| http://purl.uniprot.org/unirules/MF_01897#construct | http://www.w3.org/ns/shacl#construct | "CONSTRUCT {
_:663815 up:source unirule:MF_01897 .
_:663816 up:source unirule:MF_01897 .
_:663817 up:source unirule:MF_01897 .
_:663818 up:source unirule:MF_01897 .
_:663819 up:source unirule:MF_01897 .
_:663820 up:source unirule:MF_01897 .
_:663821 up:source unirule:MF_01897 .
_:663822 up:source unirule:MF_01897 .
_:663823 up:source unirule:MF_01897 .
_:663824 up:source unirule:MF_01897 .
_:663825 up:source unirule:MF_01897 .
_:663826 up:source unirule:MF_01897 .
_:663827 up:source unirule:MF_01897 .
_:663828 up:source unirule:MF_01897 .
_:663829 up:source unirule:MF_01897 .
_:663830 up:source unirule:MF_01897 .
_:663831 up:source unirule:MF_01897 .
_:663832 up:source unirule:MF_01897 .
_:663833 up:source unirule:MF_01897 .
_:663834 up:source unirule:MF_01897 .
_:663835 up:source unirule:MF_01897 .
_:663836 up:source unirule:MF_01897 .
?this up:annotation ?annotation2 ,
?annotation3 ,
?annotation5 ,
?annotation6 ,
?annotation8 ,
?annotation9 ;
up:classifiedWith GO:0003677 ,
GO:0003918 ,
GO:0005524 ,
GO:0005737 ,
GO:0006261 ,
GO:0006265 ,
keyword:238 ,
keyword:413 ,
keyword:547 ,
keyword:67 ,
keyword:799 ,
keyword:963 ;
up:recommendedName ?name0 .
?name0 up:ecName '5.6.2.2' ;
up:fullName 'DNA gyrase subunit A' ;
rdf:type up:Structured_Name .
?gene1 skos:prefLabel 'gyrA' .
?annotation2 a up:Function_Annotation ;
rdfs:comment '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. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.' .
?annotation3 up:activity ?activity4 ;
rdf:type up:Catalytic_Activity_Annotation .
?activity4 up:enzymeClass .
?annotation5 a up:Subunit_Annotation ;
rdfs:comment 'Heterotetramer, composed of two GyrA and two GyrB chains. In the heterotetramer, GyrA contains the active site tyrosine that forms a transient covalent intermediate with DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis.' .
?annotation6 a up:Subcellular_Location_Annotation .
?annotation6li7 up:cellularComponent .
?annotation8 a up:Annotation ;
rdfs:comment 'Few gyrases are as efficient as E.coli at forming negative supercoils. Not all organisms have 2 type II topoisomerases; in organisms with a single type II topoisomerase this enzyme also has to decatenate newly replicated chromosomes.' .
?annotation9 a up:Similarity_Annotation ;
rdfs:comment 'Belongs to the type II topoisomerase GyrA/ParC subunit family.' .
?pfs10 up:annotation ?annotation11 .
?annotation11 faldo:begin ?pfsb12 ;
faldo:end ?pfse13 ;
rdf:type up:Active_Site_Annotation ;
rdfs:comment "O-(5'-phospho-DNA)-tyrosine intermediate" .
?pfsb12 faldo:position ?thisPositionOn14 ;
rdf:type faldo:ExactPosition .
?pfse13 faldo:position ?thisPositionOn15 ;
rdf:type faldo:ExactPosition .
?pfs16 up:annotation ?annotation17 .
?annotation17 faldo:begin ?pfsb18 ;
faldo:end ?pfse19 ;
rdf:type up:Motif_Annotation ;
rdfs:comment 'GyrA-box' .
?pfsb18 faldo:position ?thisPositionOn20 ;
rdf:type faldo:ExactPosition .
?pfse19 faldo:position ?thisPositionOn21 ;
rdf:type faldo:ExactPosition .
_:663837 a rdf:Statement ;
up:attribution _:663815 ;
rdf:subject ?this ;
rdf:predicate up:recommendedName ;
rdf:object ?name0 .
_:663838 a rdf:Statement ;
up:attribution _:663816 ;
rdf:subject ?gene1 ;
rdf:predicate up:encodedBy ;
rdf:object ?gene1 .
_:663839 a rdf:Statement ;
up:attribution _:663817 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation2 .
_:663840 a rdf:Statement ;
up:attribution _:663818 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation3 .
_:663841 a rdf:Statement ;
up:attribution _:663819 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation5 .
_:663842 a rdf:Statement ;
up:attribution _:663820 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation6 .
