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Conserved domains on  [gi|950645958|gb|ALN38788|]
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DNA gyrase subunit B, partial [Rheinheimera sp. CANegra]

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
 1-354 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: 751.93  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   1 ALSDKLELTIRRKGQVHNQIYRLGVPDEPLKVIGETDSTGTEIRFWPSGTIFTDINYHYDILAKRLRELSFLNSGVSIIL 80
Cdd:PRK14939 127 ALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETDKTGTEVRFWPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRL 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  81 VDERDDKKDHFKYEGGIEAFVQYLNRTKTAIHPKAFYFSATRDdGISVEVAMQWNDSFQEGIYCFTNNIPQRDGGTHLAG 160
Cdd:PRK14939 207 KDERDGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKD-GIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAG 285

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958 161 FRSALTRVLNTYIDAEGYAKKMKVSATGDDAREGLTAVISVKVPDPKFSSQTKDKLVSSEVKSAVESVMHEKLNEYLLEN 240
Cdd:PRK14939 286 FRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEEN 365

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958 241 PNDSKIIVTKIVDAARAREAARKAREMTRRKGVLDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRNRKNQAIL 320
Cdd:PRK14939 366 PNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAIL 445

                        330       340       350
                 ....*....|....*....|....*....|....
gi 950645958 321 PLKGKILNVEKARFDKMISSQEVGTLITALGCGI 354
Cdd:PRK14939 446 PLKGKILNVEKARFDKMLSSQEIGTLITALGCGI 479
 
Name Accession Description Interval E-value
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-354 0e+00

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 751.93  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   1 ALSDKLELTIRRKGQVHNQIYRLGVPDEPLKVIGETDSTGTEIRFWPSGTIFTDINYHYDILAKRLRELSFLNSGVSIIL 80
Cdd:PRK14939 127 ALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETDKTGTEVRFWPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRL 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  81 VDERDDKKDHFKYEGGIEAFVQYLNRTKTAIHPKAFYFSATRDdGISVEVAMQWNDSFQEGIYCFTNNIPQRDGGTHLAG 160
Cdd:PRK14939 207 KDERDGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKD-GIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAG 285

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958 161 FRSALTRVLNTYIDAEGYAKKMKVSATGDDAREGLTAVISVKVPDPKFSSQTKDKLVSSEVKSAVESVMHEKLNEYLLEN 240
Cdd:PRK14939 286 FRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEEN 365

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958 241 PNDSKIIVTKIVDAARAREAARKAREMTRRKGVLDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRNRKNQAIL 320
Cdd:PRK14939 366 PNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAIL 445

                        330       340       350
                 ....*....|....*....|....*....|....
gi 950645958 321 PLKGKILNVEKARFDKMISSQEVGTLITALGCGI 354
Cdd:PRK14939 446 PLKGKILNVEKARFDKMLSSQEIGTLITALGCGI 479
gyrB TIGR01059
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ...
 1-354 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: 574.30  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958    1 ALSDKLELTIRRKGQVHNQIYRLGVPDEPLKVIGETDSTGTEIRFWPSGTIFTDINYHYDILAKRLRELSFLNSGVSIIL 80
Cdd:TIGR01059 120 ALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGTTVRFWPDPEIFETTEFDFDILAKRLRELAFLNSGVKISL 199

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   81 VDERDD--KKDHFKYEGGIEAFVQYLNRTKTAIHPKAFYFSATRDdGISVEVAMQWNDSFQEGIYCFTNNIPQRDGGTHL 158
Cdd:TIGR01059 200 EDERDGkgKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKE-GIEVEVALQWNDGYSENILSFVNNINTREGGTHL 278

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  159 AGFRSALTRVLNTYIDAEGYAKKMKVSATGDDAREGLTAVISVKVPDPKFSSQTKDKLVSSEVKSAVESVMHEKLNEYLL 238
Cdd:TIGR01059 279 EGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFE 358

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  239 ENPNDSKIIVTKIVDAARAREAARKAREMTRRKGVLDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRNRKNQA 318
Cdd:TIGR01059 359 ENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQA 438

