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Conserved domains on  [gi|56675162|emb|CAI34883|]
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DNA gyrase subunit B, partial [Aeromonas allosaccharophila]

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
 1-371 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: 808.55  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162    1 HGVGVSVVNALSDKLLLTIRRNGHVYEQTYHLGEPQAPLKQIGDSTGTGTEVRFWPSPTIFTDTLYHYEILAKRLRELSF 80
Cdd:PRK14939 118 HGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETDKTGTEVRFWPSPEIFENTEFDYDILAKRLRELAF 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   81 LNSGVSIRLLDERDGREAHFCYEGGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQR 160
Cdd:PRK14939 198 LNSGVRIRLKDERDGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQR 277

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162  161 DGGTHLVGFRTALTRTLNSYMDKEDYSKKAKSAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEK 240
Cdd:PRK14939 278 DGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEK 357

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162  241 LADFLLENPGDAKIVVNKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQGR 320
Cdd:PRK14939 358 LSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGR 437

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|.
gi 56675162  321 NRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGRDEYNPDK 371
Cdd:PRK14939 438 DRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIGRDEFNPDK 488
 
Name Accession Description Interval E-value
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-371 0e+00

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 808.55  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162    1 HGVGVSVVNALSDKLLLTIRRNGHVYEQTYHLGEPQAPLKQIGDSTGTGTEVRFWPSPTIFTDTLYHYEILAKRLRELSF 80
Cdd:PRK14939 118 HGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETDKTGTEVRFWPSPEIFENTEFDYDILAKRLRELAF 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   81 LNSGVSIRLLDERDGREAHFCYEGGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQR 160
Cdd:PRK14939 198 LNSGVRIRLKDERDGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQR 277

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162  161 DGGTHLVGFRTALTRTLNSYMDKEDYSKKAKSAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEK 240
Cdd:PRK14939 278 DGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEK 357

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162  241 LADFLLENPGDAKIVVNKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQGR 320
Cdd:PRK14939 358 LSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGR 437

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|.
gi 56675162  321 NRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGRDEYNPDK 371
Cdd:PRK14939 438 DRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIGRDEFNPDK 488
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
1-371 0e+00

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


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 620.12  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   1 HGVGVSVVNALSDKLLLTIRRNGHVYEQTYHLGEPQAPLKQIGDSTGTGTEVRFWPSPTIFTDTLYHYEILAKRLRELSF 80
Cdd:COG0187 116 HGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKTDRTGTTVRFKPDPEIFETTEFDYETLAERLRELAF 195

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162  81 LNSGVSIRLLDERDG--REAHFCYEGGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIP 158
Cdd:COG0187 196 LNKGLTITLTDEREEepKEETFHYEGGIKDFVEYLNEDKEPLHPEVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNNIN 275

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162 159 QRDGGTHLVGFRTALTRTLNSYMDKEDYSKKAKSAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMG 238
Cdd:COG0187 276 TPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREGLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVS 355

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162 239 EKLADFLLENPGDAKIVVNKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQ 318
Cdd:COG0187 356 EKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQ 435

                       330       340       350       360       370
                ....*....|....*....|....*....|....*....|....*....|...
gi 56675162 319 GRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGrDEYNPDK 371
Cdd:COG0187 436 GRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIG-DDFDLEK 487
gyrB TIGR01059
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ...
 1-371 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: 614.75  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162     1 HGVGVSVVNALSDKLLLTIRRNGHVYEQTYHLGEPQAPLKQIGDSTGTGTEVRFWPSPTIFTDTLYHYEILAKRLRELSF 80
Cdd:TIGR01059 111 HGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGTTVRFWPDPEIFETTEFDFDILAKRLRELAF 190

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162    81 LNSGVSIRLLDERD--GREAHFCYEGGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIP 158
Cdd:TIGR01059 191 LNSGVKISLEDERDgkGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKEGIEVEVALQWNDGYSENILSFVNNIN 270