_:663843 a rdf:Statement ;
up:attribution _:663821 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation8 .
_:663844 a rdf:Statement ;
up:attribution _:663822 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation9 .
_:663845 a rdf:Statement ;
up:attribution _:663823 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:67 .
_:663846 a rdf:Statement ;
up:attribution _:663824 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:963 .
_:663847 a rdf:Statement ;
up:attribution _:663825 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:238 .
_:663848 a rdf:Statement ;
up:attribution _:663826 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:413 .
_:663849 a rdf:Statement ;
up:attribution _:663827 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:547 .
_:663850 a rdf:Statement ;
up:attribution _:663828 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:799 .
_:663851 a rdf:Statement ;
up:attribution _:663829 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0005524 .
_:663852 a rdf:Statement ;
up:attribution _:663830 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0003677 .
_:663853 a rdf:Statement ;
up:attribution _:663831 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0003918 .
_:663854 a rdf:Statement ;
up:attribution _:663832 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0006265 .
_:663855 a rdf:Statement ;
up:attribution _:663833 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0006261 .
_:663856 a rdf:Statement ;
up:attribution _:663834 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0005737 .
_:663857 a rdf:Statement ;
up:source unirule:MF_01897 ;
rdf:subject ?pfs10 ;
rdf:predicate up:annotation ;
rdf:object ?annotation11 .
_:663858 a rdf:Statement ;
up:attribution _:663835 ;
rdf:subject ?pfs10 ;
rdf:predicate up:annotation ;
rdf:object ?annotation11 .
_:663859 a rdf:Statement ;
up:source unirule:MF_01897 ;
rdf:subject ?pfs16 ;
rdf:predicate up:annotation ;
rdf:object ?annotation17 .
_:663860 a rdf:Statement ;
up:attribution _:663836 ;
rdf:subject ?pfs16 ;
rdf:predicate up:annotation ;
rdf:object ?annotation17 .
}
WHERE {
#baseURI: http://purl.uniprot.org/unirule/MF_01897
#Rule MF_01897 Created by:? on:2011-05-03 Modified by:Catherine Rivoire on:2023-10-10
VALUES ?supertaxon22 {taxon:2 taxon:2157}
?this up:organism ?thisOrganism ;
rdfs:seeAlso signature:MF_01897 .
?thisOrganism rdfs:subClassOf+ ?supertaxon22 .
BIND(URI(CONCAT(STR(?this), '#MF_01897a0')) AS ?name0) .
BIND(URI(CONCAT(STR(?this), '#MF_01897a2')) AS ?annotation2) .
BIND(URI(CONCAT(STR(?this), '#MF_01897a3')) AS ?annotation3) .
BIND(URI(CONCAT(STR(?this), '#MF_01897a5')) AS ?annotation5) .
BIND(URI(CONCAT(STR(?this), '#MF_01897a6')) AS ?annotation6) .
BIND(URI(CONCAT(STR(?this), '#MF_01897a8')) AS ?annotation8) .
BIND(URI(CONCAT(STR(?this), '#MF_01897a9')) AS ?annotation9) .
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch27 faldo:location ?templateMotifSequenceMatchRegionP0AES428 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP0AES430 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP0AES4MF_0189723 .
?templateMotifSequenceMatchRegionP0AES428 faldo:begin ?templateMotifSequenceMatchBeginP0AES429 .
?templateMotifSequenceMatchBeginP0AES429 faldo:position ?templateMotifSequenceMatchBeginPositionP0AES424 ;
faldo:reference isoform:P0AES4-1 .
?templateMotifSequenceProfileAlignmentOperationP0AES430 edam:has_input signature:MF_01897 ;
rdf:type edam:operation_0300 .
?targetMotifMatch31 faldo:location ?targetMotifMatchRegionMatch32 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_0189734 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP0AES4MF_0189725 .
?targetMotifMatchRegionMatch32 faldo:begin ?targetMotifMatchRegionMatchBeginMF_0189733 .
?targetMotifMatchRegionMatchBeginMF_0189733 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_0189726 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_0189734 edam:has_input signature:MF_01897 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP0AES4MF_0189723, 1, (STRLEN(?templateMotifCigarP0AES4MF_0189723) - STRLEN(REPLACE(?templateMotifCigarP0AES4MF_0189723, CONCAT('^(?:-*[^-]){', STR(((122 - ?templateMotifSequenceMatchBeginPositionP0AES424) + 1)), '}'), '')))), '[a-z]', '')) AS ?step135) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP0AES4MF_0189725, 1, (STRLEN(?targetMotifMatchCigarP0AES4MF_0189725) - STRLEN(REPLACE(?targetMotifMatchCigarP0AES4MF_0189725, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step135), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP0AES4MF_0189725, 1, (STRLEN(?targetMotifMatchCigarP0AES4MF_0189725) - STRLEN(REPLACE(?targetMotifMatchCigarP0AES4MF_0189725, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step135), '}'), '')))), '[^-]', ''))) AS ?step236) .