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 950645958  319 ILPLKGKILNVEKARFDKMISSQEVGTLITALGCGI 354
Cdd:TIGR01059 439 ILPLRGKILNVEKARLDKILSNQEIGAIITALGCGI 474
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
1-354 0e+00

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


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 570.05  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   1 ALSDKLELTIRRKGQVHNQIYRLGVPDEPLKVIGETDSTGTEIRFWPSGTIFTDINYHYDILAKRLRELSFLNSGVSIIL 80
Cdd:COG0187  125 ALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKTDRTGTTVRFKPDPEIFETTEFDYETLAERLRELAFLNKGLTITL 204

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  81 VDERDD--KKDHFKYEGGIEAFVQYLNRTKTAIHPKAFYFSATRDDgISVEVAMQWNDSFQEGIYCFTNNIPQRDGGTHL 158
Cdd:COG0187  205 TDEREEepKEETFHYEGGIKDFVEYLNEDKEPLHPEVIYFEGEKDG-IEVEVALQWNDGYSENIHSFVNNINTPEGGTHE 283

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958 159 AGFRSALTRVLNTYIDAEGYAKKMKVSATGDDAREGLTAVISVKVPDPKFSSQTKDKLVSSEVKSAVESVMHEKLNEYLL 238
Cdd:COG0187  284 TGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREGLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLE 363

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958 239 ENPNDSKIIVTKIVDAARAREAARKAREMTRRKGVLDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRNRKNQA 318
Cdd:COG0187  364 ENPAEAKKILEKAILAARAREAARKARELVRRKSALESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQA 443

                        330       340       350
                 ....*....|....*....|....*....|....*.
gi 950645958 319 ILPLKGKILNVEKARFDKMISSQEVGTLITALGCGI 354
Cdd:COG0187  444 ILPLRGKILNVEKARLDKILKNEEIRDLITALGTGI 479
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-354 1.37e-142

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 416.57  E-value: 1.37e-142
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958     1 ALSDKLELTIRRKGQVHNQIY-RLGVPDEPLKVIGETDSTGTEIRFWPSGTIF-TDINYHYDILAKRLRELSFLNSGVSI 78
Cdd:smart00433  91 ALSTEFEVEVARDGKEYKQSFsNNGKPLSEPKIIGDTKKDGTKVTFKPDLEIFgMTTDDDFELLKRRLRELAFLNKGVKI 170

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958    79 ILVDERDDKKDHFKYEGGIEAFVQYLNRTKTAIHPKAFYFSATRDdGISVEVAMQWNDSFQEGIYCFTNNIPQRDGGTHL 158
Cdd:smart00433 171 TLNDERSDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKD-NIRVEVAFQYTDGYSENIVSFVNNIATTEGGTHE 249

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   159 AGFRSALTRVLNTYIDAEGYAKKMKVsaTGDDAREGLTAVISVKVPDPKFSSQTKDKLVSSEVKSAVESVMHEKLNEYLL 238
Cdd:smart00433 250 NGFKDALTRVINEYAKKKKKLKEKNI--KGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIVSECLLSFLE 327

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   239 ENPNDSKIIVTKIVDAARAREAARKAREMTRRKGvLDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRNRKNQA 318
Cdd:smart00433 328 ENPVEASKIVEKVLLAAKARAAAKKARELTRKKK-LSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAKSGRDRDFQA 406

                          330       340       350
                   ....*....|....*....|....*....|....*.
gi 950645958   319 ILPLKGKILNVEKARFDKMISSQEVGTLITALGCGI 354
Cdd:smart00433 407 ILPLRGKILNVEKASLDKILKNEEIQALITALGLGI 442
TopoII_Trans_DNA_gyrase cd00822
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ...
 95-253 8.13e-79

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: 238.61  E-value: 8.13e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  95 GGIEAFVQYLNRTKTAIHPKAFYFSATRDdGISVEVAMQWNDSFQEGIYCFTNNIPQRDGGTHLAGFRSALTRVLNTYID 174
Cdd:cd00822    1 GGLKDFVEELNKDKEPLHEEPIYIEGEKD-GVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAK 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 950645958 175 AEGYAKKMKVSATGDDAREGLTAVISVKVPDPKFSSQTKDKLVSSEVKSAVESVMHEKLNEYLLENPNDSKIIVTKIVD 253
Cdd:cd00822   80 KNNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAIL 158
DNA_gyraseB pfam00204
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ...
 96-253 9.08e-66

