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Conserved domains on  [gi|1173202403|emb|SFW10564|]
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DNA gyrase subunit B, partial [Aeromonas crassostreae]

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

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
gyrB super family cl36442
DNA gyrase subunit B; Provisional
 1-339 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: 691.07  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403   1 LLLTIRRNGHVYEQTYHLGEPQAPLKQIGDSSsGTGTEVRFWPSSTIFSDTLFHYDILAKRLRELSFLNSGVSIRLEDER 80
Cdd:PRK14939  132 LELTIRRDGKIHEQEFEHGVPVAPLKVVGETD-KTGTEVRFWPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRLKDER 210

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  81 DGREVHFCYEGGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRTAL 160
Cdd:PRK14939  211 DGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAAL 290

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 161 TRTLNTYMDKEDYSKKAK*SAAsGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENPGDA 240
Cdd:PRK14939  291 TRTINNYIEKEGLAKKAKVSLT-GDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEA 369

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 241 KIVVNKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQGRNRKNQAILPLKG 320
Cdd:PRK14939  370 KIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKG 449

                         330
                  ....*....|....*....
gi 1173202403 321 KILNVEKARFDKMISSQEV 339
Cdd:PRK14939  450 KILNVEKARFDKMLSSQEI 468
 
Name Accession Description Interval E-value
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-339 0e+00

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 691.07  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403   1 LLLTIRRNGHVYEQTYHLGEPQAPLKQIGDSSsGTGTEVRFWPSSTIFSDTLFHYDILAKRLRELSFLNSGVSIRLEDER 80
Cdd:PRK14939  132 LELTIRRDGKIHEQEFEHGVPVAPLKVVGETD-KTGTEVRFWPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRLKDER 210

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  81 DGREVHFCYEGGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRTAL 160
Cdd:PRK14939  211 DGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAAL 290

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 161 TRTLNTYMDKEDYSKKAK*SAAsGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENPGDA 240
Cdd:PRK14939  291 TRTINNYIEKEGLAKKAKVSLT-GDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEA 369

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 241 KIVVNKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQGRNRKNQAILPLKG 320
Cdd:PRK14939  370 KIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKG 449

                         330
                  ....*....|....*....
gi 1173202403 321 KILNVEKARFDKMISSQEV 339
Cdd:PRK14939  450 KILNVEKARFDKMLSSQEI 468
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
1-339 0e+00

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


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 533.84  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403   1 LLLTIRRNGHVYEQTYHLGEPQAPLKQIGDSSsGTGTEVRFWPSSTIFSDTLFHYDILAKRLRELSFLNSGVSIRLEDER 80
Cdd:COG0187   130 LEVEVKRDGKIYRQRFERGKPVGPLEKIGKTD-RTGTTVRFKPDPEIFETTEFDYETLAERLRELAFLNKGLTITLTDER 208

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  81 DG--REVHFCYEGGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRT 158
Cdd:COG0187   209 EEepKEETFHYEGGIKDFVEYLNEDKEPLHPEVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRT 288

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 159 ALTRTLNTYMDKEDySKKAK*SAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENPG 238
Cdd:COG0187   289 ALTRVINDYARKNG-LLKEKDKNLTGDDVREGLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPA 367

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 239 DAKIVVNKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQGRNRKNQAILPL 318
Cdd:COG0187   368 EAKKILEKAILAARAREAARKARELVRRKSALESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPL 447

                         330       340
                  ....*....|....*....|.
gi 1173202403 319 KGKILNVEKARFDKMISSQEV 339
Cdd:COG0187   448 RGKILNVEKARLDKILKNEEI 468
gyrB TIGR01059
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ...
 1-339 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: 533.47  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403   1 LLLTIRRNGHVYEQTYHLGEPQAPLKQIGDSSSgTGTEVRFWPSSTIFSDTLFHYDILAKRLRELSFLNSGVSIRLEDER 80
Cdd:TIGR01059 125 LEVTVFRDGKIYRQEFERGIPVGPLEVVGETKK-TGTTVRFWPDPEIFETTEFDFDILAKRLRELAFLNSGVKISLEDER 203