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   159 QRDGGTHLVGFRTALTRTLNSYMDKEDYSKKAKSAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMG 238
Cdd:TIGR01059 271 TREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLVY 350

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   239 EKLADFLLENPGDAKIVVNKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQ 318
Cdd:TIGR01059 351 EKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSELYIVEGDSAGGSAKQ 430

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|...
gi 56675162   319 GRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGRDeYNPDK 371
Cdd:TIGR01059 431 GRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKD-FDLEK 482
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-371 4.82e-161

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 464.34  E-value: 4.82e-161
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162      1 HGVGVSVVNALSDKLLLTIRRNGHVYEQTYH-LGEPQAPLKQIGDSTGTGTEVRFWPSPTIF-TDTLYHYEILAKRLREL 78
Cdd:smart00433  82 HGVGASVVNALSTEFEVEVARDGKEYKQSFSnNGKPLSEPKIIGDTKKDGTKVTFKPDLEIFgMTTDDDFELLKRRLREL 161

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162     79 SFLNSGVSIRLLDERDGREAHFCYEGGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIP 158
Cdd:smart00433 162 AFLNKGVKITLNDERSDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVNNIA 241

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162    159 QRDGGTHLVGFRTALTRTLNSYMDKEDYSKKAKsaASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMG 238
Cdd:smart00433 242 TTEGGTHENGFKDALTRVINEYAKKKKKLKEKN--IKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIVS 319

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162    239 EKLADFLLENPGDAKIVVNKIIDAARAREAARKARELTRRKgALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQ 318
Cdd:smart00433 320 ECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKK-KLSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAKS 398

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|...
gi 56675162    319 GRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGrDEYNPDK 371
Cdd:smart00433 399 GRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIG-KDFDIEK 450
TopoII_Trans_DNA_gyrase cd00822
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ...
 104-261 4.40e-83

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: 250.17  E-value: 4.40e-83
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162 104 GGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRTALTRTLNSYMDK 183
Cdd:cd00822   1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56675162 184 EDYSKKAKSAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLADFLLENPGDAKIVVNKIID 261
Cdd:cd00822  81 NNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAIL 158
DNA_gyraseB pfam00204
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ...
 105-261 6.30e-69

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: 214.02  E-value: 6.30e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   105 GIKAFVEYLNQNKTPIHPKVFHFTTE--QDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRTALTRTLNSYMD 182
Cdd:pfam00204   1 GLKDFVEELNKDKKPLHKEIIYFEGEspDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56675162   183 KEDYSKKAKSAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLADFLLENPGDAKIVVNKIID 261
Cdd:pfam00204  81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQ 159
 
Name Accession Description Interval E-value
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-371 0e+00

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 808.55  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162    1 HGVGVSVVNALSDKLLLTIRRNGHVYEQTYHLGEPQAPLKQIGDSTGTGTEVRFWPSPTIFTDTLYHYEILAKRLRELSF 80
Cdd:PRK14939 118 HGVGVSVVNALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETDKTGTEVRFWPSPEIFENTEFDYDILAKRLRELAF 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   81 LNSGVSIRLLDERDGREAHFCYEGGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQR 160
Cdd:PRK14939 198 LNSGVRIRLKDERDGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQR 277

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162  161 DGGTHLVGFRTALTRTLNSYMDKEDYSKKAKSAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEK 240
Cdd:PRK14939 278 DGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEK 357

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162  241 LADFLLENPGDAKIVVNKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQGR 320
Cdd:PRK14939 358 LSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGR 437

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|.
gi 56675162  321 NRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGRDEYNPDK 371
Cdd:PRK14939 438 DRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIGRDEFNPDK 488
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
1-371 0e+00

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


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 620.12  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   1 HGVGVSVVNALSDKLLLTIRRNGHVYEQTYHLGEPQAPLKQIGDSTGTGTEVRFWPSPTIFTDTLYHYEILAKRLRELSF 80
Cdd:COG0187 116 HGVGASVVNALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKTDRTGTTVRFKPDPEIFETTEFDYETLAERLRELAF 195