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: 205.54  E-value: 9.08e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   96 GIEAFVQYLNRTKTAIHPKAFYFSAT-RDDGISVEVAMQWNDSFQEGIYCFTNNIPQRDGGTHLAGFRSALTRVLNTYID 174
Cdd:pfam00204   1 GLKDFVEELNKDKKPLHKEIIYFEGEsPDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 950645958  175 AEGYAKKMKVSATGDDAREGLTAVISVKVPDPKFSSQTKDKLVSSEVKSAVESVMHEKLNEYLLENPNDSKIIVTKIVD 253
Cdd:pfam00204  81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQ 159
 
Name Accession Description Interval E-value
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-354 0e+00

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 751.93  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   1 ALSDKLELTIRRKGQVHNQIYRLGVPDEPLKVIGETDSTGTEIRFWPSGTIFTDINYHYDILAKRLRELSFLNSGVSIIL 80
Cdd:PRK14939 127 ALSEWLELTIRRDGKIHEQEFEHGVPVAPLKVVGETDKTGTEVRFWPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRL 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  81 VDERDDKKDHFKYEGGIEAFVQYLNRTKTAIHPKAFYFSATRDdGISVEVAMQWNDSFQEGIYCFTNNIPQRDGGTHLAG 160
Cdd:PRK14939 207 KDERDGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKD-GIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAG 285

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958 161 FRSALTRVLNTYIDAEGYAKKMKVSATGDDAREGLTAVISVKVPDPKFSSQTKDKLVSSEVKSAVESVMHEKLNEYLLEN 240
Cdd:PRK14939 286 FRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEEN 365

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958 241 PNDSKIIVTKIVDAARAREAARKAREMTRRKGVLDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRNRKNQAIL 320
Cdd:PRK14939 366 PNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAIL 445

                        330       340       350
                 ....*....|....*....|....*....|....
gi 950645958 321 PLKGKILNVEKARFDKMISSQEVGTLITALGCGI 354
Cdd:PRK14939 446 PLKGKILNVEKARFDKMLSSQEIGTLITALGCGI 479
gyrB TIGR01059
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ...
 1-354 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: 574.30  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958    1 ALSDKLELTIRRKGQVHNQIYRLGVPDEPLKVIGETDSTGTEIRFWPSGTIFTDINYHYDILAKRLRELSFLNSGVSIIL 80
Cdd:TIGR01059 120 ALSEWLEVTVFRDGKIYRQEFERGIPVGPLEVVGETKKTGTTVRFWPDPEIFETTEFDFDILAKRLRELAFLNSGVKISL 199

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   81 VDERDD--KKDHFKYEGGIEAFVQYLNRTKTAIHPKAFYFSATRDdGISVEVAMQWNDSFQEGIYCFTNNIPQRDGGTHL 158
Cdd:TIGR01059 200 EDERDGkgKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKE-GIEVEVALQWNDGYSENILSFVNNINTREGGTHL 278

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  159 AGFRSALTRVLNTYIDAEGYAKKMKVSATGDDAREGLTAVISVKVPDPKFSSQTKDKLVSSEVKSAVESVMHEKLNEYLL 238
Cdd:TIGR01059 279 EGFRSALTRVINSYAKNNKLLKESKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFE 358

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  239 ENPNDSKIIVTKIVDAARAREAARKAREMTRRKGVLDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRNRKNQA 318
Cdd:TIGR01059 359 ENPQEAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQA 438

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 950645958  319 ILPLKGKILNVEKARFDKMISSQEVGTLITALGCGI 354
Cdd:TIGR01059 439 ILPLRGKILNVEKARLDKILSNQEIGAIITALGCGI 474
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
1-354 0e+00

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


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 570.05  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   1 ALSDKLELTIRRKGQVHNQIYRLGVPDEPLKVIGETDSTGTEIRFWPSGTIFTDINYHYDILAKRLRELSFLNSGVSIIL 80
Cdd:COG0187  125 ALSERLEVEVKRDGKIYRQRFERGKPVGPLEKIGKTDRTGTTVRFKPDPEIFETTEFDYETLAERLRELAFLNKGLTITL 204

