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Conserved domains on  [gi|1139875201|gb|APZ88672|]
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DNA gyrase subunit B, partial [Psychrobacter pocilloporae]

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
 1-217 2.48e-151

DNA gyrase subunit B; Provisional


The actual alignment was detected with superfamily member PRK14939:

Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 441.46  E-value: 2.48e-151
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201   1 EKDPVLSELYIVEGDSAGGSAKQGRSRKTQAILPLKGKILNVERARFDKMLSSAEVGNLITALGCGIGPDEYNPDKVRYH 80
Cdd:PRK14939  413 EKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIGRDEFNPDKLRYH 492

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201  81 KIIIMTDADVDGSHIRTLLLTFFFRQTPELIERGYVYIAQPPLYKVKKGRQELYLKDDEALKAYLLSSTIDSTKLHVsAD 160
Cdd:PRK14939  493 KIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDYLIELALEGATLHL-AD 571

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1139875201 161 APAITGQALESLLNDYNQTQLIKARLQIRFPAVILDALTHTPKLSVDMTYDESAMQD 217
Cdd:PRK14939  572 GPAISGEALEKLVKEYRAVRKIIDRLERRYPRAVLEALIYAPALDLDDLADEAAVAA 628
 
Name Accession Description Interval E-value
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-217 2.48e-151

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 441.46  E-value: 2.48e-151
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201   1 EKDPVLSELYIVEGDSAGGSAKQGRSRKTQAILPLKGKILNVERARFDKMLSSAEVGNLITALGCGIGPDEYNPDKVRYH 80
Cdd:PRK14939  413 EKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIGRDEFNPDKLRYH 492

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201  81 KIIIMTDADVDGSHIRTLLLTFFFRQTPELIERGYVYIAQPPLYKVKKGRQELYLKDDEALKAYLLSSTIDSTKLHVsAD 160
Cdd:PRK14939  493 KIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDYLIELALEGATLHL-AD 571

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1139875201 161 APAITGQALESLLNDYNQTQLIKARLQIRFPAVILDALTHTPKLSVDMTYDESAMQD 217
Cdd:PRK14939  572 GPAISGEALEKLVKEYRAVRKIIDRLERRYPRAVLEALIYAPALDLDDLADEAAVAA 628
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
1-145 3.86e-103

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


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 313.89  E-value: 3.86e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201   1 EKDPVLSELYIVEGDSAGGSAKQGRSRKTQAILPLKGKILNVERARFDKMLSSAEVGNLITALGCGIGpDEYNPDKVRYH 80
Cdd:COG0187   413 SKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIG-DDFDLEKLRYH 491

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1139875201  81 KIIIMTDADVDGSHIRTLLLTFFFRQTPELIERGYVYIAQPPLYKVKKGRQELYLKDDEALKAYL 145
Cdd:COG0187   492 KIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDELL 556
gyrB TIGR01059
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ...
 1-140 3.03e-95

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: 294.26  E-value: 3.03e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201   1 EKDPVLSELYIVEGDSAGGSAKQGRSRKTQAILPLKGKILNVERARFDKMLSSAEVGNLITALGCGIGPDeYNPDKVRYH 80
Cdd:TIGR01059 408 SKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKD-FDLEKLRYH 486

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201  81 KIIIMTDADVDGSHIRTLLLTFFFRQTPELIERGYVYIAQPPLYKVKKGRQELYLKDDEA 140
Cdd:TIGR01059 487 KIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIKDDKE 546
TOPRIM_TopoIIA_GyrB cd03366
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 7-121 7.93e-82

TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. 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. DNA gyrase is more effective at relaxing supercoils than decatentating DNA. DNA gyrase in addition inserts negative supercoils in the presence of ATP. 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: 173786 [Multi-domain]  Cd Length: 114  Bit Score: 242.18  E-value: 7.93e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201   7 SELYIVEGDSAGGSAKQGRSRKTQAILPLKGKILNVERARFDKMLSSAEVGNLITALGCGIGpDEYNPDKVRYHKIIIMT 86
Cdd:cd03366     1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIG-EDFDLEKLRYHKIIIMT 79

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1139875201  87 DADVDGSHIRTLLLTFFFRQTPELIERGYVYIAQP 121
Cdd:cd03366    80 DADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-142 3.51e-79