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162  81 LNSGVSIRLLDERDG--REAHFCYEGGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIP 158
Cdd:COG0187 196 LNKGLTITLTDEREEepKEETFHYEGGIKDFVEYLNEDKEPLHPEVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNNIN 275

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162 159 QRDGGTHLVGFRTALTRTLNSYMDKEDYSKKAKSAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMG 238
Cdd:COG0187 276 TPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREGLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVS 355

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162 239 EKLADFLLENPGDAKIVVNKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQ 318
Cdd:COG0187 356 EKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQ 435

                       330       340       350       360       370
                ....*....|....*....|....*....|....*....|....*....|...
gi 56675162 319 GRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGrDEYNPDK 371
Cdd:COG0187 436 GRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIG-DDFDLEK 487
gyrB TIGR01059
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ...
 1-371 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: 614.75  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162     1 HGVGVSVVNALSDKLLLTIRRNGHVYEQTYHLGEPQAPLKQIGDSTGTGTEVRFWPSPTIFTDTLYHYEILAKRLRELSF 80
Cdd:TIGR01059 111 HGVGVSVVNALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGTTVRFWPDPEIFETTEFDFDILAKRLRELAF 190

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162    81 LNSGVSIRLLDERD--GREAHFCYEGGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIP 158
Cdd:TIGR01059 191 LNSGVKISLEDERDgkGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKEGIEVEVALQWNDGYSENILSFVNNIN 270

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   159 QRDGGTHLVGFRTALTRTLNSYMDKEDYSKKAKSAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMG 238
Cdd:TIGR01059 271 TREGGTHLEGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLVY 350

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   239 EKLADFLLENPGDAKIVVNKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQ 318
Cdd:TIGR01059 351 EKLTEFFEENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSELYIVEGDSAGGSAKQ 430

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|...
gi 56675162   319 GRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGRDeYNPDK 371
Cdd:TIGR01059 431 GRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKD-FDLEK 482
gyrB PRK05644
DNA gyrase subunit B; Validated
 1-371 0e+00

DNA gyrase subunit B; Validated


Pssm-ID: 235542 [Multi-domain]  Cd Length: 638  Bit Score: 610.94  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162    1 HGVGVSVVNALSDKLLLTIRRNGHVYEQTYHLGEPQAPLKQIGDSTGTGTEVRFWPSPTIFTDTLYHYEILAKRLRELSF 80
Cdd:PRK05644 118 HGVGVSVVNALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIGETDETGTTVTFKPDPEIFETTEFDYDTLATRLRELAF 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   81 LNSGVSIRLLDERDGREAH--FCYEGGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIP 158
Cdd:PRK05644 198 LNKGLKITLTDEREGEEKEetFHYEGGIKEYVEYLNRNKEPLHEEPIYFEGEKDGIEVEVAMQYNDGYSENILSFANNIN 277

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162  159 QRDGGTHLVGFRTALTRTLNSYMDKEDYSKKAKSAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMG 238
Cdd:PRK05644 278 THEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVREGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVS 357

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162  239 EKLADFLLENPGDAKIVVNKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQ 318
Cdd:PRK05644 358 EALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQ 437

                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|...
gi 56675162  319 GRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGrDEYNPDK 371
Cdd:PRK05644 438 GRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIG-DDFDISK 489
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-371 4.82e-161

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 464.34  E-value: 4.82e-161
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162      1 HGVGVSVVNALSDKLLLTIRRNGHVYEQTYH-LGEPQAPLKQIGDSTGTGTEVRFWPSPTIF-TDTLYHYEILAKRLREL 78
Cdd:smart00433  82 HGVGASVVNALSTEFEVEVARDGKEYKQSFSnNGKPLSEPKIIGDTKKDGTKVTFKPDLEIFgMTTDDDFELLKRRLREL 161

