

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*....
gi 66474593   314 GGSAKQGRNRKNQAILPLKGKILNVERARFDRMISSQEVGTLITALGCG 362
Cdd:TIGR01055 422 GGSAKQARDREYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALGID 470
DNA_gyraseB pfam00204
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ...
 105-262 1.29e-64

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: 203.23  E-value: 1.29e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   105 GIKAFVEYLNQNKTPIHQNVFHFSTE--QDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRTALTRTLNTYMD 182
Cdd:pfam00204   1 GLKDFVEELNKDKKPLHKEIIYFEGEspDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   183 REDYSKKAKIsAASGDDVREDLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENPGDAKIVVNKIID 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 8.98e-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: 157.31  E-value: 8.98e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   1 HGVGVSVVNALSEKLLLTIRRNGHVYEQTYHMGEPQAPLKQIGDSNGTGTEVRFWPSATIFTDTLYHYDILAKRLRELSF 80
Cdd:cd16928  81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIFEKTEFDFDTLKRRLRELAF 160

                        90       100
                ....*....|....*....|
gi 66474593  81 LNSGVSIRLEDERDGREVHF 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 1.56e-21

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


Pssm-ID: 238202 [Multi-domain]  Cd Length: 107  Bit Score: 88.47  E-value: 1.56e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593 106 IKAFVEYLNQNKTpiHQNVFHFSTEQDGIGVEVAMQWND---AYQEGVYCFTNNIPQRDGGTHLVGFRTALTRTLNtymd 182
Cdd:cd00329   1 LKDRLAEILGDKV--ADKLIYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---- 74

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 66474593 183 redyskkakisaasGDDVREDLIAVISVKVPD--PKFS-SQTKDKL 225
Cdd:cd00329  75 --------------GDDVRRYPVAVLSLKIPPslVDVNvHPTKEEV 106
PTZ00108 PTZ00108
DNA topoisomerase 2-like protein; Provisional
 1-371 1.44e-19

DNA topoisomerase 2-like protein; Provisional


Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 90.49  E-value: 1.44e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593     1 HGVGVSVVNALSEKLLLTIR--RNGHVYEQTY--HMGEPQAPlkQIGDSNGTG--TEVRFWPSATIFTDTLY---HYDIL 71
Cdd:PTZ00108  143 NGFGAKLTNIFSTKFTVECVdsKSGKKFKMTWtdNMSKKSEP--RITSYDGKKdyTKVTFYPDYAKFGMTEFdddMLRLL 220

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593    72 AKRLRELSFLNSGVSIRLEDERDGrevhfcyeggIKAFVEYLN---QNKTPIHQNVFHFSTEQDGIGVEVAMQWNDAYQE 148
Cdd:PTZ00108  221 KKRVYDLAGCFGKLKVYLNGERIA----------IKSFKDYVDlylPDGEEGKKPPYPFVYTSVNGRWEVVVSLSDGQFQ 290

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   149 GVyCFTNNIPQRDGGTHLvgfrTALTRTLNTYMDREDYSKKAKISAASGDDVREDLIAVISVKVPDPKFSSQTKDKLVSS 228
Cdd:PTZ00108  291 QV-SFVNSICTTKGGTHV----NYILDQLISKLQEKAKKKKKKGKEIKPNQIKNHLWVFVNCLIVNPSFDSQTKETLTTK 365

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   229 EVKTAVEQAMGEKLGEFLLENPgdakiVVNKIIDAARAREAARKAREM--TRRKGaldIAGLPgKLADCQEKDPALSE-- 304
Cdd:PTZ00108  366 PSKFGSTCELSEKLIKYVLKSP-----ILENIVEWAQAKLAAELNKKMkaGKKSR---ILGIP-KLDDANDAGGKNSEec 436

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 66474593   305 -LYIVEGDSAGGSAKQG---RNRKNQAILPLKGKILNVERARFDRMISSQEVGTLITALGCGIGRDEYNPD 371
Cdd:PTZ00108  437 tLILTEGDSAKALALAGlsvVGRDYYGVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYEDPK 507
PLN03128 PLN03128
DNA topoisomerase 2; Provisional
 1-371 3.62e-11

DNA topoisomerase 2; Provisional


Pssm-ID: 215593 [Multi-domain]  Cd Length: 1135  Bit Score: 64.73  E-value: 3.62e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593     1 HGVGVSVVNALSEKLLLTIR--RNGHVYEQTY--HMGEPQAPLKQIGDSNGTGTEVRFWPSATIFTDTLYHYDI---LAK 73
Cdd:PLN03128  135 NGYGAKLANIFSTEFTVETAdgNRGKKYKQVFtnNMSVKSEPKITSCKASENWTKITFKPDLAKFNMTRLDEDVvalMSK 214

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593    74 RLRELS-FLNSGVSIRLEDERDGrevhfcyeggIKAFVEYLN-----QNKTPIHQNVFHFSTEQDGIGVEVAmqwNDAYQ 147
Cdd:PLN03128  215 RVYDIAgCLGKKLKVELNGKKLP----------VKSFQDYVGlylgpNSREDPLPRIYEKVNDRWEVCVSLS---DGSFQ 281