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  81 VDERDD--KKDHFKYEGGIEAFVQYLNRTKTAIHPKAFYFSATRDDgISVEVAMQWNDSFQEGIYCFTNNIPQRDGGTHL 158
Cdd:COG0187  205 TDEREEepKEETFHYEGGIKDFVEYLNEDKEPLHPEVIYFEGEKDG-IEVEVALQWNDGYSENIHSFVNNINTPEGGTHE 283

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958 159 AGFRSALTRVLNTYIDAEGYAKKMKVSATGDDAREGLTAVISVKVPDPKFSSQTKDKLVSSEVKSAVESVMHEKLNEYLL 238
Cdd:COG0187  284 TGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREGLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLE 363

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958 239 ENPNDSKIIVTKIVDAARAREAARKAREMTRRKGVLDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRNRKNQA 318
Cdd:COG0187  364 ENPAEAKKILEKAILAARAREAARKARELVRRKSALESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQA 443

                        330       340       350
                 ....*....|....*....|....*....|....*.
gi 950645958 319 ILPLKGKILNVEKARFDKMISSQEVGTLITALGCGI 354
Cdd:COG0187  444 ILPLRGKILNVEKARLDKILKNEEIRDLITALGTGI 479
gyrB PRK05644
DNA gyrase subunit B; Validated
 1-354 0e+00

DNA gyrase subunit B; Validated


Pssm-ID: 235542 [Multi-domain]  Cd Length: 638  Bit Score: 561.64  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   1 ALSDKLELTIRRKGQVHNQIYRLGVPDEPLKVIGETDSTGTEIRFWPSGTIFTDINYHYDILAKRLRELSFLNSGVSIIL 80
Cdd:PRK05644 127 ALSTWLEVEVKRDGKIYYQEYERGVPVTPLEVIGETDETGTTVTFKPDPEIFETTEFDYDTLATRLRELAFLNKGLKITL 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  81 VDERDD--KKDHFKYEGGIEAFVQYLNRTKTAIHPKAFYFSATRDDgISVEVAMQWNDSFQEGIYCFTNNIPQRDGGTHL 158
Cdd:PRK05644 207 TDEREGeeKEETFHYEGGIKEYVEYLNRNKEPLHEEPIYFEGEKDG-IEVEVAMQYNDGYSENILSFANNINTHEGGTHE 285

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958 159 AGFRSALTRVLNTYIDAEGYAKKMKVSATGDDAREGLTAVISVKVPDPKFSSQTKDKLVSSEVKSAVESVMHEKLNEYLL 238
Cdd:PRK05644 286 EGFKTALTRVINDYARKNKLLKEKDDNLTGEDVREGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLE 365

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958 239 ENPNDSKIIVTKIVDAARAREAARKAREMTRRKGVLDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRNRKNQA 318
Cdd:PRK05644 366 ENPNVAKKIVEKAILAARAREAARKARELTRRKSALESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQA 445

                        330       340       350
                 ....*....|....*....|....*....|....*.
gi 950645958 319 ILPLKGKILNVEKARFDKMISSQEVGTLITALGCGI 354
Cdd:PRK05644 446 ILPLRGKILNVEKARLDKILKNEEIRALITALGTGI 481
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-354 1.37e-142

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 416.57  E-value: 1.37e-142
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958     1 ALSDKLELTIRRKGQVHNQIY-RLGVPDEPLKVIGETDSTGTEIRFWPSGTIF-TDINYHYDILAKRLRELSFLNSGVSI 78
Cdd:smart00433  91 ALSTEFEVEVARDGKEYKQSFsNNGKPLSEPKIIGDTKKDGTKVTFKPDLEIFgMTTDDDFELLKRRLRELAFLNKGVKI 170

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958    79 ILVDERDDKKDHFKYEGGIEAFVQYLNRTKTAIHPKAFYFSATRDdGISVEVAMQWNDSFQEGIYCFTNNIPQRDGGTHL 158
Cdd:smart00433 171 TLNDERSDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKD-NIRVEVAFQYTDGYSENIVSFVNNIATTEGGTHE 249