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162     79 SFLNSGVSIRLLDERDGREAHFCYEGGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIP 158
Cdd:smart00433 162 AFLNKGVKITLNDERSDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVNNIA 241

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162    159 QRDGGTHLVGFRTALTRTLNSYMDKEDYSKKAKsaASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMG 238
Cdd:smart00433 242 TTEGGTHENGFKDALTRVINEYAKKKKKLKEKN--IKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIVS 319

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162    239 EKLADFLLENPGDAKIVVNKIIDAARAREAARKARELTRRKgALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQ 318
Cdd:smart00433 320 ECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRKK-KLSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAKS 398

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|...
gi 56675162    319 GRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGrDEYNPDK 371
Cdd:smart00433 399 GRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIG-KDFDIEK 450
PRK05559 PRK05559
DNA topoisomerase IV subunit B; Reviewed
 1-366 1.79e-156

DNA topoisomerase IV subunit B; Reviewed


Pssm-ID: 235501 [Multi-domain]  Cd Length: 631  Bit Score: 453.79  E-value: 1.79e-156
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162    1 HGVGVSVVNALSDKLLLTIRRNGHVYEQTYHLGEPQAPLKQIGDSTG--TGTEVRFWPSPTIFTDTLYHYEILAKRLREL 78
Cdd:PRK05559 118 HGVGVSVVNALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVGTAGKrkTGTRVRFWPDPKIFDSPKFSPERLKERLRSK 197

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   79 SFLNSGVSIRLLDERDgrEAHFCYEGGIKAFVEYLNQNKTPIHP-KVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNI 157
Cdd:PRK05559 198 AFLLPGLTITLNDERE--RQTFHYENGLKDYLAELNEGKETLPEeFVGSFEGEAEGEAVEWALQWTDEGGENIESYVNLI 275

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162  158 PQRDGGTHLVGFRTALTRTLNSYMDKEDYSKKAKsAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAM 237
Cdd:PRK05559 276 PTPQGGTHENGFREGLLKAVREFAEKRNLLPKGK-KLEGEDVREGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVV 354

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162  238 GEKLADFLLENPGDAKIVVNKIIDAARAREAARKARelTRRKGALDIAgLPGKLADCQEKDPALSELYIVEGDSAGGSAK 317
Cdd:PRK05559 355 KDAFDLWLNQNPELAEKLAEKAIKAAQARLRAAKKV--KRKKKTSGPA-LPGKLADCTSQDPERTELFLVEGDSAGGSAK 431

                        330       340       350       360
                 ....*....|....*....|....*....|....*....|....*....
gi 56675162  318 QGRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGRDE 366
Cdd:PRK05559 432 QARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAIGIGPGDSF 480
TopoII_Trans_DNA_gyrase cd00822
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ...
 104-261 4.40e-83

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: 250.17  E-value: 4.40e-83
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162 104 GGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRTALTRTLNSYMDK 183
Cdd:cd00822   1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56675162 184 EDYSKKAKSAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLADFLLENPGDAKIVVNKIID 261
Cdd:cd00822  81 NNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAIL 158
PTZ00109 PTZ00109
DNA gyrase subunit b; Provisional
 1-365 1.02e-75

DNA gyrase subunit b; Provisional


Pssm-ID: 240272 [Multi-domain]  Cd Length: 903  Bit Score: 250.95  E-value: 1.02e-75
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162    1 HGVGVSVVNALSDKLLLTIRRNGHVY-------EQTYHLGEPQAPLKQigdstgTGTEVRFWPS-PTIFTDTLYHY---- 68
Cdd:PTZ00109 250 HGVGLSVVNALSSFLKVDVFKGGKIYsielskgKVTKPLSVFSCPLKK------RGTTIHFLPDyKHIFKTHHQHTetee 323

