| http://purl.uniprot.org/unirules/MF_01898#construct | http://www.w3.org/ns/shacl#construct | "CONSTRUCT {
_:664330 up:source unirule:MF_01898 .
_:664331 up:source unirule:MF_01898 .
_:664332 up:source unirule:MF_01898 .
_:664333 up:source unirule:MF_01898 .
_:664334 up:source unirule:MF_01898 .
_:664335 up:source unirule:MF_01898 .
_:664336 up:source unirule:MF_01898 .
_:664337 up:source unirule:MF_01898 .
_:664338 up:source unirule:MF_01898 .
_:664339 up:source unirule:MF_01898 .
_:664340 up:source unirule:MF_01898 .
_:664341 up:source unirule:MF_01898 .
_:664342 up:source unirule:MF_01898 .
_:664343 up:source unirule:MF_01898 .
_:664344 up:source unirule:MF_01898 .
_:664345 up:source unirule:MF_01898 .
_:664346 up:source unirule:MF_01898 .
_:664347 up:source unirule:MF_01898 .
_:664348 up:source unirule:MF_01898 .
_:664349 up:source unirule:MF_01898 .
_:664350 up:source unirule:MF_01898 .
_:664351 up:source unirule:MF_01898 .
_:664352 up:source unirule:MF_01898 .
_:664353 up:source unirule:MF_01898 .
_:664354 up:source unirule:MF_01898 .
_:664355 up:source unirule:MF_01898 .
_:664356 up:source unirule:MF_01898 .
?this up:annotation ?annotation2 ,
?annotation3 ,
?annotation5 ,
?annotation6 ,
?annotation7 ,
?annotation9 ,
?annotation10 ;
up:classifiedWith GO:0003918 ,
GO:0005524 ,
GO:0005737 ,
GO:0006261 ,
GO:0006265 ,
keyword:413 ,
keyword:460 ,
keyword:479 ,
keyword:547 ,
keyword:67 ,
keyword:799 ,
keyword:963 ;
up:recommendedName ?name0 .
?name0 up:ecName '5.6.2.2' ;
up:fullName 'DNA gyrase subunit B' ;
rdf:type up:Structured_Name .
?gene1 skos:prefLabel 'gyrB' .
?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 up:cofactor chebi:18420 ,
chebi:29035 ,
chebi:29108 ;
rdf:type up:Cofactor_Annotation ;
rdfs:comment 'Binds two Mg(2+) per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn(2+) or Ca(2+).' .
?annotation6 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.' .
?annotation7 a up:Subcellular_Location_Annotation .
?annotation7li8 up:cellularComponent .
?annotation9 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.' .
?annotation10 a up:Similarity_Annotation ;
rdfs:comment 'Belongs to the type II topoisomerase GyrB family.' .
?pfs11 up:annotation ?annotation12 .
?annotation12 faldo:begin ?pfsb13 ;
faldo:end ?pfse14 ;
up:ligand ?ligand15 ;
rdf:type up:Binding_Site_Annotation .
?pfsb13 faldo:position ?thisPositionOn16 ;
rdf:type faldo:ExactPosition .
?pfse14 faldo:position ?thisPositionOn17 ;
rdf:type faldo:ExactPosition .
?ligand15 rdfs:subClassOf chebi:18420 .
?pfs18 up:annotation ?annotation19 .
?annotation19 faldo:begin ?pfsb20 ;
faldo:end ?pfse21 ;
up:ligand ?ligand22 ;
rdf:type up:Binding_Site_Annotation .
?pfsb20 faldo:position ?thisPositionOn23 ;
rdf:type faldo:ExactPosition .
?pfse21 faldo:position ?thisPositionOn24 ;
rdf:type faldo:ExactPosition .
?ligand22 rdfs:subClassOf chebi:18420 .
?pfs25 up:annotation ?annotation26 .
?annotation26 faldo:begin ?pfsb27 ;
faldo:end ?pfse28 ;
up:ligand ?ligand29 ;
rdf:type up:Binding_Site_Annotation .
?pfsb27 faldo:position ?thisPositionOn30 ;
rdf:type faldo:ExactPosition .
?pfse28 faldo:position ?thisPositionOn31 ;
rdf:type faldo:ExactPosition .
?ligand29 rdfs:subClassOf chebi:18420 .
?pfs32 up:annotation ?annotation33 .