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   159 AGFRSALTRVLNTYIDAEGYAKKMKVsaTGDDAREGLTAVISVKVPDPKFSSQTKDKLVSSEVKSAVESVMHEKLNEYLL 238
Cdd:smart00433 250 NGFKDALTRVINEYAKKKKKLKEKNI--KGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIVSECLLSFLE 327

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   239 ENPNDSKIIVTKIVDAARAREAARKAREMTRRKGvLDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRNRKNQA 318
Cdd:smart00433 328 ENPVEASKIVEKVLLAAKARAAAKKARELTRKKK-LSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAKSGRDRDFQA 406

                          330       340       350
                   ....*....|....*....|....*....|....*.
gi 950645958   319 ILPLKGKILNVEKARFDKMISSQEVGTLITALGCGI 354
Cdd:smart00433 407 ILPLRGKILNVEKASLDKILKNEEIQALITALGLGI 442
PRK05559 PRK05559
DNA topoisomerase IV subunit B; Reviewed
 1-354 3.77e-136

DNA topoisomerase IV subunit B; Reviewed


Pssm-ID: 235501 [Multi-domain]  Cd Length: 631  Bit Score: 401.02  E-value: 3.77e-136
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   1 ALSDKLELTIRRKGQVHNQIYRLGVPDEPLKVIGETDS--TGTEIRFWPSGTIFTDINYHYDILAKRLRELSFLNSGVSI 78
Cdd:PRK05559 127 ALSSRLEVEVKRDGKVYRQRFEGGDPVGPLEVVGTAGKrkTGTRVRFWPDPKIFDSPKFSPERLKERLRSKAFLLPGLTI 206

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  79 ILVDERddKKDHFKYEGGIEAFVQYLNRTKTAIHPKAFYFSATRDDGISVEVAMQWNDSFQEGIYCFTNNIPQRDGGTHL 158
Cdd:PRK05559 207 TLNDER--ERQTFHYENGLKDYLAELNEGKETLPEEFVGSFEGEAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHE 284

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958 159 AGFRSALTRVLNTYIDAEGYAKKMKvSATGDDAREGLTAVISVKVPDPKFSSQTKDKLVSSEVKSAVESVMHEKLNEYLL 238
Cdd:PRK05559 285 NGFREGLLKAVREFAEKRNLLPKGK-KLEGEDVREGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLN 363

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958 239 ENPNDSKIIVTKIVDAARAREAARKAremTRRKGVLDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRNRKNQA 318
Cdd:PRK05559 364 QNPELAEKLAEKAIKAAQARLRAAKK---VKRKKKTSGPALPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQA 440

                        330       340       350
                 ....*....|....*....|....*....|....*.
gi 950645958 319 ILPLKGKILNVEKARFDKMISSQEVGTLITALGCGI 354
Cdd:PRK05559 441 ILPLRGKILNTWEASLDDVLANEEIHDIIVAIGIGP 476
TopoII_Trans_DNA_gyrase cd00822
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ...
 95-253 8.13e-79

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: 238.61  E-value: 8.13e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  95 GGIEAFVQYLNRTKTAIHPKAFYFSATRDdGISVEVAMQWNDSFQEGIYCFTNNIPQRDGGTHLAGFRSALTRVLNTYID 174
Cdd:cd00822    1 GGLKDFVEELNKDKEPLHEEPIYIEGEKD-GVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAK 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 950645958 175 AEGYAKKMKVSATGDDAREGLTAVISVKVPDPKFSSQTKDKLVSSEVKSAVESVMHEKLNEYLLENPNDSKIIVTKIVD 253
Cdd:cd00822   80 KNNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAIL 158
PTZ00109 PTZ00109
DNA gyrase subunit b; Provisional
 1-354 3.39e-68

DNA gyrase subunit b; Provisional


Pssm-ID: 240272 [Multi-domain]  Cd Length: 903  Bit Score: 229.77  E-value: 3.39e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   1 ALSDKLELTIRRKGQVHNQIYRLGVPDEPLKVIGETDS-TGTEIRFWPSG-TIFTDINYHY--------------DILAK 64
Cdd:PTZ00109 259 ALSSFLKVDVFKGGKIYSIELSKGKVTKPLSVFSCPLKkRGTTIHFLPDYkHIFKTHHQHTeteeeegckngfnlDLIKN 338