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   69 ----------EILAKRLRELSFLNSGVSIRLLDERDGREAHFC------YEGGIKAFVEYLNQNKTPIHP--KVFHFTTE 130
Cdd:PTZ00109 324 eegckngfnlDLIKNRIHELSYLNPGLTFYLVDERIANENNFYpyetikHEGGTREFLEELIKDKTPLYKdiNIISIRGV 403

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162  131 QDGIGVEVAMQWN-DAYQEGVYCFTNNIpQRDGGTHLVGFRTALTRTLNSYMDKEDYSKKAKSAASGDDVREGLIAVISV 209
Cdd:PTZ00109 404 IKNVNVEVSLSWSlESYTALIKSFANNV-STTAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISV 482

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162  210 KVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLADFLLENPGDAKIVVNKIIDAARAREAARKARELTRRKGALDIA-GLP 288
Cdd:PTZ00109 483 KLNGAEFDGQTKTKLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYStILP 562

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56675162  289 GKLADCQEKDPALSELYIVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMI-SSQEVGTLITALGCGIGRD 365
Cdd:PTZ00109 563 GKLVDCISDDIERNELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNKKVfENSEIKLLITSIGLSVNPV 640
parE_Gneg TIGR01055
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ...
 1-361 2.93e-72

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: 236.74  E-value: 2.93e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162     1 HGVGVSVVNALSDKLLLTIRRNGHVYEQTYHLGEPQAPLKQIGDSTG--TGTEVRFWPSPTIFTDTLYHYEILAKRLREL 78
Cdd:TIGR01055 111 HGVGISVVNALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCGKrlTGTSVHFTPDPEIFDSLHFSVSRLYHILRAK 190

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162    79 SFLNSGVSIRLLDERDGREAHFCYEGGIKAFV-EYLNQNKTPIhPKVFHFTTEQDGIGVEVAMQWNDAYQEGV---YCft 154
Cdd:TIGR01055 191 AVLCRGVEIEFEDEVNNTKALWNYPDGLKDYLsEAVNGDNTLP-PKPFSGNFEGDDEAVEWALLWLPEGGELFmesYV-- 267

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   155 NNIPQRDGGTHLVGFRTALTRTLNSYMDKEDYSKKAkSAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVE 234
Cdd:TIGR01055 268 NLIPTPQGGTHVNGLRQGLLDALREFCEMRNNLPRG-VKLTAEDIWDRCSYVLSIKMQDPQFAGQTKERLSSRQVAKFVS 346

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   235 QAMGEKLADFLLENPGDAKIVVNKIIDAARAREAARKAREltrRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGG 314
Cdd:TIGR01055 347 GVIKDAFDLWLNQNVQLAEHLAEHAISSAQRRKRAAKKVV---RKKLTSGPALPGKLADCTRQDLEGTELFLVEGDSAGG 423

                         330       340       350       360
                  ....*....|....*....|....*....|....*....|....*..
gi 56675162   315 SAKQGRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCG 361
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 ...
 105-261 6.30e-69

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: 214.02  E-value: 6.30e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   105 GIKAFVEYLNQNKTPIHPKVFHFTTE--QDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRTALTRTLNSYMD 182
Cdd:pfam00204   1 GLKDFVEELNKDKKPLHKEIIYFEGEspDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56675162   183 KEDYSKKAKSAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLADFLLENPGDAKIVVNKIID 261
Cdd:pfam00204  81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQ 159
HATPase_GyrB-like cd16928
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ...
 1-100 1.74e-46

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: 156.54  E-value: 1.74e-46
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   1 HGVGVSVVNALSDKLLLTIRRNGHVYEQTYHLGEPQAPLKQIGDSTGTGTEVRFWPSPTIFTDTLYHYEILAKRLRELSF 80
Cdd:cd16928  81 HGVGVSVVNALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIFEKTEFDFDTLKRRLRELAF 160

                        90       100
                ....*....|....*....|
gi 56675162  81 LNSGVSIRLLDERDGREAHF 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 ...
 106-224 9.40e-23