?annotation33 faldo:begin ?pfsb34 ;
faldo:end ?pfse35 ;
up:ligand ?ligand36 ;
rdf:type up:Binding_Site_Annotation .
?pfsb34 faldo:position ?thisPositionOn37 ;
rdf:type faldo:ExactPosition .
?pfse35 faldo:position ?thisPositionOn38 ;
rdf:type faldo:ExactPosition .
?ligand36 rdfs:subClassOf chebi:18420 .
?pfs39 up:annotation ?annotation40 .
?annotation40 faldo:begin ?pfsb41 ;
faldo:end ?pfse42 ;
rdf:type up:Site_Annotation ;
rdfs:comment 'Interaction with DNA' .
?pfsb41 faldo:position ?thisPositionOn43 ;
rdf:type faldo:ExactPosition .
?pfse42 faldo:position ?thisPositionOn44 ;
rdf:type faldo:ExactPosition .
?pfs45 up:annotation ?annotation46 .
?annotation46 faldo:begin ?pfsb47 ;
faldo:end ?pfse48 ;
rdf:type up:Site_Annotation ;
rdfs:comment 'Interaction with DNA' .
?pfsb47 faldo:position ?thisPositionOn49 ;
rdf:type faldo:ExactPosition .
?pfse48 faldo:position ?thisPositionOn50 ;
rdf:type faldo:ExactPosition .
_:664357 a rdf:Statement ;
up:attribution _:664330 ;
rdf:subject ?this ;
rdf:predicate up:recommendedName ;
rdf:object ?name0 .
_:664358 a rdf:Statement ;
up:attribution _:664331 ;
rdf:subject ?gene1 ;
rdf:predicate up:encodedBy ;
rdf:object ?gene1 .
_:664359 a rdf:Statement ;
up:attribution _:664332 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation2 .
_:664360 a rdf:Statement ;
up:attribution _:664333 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation3 .
_:664361 a rdf:Statement ;
up:attribution _:664334 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation5 .
_:664362 a rdf:Statement ;
up:attribution _:664335 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation6 .
_:664363 a rdf:Statement ;
up:attribution _:664336 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation7 .
_:664364 a rdf:Statement ;
up:attribution _:664337 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation9 .
_:664365 a rdf:Statement ;
up:attribution _:664338 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation10 .
_:664366 a rdf:Statement ;
up:attribution _:664339 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:67 .
_:664367 a rdf:Statement ;
up:attribution _:664340 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:963 .
_:664368 a rdf:Statement ;
up:attribution _:664341 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:413 .
_:664369 a rdf:Statement ;
up:attribution _:664342 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:460 .
_:664370 a rdf:Statement ;
up:attribution _:664343 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:479 .
_:664371 a rdf:Statement ;
up:attribution _:664344 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:547 .
_:664372 a rdf:Statement ;
up:attribution _:664345 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:799 .
_:664373 a rdf:Statement ;
up:attribution _:664346 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0005524 .
_:664374 a rdf:Statement ;
up:attribution _:664347 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0003918 .
_:664375 a rdf:Statement ;
up:attribution _:664348 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0006261 .
_:664376 a rdf:Statement ;
up:attribution _:664349 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0006265 .
_:664377 a rdf:Statement ;
up:attribution _:664350 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0005737 .
_:664378 a rdf:Statement ;
up:source unirule:MF_01898 ;
rdf:subject ?pfs11 ;
rdf:predicate up:annotation ;
rdf:object ?annotation12 .
_:664379 a rdf:Statement ;
up:attribution _:664351 ;
rdf:subject ?pfs11 ;
rdf:predicate up:annotation ;
rdf:object ?annotation12 .
_:664380 a rdf:Statement ;
up:source unirule:MF_01898 ;
rdf:subject ?pfs18 ;
rdf:predicate up:annotation ;
rdf:object ?annotation19 .
_:664381 a rdf:Statement ;
up:attribution _:664352 ;
rdf:subject ?pfs18 ;
rdf:predicate up:annotation ;
rdf:object ?annotation19 .
_:664382 a rdf:Statement ;
up:source unirule:MF_01898 ;
rdf:subject ?pfs25 ;
rdf:predicate up:annotation ;
rdf:object ?annotation26 .
_:664383 a rdf:Statement ;
up:attribution _:664353 ;
rdf:subject ?pfs25 ;
rdf:predicate up:annotation ;
rdf:object ?annotation26 .