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  65 RLRELSFLNSGVSIILVDERDDKKDHF------KYEGGIEAFVQYLNRTKTAIHPKAFYFSAT-RDDGISVEVAMQWN-D 136
Cdd:PTZ00109 339 RIHELSYLNPGLTFYLVDERIANENNFypyetiKHEGGTREFLEELIKDKTPLYKDINIISIRgVIKNVNVEVSLSWSlE 418

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958 137 SFQEGIYCFTNNIpQRDGGTHLAGFRSALTRVLNTYIDAEGYAKKMKVSATGDDAREGLTAVISVKVPDPKFSSQTKDKL 216
Cdd:PTZ00109 419 SYTALIKSFANNV-STTAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISVKLNGAEFDGQTKTKL 497

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958 217 VSSEVKSAVESVMHEKLNEYLLENPNDSKIIVTKIVDAARAREAARKAREMTRRKGVLDIA-GLPGKLADCQEKDPALSE 295
Cdd:PTZ00109 498 GNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYStILPGKLVDCISDDIERNE 577

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958 296 LYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMI-SSQEVGTLITALGCGI 354
Cdd:PTZ00109 578 LFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNKKVfENSEIKLLITSIGLSV 637
DNA_gyraseB pfam00204
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ...
 96-253 9.08e-66

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: 205.54  E-value: 9.08e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   96 GIEAFVQYLNRTKTAIHPKAFYFSAT-RDDGISVEVAMQWNDSFQEGIYCFTNNIPQRDGGTHLAGFRSALTRVLNTYID 174
Cdd:pfam00204   1 GLKDFVEELNKDKKPLHKEIIYFEGEsPDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 950645958  175 AEGYAKKMKVSATGDDAREGLTAVISVKVPDPKFSSQTKDKLVSSEVKSAVESVMHEKLNEYLLENPNDSKIIVTKIVD 253
Cdd:pfam00204  81 KKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQ 159
parE_Gneg TIGR01055
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ...
 1-353 8.83e-64

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: 213.63  E-value: 8.83e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958    1 ALSDKLELTIRRKGQVHNQIYRLGVPDEPLKVIGETD--STGTEIRFWPSGTIFTDINYHYDILAKRLRELSFLNSGVSI 78
Cdd:TIGR01055 120 ALSKRVKIKVYRQGKLYSIAFENGAKVTDLISAGTCGkrLTGTSVHFTPDPEIFDSLHFSVSRLYHILRAKAVLCRGVEI 199

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   79 ILVDERDDKKDHFKYEGGIEAFV-QYLNRTKTAIhPKAFYFSATRDDgISVEVAMQWNDSFQEGI---YCftNNIPQRDG 154
Cdd:TIGR01055 200 EFEDEVNNTKALWNYPDGLKDYLsEAVNGDNTLP-PKPFSGNFEGDD-EAVEWALLWLPEGGELFmesYV--NLIPTPQG 275

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  155 GTHLAGFRSALTRVLNTYIDAEGYAKKmKVSATGDDAREGLTAVISVKVPDPKFSSQTKDKLVSSEVKSAVESVMHEKLN 234
Cdd:TIGR01055 276 GTHVNGLRQGLLDALREFCEMRNNLPR-GVKLTAEDIWDRCSYVLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFD 354

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  235 EYLLENPNDSKIIVTKIVDAARAREAARKAREmtrRKGVLDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRNR 314
Cdd:TIGR01055 355 LWLNQNVQLAEHLAEHAISSAQRRKRAAKKVV---RKKLTSGPALPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDR 431

                         330       340       350
                  ....*....|....*....|....*....|....*....
gi 950645958  315 KNQAILPLKGKILNVEKARFDKMISSQEVGTLITALGCG 353
Cdd:TIGR01055 432 EYQAILPLWGKILNTWEVSLDKVLNSQEIHDIEVALGID 470
HATPase_GyrB-like cd16928
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ...
 1-91 4.54e-38