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 250.94  E-value: 3.51e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201    1 EKDPVLSELYIVEGDSAGGSAKQGRSRKTQAILPLKGKILNVERARFDKMLSSAEVGNLITALGCGIGpDEYNPDKVRYH 80
Cdd:smart00433 376 SAGPKKCELFLVEGDSAGGSAKSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIG-KDFDIEKLRYG 454

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1139875201   81 KIIIMTDADVDGSHIRTLLLTFFFRQTPELIERGYVYIAQPPLYKVKKGRQEL---YLKDDEALK 142
Cdd:smart00433 455 KIIIMTDADVDGSHIKGLLLTFFYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYvysFYSLDEYEK 519
GyrB_insert pfam18053
DNA gyrase B subunit insert domain; This is the insert domain found in DNA gyrase B subunit ...
 155-231 2.51e-18

DNA gyrase B subunit insert domain; This is the insert domain found in DNA gyrase B subunit proteins. Studies indicate that the insert has two functions, acting as a steric buttress to pre-configure the primary DNA-binding site, and serving as a relay that may help coordinate communication between different functional domains.


Pssm-ID: 465629  Cd Length: 167  Bit Score: 80.26  E-value: 2.51e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1139875201 155 LHVSADAPAITGQALESLLNDYNQTQLIKARLQIRFPAVILDALTHTPKLSVDMTYDESAMQDWQKAMQAQLDVFGS 231
Cdd:pfam18053   3 LYPNEGAPPISGEALEELARQYRLAEAIIKRLSRRYDPAVLEALLYLPPLDAEDLDDEAAAEAWAAALEARLNQDGL 79
 
Name Accession Description Interval E-value
gyrB PRK14939
DNA gyrase subunit B; Provisional
 1-217 2.48e-151

DNA gyrase subunit B; Provisional


Pssm-ID: 237860 [Multi-domain]  Cd Length: 756  Bit Score: 441.46  E-value: 2.48e-151
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201   1 EKDPVLSELYIVEGDSAGGSAKQGRSRKTQAILPLKGKILNVERARFDKMLSSAEVGNLITALGCGIGPDEYNPDKVRYH 80
Cdd:PRK14939  413 EKDPALSELYLVEGDSAGGSAKQGRDRKFQAILPLKGKILNVEKARFDKMLSSQEIGTLITALGCGIGRDEFNPDKLRYH 492

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201  81 KIIIMTDADVDGSHIRTLLLTFFFRQTPELIERGYVYIAQPPLYKVKKGRQELYLKDDEALKAYLLSSTIDSTKLHVsAD 160
Cdd:PRK14939  493 KIIIMTDADVDGSHIRTLLLTFFYRQMPELIERGHLYIAQPPLYKVKKGKQEQYLKDDEALDDYLIELALEGATLHL-AD 571

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1139875201 161 APAITGQALESLLNDYNQTQLIKARLQIRFPAVILDALTHTPKLSVDMTYDESAMQD 217
Cdd:PRK14939  572 GPAISGEALEKLVKEYRAVRKIIDRLERRYPRAVLEALIYAPALDLDDLADEAAVAA 628
GyrB COG0187
DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair];
1-145 3.86e-103

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


Pssm-ID: 439957 [Multi-domain]  Cd Length: 635  Bit Score: 313.89  E-value: 3.86e-103
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201   1 EKDPVLSELYIVEGDSAGGSAKQGRSRKTQAILPLKGKILNVERARFDKMLSSAEVGNLITALGCGIGpDEYNPDKVRYH 80
Cdd:COG0187   413 SKDPEESELFIVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIRDLITALGTGIG-DDFDLEKLRYH 491

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1139875201  81 KIIIMTDADVDGSHIRTLLLTFFFRQTPELIERGYVYIAQPPLYKVKKGRQELYLKDDEALKAYL 145
Cdd:COG0187   492 KIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGHVYIAQPPLYRIKKGKKTYYAYSDAELDELL 556
gyrB PRK05644
DNA gyrase subunit B; Validated
 1-145 5.10e-97

DNA gyrase subunit B; Validated


Pssm-ID: 235542 [Multi-domain]  Cd Length: 638  Bit Score: 298.16  E-value: 5.10e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201   1 EKDPVLSELYIVEGDSAGGSAKQGRSRKTQAILPLKGKILNVERARFDKMLSSAEVGNLITALGCGIGpDEYNPDKVRYH 80
Cdd:PRK05644  415 SKDPEESELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIG-DDFDISKLRYH 493