_:664384 a rdf:Statement ;
up:source unirule:MF_01898 ;
rdf:subject ?pfs32 ;
rdf:predicate up:annotation ;
rdf:object ?annotation33 .
_:664385 a rdf:Statement ;
up:attribution _:664354 ;
rdf:subject ?pfs32 ;
rdf:predicate up:annotation ;
rdf:object ?annotation33 .
_:664386 a rdf:Statement ;
up:source unirule:MF_01898 ;
rdf:subject ?pfs39 ;
rdf:predicate up:annotation ;
rdf:object ?annotation40 .
_:664387 a rdf:Statement ;
up:attribution _:664355 ;
rdf:subject ?pfs39 ;
rdf:predicate up:annotation ;
rdf:object ?annotation40 .
_:664388 a rdf:Statement ;
up:source unirule:MF_01898 ;
rdf:subject ?pfs45 ;
rdf:predicate up:annotation ;
rdf:object ?annotation46 .
_:664389 a rdf:Statement ;
up:attribution _:664356 ;
rdf:subject ?pfs45 ;
rdf:predicate up:annotation ;
rdf:object ?annotation46 .
}
WHERE {
#baseURI: http://purl.uniprot.org/unirule/MF_01898
#Rule MF_01898 Created by:? on:2011-05-18 Modified by:Andrea Auchincloss on:2023-06-15
VALUES ?supertaxon51 {taxon:2 taxon:2157}
?this up:organism ?thisOrganism ;
rdfs:seeAlso signature:MF_01898 .
?thisOrganism rdfs:subClassOf+ ?supertaxon51 .
BIND(URI(CONCAT(STR(?this), '#MF_01898a0')) AS ?name0) .
BIND(URI(CONCAT(STR(?this), '#MF_01898a2')) AS ?annotation2) .
BIND(URI(CONCAT(STR(?this), '#MF_01898a3')) AS ?annotation3) .
BIND(URI(CONCAT(STR(?this), '#MF_01898a5')) AS ?annotation5) .
BIND(URI(CONCAT(STR(?this), '#MF_01898a6')) AS ?annotation6) .
BIND(URI(CONCAT(STR(?this), '#MF_01898a7')) AS ?annotation7) .
BIND(URI(CONCAT(STR(?this), '#MF_01898a9')) AS ?annotation9) .
BIND(URI(CONCAT(STR(?this), '#MF_01898a10')) AS ?annotation10) .
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch56 faldo:location ?templateMotifSequenceMatchRegionP0AES657 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP0AES659 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP0AES6MF_0189852 .
?templateMotifSequenceMatchRegionP0AES657 faldo:begin ?templateMotifSequenceMatchBeginP0AES658 .
?templateMotifSequenceMatchBeginP0AES658 faldo:position ?templateMotifSequenceMatchBeginPositionP0AES653 ;
faldo:reference isoform:P0AES6-1 .
?templateMotifSequenceProfileAlignmentOperationP0AES659 edam:has_input signature:MF_01898 ;
rdf:type edam:operation_0300 .
?targetMotifMatch60 faldo:location ?targetMotifMatchRegionMatch61 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_0189863 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP0AES6MF_0189854 .
?targetMotifMatchRegionMatch61 faldo:begin ?targetMotifMatchRegionMatchBeginMF_0189862 .
?targetMotifMatchRegionMatchBeginMF_0189862 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_0189855 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_0189863 edam:has_input signature:MF_01898 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP0AES6MF_0189852, 1, (STRLEN(?templateMotifCigarP0AES6MF_0189852) - STRLEN(REPLACE(?templateMotifCigarP0AES6MF_0189852, CONCAT('^(?:-*[^-]){', STR(((424 - ?templateMotifSequenceMatchBeginPositionP0AES653) + 1)), '}'), '')))), '[a-z]', '')) AS ?step164) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP0AES6MF_0189854, 1, (STRLEN(?targetMotifMatchCigarP0AES6MF_0189854) - STRLEN(REPLACE(?targetMotifMatchCigarP0AES6MF_0189854, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step164), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP0AES6MF_0189854, 1, (STRLEN(?targetMotifMatchCigarP0AES6MF_0189854) - STRLEN(REPLACE(?targetMotifMatchCigarP0AES6MF_0189854, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step164), '}'), '')))), '[^-]', ''))) AS ?step265) .
BIND(((?step265 + ?targetMotifMatchRegionMatchBeginPositionMF_0189855) - 1) AS ?thisPositionOn16) .
