NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1275020626|gb|ARH02093|]
View 

gyrase B subunit, partial [Leuconostoc mesenteroides]

Protein Classification

DNA topoisomerase subunit B( domain architecture ID 1750046)

DNA topoisomerase subunit B relaxes positive DNA supercoils generated during DNA replication; such as Mycoplasma capricolum DNA topoisomerase 4 subunit B and Arabidopsis thaliana mitochondrial DNA gyrase subunit B

EC:  5.6.2.2
Gene Ontology:  GO:0003918|GO:0006265|GO:0003677|GO:0005524
PubMed:  11395412

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
TOP2c super family cl40739
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-204 1.68e-148

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


The actual alignment was detected with superfamily member PRK05644:

Pssm-ID: 454823 [Multi-domain]  Cd Length: 638  Bit Score: 426.43  E-value: 1.68e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   1 QYTTDIKDSLRTFANNINTYEGGTHETGFKTALTRVINDYARKSGQIKDGAESLTGEDVREGMTAIVSIKHPDPQFEGQT 80
Cdd:PRK05644  260 QYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVREGLTAVISVKHPEPQFEGQT 339

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626  81 KTKLGNSDARQATDRMFSETFSRFMMENPNVAKQIVEKGVLAQKARLAAKRAREMTRKQSGLEIGNLPGKLADNTSNDPA 160
Cdd:PRK05644  340 KTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALESSSLPGKLADCSSKDPE 419

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1275020626 161 ISELFIVEGDSAGGSAKQGRNRVTQAILPIRGKILNVGKASLER 204
Cdd:PRK05644  420 ESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDK 463
 
Name Accession Description Interval E-value
gyrB PRK05644
DNA gyrase subunit B; Validated
 1-204 1.68e-148

DNA gyrase subunit B; Validated


Pssm-ID: 235542 [Multi-domain]  Cd Length: 638  Bit Score: 426.43  E-value: 1.68e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   1 QYTTDIKDSLRTFANNINTYEGGTHETGFKTALTRVINDYARKSGQIKDGAESLTGEDVREGMTAIVSIKHPDPQFEGQT 80
Cdd:PRK05644  260 QYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVREGLTAVISVKHPEPQFEGQT 339

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626  81 KTKLGNSDARQATDRMFSETFSRFMMENPNVAKQIVEKGVLAQKARLAAKRAREMTRKQSGLEIGNLPGKLADNTSNDPA 160
Cdd:PRK05644  340 KTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALESSSLPGKLADCSSKDPE 419

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1275020626 161 ISELFIVEGDSAGGSAKQGRNRVTQAILPIRGKILNVGKASLER 204
Cdd:PRK05644  420 ESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDK 463
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
1-204 2.60e-134

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


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 390.16  E-value: 2.60e-134
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   1 QYTTDIKDSLRTFANNINTYEGGTHETGFKTALTRVINDYARKSGQIKDGAESLTGEDVREGMTAIVSIKHPDPQFEGQT 80
Cdd:COG0187   258 QWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREGLTAVISVKLPEPQFEGQT 337

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626  81 KTKLGNSDARQATDRMFSETFSRFMMENPNVAKQIVEKGVLAQKARLAAKRAREMTRKQSGLEIGNLPGKLADNTSNDPA 160
Cdd:COG0187   338 KTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALESSGLPGKLADCSSKDPE 417

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1275020626 161 ISELFIVEGDSAGGSAKQGRNRVTQAILPIRGKILNVGKASLER 204
Cdd:COG0187   418 ESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDK 461
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-204 3.25e-102

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 306.79  E-value: 3.25e-102
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626    1 QYTTDIKDSLRTFANNINTYEGGTHETGFKTALTRVINDYARKSGqiKDGAESLTGEDVREGMTAIVSIKHPDPQFEGQT 80
Cdd:smart00433 224 QYTDGYSENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKK--KLKEKNIKGEDVREGLTAFISVKIPEPQFEGQT 301

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   81 KTKLGNSDARQATDRMFSETFSRFMMENPNVAKQIVEKGVLAQKARLAAKRAREMTRKqSGLEIGNLPGKLADNTSNDPA 160
Cdd:smart00433 302 KEKLGTSEVRFGVEKIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRK-KKLSSISLPGKLADASSAGPK 380