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1139875201  81 KIIIMTDADVDGSHIRTLLLTFFFRQTPELIERGYVYIAQPPLYKVKKGRQElYLKDDEALKAYL 145
Cdd:PRK05644  494 KIIIMTDADVDGAHIRTLLLTFFYRYMRPLIEAGYVYIAQPPLYKIKKGGKE-YAYSDEELDEIL 557
gyrB TIGR01059
DNA gyrase, B subunit; This model describes the common type II DNA topoisomerase (DNA gyrase). ...
 1-140 3.03e-95

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: 294.26  E-value: 3.03e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201   1 EKDPVLSELYIVEGDSAGGSAKQGRSRKTQAILPLKGKILNVERARFDKMLSSAEVGNLITALGCGIGPDeYNPDKVRYH 80
Cdd:TIGR01059 408 SKDPSKSELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILSNQEIGAIITALGCGIGKD-FDLEKLRYH 486

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201  81 KIIIMTDADVDGSHIRTLLLTFFFRQTPELIERGYVYIAQPPLYKVKKGRQELYLKDDEA 140
Cdd:TIGR01059 487 KIIIMTDADVDGSHIRTLLLTFFYRYMRPLIENGYVYIAQPPLYKVKKGKKERYIKDDKE 546
TOPRIM_TopoIIA_GyrB cd03366
TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 7-121 7.93e-82

TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. 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. DNA gyrase is more effective at relaxing supercoils than decatentating DNA. DNA gyrase in addition inserts negative supercoils in the presence of ATP. 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: 173786 [Multi-domain]  Cd Length: 114  Bit Score: 242.18  E-value: 7.93e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201   7 SELYIVEGDSAGGSAKQGRSRKTQAILPLKGKILNVERARFDKMLSSAEVGNLITALGCGIGpDEYNPDKVRYHKIIIMT 86
Cdd:cd03366     1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTGIG-EDFDLEKLRYHKIIIMT 79

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1139875201  87 DADVDGSHIRTLLLTFFFRQTPELIERGYVYIAQP 121
Cdd:cd03366    80 DADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
TOP2c smart00433
TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE
 1-142 3.51e-79

TopoisomeraseII; Eukaryotic DNA topoisomerase II, GyrB, ParE


Pssm-ID: 214659 [Multi-domain]  Cd Length: 594  Bit Score: 250.94  E-value: 3.51e-79
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201    1 EKDPVLSELYIVEGDSAGGSAKQGRSRKTQAILPLKGKILNVERARFDKMLSSAEVGNLITALGCGIGpDEYNPDKVRYH 80
Cdd:smart00433 376 SAGPKKCELFLVEGDSAGGSAKSGRDRDFQAILPLRGKILNVEKASLDKILKNEEIQALITALGLGIG-KDFDIEKLRYG 454

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1139875201   81 KIIIMTDADVDGSHIRTLLLTFFFRQTPELIERGYVYIAQPPLYKVKKGRQEL---YLKDDEALK 142
Cdd:smart00433 455 KIIIMTDADVDGSHIKGLLLTFFYRYMPPLIEAGFVYIAIPPLYKVTKGKKKYvysFYSLDEYEK 519
PRK05559 PRK05559
DNA topoisomerase IV subunit B; Reviewed
 2-145 1.08e-78

DNA topoisomerase IV subunit B; Reviewed


Pssm-ID: 235501 [Multi-domain]  Cd Length: 631  Bit Score: 250.40  E-value: 1.08e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201   2 KDPVLSELYIVEGDSAGGSAKQGRSRKTQAILPLKGKILNVERARFDKMLSSAEVGNLITALGCGIGpDEYNPDKVRYHK 81
Cdd:PRK05559  411 QDPERTELFLVEGDSAGGSAKQARDREFQAILPLRGKILNTWEASLDDVLANEEIHDIIVAIGIGPG-DSFDLEDLRYGK 489

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1139875201  82 IIIMTDADVDGSHIRTLLLTFFFRQTPELIERGYVYIAQPPLYKVKKGRQELYLKDDEALKAYL 145
Cdd:PRK05559  490 IIIMTDADVDGAHIATLLLTFFYRHFPPLVEAGHVYIALPPLYRVDKGKKKIYALDEEEKEELL 553
TOPRIM_TopoIIA_like cd01030
TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain ...
 7-121 6.14e-73