BIND(?thisPositionOn16 AS ?thisPositionOn17) .
BIND(?this AS ?pfs1t66) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn16))) AS ?pfsb13) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn17))) AS ?pfse14) .
FILTER ((SUBSTR(?thisSequenceValue, ?thisPositionOn16, 1) = 'E')) .
BIND(URI(CONCAT(STR(?this), '#MF_01898a12')) AS ?annotation12) .
BIND(?this AS ?pfs11) .
}
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch71 faldo:location ?templateMotifSequenceMatchRegionP0AES672 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP0AES674 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP0AES6MF_0189867 .
?templateMotifSequenceMatchRegionP0AES672 faldo:begin ?templateMotifSequenceMatchBeginP0AES673 .
?templateMotifSequenceMatchBeginP0AES673 faldo:position ?templateMotifSequenceMatchBeginPositionP0AES668 ;
faldo:reference isoform:P0AES6-1 .
?templateMotifSequenceProfileAlignmentOperationP0AES674 edam:has_input signature:MF_01898 ;
rdf:type edam:operation_0300 .
?targetMotifMatch75 faldo:location ?targetMotifMatchRegionMatch76 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_0189878 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP0AES6MF_0189869 .
?targetMotifMatchRegionMatch76 faldo:begin ?targetMotifMatchRegionMatchBeginMF_0189877 .
?targetMotifMatchRegionMatchBeginMF_0189877 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_0189870 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_0189878 edam:has_input signature:MF_01898 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP0AES6MF_0189867, 1, (STRLEN(?templateMotifCigarP0AES6MF_0189867) - STRLEN(REPLACE(?templateMotifCigarP0AES6MF_0189867, CONCAT('^(?:-*[^-]){', STR(((498 - ?templateMotifSequenceMatchBeginPositionP0AES668) + 1)), '}'), '')))), '[a-z]', '')) AS ?step179) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP0AES6MF_0189869, 1, (STRLEN(?targetMotifMatchCigarP0AES6MF_0189869) - STRLEN(REPLACE(?targetMotifMatchCigarP0AES6MF_0189869, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step179), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP0AES6MF_0189869, 1, (STRLEN(?targetMotifMatchCigarP0AES6MF_0189869) - STRLEN(REPLACE(?targetMotifMatchCigarP0AES6MF_0189869, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step179), '}'), '')))), '[^-]', ''))) AS ?step280) .
BIND(((?step280 + ?targetMotifMatchRegionMatchBeginPositionMF_0189870) - 1) AS ?thisPositionOn23) .
BIND(?thisPositionOn23 AS ?thisPositionOn24) .
BIND(?this AS ?pfs1t81) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn23))) AS ?pfsb20) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn24))) AS ?pfse21) .
FILTER ((SUBSTR(?thisSequenceValue, ?thisPositionOn23, 1) = 'D')) .
BIND(URI(CONCAT(STR(?this), '#MF_01898a19')) AS ?annotation19) .
BIND(?this AS ?pfs18) .
}
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch86 faldo:location ?templateMotifSequenceMatchRegionP0AES687 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP0AES689 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP0AES6MF_0189882 .
?templateMotifSequenceMatchRegionP0AES687 faldo:begin ?templateMotifSequenceMatchBeginP0AES688 .
?templateMotifSequenceMatchBeginP0AES688 faldo:position ?templateMotifSequenceMatchBeginPositionP0AES683 ;
faldo:reference isoform:P0AES6-1 .
?templateMotifSequenceProfileAlignmentOperationP0AES689 edam:has_input signature:MF_01898 ;
rdf:type edam:operation_0300 .
?targetMotifMatch90 faldo:location ?targetMotifMatchRegionMatch91 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_0189893 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP0AES6MF_0189884 .
?targetMotifMatchRegionMatch91 faldo:begin ?targetMotifMatchRegionMatchBeginMF_0189892 .