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   148 EgvYCFTNNIPQRDGGTHLvgfrTALTRTLNTYMdREDYSKKAKISAA-SGDDVREDLIAVISVKVPDPKFSSQTKDKLV 226
Cdd:PLN03128  282 Q--VSFVNSIATIKGGTHV----DYVADQIVKHI-QEKVKKKNKNATHvKPFQIKNHLWVFVNCLIENPTFDSQTKETLT 354

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   227 SSEVKTAVEQAMGEklgEFL--LENPGdakiVVNKIIDAARAREAARKAREMTRRKGALdiAGLPgKLADCQEKDPALSE 304
Cdd:PLN03128  355 TRPSSFGSKCELSE---EFLkkVEKCG----VVENILSWAQFKQQKELKKKDGAKRQRL--TGIP-KLDDANDAGGKKSK 424

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 66474593   305 ---LYIVEGDSAGGSAKQGR---NRKNQAILPLKGKILNVERARFDRMISSQEVGTLITALGCGIGRdEYNPD 371
Cdd:PLN03128  425 dctLILTEGDSAKALAMSGLsvvGRDHYGVFPLRGKLLNVREASHKQIMKNAEITNIKQILGLQFGK-TYDEE 496
39 PHA02569
DNA topoisomerase II large subunit; Provisional
 153-370 5.11e-11

DNA topoisomerase II large subunit; Provisional


Pssm-ID: 177398 [Multi-domain]  Cd Length: 602  Bit Score: 64.00  E-value: 5.11e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593  153 FTNNIPQRDGGTHLVGFRTALTRTLNTYMDREdysKKAKISAASgddVREDLIAVISVK-VPDPKFSSQTKDKLVSS--E 229
Cdd:PHA02569 264 FVNGLHTKNGGHHVDCVMDDICEELIPMIKKK---HKIEVTKAR---VKECLTIVLFVRnMSNPRFDSQTKERLTSPfgE 337

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593  230 VKTAVeQAMGEKLGEFLLENPGdakiVVNKIIDAARAREAARKAREMTR-RKGALDI-------AGLPGKLADcqekdpa 301
Cdd:PHA02569 338 IRNHI-DLDYKKIAKQILKTEA----IIMPIIEAALARKLAAEKAAETKaAKKAKKAkvakhikANLIGKDAE------- 405

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 66474593  302 lSELYIVEGDSAGGSAKQGRNRKNQAILPLKGKILNVERARFDRMISSQEVGTLITALGCGIGRDEYNP 370
Cdd:PHA02569 406 -TTLFLTEGDSAIGYLIEVRDEELHGGYPLRGKVLNTWGMSYADILKNKELFDICAITGLVLGEKAENM 473
TOPRIM_TopoIIA cd03365
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 305-369 1.74e-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: 1.74e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 66474593 305 LYIVEGDSAGGSAKQGRN---RKNQAILPLKGKILNVERARFDRMISSQEVGTLITALGCGIGRDEYN 369
Cdd:cd03365   3 LILTEGDSAKALAVAGLSvvgRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGKSDYE 70
PLN03237 PLN03237
DNA topoisomerase 2; Provisional
 26-360 2.19e-06

DNA topoisomerase 2; Provisional


Pssm-ID: 215641 [Multi-domain]  Cd Length: 1465  Bit Score: 49.86  E-value: 2.19e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593    26 YEQTY--HMGEPQAPLKQIGDSNGTGTEVRFWPSATIFTDTLYHYDILA---KRLRELSFlNSGVSIRLEdeRDGREVHf 100
Cdd:PLN03237  187 YKQVFsnNMGKKSEPVITKCKKSENWTKVTFKPDLAKFNMTHLEDDVVAlmkKRVVDIAG-CLGKTVKVE--LNGKRIP- 262

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   101 cyeggIKAFVEYLN---QNKTPIHQNVFHFSTEQDGIGVEVAMQWNDAYQEGVyCFTNNIPQRDGGTHLvgfrTALTRTL 177
Cdd:PLN03237  263 -----VKSFSDYVDlylESANKSRPENLPRIYEKVNDRWEVCVSLSEGQFQQV-SFVNSIATIKGGTHV----DYVTNQI 332

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   178 NTYMdREDYSKKAKISAASGDDVREDLIAVISVKVPDPKFSSQTKDKLvssevkTAVEQAMGEK--LGEFLLEnpgdaKI 255
Cdd:PLN03237  333 ANHV-MEAVNKKNKNANIKAHNVKNHLWVFVNALIDNPAFDSQTKETL------TLRQSSFGSKceLSEDFLK-----KV 400

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474593   256 VVNKIIDAARAREAARKAREMTRRKGA--LDIAGLPgKLADCQE---KDPALSELYIVEGDSAGGSAKQGRN---RKNQA 327
Cdd:PLN03237  401 MKSGIVENLLSWADFKQSKELKKTDGAktTRVTGIP-KLEDANEaggKNSEKCTLILTEGDSAKALAVAGLSvvgRNYYG 479

                         330       340       350
                  ....*....|....*....|....*....|...
gi 66474593   328 ILPLKGKILNVERARFDRMISSQEVGTLITALG 360
Cdd:PLN03237  480 VFPLRGKLLNVREASHKQIMNNAEIENIKQILG 512
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 304-339 3.12e-06

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: 45.04  E-value: 3.12e-06
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 66474593   304 ELYIVEGDSAGGSAKQGRNRKNQAILPLKGKILNVE 339
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLE 36
 
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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