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  81 D--GREVHFCYEGGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRT 158
Cdd:TIGR01059 204 DgkGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRS 283

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 159 ALTRTLNTYMDKEDYsKKAK*SAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENPG 238
Cdd:TIGR01059 284 ALTRVINSYAKNNKL-LKESKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQ 362

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 239 DAKIVVNKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQGRNRKNQAILPL 318
Cdd:TIGR01059 363 EAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPL 442

                         330       340
                  ....*....|....*....|.
gi 1173202403 319 KGKILNVEKARFDKMISSQEV 339
Cdd:TIGR01059 443 RGKILNVEKARLDKILSNQEI 463
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-339 9.50e-136

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 398.47  E-value: 9.50e-136
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403    1 LLLTIRRNGHVYEQTYH-LGEPQAPLKQIGDSSSgTGTEVRFWPSSTIFS-DTLFHYDILAKRLRELSFLNSGVSIRLED 78
Cdd:smart00433  96 FEVEVARDGKEYKQSFSnNGKPLSEPKIIGDTKK-DGTKVTFKPDLEIFGmTTDDDFELLKRRLRELAFLNKGVKITLND 174

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403   79 ERDGREVHFCYEGGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRT 158
Cdd:smart00433 175 ERSDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVNNIATTEGGTHENGFKD 254

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  159 ALTRTLNTYMDKedySKKAK*SAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENPG 238
Cdd:smart00433 255 ALTRVINEYAKK---KKKLKEKNIKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIVSECLLSFLEENPV 331

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  239 DAKIVVNKIIDAARAREAARKARELTRRKgALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQGRNRKNQAILPL 318
Cdd:smart00433 332 EASKIVEKVLLAAKARAAAKKARELTRKK-KLSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAKSGRDRDFQAILPL 410

                          330       340
                   ....*....|....*....|.
gi 1173202403  319 KGKILNVEKARFDKMISSQEV 339
Cdd:smart00433 411 RGKILNVEKASLDKILKNEEI 431
TopoII_Trans_DNA_gyrase cd00822
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ...
 91-249 1.34e-78

TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are heterodimers composed of two subunits. The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and eukaryotes. All type IIA topoisomerases are related to each other at amino acid sequence level, though their oligomeric organization sometimes differs. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. TopoIIA enzymes also catenate/ decatenate duplex rings. E.coli DNA gyrase is a heterodimer composed of two subunits. E. coli DNA gyrase B subunit is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.


Pssm-ID: 238419 [Multi-domain]  Cd Length: 172  Bit Score: 237.84  E-value: 1.34e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  91 GGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRTALTRTLNTYMDK 170
Cdd:cd00822     1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1173202403 171 EDYsKKAK*SAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENPGDAKIVVNKIID 249
Cdd:cd00822    81 NNL-LKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAIL 158
DNA_gyraseB pfam00204
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ...
 92-249 2.35e-65

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: 204.00  E-value: 2.35e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  92 GIKAFVEYLNQNKTPIHPKVFHFTTE--QDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRTALTRTLNTYMD 169
Cdd:pfam00204   1 GLKDFVEELNKDKKPLHKEIIYFEGEspDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 170 KEDYSKKAK*SAAsGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENPGDAKIVVNKIID 249
Cdd:pfam00204  81 KKGLLKKKDEKIT-GEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQ 159
 
Name Accession Description Interval E-value
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-339 0e+00

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 691.07  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403   1 LLLTIRRNGHVYEQTYHLGEPQAPLKQIGDSSsGTGTEVRFWPSSTIFSDTLFHYDILAKRLRELSFLNSGVSIRLEDER 80
Cdd:PRK14939  132 LELTIRRDGKIHEQEFEHGVPVAPLKVVGETD-KTGTEVRFWPSPEIFENTEFDYDILAKRLRELAFLNSGVRIRLKDER 210

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  81 DGREVHFCYEGGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRTAL 160
Cdd:PRK14939  211 DGKEEEFHYEGGIKAFVEYLNRNKTPLHPNIFYFSGEKDGIGVEVALQWNDSYQENVLCFTNNIPQRDGGTHLAGFRAAL 290