?targetMotifMatchRegionMatchBeginMF_0189892 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_0189885 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_0189893 edam:has_input signature:MF_01898 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP0AES6MF_0189882, 1, (STRLEN(?templateMotifCigarP0AES6MF_0189882) - STRLEN(REPLACE(?templateMotifCigarP0AES6MF_0189882, CONCAT('^(?:-*[^-]){', STR(((498 - ?templateMotifSequenceMatchBeginPositionP0AES683) + 1)), '}'), '')))), '[a-z]', '')) AS ?step194) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP0AES6MF_0189884, 1, (STRLEN(?targetMotifMatchCigarP0AES6MF_0189884) - STRLEN(REPLACE(?targetMotifMatchCigarP0AES6MF_0189884, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step194), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP0AES6MF_0189884, 1, (STRLEN(?targetMotifMatchCigarP0AES6MF_0189884) - STRLEN(REPLACE(?targetMotifMatchCigarP0AES6MF_0189884, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step194), '}'), '')))), '[^-]', ''))) AS ?step295) .
BIND(((?step295 + ?targetMotifMatchRegionMatchBeginPositionMF_0189885) - 1) AS ?thisPositionOn30) .
BIND(?thisPositionOn30 AS ?thisPositionOn31) .
BIND(?this AS ?pfs1t96) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn30))) AS ?pfsb27) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn31))) AS ?pfse28) .
FILTER ((SUBSTR(?thisSequenceValue, ?thisPositionOn30, 1) = 'D')) .
BIND(URI(CONCAT(STR(?this), '#MF_01898a26')) AS ?annotation26) .
BIND(?this AS ?pfs25) .
}
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch101 faldo:location ?templateMotifSequenceMatchRegionP0AES6102 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP0AES6104 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP0AES6MF_0189897 .
?templateMotifSequenceMatchRegionP0AES6102 faldo:begin ?templateMotifSequenceMatchBeginP0AES6103 .
?templateMotifSequenceMatchBeginP0AES6103 faldo:position ?templateMotifSequenceMatchBeginPositionP0AES698 ;
faldo:reference isoform:P0AES6-1 .
?templateMotifSequenceProfileAlignmentOperationP0AES6104 edam:has_input signature:MF_01898 ;
rdf:type edam:operation_0300 .
?targetMotifMatch105 faldo:location ?targetMotifMatchRegionMatch106 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_01898108 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP0AES6MF_0189899 .
?targetMotifMatchRegionMatch106 faldo:begin ?targetMotifMatchRegionMatchBeginMF_01898107 .
?targetMotifMatchRegionMatchBeginMF_01898107 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_01898100 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_01898108 edam:has_input signature:MF_01898 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP0AES6MF_0189897, 1, (STRLEN(?templateMotifCigarP0AES6MF_0189897) - STRLEN(REPLACE(?templateMotifCigarP0AES6MF_0189897, CONCAT('^(?:-*[^-]){', STR(((500 - ?templateMotifSequenceMatchBeginPositionP0AES698) + 1)), '}'), '')))), '[a-z]', '')) AS ?step1109) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP0AES6MF_0189899, 1, (STRLEN(?targetMotifMatchCigarP0AES6MF_0189899) - STRLEN(REPLACE(?targetMotifMatchCigarP0AES6MF_0189899, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1109), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP0AES6MF_0189899, 1, (STRLEN(?targetMotifMatchCigarP0AES6MF_0189899) - STRLEN(REPLACE(?targetMotifMatchCigarP0AES6MF_0189899, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1109), '}'), '')))), '[^-]', ''))) AS ?step2110) .
BIND(((?step2110 + ?targetMotifMatchRegionMatchBeginPositionMF_01898100) - 1) AS ?thisPositionOn37) .
BIND(?thisPositionOn37 AS ?thisPositionOn38) .
BIND(?this AS ?pfs1t111) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn37))) AS ?pfsb34) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn38))) AS ?pfse35) .
FILTER ((SUBSTR(?thisSequenceValue, ?thisPositionOn37, 1) = 'D')) .
BIND(URI(CONCAT(STR(?this), '#MF_01898a33')) AS ?annotation33) .
BIND(?this AS ?pfs32) .
}
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch116 faldo:location ?templateMotifSequenceMatchRegionP0AES6117 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP0AES6119 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP0AES6MF_01898112 .
?templateMotifSequenceMatchRegionP0AES6117 faldo:begin ?templateMotifSequenceMatchBeginP0AES6118 .
?templateMotifSequenceMatchBeginP0AES6118 faldo:position ?templateMotifSequenceMatchBeginPositionP0AES6113 ;
faldo:reference isoform:P0AES6-1 .
?templateMotifSequenceProfileAlignmentOperationP0AES6119 edam:has_input signature:MF_01898 ;
rdf:type edam:operation_0300 .
?targetMotifMatch120 faldo:location ?targetMotifMatchRegionMatch121 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_01898123 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP0AES6MF_01898114 .