BIND(((?step236 + ?targetMotifMatchRegionMatchBeginPositionMF_0189726) - 1) AS ?thisPositionOn14) .
BIND(?thisPositionOn14 AS ?thisPositionOn15) .
BIND(?this AS ?pfs1t37) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn14))) AS ?pfsb12) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn15))) AS ?pfse13) .
FILTER ((SUBSTR(?thisSequenceValue, ?thisPositionOn14, 1) = 'Y')) .
BIND(URI(CONCAT(STR(?this), '#MF_01897a11')) AS ?annotation11) .
BIND(?this AS ?pfs10) .
}
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch42 faldo:location ?templateMotifSequenceMatchRegionP0AES443 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP0AES445 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP0AES4MF_0189738 .
?templateMotifSequenceMatchRegionP0AES443 faldo:begin ?templateMotifSequenceMatchBeginP0AES444 .
?templateMotifSequenceMatchBeginP0AES444 faldo:position ?templateMotifSequenceMatchBeginPositionP0AES439 ;
faldo:reference isoform:P0AES4-1 .
?templateMotifSequenceProfileAlignmentOperationP0AES445 edam:has_input signature:MF_01897 ;
rdf:type edam:operation_0300 .
?targetMotifMatch46 faldo:location ?targetMotifMatchRegionMatch47 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_0189749 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP0AES4MF_0189740 .
?targetMotifMatchRegionMatch47 faldo:begin ?targetMotifMatchRegionMatchBeginMF_0189748 .
?targetMotifMatchRegionMatchBeginMF_0189748 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_0189741 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_0189749 edam:has_input signature:MF_01897 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP0AES4MF_0189738, 1, (STRLEN(?templateMotifCigarP0AES4MF_0189738) - STRLEN(REPLACE(?templateMotifCigarP0AES4MF_0189738, CONCAT('^(?:-*[^-]){', STR(((560 - ?templateMotifSequenceMatchBeginPositionP0AES439) + 1)), '}'), '')))), '[a-z]', '')) AS ?step150) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP0AES4MF_0189740, 1, (STRLEN(?targetMotifMatchCigarP0AES4MF_0189740) - STRLEN(REPLACE(?targetMotifMatchCigarP0AES4MF_0189740, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step150), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP0AES4MF_0189740, 1, (STRLEN(?targetMotifMatchCigarP0AES4MF_0189740) - STRLEN(REPLACE(?targetMotifMatchCigarP0AES4MF_0189740, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step150), '}'), '')))), '[^-]', ''))) AS ?step251) .
BIND(((?step251 + ?targetMotifMatchRegionMatchBeginPositionMF_0189741) - 1) AS ?thisPositionOn20) .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP0AES4MF_0189738, 1, (STRLEN(?templateMotifCigarP0AES4MF_0189738) - STRLEN(REPLACE(?templateMotifCigarP0AES4MF_0189738, CONCAT('^(?:-*[^-]){', STR(((566 - ?templateMotifSequenceMatchBeginPositionP0AES439) + 1)), '}'), '')))), '[a-z]', '')) AS ?step152) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP0AES4MF_0189740, 1, (STRLEN(?targetMotifMatchCigarP0AES4MF_0189740) - STRLEN(REPLACE(?targetMotifMatchCigarP0AES4MF_0189740, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step152), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP0AES4MF_0189740, 1, (STRLEN(?targetMotifMatchCigarP0AES4MF_0189740) - STRLEN(REPLACE(?targetMotifMatchCigarP0AES4MF_0189740, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step152), '}'), '')))), '[^-]', ''))) AS ?step253) .
BIND(((?step253 + ?targetMotifMatchRegionMatchBeginPositionMF_0189741) - 1) AS ?thisPositionOn21) .
BIND(?this AS ?pfs1t54) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn20))) AS ?pfsb18) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn21))) AS ?pfse19) .
FILTER (REGEX('Q[KNRHGA][RIT][GA][GT][KRVIQH]G', SUBSTR(?thisSequenceValue, ?thisPositionOn20, (?thisPositionOn21 - ?thisPositionOn20)))) .
BIND(URI(CONCAT(STR(?this), '#MF_01897a17')) AS ?annotation17) .
BIND(?this AS ?pfs16) .
}
}
"xsd:string |