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 161 TRTLNTYMDKEDYSKKAK*SAAsGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENPGDA 240
Cdd:PRK14939  291 TRTINNYIEKEGLAKKAKVSLT-GDDAREGLTAVLSVKVPDPKFSSQTKDKLVSSEVRPAVESLVNEKLSEFLEENPNEA 369

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 241 KIVVNKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQGRNRKNQAILPLKG 320
Cdd:PRK14939  370 KIIVGKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKG 449

                         330
                  ....*....|....*....
gi 1173202403 321 KILNVEKARFDKMISSQEV 339
Cdd:PRK14939  450 KILNVEKARFDKMLSSQEI 468
gyrB PRK05644
DNA gyrase subunit B; Validated
 4-339 0e+00

DNA gyrase subunit B; Validated


Pssm-ID: 235542 [Multi-domain]  Cd Length: 638  Bit Score: 533.90  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403   4 TIRRNGHVYEQTYHLGEPQAPLKQIGDSSsGTGTEVRFWPSSTIFSDTLFHYDILAKRLRELSFLNSGVSIRLEDERDG- 82
Cdd:PRK05644  135 EVKRDGKIYYQEYERGVPVTPLEVIGETD-ETGTTVTFKPDPEIFETTEFDYDTLATRLRELAFLNKGLKITLTDEREGe 213

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  83 -REVHFCYEGGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRTALT 161
Cdd:PRK05644  214 eKEETFHYEGGIKEYVEYLNRNKEPLHEEPIYFEGEKDGIEVEVAMQYNDGYSENILSFANNINTHEGGTHEEGFKTALT 293

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 162 RTLNTYMDKEDYSKKAK*SAAsGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENPGDAK 241
Cdd:PRK05644  294 RVINDYARKNKLLKEKDDNLT-GEDVREGLTAVISVKHPEPQFEGQTKTKLGNSEVRGIVDSVVSEALSEFLEENPNVAK 372

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 242 IVVNKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQGRNRKNQAILPLKGK 321
Cdd:PRK05644  373 KIVEKAILAARAREAARKARELTRRKSALESSSLPGKLADCSSKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGK 452

                         330
                  ....*....|....*...
gi 1173202403 322 ILNVEKARFDKMISSQEV 339
Cdd:PRK05644  453 ILNVEKARLDKILKNEEI 470
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
1-339 0e+00

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


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 533.84  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403   1 LLLTIRRNGHVYEQTYHLGEPQAPLKQIGDSSsGTGTEVRFWPSSTIFSDTLFHYDILAKRLRELSFLNSGVSIRLEDER 80
Cdd:COG0187   130 LEVEVKRDGKIYRQRFERGKPVGPLEKIGKTD-RTGTTVRFKPDPEIFETTEFDYETLAERLRELAFLNKGLTITLTDER 208

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  81 DG--REVHFCYEGGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRT 158
Cdd:COG0187   209 EEepKEETFHYEGGIKDFVEYLNEDKEPLHPEVIYFEGEKDGIEVEVALQWNDGYSENIHSFVNNINTPEGGTHETGFRT 288

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 159 ALTRTLNTYMDKEDySKKAK*SAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENPG 238
Cdd:COG0187   289 ALTRVINDYARKNG-LLKEKDKNLTGDDVREGLTAVISVKLPEPQFEGQTKTKLGNSEARGIVESVVSEKLEHYLEENPA 367

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 239 DAKIVVNKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQGRNRKNQAILPL 318
Cdd:COG0187   368 EAKKILEKAILAARAREAARKARELVRRKSALESSGLPGKLADCSSKDPEESELFIVEGDSAGGSAKQGRDREFQAILPL 447

                         330       340
                  ....*....|....*....|.
gi 1173202403 319 KGKILNVEKARFDKMISSQEV 339
Cdd:COG0187   448 RGKILNVEKARLDKILKNEEI 468
gyrB TIGR01059
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ...
 1-339 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: 533.47  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403   1 LLLTIRRNGHVYEQTYHLGEPQAPLKQIGDSSSgTGTEVRFWPSSTIFSDTLFHYDILAKRLRELSFLNSGVSIRLEDER 80
Cdd:TIGR01059 125 LEVTVFRDGKIYRQEFERGIPVGPLEVVGETKK-TGTTVRFWPDPEIFETTEFDFDILAKRLRELAFLNSGVKISLEDER 203