?targetMotifMatchRegionMatch121 faldo:begin ?targetMotifMatchRegionMatchBeginMF_01898122 .
?targetMotifMatchRegionMatchBeginMF_01898122 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_01898115 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_01898123 edam:has_input signature:MF_01898 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP0AES6MF_01898112, 1, (STRLEN(?templateMotifCigarP0AES6MF_01898112) - STRLEN(REPLACE(?templateMotifCigarP0AES6MF_01898112, CONCAT('^(?:-*[^-]){', STR(((449 - ?templateMotifSequenceMatchBeginPositionP0AES6113) + 1)), '}'), '')))), '[a-z]', '')) AS ?step1124) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP0AES6MF_01898114, 1, (STRLEN(?targetMotifMatchCigarP0AES6MF_01898114) - STRLEN(REPLACE(?targetMotifMatchCigarP0AES6MF_01898114, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1124), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP0AES6MF_01898114, 1, (STRLEN(?targetMotifMatchCigarP0AES6MF_01898114) - STRLEN(REPLACE(?targetMotifMatchCigarP0AES6MF_01898114, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1124), '}'), '')))), '[^-]', ''))) AS ?step2125) .
BIND(((?step2125 + ?targetMotifMatchRegionMatchBeginPositionMF_01898115) - 1) AS ?thisPositionOn43) .
BIND(?thisPositionOn43 AS ?thisPositionOn44) .
BIND(?this AS ?pfs1t126) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn43))) AS ?pfsb41) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn44))) AS ?pfse42) .
FILTER ((SUBSTR(?thisSequenceValue, ?thisPositionOn43, 1) = 'K')) .
BIND(URI(CONCAT(STR(?this), '#MF_01898a40')) AS ?annotation40) .
BIND(?this AS ?pfs39) .
}
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch131 faldo:location ?templateMotifSequenceMatchRegionP0AES6132 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP0AES6134 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP0AES6MF_01898127 .
?templateMotifSequenceMatchRegionP0AES6132 faldo:begin ?templateMotifSequenceMatchBeginP0AES6133 .
?templateMotifSequenceMatchBeginP0AES6133 faldo:position ?templateMotifSequenceMatchBeginPositionP0AES6128 ;
faldo:reference isoform:P0AES6-1 .
?templateMotifSequenceProfileAlignmentOperationP0AES6134 edam:has_input signature:MF_01898 ;
rdf:type edam:operation_0300 .
?targetMotifMatch135 faldo:location ?targetMotifMatchRegionMatch136 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_01898138 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP0AES6MF_01898129 .
?targetMotifMatchRegionMatch136 faldo:begin ?targetMotifMatchRegionMatchBeginMF_01898137 .
?targetMotifMatchRegionMatchBeginMF_01898137 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_01898130 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_01898138 edam:has_input signature:MF_01898 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP0AES6MF_01898127, 1, (STRLEN(?templateMotifCigarP0AES6MF_01898127) - STRLEN(REPLACE(?templateMotifCigarP0AES6MF_01898127, CONCAT('^(?:-*[^-]){', STR(((452 - ?templateMotifSequenceMatchBeginPositionP0AES6128) + 1)), '}'), '')))), '[a-z]', '')) AS ?step1139) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP0AES6MF_01898129, 1, (STRLEN(?targetMotifMatchCigarP0AES6MF_01898129) - STRLEN(REPLACE(?targetMotifMatchCigarP0AES6MF_01898129, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1139), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP0AES6MF_01898129, 1, (STRLEN(?targetMotifMatchCigarP0AES6MF_01898129) - STRLEN(REPLACE(?targetMotifMatchCigarP0AES6MF_01898129, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1139), '}'), '')))), '[^-]', ''))) AS ?step2140) .
BIND(((?step2140 + ?targetMotifMatchRegionMatchBeginPositionMF_01898130) - 1) AS ?thisPositionOn49) .
BIND(?thisPositionOn49 AS ?thisPositionOn50) .
BIND(?this AS ?pfs1t141) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn49))) AS ?pfsb47) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn50))) AS ?pfse48) .
FILTER ((SUBSTR(?thisSequenceValue, ?thisPositionOn49, 1) = 'N')) .
BIND(URI(CONCAT(STR(?this), '#MF_01898a46')) AS ?annotation46) .
BIND(?this AS ?pfs45) .
}
}
"xsd:string |