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 1275020626  161 ISELFIVEGDSAGGSAKQGRNRVTQAILPIRGKILNVGKASLER 204
Cdd:smart00433 381 KCELFLVEGDSAGGSAKSGRDRDFQAILPLRGKILNVEKASLDK 424
TopoII_Trans_DNA_gyrase cd00822
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ...
 1-135 9.09e-70

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: 210.11  E-value: 9.09e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   1 QYTTDIKDSLRTFANNINTYEGGTHETGFKTALTRVINDYARKSGQIKDGAESLTGEDVREGMTAIVSIKHPDPQFEGQT 80
Cdd:cd00822    38 QWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKKNNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQT 117

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1275020626  81 KTKLGNSDARQATDRMFSETFSRFMMENPNVAKQIVEKGVLAQKARLAAKRAREM 135
Cdd:cd00822   118 KDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAILAAKAREAARKAREL 172
DNA_gyraseB pfam00204
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ...
 1-135 2.29e-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: 201.30  E-value: 2.29e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   1 QYTTDIKDSLRTFANNINTYEGGTHETGFKTALTRVINDYARKSGQIKDGAESLTGEDVREGMTAIVSIKHPDPQFEGQT 80
Cdd:pfam00204  39 QWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAKKKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQT 118

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1275020626  81 KTKLGNSDARQATDRMFSETFSRFMMENPNVAKQIVEKGVLAQKARLAAKRAREM 135
Cdd:pfam00204 119 KEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQAAKARLAARKAREA 173
 
Name Accession Description Interval E-value
gyrB PRK05644
DNA gyrase subunit B; Validated
 1-204 1.68e-148

DNA gyrase subunit B; Validated


Pssm-ID: 235542 [Multi-domain]  Cd Length: 638  Bit Score: 426.43  E-value: 1.68e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   1 QYTTDIKDSLRTFANNINTYEGGTHETGFKTALTRVINDYARKSGQIKDGAESLTGEDVREGMTAIVSIKHPDPQFEGQT 80
Cdd:PRK05644  260 QYNDGYSENILSFANNINTHEGGTHEEGFKTALTRVINDYARKNKLLKEKDDNLTGEDVREGLTAVISVKHPEPQFEGQT 339

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626  81 KTKLGNSDARQATDRMFSETFSRFMMENPNVAKQIVEKGVLAQKARLAAKRAREMTRKQSGLEIGNLPGKLADNTSNDPA 160
Cdd:PRK05644  340 KTKLGNSEVRGIVDSVVSEALSEFLEENPNVAKKIVEKAILAARAREAARKARELTRRKSALESSSLPGKLADCSSKDPE 419

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1275020626 161 ISELFIVEGDSAGGSAKQGRNRVTQAILPIRGKILNVGKASLER 204
Cdd:PRK05644  420 ESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDK 463
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
1-204 2.60e-134

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


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 390.16  E-value: 2.60e-134
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   1 QYTTDIKDSLRTFANNINTYEGGTHETGFKTALTRVINDYARKSGQIKDGAESLTGEDVREGMTAIVSIKHPDPQFEGQT 80
Cdd:COG0187   258 QWNDGYSENIHSFVNNINTPEGGTHETGFRTALTRVINDYARKNGLLKEKDKNLTGDDVREGLTAVISVKLPEPQFEGQT 337

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626  81 KTKLGNSDARQATDRMFSETFSRFMMENPNVAKQIVEKGVLAQKARLAAKRAREMTRKQSGLEIGNLPGKLADNTSNDPA 160
Cdd:COG0187   338 KTKLGNSEARGIVESVVSEKLEHYLEENPAEAKKILEKAILAARAREAARKARELVRRKSALESSGLPGKLADCSSKDPE 417

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1275020626 161 ISELFIVEGDSAGGSAKQGRNRVTQAILPIRGKILNVGKASLER 204
Cdd:COG0187   418 ESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDK 461
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-204 4.65e-112

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 336.68  E-value: 4.65e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   1 QYTTDIKDSLRTFANNINTYEGGTHETGFKTALTRVINDYARKSGQIKDGAESLTGEDVREGMTAIVSIKHPDPQFEGQT 80
Cdd:PRK14939  258 QWNDSYQENVLCFTNNIPQRDGGTHLAGFRAALTRTINNYIEKEGLAKKAKVSLTGDDAREGLTAVLSVKVPDPKFSSQT 337