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: 134.20  E-value: 4.54e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   1 ALSDKLELTIRRKGQVHNQIYRLGVPDEPLKVIGETDSTGTEIRFWPSGTIFTDINYHYDILAKRLRELSFLNSGVSIIL 80
Cdd:cd16928   90 ALSERLEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKKTGTTVRFWPDPEIFEKTEFDFDTLKRRLRELAFLNKGLKIVL 169

                         90
                 ....*....|.
gi 950645958  81 VDERDDKKDHF 91
Cdd:cd16928  170 EDERTGKEEVF 180
TopoII_MutL_Trans cd00329
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ...
 97-216 4.14e-20

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: 84.23  E-value: 4.14e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  97 IEAFVQYLNRTKTaiHPKAFYFSATrDDGISVEVAMQWND---SFQEGIYCFTNNIPQRDGGTHLAGFRSALTRVLNtyi 173
Cdd:cd00329    1 LKDRLAEILGDKV--ADKLIYVEGE-SDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN--- 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 950645958 174 daegyakkmkvsatGDDAREGLTAVISVKVPD--PKFS-SQTKDKL 216
Cdd:cd00329   75 --------------GDDVRRYPVAVLSLKIPPslVDVNvHPTKEEV 106
PTZ00108 PTZ00108
DNA topoisomerase 2-like protein; Provisional
 58-351 1.19e-17

DNA topoisomerase 2-like protein; Provisional


Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 84.33  E-value: 1.19e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   58 HYDILAKRLRELSFLNSGVSIILVDERDdkkdhfkyegGIEAFVQY--LNRTKTAIHPKAFYFSATRDDGISVEVAMQWN 135
Cdd:PTZ00108  216 MLRLLKKRVYDLAGCFGKLKVYLNGERI----------AIKSFKDYvdLYLPDGEEGKKPPYPFVYTSVNGRWEVVVSLS 285

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  136 DS-FQegIYCFTNNIPQRDGGTHLagfrSALTRVLNTYIDaeGYAKKMKVSATGDDA---REGLTAVISVKVPDPKFSSQ 211
Cdd:PTZ00108  286 DGqFQ--QVSFVNSICTTKGGTHV----NYILDQLISKLQ--EKAKKKKKKGKEIKPnqiKNHLWVFVNCLIVNPSFDSQ 357

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  212 TKDKLVSSEVKSAVESVMHEKLNEYLLENPndskiIVTKIVDAARAREAARKAREM--TRRKGvldIAGLPgKLADCQEK 289
Cdd:PTZ00108  358 TKETLTTKPSKFGSTCELSEKLIKYVLKSP-----ILENIVEWAQAKLAAELNKKMkaGKKSR---ILGIP-KLDDANDA 428

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 950645958  290 DPALSE---LYLVEGDSAGGSAKQG---RNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALG 351
Cdd:PTZ00108  429 GGKNSEectLILTEGDSAKALALAGlsvVGRDYYGVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILG 496
39 PHA02569
DNA topoisomerase II large subunit; Provisional
 145-351 1.01e-13

DNA topoisomerase II large subunit; Provisional


Pssm-ID: 177398 [Multi-domain]  Cd Length: 602  Bit Score: 72.09  E-value: 1.01e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958 145 FTNNIPQRDGGTHLAGFRSALTRVLNTYIDaegyaKKMKVSATGDDAREGLTAVISVK-VPDPKFSSQTKDKLVSS--EV 221
Cdd:PHA02569 264 FVNGLHTKNGGHHVDCVMDDICEELIPMIK-----KKHKIEVTKARVKECLTIVLFVRnMSNPRFDSQTKERLTSPfgEI 338

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958 222 KSAVEsVMHEKLNEYLLENPNdskiIVTKIVDAARAREAARKAREMTRR-------KGVLDI-AGLPGKLADcqekdpal 293
Cdd:PHA02569 339 RNHID-LDYKKIAKQILKTEA----IIMPIIEAALARKLAAEKAAETKAakkakkaKVAKHIkANLIGKDAE-------- 405