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: 91.55  E-value: 9.40e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162 106 IKAFVEYLNQNKTpiHPKVFHFTTEQDGIGVEVAMQWND---AYQEGVYCFTNNIPQRDGGTHLVGFRTALTRTLNsymd 182
Cdd:cd00329   1 LKDRLAEILGDKV--ADKLIYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---- 74

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
gi 56675162 183 kedyskkaksaasGDDVREGLIAVISVKVPD--PKFS-SQTKDKL 224
Cdd:cd00329  75 -------------GDDVRRYPVAVLSLKIPPslVDVNvHPTKEEV 106
PTZ00108 PTZ00108
DNA topoisomerase 2-like protein; Provisional
 1-370 2.33e-18

DNA topoisomerase 2-like protein; Provisional


Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 87.02  E-value: 2.33e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162     1 HGVGVSVVNALSDKLLLTIR--RNGHVYEQTY--HLGEPQAPlkQIGDSTGTG--TEVRFWPSPTIFTDTLY---HYEIL 71
Cdd:PTZ00108  143 NGFGAKLTNIFSTKFTVECVdsKSGKKFKMTWtdNMSKKSEP--RITSYDGKKdyTKVTFYPDYAKFGMTEFdddMLRLL 220

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162    72 AKRLRELSFLNSGVSIRLLDERDGreahfcyeggIKAFVEYLN---QNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQE 148
Cdd:PTZ00108  221 KKRVYDLAGCFGKLKVYLNGERIA----------IKSFKDYVDlylPDGEEGKKPPYPFVYTSVNGRWEVVVSLSDGQFQ 290

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   149 GVyCFTNNIPQRDGGTHLvgfrTALTRTLNSYMDKEDYSKKAKSAA-SGDDVREGLIAVISVKVPDPKFSSQTKDKLVSS 227
Cdd:PTZ00108  291 QV-SFVNSICTTKGGTHV----NYILDQLISKLQEKAKKKKKKGKEiKPNQIKNHLWVFVNCLIVNPSFDSQTKETLTTK 365

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   228 EVKTAVEQAMGEKLADFLLENPgdakivvnkIIDAARAREAARKARELTRRKGALD---IAGLPgKLADCQEKDPALSE- 303
Cdd:PTZ00108  366 PSKFGSTCELSEKLIKYVLKSP---------ILENIVEWAQAKLAAELNKKMKAGKksrILGIP-KLDDANDAGGKNSEe 435

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56675162   304 --LYIVEGDSAGGSAKQG---RNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGRDEYNPD 370
Cdd:PTZ00108  436 ctLILTEGDSAKALALAGlsvVGRDYYGVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYEDPK 507
PLN03128 PLN03128
DNA topoisomerase 2; Provisional
 106-370 1.66e-12

DNA topoisomerase 2; Provisional


Pssm-ID: 215593 [Multi-domain]  Cd Length: 1135  Bit Score: 68.97  E-value: 1.66e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   106 IKAFVEYLN-----QNKTPIHPKVFHFTTEQDGIGVEVAmqwNDAYQEgvYCFTNNIPQRDGGTHLvgfrTALTRTLNSY 180
Cdd:PLN03128  238 VKSFQDYVGlylgpNSREDPLPRIYEKVNDRWEVCVSLS---DGSFQQ--VSFVNSIATIKGGTHV----DYVADQIVKH 308

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   181 MdKEDYSKKAKSAAS--GDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEklaDFL--LENPGdakiVV 256
Cdd:PLN03128  309 I-QEKVKKKNKNATHvkPFQIKNHLWVFVNCLIENPTFDSQTKETLTTRPSSFGSKCELSE---EFLkkVEKCG----VV 380

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   257 NKIIDAARAREAARKARELTRRKGALdiAGLPgKLADCQEKDPALSE---LYIVEGDSAGGSAKQGR---NRKNQAILPL 330
Cdd:PLN03128  381 ENILSWAQFKQQKELKKKDGAKRQRL--TGIP-KLDDANDAGGKKSKdctLILTEGDSAKALAMSGLsvvGRDHYGVFPL 457