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626  81 KTKLGNSDARQATDRMFSETFSRFMMENPNVAKQIVEKGVLAQKARLAAKRAREMTRKQSGLEIGNLPGKLADNTSNDPA 160
Cdd:PRK14939  338 KDKLVSSEVRPAVESLVNEKLSEFLEENPNEAKIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPA 417

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1275020626 161 ISELFIVEGDSAGGSAKQGRNRVTQAILPIRGKILNVGKASLER 204
Cdd:PRK14939  418 LSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDK 461
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-204 3.25e-102

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 306.79  E-value: 3.25e-102
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626    1 QYTTDIKDSLRTFANNINTYEGGTHETGFKTALTRVINDYARKSGqiKDGAESLTGEDVREGMTAIVSIKHPDPQFEGQT 80
Cdd:smart00433 224 QYTDGYSENIVSFVNNIATTEGGTHENGFKDALTRVINEYAKKKK--KLKEKNIKGEDVREGLTAFISVKIPEPQFEGQT 301

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   81 KTKLGNSDARQATDRMFSETFSRFMMENPNVAKQIVEKGVLAQKARLAAKRAREMTRKqSGLEIGNLPGKLADNTSNDPA 160
Cdd:smart00433 302 KEKLGTSEVRFGVEKIVSECLLSFLEENPVEASKIVEKVLLAAKARAAAKKARELTRK-KKLSSISLPGKLADASSAGPK 380

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 1275020626  161 ISELFIVEGDSAGGSAKQGRNRVTQAILPIRGKILNVGKASLER 204
Cdd:smart00433 381 KCELFLVEGDSAGGSAKSGRDRDFQAILPLRGKILNVEKASLDK 424
PRK05559 PRK05559
DNA topoisomerase IV subunit B; Reviewed
 1-204 1.27e-88

DNA topoisomerase IV subunit B; Reviewed


Pssm-ID: 235501 [Multi-domain]  Cd Length: 631  Bit Score: 272.74  E-value: 1.27e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   1 QYTTDIKDSLRTFANNINTYEGGTHETGFKTALTRVINDYARKSGQIKDGAEsLTGEDVREGMTAIVSIKHPDPQFEGQT 80
Cdd:PRK05559  259 QWTDEGGENIESYVNLIPTPQGGTHENGFREGLLKAVREFAEKRNLLPKGKK-LEGEDVREGLAAVLSVKIPEPQFEGQT 337

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626  81 KTKLGNSDARQATDRMFSETFSRFMMENPNVAKQIVEKGVLAQKARLAAKRAREMTRKQSGLeigNLPGKLADNTSNDPA 160
Cdd:PRK05559  338 KEKLGSREARRFVSGVVKDAFDLWLNQNPELAEKLAEKAIKAAQARLRAAKKVKRKKKTSGP---ALPGKLADCTSQDPE 414

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1275020626 161 ISELFIVEGDSAGGSAKQGRNRVTQAILPIRGKILNVGKASLER 204
Cdd:PRK05559  415 RTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDD 458
TopoII_Trans_DNA_gyrase cd00822
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ...
 1-135 9.09e-70

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: 210.11  E-value: 9.09e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   1 QYTTDIKDSLRTFANNINTYEGGTHETGFKTALTRVINDYARKSGQIKDGAESLTGEDVREGMTAIVSIKHPDPQFEGQT 80
Cdd:cd00822    38 QWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKKNNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQT 117

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1275020626  81 KTKLGNSDARQATDRMFSETFSRFMMENPNVAKQIVEKGVLAQKARLAAKRAREM 135
Cdd:cd00822   118 KDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAILAAKAREAARKAREL 172
DNA_gyraseB pfam00204
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ...
 1-135 2.29e-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: 201.30  E-value: 2.29e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   1 QYTTDIKDSLRTFANNINTYEGGTHETGFKTALTRVINDYARKSGQIKDGAESLTGEDVREGMTAIVSIKHPDPQFEGQT 80
Cdd:pfam00204  39 QWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAKKKGLLKKKDEKITGEDIREGLTAVVSVKIPDPQFEGQT 118

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1275020626  81 KTKLGNSDARQATDRMFSETFSRFMMENPNVAKQIVEKGVLAQKARLAAKRAREM 135
Cdd:pfam00204 119 KEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQAAKARLAARKAREA 173
PTZ00109 PTZ00109
DNA gyrase subunit b; Provisional
 1-201 1.51e-59