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: 219.68  E-value: 6.14e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201   7 SELYIVEGDSAGGSAKQGRSRKTQAILPLKGKILNVERARFDKMLSSAEVGNLITALGCGIGPDEYNPDKVRYHKIIIMT 86
Cdd:cd01030     1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLGIGKDDFDLDKLRYGKIIIMT 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1139875201  87 DADVDGSHIRTLLLTFFFRQTPELIERGYVYIAQP 121
Cdd:cd01030    81 DADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
PTZ00109 PTZ00109
DNA gyrase subunit b; Provisional
 6-147 7.99e-44

DNA gyrase subunit b; Provisional


Pssm-ID: 240272 [Multi-domain]  Cd Length: 903  Bit Score: 159.28  E-value: 7.99e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201   6 LSELYIVEGDSAGGSAKQGRSRKTQAILPLKGKILNVERARFD-KMLSSAEVGNLITALGCGIGPDEYNPD--------- 75
Cdd:PTZ00109  575 RNELFIVEGESAAGNAKQARNREFQAVLPLKGKILNIEKIKNNkKVFENSEIKLLITSIGLSVNPVTWRQYdlshgtkas 654

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201  76 ----------------------KVRYHKIIIMTDADVDGSHIRTLLLTFFFRQTPELIERGYVYIAQPPLYKVKKGRQEL 133
Cdd:PTZ00109  655 kdesvqnnnstltkkknslfdtPLRYGKIILLTDADVDGEHLRILLLTLLYRFCPSLYEHGRVYVACPPLYRITNNRMKQ 734

                         170
                  ....*....|....
gi 1139875201 134 YLKDDEALKAYLLS 147
Cdd:PTZ00109  735 FNVSTKNSKKYIYT 748
TOPRIM_TopoIIA cd03365
TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the ...
 9-113 2.83e-26

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: 100.07  E-value: 2.83e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201   9 LYIVEGDSAGGSAKQGRS---RKTQAILPLKGKILNVERARFDKMLSSAEVGNLITALGCGIGPDEY-NPDKVRYHKIII 84
Cdd:cd03365     3 LILTEGDSAKALAVAGLSvvgRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGLQHGKSDYeSTKSLRYGRLMI 82

                          90       100
                  ....*....|....*....|....*....
gi 1139875201  85 MTDADVDGSHIRTLLLTFFFRQTPELIER 113
Cdd:cd03365    83 MTDQDHDGSHIKGLLINFIHSFWPSLLKI 111
PTZ00108 PTZ00108
DNA topoisomerase 2-like protein; Provisional
 9-133 1.91e-23

DNA topoisomerase 2-like protein; Provisional


Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 100.12  E-value: 1.91e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201    9 LYIVEGDSAGGSAKQGRS---RKTQAILPLKGKILNVERARFDKMLSSAEVGNLITALGCGIGPDEYNPDKVRYHKIIIM 85
Cdd:PTZ00108   438 LILTEGDSAKALALAGLSvvgRDYYGVFPLRGKLLNVRDASLKQLMNNKEIQNLFKILGLDIGKKYEDPKGLRYGSLMIM 517

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|
gi 1139875201   86 TDADVDGSHIRTLLLTFFFRQTPELIE-RGYVYIAQPPLYKV-KKGRQEL 133
Cdd:PTZ00108   518 TDQDHDGSHIKGLLINMIHHFWPSLLKnPGFLKEFITPIVKAtKKGNQVI 567
39 PHA02569
DNA topoisomerase II large subunit; Provisional
 9-132 3.70e-20

DNA topoisomerase II large subunit; Provisional


Pssm-ID: 177398 [Multi-domain]  Cd Length: 602  Bit Score: 90.20  E-value: 3.70e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201   9 LYIVEGDSAGGSAKQGRSRKTQAILPLKGKILNVERARFDKMLSSAEVGNLITALGCGIGPDEYNPdkvRYHKIIIMTDA 88
Cdd:PHA02569  408 LFLTEGDSAIGYLIEVRDEELHGGYPLRGKVLNTWGMSYADILKNKELFDICAITGLVLGEKAENM---NYKNIAIMTDA 484

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1139875201  89 DVDG-SHIRTLLLTFFFRQtPELIERGYVYIAQPPLYKVKKGRQE 132
Cdd:PHA02569  485 DVDGkGSIYPLLLAFFSRW-PELFEQGRIRFVKTPVIIAQVGKET 528
PLN03128 PLN03128
DNA topoisomerase 2; Provisional
 9-131 2.22e-18