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 950645958 294 SELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALG 351
Cdd:PHA02569 406 TTLFLTEGDSAIGYLIEVRDEELHGGYPLRGKVLNTWGMSYADILKNKELFDICAITG 463
PLN03128 PLN03128
DNA topoisomerase 2; Provisional
 12-351 4.13e-10

DNA topoisomerase 2; Provisional


Pssm-ID: 215593 [Multi-domain]  Cd Length: 1135  Bit Score: 61.26  E-value: 4.13e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   12 RKGQVHNQIYR--LGVPDEPLKVIGETDSTGTEIRFWPSGTIFT------DInyhYDILAKRLRELS-FLNSGVSIILVD 82
Cdd:PLN03128  157 NRGKKYKQVFTnnMSVKSEPKITSCKASENWTKITFKPDLAKFNmtrldeDV---VALMSKRVYDIAgCLGKKLKVELNG 233

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958   83 ERDDKKDHFKYEGgieafvQYLNRTKTAIHPKAFYfsATRDDGISVEVAMQwNDSFQEgiYCFTNNIPQRDGGTHLAgfr 162
Cdd:PLN03128  234 KKLPVKSFQDYVG------LYLGPNSREDPLPRIY--EKVNDRWEVCVSLS-DGSFQQ--VSFVNSIATIKGGTHVD--- 299

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  163 sALTRVLNTYIdAEGYAKKMK--VSATGDDAREGLTAVISVKVPDPKFSSQTKDKLVSSEvkSAVESvmHEKLNEYLLEn 240
Cdd:PLN03128  300 -YVADQIVKHI-QEKVKKKNKnaTHVKPFQIKNHLWVFVNCLIENPTFDSQTKETLTTRP--SSFGS--KCELSEEFLK- 372

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  241 pndsKIIVTKIVDAARAREAARKAREMTRRKGV--LDIAGLPgKLADCQEKDPALSE---LYLVEGDSAGGSAKQGR--- 312
Cdd:PLN03128  373 ----KVEKCGVVENILSWAQFKQQKELKKKDGAkrQRLTGIP-KLDDANDAGGKKSKdctLILTEGDSAKALAMSGLsvv 447

                         330       340       350
                  ....*....|....*....|....*....|....*....
gi 950645958  313 NRKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALG 351
Cdd:PLN03128  448 GRDHYGVFPLRGKLLNVREASHKQIMKNAEITNIKQILG 486
TOPRIM_TopoIIA cd03365
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 296-351 6.66e-08

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: 50.38  E-value: 6.66e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 950645958 296 LYLVEGDSAGGSAKQGRN---RKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALG 351
Cdd:cd03365    3 LILTEGDSAKALAVAGLSvvgRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILG 61
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 295-339 3.80e-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: 44.65  E-value: 3.80e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 950645958  295 ELYLVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMIS 339
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKALK 45
PLN03237 PLN03237
DNA topoisomerase 2; Provisional
 145-351 8.54e-05

DNA topoisomerase 2; Provisional


Pssm-ID: 215641 [Multi-domain]  Cd Length: 1465  Bit Score: 44.47  E-value: 8.54e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  145 FTNNIPQRDGGTHLAGFRSALTRVLNTYIDAEGYAKKMKVSatgdDAREGLTAVISVKVPDPKFSSQTKDKLV--SSEVK 222
Cdd:PLN03237  312 FVNSIATIKGGTHVDYVTNQIANHVMEAVNKKNKNANIKAH----NVKNHLWVFVNALIDNPAFDSQTKETLTlrQSSFG 387

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 950645958  223 SAVEsvmhekLNEYLLEnpndsKIIVTKIVDAARAREAARKAREMTRRKGV--LDIAGLPgKLADCQE---KDPALSELY 297
Cdd:PLN03237  388 SKCE------LSEDFLK-----KVMKSGIVENLLSWADFKQSKELKKTDGAktTRVTGIP-KLEDANEaggKNSEKCTLI 455

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 950645958  298 LVEGDSAGGSAKQGRN---RKNQAILPLKGKILNVEKARFDKMISSQEVGTLITALG 351
Cdd:PLN03237  456 LTEGDSAKALAVAGLSvvgRNYYGVFPLRGKLLNVREASHKQIMNNAEIENIKQILG 512
 
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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