DNA gyrase subunit b; Provisional


Pssm-ID: 240272 [Multi-domain]  Cd Length: 903  Bit Score: 200.11  E-value: 1.51e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   1 QYTTDIKdslrTFANNINTyEGGTHETGFKTALTRVINDYARKSGQIKDGAESLTGEDVREGMTAIVSIKHPDPQFEGQT 80
Cdd:PTZ00109  419 SYTALIK----SFANNVST-TAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIPGEFIREGMTAIISVKLNGAEFDGQT 493

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626  81 KTKLGNSDARQATDRMFSETFSRFMMENPNVAKQIVEKGVLAQKARLAAKRAREMTRKQSGLEIGN-LPGKLADNTSNDP 159
Cdd:PTZ00109  494 KTKLGNHLLKTILESIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYSTiLPGKLVDCISDDI 573

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1275020626 160 AISELFIVEGDSAGGSAKQGRNRVTQAILPIRGKILNVGKAS 201
Cdd:PTZ00109  574 ERNELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIK 615
TOPRIM_TopoIIA_like cd01030
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 162-204 7.95e-22

TOPRIM_TopoIIA_like: 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). 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: 173780 [Multi-domain]  Cd Length: 115  Bit Score: 85.63  E-value: 7.95e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1275020626 162 SELFIVEGDSAGGSAKQGRNRVTQAILPIRGKILNVGKASLER 204
Cdd:cd01030     1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKK 43
39 PHA02569
DNA topoisomerase II large subunit; Provisional
 12-197 2.08e-15

DNA topoisomerase II large subunit; Provisional


Pssm-ID: 177398 [Multi-domain]  Cd Length: 602  Bit Score: 73.63  E-value: 2.08e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626  12 TFANNINTYEGGTHETGFKTALTRVINDYARKSGQIKdgaesLTGEDVREGMTAIVSIKH-PDPQFEGQTKTKLGNS--D 88
Cdd:PHA02569  263 SFVNGLHTKNGGHHVDCVMDDICEELIPMIKKKHKIE-----VTKARVKECLTIVLFVRNmSNPRFDSQTKERLTSPfgE 337

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626  89 ARQATDRMFSEtFSRFMMENPNVAKQIVEkGVLAQKarLAAKRArEMTRKQSGLE--------IGNLPGKLADNTsndpa 160
Cdd:PHA02569  338 IRNHIDLDYKK-IAKQILKTEAIIMPIIE-AALARK--LAAEKA-AETKAAKKAKkakvakhiKANLIGKDAETT----- 407

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 1275020626 161 iseLFIVEGDSAGGSAKQGRNRVTQAILPIRGKILNV 197
Cdd:PHA02569  408 ---LFLTEGDSAIGYLIEVRDEELHGGYPLRGKVLNT 441
TopoII_MutL_Trans cd00329
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ...
 7-85 4.90e-15

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: 68.06  E-value: 4.90e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   7 KDSLRTFANNINTYEGGTHETGFKTALTRVINdyarksgqikdgaesltGEDVREGMTAIVSIKHPD--PQFE-GQTKTK 83
Cdd:cd00329    43 KDRQFSFVNGRPVREGGTHVKAVREAYTRALN-----------------GDDVRRYPVAVLSLKIPPslVDVNvHPTKEE 105


                  ..
gi 1275020626  84 LG 85
Cdd:cd00329   106 VR 107
PTZ00108 PTZ00108
DNA topoisomerase 2-like protein; Provisional
 13-204 4.26e-12

DNA topoisomerase 2-like protein; Provisional


Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 64.30  E-value: 4.26e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   13 FANNINTYEGGTHETGFKTALTRVINDYARKSgqiKDGAESLTGEDVREGMTAIVSIKHPDPQFEGQTKTKLGNSDARQA 92
Cdd:PTZ00108   294 FVNSICTTKGGTHVNYILDQLISKLQEKAKKK---KKKGKEIKPNQIKNHLWVFVNCLIVNPSFDSQTKETLTTKPSKFG 370

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   93 TDRMFSETFSRFMMENPnvakqIVEKGVLAQKARLAAKRAREMTRKQSGLEIGnLPgKLADNTSNDPAISE---LFIVEG 169
Cdd:PTZ00108   371 STCELSEKLIKYVLKSP-----ILENIVEWAQAKLAAELNKKMKAGKKSRILG-IP-KLDDANDAGGKNSEectLILTEG 443