DNA topoisomerase 2; Provisional


Pssm-ID: 215593 [Multi-domain]  Cd Length: 1135  Bit Score: 85.15  E-value: 2.22e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201    9 LYIVEGDSAGGSAKQGRS---RKTQAILPLKGKILNVERARFDKMLSSAEVGNLITALGCGIGP--DEYNPDKVRYHKII 83
Cdd:PLN03128   428 LILTEGDSAKALAMSGLSvvgRDHYGVFPLRGKLLNVREASHKQIMKNAEITNIKQILGLQFGKtyDEENTKSLRYGHLM 507

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 1139875201   84 IMTDADVDGSHIRTLLLTFFFRQTPELIER-GYVYIAQPPLYKVKKGRQ 131
Cdd:PLN03128   508 IMTDQDHDGSHIKGLIINFFHSFWPSLLKIpGFLVEFITPIVKATKGGK 556
GyrB_insert pfam18053
DNA gyrase B subunit insert domain; This is the insert domain found in DNA gyrase B subunit ...
 155-231 2.51e-18

DNA gyrase B subunit insert domain; This is the insert domain found in DNA gyrase B subunit proteins. Studies indicate that the insert has two functions, acting as a steric buttress to pre-configure the primary DNA-binding site, and serving as a relay that may help coordinate communication between different functional domains.


Pssm-ID: 465629  Cd Length: 167  Bit Score: 80.26  E-value: 2.51e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1139875201 155 LHVSADAPAITGQALESLLNDYNQTQLIKARLQIRFPAVILDALTHTPKLSVDMTYDESAMQDWQKAMQAQLDVFGS 231
Cdd:pfam18053   3 LYPNEGAPPISGEALEELARQYRLAEAIIKRLSRRYDPAVLEALLYLPPLDAEDLDDEAAAEAWAAALEARLNQDGL 79
Toprim pfam01751
Toprim domain; This is a conserved region from DNA primase. This corresponds to the Toprim ...
 8-121 4.21e-16

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: 72.00  E-value: 4.21e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201   8 ELYIVEGDSAGGSAKQGRSRKTQAILPLKGKILNVERARFDKMLSSAevgnlitalgcgigpdeyNPDKVRYHKIIIMTD 87
Cdd:pfam01751   1 ELIIVEGPSDAIALEKALGGGFQAVVAVLGHLLSLEKGPKKKALKAL------------------KELALKAKEVILATD 62

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1139875201  88 ADVDGSHIRTLLLTFFfrqtpELIER--GYVYIAQP 121
Cdd:pfam01751  63 PDREGEAIALKLLELK-----ELLENagGRVEFSEL 93
PLN03237 PLN03237
DNA topoisomerase 2; Provisional
 2-112 2.41e-15

DNA topoisomerase 2; Provisional


Pssm-ID: 215641 [Multi-domain]  Cd Length: 1465  Bit Score: 76.44  E-value: 2.41e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201    2 KDPVLSELYIVEGDSAGGSAKQGRS---RKTQAILPLKGKILNVERARFDKMLSSAEVGNLITALGCGIGPDEYNPDKVR 78
Cdd:PLN03237   447 KNSEKCTLILTEGDSAKALAVAGLSvvgRNYYGVFPLRGKLLNVREASHKQIMNNAEIENIKQILGLQHGKQYESVKSLR 526

                           90       100       110
                   ....*....|....*....|....*....|....
gi 1139875201   79 YHKIIIMTDADVDGSHIRTLLLTFFFRQTPELIE 112
Cdd:PLN03237   527 YGHLMIMTDQDHDGSHIKGLLINFIHSFWPSLLK 560
TOPRIM cd00188
Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type ...
 7-111 3.47e-07

Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This 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 nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.


Pssm-ID: 173773 [Multi-domain]  Cd Length: 83  Bit Score: 47.04  E-value: 3.47e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1139875201   7 SELYIVEGDSAGGSAKQGRSRKtQAILPLKGKILNVERARFDKMLSsaevgnlitalgcgigpdeynpdkvRYHKIIIMT 86
Cdd:cd00188     1 KKLIIVEGPSDALALAQAGGYG-GAVVALGGHALNKTRELLKRLLG-------------------------EAKEVIIAT 54

                          90       100
                  ....*....|....*....|....*
gi 1139875201  87 DADVDGSHIRTLLLTFFFRQTPELI 111
Cdd:cd00188    55 DADREGEAIALRLLELLKSLGKKVR 79
 
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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