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 56675162   331 KGKILNVEKARFDKMISSQEVGTLITALGCGIGRdEYNPD 370
Cdd:PLN03128  458 RGKLLNVREASHKQIMKNAEITNIKQILGLQFGK-TYDEE 496
39 PHA02569
DNA topoisomerase II large subunit; Provisional
 153-369 2.72e-12

DNA topoisomerase II large subunit; Provisional


Pssm-ID: 177398 [Multi-domain]  Cd Length: 602  Bit Score: 67.86  E-value: 2.72e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162  153 FTNNIPQRDGGTHLVGFRTALTRTLNSyMDKedysKKAKSAASGDDVREGLIAVISVK-VPDPKFSSQTKDKLVSS--EV 229
Cdd:PHA02569 264 FVNGLHTKNGGHHVDCVMDDICEELIP-MIK----KKHKIEVTKARVKECLTIVLFVRnMSNPRFDSQTKERLTSPfgEI 338

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162  230 KTAVeQAMGEKLADFLLENPGdakiVVNKIIDAARAREAARKARELTR-RKGALDI-------AGLPGKLADcqekdpal 301
Cdd:PHA02569 339 RNHI-DLDYKKIAKQILKTEA----IIMPIIEAALARKLAAEKAAETKaAKKAKKAkvakhikANLIGKDAE-------- 405

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56675162  302 SELYIVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGRDEYNP 369
Cdd:PHA02569 406 TTLFLTEGDSAIGYLIEVRDEELHGGYPLRGKVLNTWGMSYADILKNKELFDICAITGLVLGEKAENM 473
TOPRIM_TopoIIA cd03365
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 304-368 2.29e-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: 54.61  E-value: 2.29e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56675162 304 LYIVEGDSAGGSAKQGRN---RKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCGIGRDEYN 368
Cdd:cd03365   3 LILTEGDSAKALAVAGLSvvgRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGKSDYE 70
PLN03237 PLN03237
DNA topoisomerase 2; Provisional
 106-359 3.70e-07

DNA topoisomerase 2; Provisional


Pssm-ID: 215641 [Multi-domain]  Cd Length: 1465  Bit Score: 52.17  E-value: 3.70e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   106 IKAFVEYLN---QNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVyCFTNNIPQRDGGTHLVGFRTALTRTLNSYMD 182
Cdd:PLN03237  263 VKSFSDYVDlylESANKSRPENLPRIYEKVNDRWEVCVSLSEGQFQQV-SFVNSIATIKGGTHVDYVTNQIANHVMEAVN 341

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   183 KEDYSKKAKSAasgdDVREGLIAVISVKVPDPKFSSQTKDKLvssevkTAVEQAMGEKLA---DFLlenpgdAKIVVNKI 259
Cdd:PLN03237  342 KKNKNANIKAH----NVKNHLWVFVNALIDNPAFDSQTKETL------TLRQSSFGSKCElseDFL------KKVMKSGI 405

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56675162   260 IDAARAREAARKARELTRRKGA--LDIAGLPgKLADCQE---KDPALSELYIVEGDSAGGSAKQGRN---RKNQAILPLK 331
Cdd:PLN03237  406 VENLLSWADFKQSKELKKTDGAktTRVTGIP-KLEDANEaggKNSEKCTLILTEGDSAKALAVAGLSvvgRNYYGVFPLR 484

                         250       260
                  ....*....|....*....|....*...
gi 56675162   332 GKILNVEKARFDKMISSQEVGTLITALG 359
Cdd:PLN03237  485 GKLLNVREASHKQIMNNAEIENIKQILG 512
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 303-347 6.46e-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: 46.97  E-value: 6.46e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 56675162   303 ELYIVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMIS 347
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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