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  81 D--GREVHFCYEGGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRT 158
Cdd:TIGR01059 204 DgkGKKVTFHYEGGIKSFVKYLNRNKEPLHEEIIYIKGEKEGIEVEVALQWNDGYSENILSFVNNINTREGGTHLEGFRS 283

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 159 ALTRTLNTYMDKEDYsKKAK*SAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENPG 238
Cdd:TIGR01059 284 ALTRVINSYAKNNKL-LKESKPNLTGEDIREGLTAVISVKVPDPQFEGQTKTKLGNSEVRSIVESLVYEKLTEFFEENPQ 362

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 239 DAKIVVNKIIDAARAREAARKARELTRRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQGRNRKNQAILPL 318
Cdd:TIGR01059 363 EAKAIVEKAILAAQAREAARKARELTRRKSALDSGGLPGKLADCSSKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPL 442

                         330       340
                  ....*....|....*....|.
gi 1173202403 319 KGKILNVEKARFDKMISSQEV 339
Cdd:TIGR01059 443 RGKILNVEKARLDKILSNQEI 463
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-339 9.50e-136

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 398.47  E-value: 9.50e-136
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403    1 LLLTIRRNGHVYEQTYH-LGEPQAPLKQIGDSSSgTGTEVRFWPSSTIFS-DTLFHYDILAKRLRELSFLNSGVSIRLED 78
Cdd:smart00433  96 FEVEVARDGKEYKQSFSnNGKPLSEPKIIGDTKK-DGTKVTFKPDLEIFGmTTDDDFELLKRRLRELAFLNKGVKITLND 174

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403   79 ERDGREVHFCYEGGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRT 158
Cdd:smart00433 175 ERSDEEKTFLFEGGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAFQYTDGYSENIVSFVNNIATTEGGTHENGFKD 254

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  159 ALTRTLNTYMDKedySKKAK*SAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENPG 238
Cdd:smart00433 255 ALTRVINEYAKK---KKKLKEKNIKGEDVREGLTAFISVKIPEPQFEGQTKEKLGTSEVRFGVEKIVSECLLSFLEENPV 331

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  239 DAKIVVNKIIDAARAREAARKARELTRRKgALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQGRNRKNQAILPL 318
Cdd:smart00433 332 EASKIVEKVLLAAKARAAAKKARELTRKK-KLSSISLPGKLADASSAGPKKCELFLVEGDSAGGSAKSGRDRDFQAILPL 410

                          330       340
                   ....*....|....*....|.
gi 1173202403  319 KGKILNVEKARFDKMISSQEV 339
Cdd:smart00433 411 RGKILNVEKASLDKILKNEEI 431
PRK05559 PRK05559
DNA topoisomerase IV subunit B; Reviewed
 4-339 4.56e-133

DNA topoisomerase IV subunit B; Reviewed


Pssm-ID: 235501 [Multi-domain]  Cd Length: 631  Bit Score: 392.54  E-value: 4.56e-133
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403   4 TIRRNGHVYEQTYHLGEPQAPLKQIGDSSSG-TGTEVRFWPSSTIFSDTLFHYDILAKRLRELSFLNSGVSIRLEDERDG 82
Cdd:PRK05559  135 EVKRDGKVYRQRFEGGDPVGPLEVVGTAGKRkTGTRVRFWPDPKIFDSPKFSPERLKERLRSKAFLLPGLTITLNDERER 214

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  83 REvhFCYEGGIKAFVEYLNQNKTPIHP-KVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRTALT 161
Cdd:PRK05559  215 QT--FHYENGLKDYLAELNEGKETLPEeFVGSFEGEAEGEAVEWALQWTDEGGENIESYVNLIPTPQGGTHENGFREGLL 292

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 162 RTLNTYMDKedYSKKAK*SAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENPGDAK 241
Cdd:PRK05559  293 KAVREFAEK--RNLLPKGKKLEGEDVREGLAAVLSVKIPEPQFEGQTKEKLGSREARRFVSGVVKDAFDLWLNQNPELAE 370

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 242 IVVNKIIDAARAREAARKARelTRRKGALDIAgLPGKLADCQEKDPALSELYIVEGDSAGGSAKQGRNRKNQAILPLKGK 321
Cdd:PRK05559  371 KLAEKAIKAAQARLRAAKKV--KRKKKTSGPA-LPGKLADCTSQDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGK 447

                         330
                  ....*....|....*...
gi 1173202403 322 ILNVEKARFDKMISSQEV 339
Cdd:PRK05559  448 ILNTWEASLDDVLANEEI 465
TopoII_Trans_DNA_gyrase cd00822
TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the ...
 91-249 1.34e-78

TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are heterodimers composed of two subunits. The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and eukaryotes. All type IIA topoisomerases are related to each other at amino acid sequence level, though their oligomeric organization sometimes differs. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. TopoIIA enzymes also catenate/ decatenate duplex rings. E.coli DNA gyrase is a heterodimer composed of two subunits. E. coli DNA gyrase B subunit is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes.


Pssm-ID: 238419 [Multi-domain]  Cd Length: 172  Bit Score: 237.84  E-value: 1.34e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  91 GGIKAFVEYLNQNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRTALTRTLNTYMDK 170
Cdd:cd00822     1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGGTHETGFRAALTRAINDYAKK 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1173202403 171 EDYsKKAK*SAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENPGDAKIVVNKIID 249
Cdd:cd00822    81 NNL-LKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDKLGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAIL 158
DNA_gyraseB pfam00204
DNA gyrase B; This family represents the second domain of DNA gyrase B which has a ribosomal ...
 92-249 2.35e-65

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: 204.00  E-value: 2.35e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  92 GIKAFVEYLNQNKTPIHPKVFHFTTE--QDGIGVEVAMQWNDAYQEGVYCFTNNIPQRDGGTHLVGFRTALTRTLNTYMD 169
Cdd:pfam00204   1 GLKDFVEELNKDKKPLHKEIIYFEGEspDNRIEVEVALQWTDSYSENILSFVNNIATPEGGTHVDGFKSALTRTINEYAK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 170 KEDYSKKAK*SAAsGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENPGDAKIVVNKIID 249
Cdd:pfam00204  81 KKGLLKKKDEKIT-GEDIREGLTAVVSVKIPDPQFEGQTKEKLGNPEVKSAVEKIVSEKLEEFLEENPEIAKKILEKALQ 159
PTZ00109 PTZ00109
DNA gyrase subunit b; Provisional
 7-334 4.02e-62

DNA gyrase subunit b; Provisional


Pssm-ID: 240272 [Multi-domain]  Cd Length: 903  Bit Score: 212.82  E-value: 4.02e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403   7 RNGHVYEQTYHLGEPQAPLKQIGDSSSGTGTEVRFWPS-STIFSDTLFHY--------------DILAKRLRELSFLNSG 71
Cdd:PTZ00109  270 KGGKIYSIELSKGKVTKPLSVFSCPLKKRGTTIHFLPDyKHIFKTHHQHTeteeeegckngfnlDLIKNRIHELSYLNPG 349

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  72 VSIRLEDERDGREVHFC------YEGGIKAFVEYLNQNKTPIHP--KVFHFTTEQDGIGVEVAMQWN-DAYQEGVYCFTN 142
Cdd:PTZ00109  350 LTFYLVDERIANENNFYpyetikHEGGTREFLEELIKDKTPLYKdiNIISIRGVIKNVNVEVSLSWSlESYTALIKSFAN 429

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 143 NIpQRDGGTHLVGFRTALTRTLNTYMDKEDYSKKAK*SAAsGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVE 222
Cdd:PTZ00109  430 NV-STTAGTHIDGFKYAITRCVNGNIKKNGYFKGNFVNIP-GEFIREGMTAIISVKLNGAEFDGQTKTKLGNHLLKTILE 507

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 223 QAMGEKLGEFLLENPGDAKIVVNKIIDAARAREAARKARELTRRKGALDIA-GLPGKLADCQEKDPALSELYIVEGDSAG 301
Cdd:PTZ00109  508 SIVFEQLSEILEFEPNLLLAIYNKSLAAKKAFEEAKAAKDLIRQKNNQYYStILPGKLVDCISDDIERNELFIVEGESAA 587

                         330       340       350
                  ....*....|....*....|....*....|...
gi 1173202403 302 GSAKQGRNRKNQAILPLKGKILNVEKARFDKMI 334
Cdd:PTZ00109  588 GNAKQARNREFQAVLPLKGKILNIEKIKNNKKV 620
parE_Gneg TIGR01055
DNA topoisomerase IV, B subunit, proteobacterial; Operationally, topoisomerase IV is a type II ...
 3-339 9.99e-59

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: 199.76  E-value: 9.99e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403   3 LTIRRNGHVYEQTYHLGEPQAPLKQIGDSSS-GTGTEVRFWPSSTIFSDTLFHYDILAKRLRELSFLNSGVSIRLEDERD 81
Cdd:TIGR01055 127 IKVYRQGKLYSIAFENGAKVTDLISAGTCGKrLTGTSVHFTPDPEIFDSLHFSVSRLYHILRAKAVLCRGVEIEFEDEVN 206

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  82 GREVHFCYEGGIKAFV-EYLNQNKTPIhPKVFHFTTEQDGIGVEVAMQWNDAYQEGV---YCftNNIPQRDGGTHLVGFR 157
Cdd:TIGR01055 207 NTKALWNYPDGLKDYLsEAVNGDNTLP-PKPFSGNFEGDDEAVEWALLWLPEGGELFmesYV--NLIPTPQGGTHVNGLR 283

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 158 TALTRTLNTYMdkEDYSKKAK*SAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENP 237
Cdd:TIGR01055 284 QGLLDALREFC--EMRNNLPRGVKLTAEDIWDRCSYVLSIKMQDPQFAGQTKERLSSRQVAKFVSGVIKDAFDLWLNQNV 361

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 238 GDAKIVVNKIIDAARAREAARKAREltrRKGALDIAGLPGKLADCQEKDPALSELYIVEGDSAGGSAKQGRNRKNQAILP 317
Cdd:TIGR01055 362 QLAEHLAEHAISSAQRRKRAAKKVV---RKKLTSGPALPGKLADCTRQDLEGTELFLVEGDSAGGSAKQARDREYQAILP 438

                         330       340
                  ....*....|....*....|..
gi 1173202403 318 LKGKILNVEKARFDKMISSQEV 339
Cdd:TIGR01055 439 LWGKILNTWEVSLDKVLNSQEI 460
HATPase_GyrB-like cd16928
Histidine kinase-like ATPase domain of the B subunit of DNA gyrase; This family includes ...
 1-87 3.14e-33

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: 121.10  E-value: 3.14e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403   1 LLLTIRRNGHVYEQTYHLGEPQAPLKQIGDSSSgTGTEVRFWPSSTIFSDTLFHYDILAKRLRELSFLNSGVSIRLEDER 80
Cdd:cd16928    95 LEVEVKRDGKIYRQEFSRGGPLTPLEVIGETKK-TGTTVRFWPDPEIFEKTEFDFDTLKRRLRELAFLNKGLKIVLEDER 173


                  ....*..
gi 1173202403  81 DGREVHF 87
Cdd:cd16928   174 TGKEEVF 180
TopoII_MutL_Trans cd00329
MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the ...
 93-212 1.92e-22

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


Pssm-ID: 238202 [Multi-domain]  Cd Length: 107  Bit Score: 90.40  E-value: 1.92e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  93 IKAFVEYLNQNKTpiHPKVFHFTTEQDGIGVEVAMQWND---AYQEGVYCFTNNIPQRDGGTHLVGFRTALTRTLNtymd 169
Cdd:cd00329     1 LKDRLAEILGDKV--ADKLIYVEGESDGFRVEGAISYPDsgrSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALN---- 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1173202403 170 kedyskkak*saasGDDVREGLIAVISVKVPD--PKFS-SQTKDKL 212
Cdd:cd00329    75 --------------GDDVRRYPVAVLSLKIPPslVDVNvHPTKEEV 106
PTZ00108 PTZ00108
DNA topoisomerase 2-like protein; Provisional
 7-339 3.97e-13

DNA topoisomerase 2-like protein; Provisional


Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 70.46  E-value: 3.97e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403    7 RNGHVYEQTY--HLGEPQAPlkQIGDSSSGTG-TEVRFWPSSTIFSDTLF---HYDILAKRLRELSFLNSGVSIRLEDER 80
Cdd:PTZ00108   165 KSGKKFKMTWtdNMSKKSEP--RITSYDGKKDyTKVTFYPDYAKFGMTEFdddMLRLLKKRVYDLAGCFGKLKVYLNGER 242

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403   81 DGrevhfcyeggIKAFVEYLN---QNKTPIHPKVFHFTTEQDGIGVEVAMQWNDAYQEGVyCFTNNIPQRDGGTHLvgfr 157
Cdd:PTZ00108   243 IA----------IKSFKDYVDlylPDGEEGKKPPYPFVYTSVNGRWEVVVSLSDGQFQQV-SFVNSICTTKGGTHV---- 307

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  158 TALTRTLNTYMDKEDYSKKAK*SAASGDDVREGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEKLGEFLLENP 237
Cdd:PTZ00108   308 NYILDQLISKLQEKAKKKKKKGKEIKPNQIKNHLWVFVNCLIVNPSFDSQTKETLTTKPSKFGSTCELSEKLIKYVLKSP 387

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  238 gdakivvnkIIDAARAREAARKARELTRRKGALD---IAGLPgKLADCQEKDPALSE---LYIVEGDSAGGSAKQG---R 308
Cdd:PTZ00108   388 ---------ILENIVEWAQAKLAAELNKKMKAGKksrILGIP-KLDDANDAGGKNSEectLILTEGDSAKALALAGlsvV 457

                          330       340       350
                   ....*....|....*....|....*....|.
gi 1173202403  309 NRKNQAILPLKGKILNVEKARFDKMISSQEV 339
Cdd:PTZ00108   458 GRDYYGVFPLRGKLLNVRDASLKQLMNNKEI 488
PLN03128 PLN03128
DNA topoisomerase 2; Provisional
 37-339 1.63e-09

DNA topoisomerase 2; Provisional


Pssm-ID: 215593 [Multi-domain]  Cd Length: 1135  Bit Score: 59.34  E-value: 1.63e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403   37 TEVRFWPSSTIFSDTLFHYDI---LAKRLRELS-FLNSGVSIRLEDERDGrevhfcyeggIKAFVEYLN-----QNKTPI 107
Cdd:PLN03128   188 TKITFKPDLAKFNMTRLDEDVvalMSKRVYDIAgCLGKKLKVELNGKKLP----------VKSFQDYVGlylgpNSREDP 257

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  108 HPKVFHFTTEQDGIGVEVAmqwNDAYQEgvYCFTNNIPQRDGGTHLvgfrTALTRTLNTYMDKEDYSKKAK*SAASGDDV 187
Cdd:PLN03128   258 LPRIYEKVNDRWEVCVSLS---DGSFQQ--VSFVNSIATIKGGTHV----DYVADQIVKHIQEKVKKKNKNATHVKPFQI 328

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  188 REGLIAVISVKVPDPKFSSQTKDKLVSSEVKTAVEQAMGEklgEFL--LENPGdakiVVNKIIDAARAREAARKARELTR 265
Cdd:PLN03128   329 KNHLWVFVNCLIENPTFDSQTKETLTTRPSSFGSKCELSE---EFLkkVEKCG----VVENILSWAQFKQQKELKKKDGA 401

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  266 RKGALdiAGLPgKLADCQEKDPALSE---LYIVEGDSAGGSAKQGR---NRKNQAILPLKGKILNVEKARFDKMISSQEV 339
Cdd:PLN03128   402 KRQRL--TGIP-KLDDANDAGGKKSKdctLILTEGDSAKALAMSGLsvvGRDHYGVFPLRGKLLNVREASHKQIMKNAEI 478
39 PHA02569
DNA topoisomerase II large subunit; Provisional
 140-339 3.23e-09

DNA topoisomerase II large subunit; Provisional


Pssm-ID: 177398 [Multi-domain]  Cd Length: 602  Bit Score: 58.23  E-value: 3.23e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 140 FTNNIPQRDGGTHLVGFRTALTRTLNTyMDKEDYSKKAK*SAasgddVREGLIAVISVK-VPDPKFSSQTKDKLVSS--E 216
Cdd:PHA02569  264 FVNGLHTKNGGHHVDCVMDDICEELIP-MIKKKHKIEVTKAR-----VKECLTIVLFVRnMSNPRFDSQTKERLTSPfgE 337

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403 217 VKTAVeQAMGEKLGEFLLENPGdakiVVNKIIDAARAREAARKARELTR-RKGALDI-------AGLPGKLADcqekdpa 288
Cdd:PHA02569  338 IRNHI-DLDYKKIAKQILKTEA----IIMPIIEAALARKLAAEKAAETKaAKKAKKAkvakhikANLIGKDAE------- 405

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1173202403 289 lSELYIVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMISSQEV 339
Cdd:PHA02569  406 -TTLFLTEGDSAIGYLIEVRDEELHGGYPLRGKVLNTWGMSYADILKNKEL 455
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 291-335 4.78e-07

Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks.


Pssm-ID: 396354 [Multi-domain]  Cd Length: 93  Bit Score: 47.35  E-value: 4.78e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1173202403 291 ELYIVEGDSAGGSAKQGRNRKNQAILPLKGKILNVEKARFDKMIS 335
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKALK 45
TOPRIM_TopoIIA cd03365
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 292-339 8.85e-06

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: 44.21  E-value: 8.85e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1173202403 292 LYIVEGDSAGGSAKQGRN---RKNQAILPLKGKILNVEKARFDKMISSQEV 339
Cdd:cd03365     3 LILTEGDSAKALAVAGLSvvgRDYYGVFPLRGKLLNVREASHKQIMENAEI 53
PLN03237 PLN03237
DNA topoisomerase 2; Provisional
 37-339 4.45e-05

DNA topoisomerase 2; Provisional


Pssm-ID: 215641 [Multi-domain]  Cd Length: 1465  Bit Score: 45.24  E-value: 4.45e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403   37 TEVRFWPSSTIFSDTLFHYDILA---KRLRELSFlNSGVSIRLEdeRDGREVHfcyeggIKAFVEYLN---QNKTPIHPK 110
Cdd:PLN03237   213 TKVTFKPDLAKFNMTHLEDDVVAlmkKRVVDIAG-CLGKTVKVE--LNGKRIP------VKSFSDYVDlylESANKSRPE 283

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  111 VFHFTTEQDGIGVEVAMQWNDAYQEGVyCFTNNIPQRDGGTHLVGFRTALTRTLNTYMDKEDyskkaK*SAASGDDVREG 190
Cdd:PLN03237   284 NLPRIYEKVNDRWEVCVSLSEGQFQQV-SFVNSIATIKGGTHVDYVTNQIANHVMEAVNKKN-----KNANIKAHNVKNH 357

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1173202403  191 LIAVISVKVPDPKFSSQTKDKLvssevkTAVEQAMGEK--LGEFLLEnpgdaKIVVNKIIDAARAREAARKARELTRRKG 268
Cdd:PLN03237   358 LWVFVNALIDNPAFDSQTKETL------TLRQSSFGSKceLSEDFLK-----KVMKSGIVENLLSWADFKQSKELKKTDG 426

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1173202403  269 A--LDIAGLPgKLADCQE---KDPALSELYIVEGDSAGGSAKQGRN---RKNQAILPLKGKILNVEKARFDKMISSQEV 339
Cdd:PLN03237   427 AktTRVTGIP-KLEDANEaggKNSEKCTLILTEGDSAKALAVAGLSvvgRNYYGVFPLRGKLLNVREASHKQIMNNAEI 504
 
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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