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|
gi 1275020626  170 DSA-----GGSAKQGRNRVtqAILPIRGKILNVGKASLER 204
Cdd:PTZ00108   444 DSAkalalAGLSVVGRDYY--GVFPLRGKLLNVRDASLKQ 481
PLN03128 PLN03128
DNA topoisomerase 2; Provisional
 12-204 1.02e-07

DNA topoisomerase 2; Provisional


Pssm-ID: 215593 [Multi-domain]  Cd Length: 1135  Bit Score: 51.25  E-value: 1.02e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   12 TFANNINTYEGGTHetgfKTALTRVINDYARKSGQIKD-GAESLTGEDVREGMTAIVSIKHPDPQFEGQTKTKLGNSDAR 90
Cdd:PLN03128   284 SFVNSIATIKGGTH----VDYVADQIVKHIQEKVKKKNkNATHVKPFQIKNHLWVFVNCLIENPTFDSQTKETLTTRPSS 359

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   91 QATDRMFSETFsrfmmenpnvAKQIVEKGVLAQKARLAAKRAREMTRKQSGLEIGNLPG--KLADNTSNDPAISE---LF 165
Cdd:PLN03128   360 FGSKCELSEEF----------LKKVEKCGVVENILSWAQFKQQKELKKKDGAKRQRLTGipKLDDANDAGGKKSKdctLI 429

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 1275020626  166 IVEGDSAGGSAKQGR---NRVTQAILPIRGKILNVGKASLER 204
Cdd:PLN03128   430 LTEGDSAKALAMSGLsvvGRDHYGVFPLRGKLLNVREASHKQ 471
PLN03237 PLN03237
DNA topoisomerase 2; Provisional
 12-201 6.11e-06

DNA topoisomerase 2; Provisional


Pssm-ID: 215641 [Multi-domain]  Cd Length: 1465  Bit Score: 46.01  E-value: 6.11e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   12 TFANNINTYEGGTHetgfKTALTRVINDYARKSGQIKDGAESLTGEDVREGMTAIVSIKHPDPQFEGQTKTKLgnsDARQ 91
Cdd:PLN03237   311 SFVNSIATIKGGTH----VDYVTNQIANHVMEAVNKKNKNANIKAHNVKNHLWVFVNALIDNPAFDSQTKETL---TLRQ 383

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1275020626   92 ATdrmFSETFSRfmmeNPNVAKQIVEKGVLAQKARLAA-KRAREMtRKQSGLEIGNLPG--KLADNTSNDPAISE---LF 165
Cdd:PLN03237   384 SS---FGSKCEL----SEDFLKKVMKSGIVENLLSWADfKQSKEL-KKTDGAKTTRVTGipKLEDANEAGGKNSEkctLI 455

                          170       180       190
                   ....*....|....*....|....*....|....*....
gi 1275020626  166 IVEGDSAGGSAKQGRNRVTQ---AILPIRGKILNVGKAS 201
Cdd:PLN03237   456 LTEGDSAKALAVAGLSVVGRnyyGVFPLRGKLLNVREAS 494
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 163-197 7.71e-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: 42.73  E-value: 7.71e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1275020626 163 ELFIVEGDSAGGSAKQGRNRVTQAILPIRGKILNV 197
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSL 35
TOPRIM_TopoIIA cd03365
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 164-204 1.62e-03

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: 36.89  E-value: 1.62e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1275020626 164 LFIVEGDSAGGSAKQGRN---RVTQAILPIRGKILNVGKASLER 204
Cdd:cd03365     3 LILTEGDSAKALAVAGLSvvgRDYYGVFPLRGKLLNVREASHKQ 46
TopoIIA_Trans_ScTopoIIA cd03481
TopoIIA_Trans_ScTopoIIA: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ...
 13-84 1.91e-03

TopoIIA_Trans_ScTopoIIA: 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 Saccharomyces cerevisiae Topo IIA. S. cerevisiae Topo IIA is a homodimer encoded by a single gene. 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. 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.


Pssm-ID: 239563 [Multi-domain]  Cd Length: 153  Bit Score: 37.27  E-value: 1.91e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1275020626  13 FANNINTYEGGTHETGFKTALTRVINDYARKSgqiKDGAESLTGEDVREGMTAIVSIKHPDPQFEGQTKTKL 84
Cdd:cd03481    49 FVNSIATTKGGTHVDYVADQIVKKLDEVVKKK---NKGGINVKPFQVKNHLWIFVNCLIENPSFDSQTKETL 117
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH