| http://purl.uniprot.org/unirules/MF_01487#construct | http://www.w3.org/ns/shacl#construct | "CONSTRUCT {
_:539122 up:source unirule:MF_01487 .
_:539123 up:source unirule:MF_01487 .
_:539124 up:source unirule:MF_01487 .
_:539125 up:source unirule:MF_01487 .
_:539126 up:source unirule:MF_01487 .
_:539127 up:source unirule:MF_01487 .
_:539128 up:source unirule:MF_01487 .
_:539129 up:source unirule:MF_01487 .
_:539130 up:source unirule:MF_01487 .
_:539131 up:source unirule:MF_01487 .
_:539132 up:source unirule:MF_01487 .
_:539133 up:source unirule:MF_01487 .
_:539134 up:source unirule:MF_01487 .
_:539135 up:source unirule:MF_01487 .
_:539136 up:source unirule:MF_01487 .
_:539137 up:source unirule:MF_01487 .
_:539138 up:source unirule:MF_01487 .
_:539139 up:source unirule:MF_01487 .
_:539140 up:source unirule:MF_01487 .
_:539141 up:source unirule:MF_01487 .
_:539142 up:source unirule:MF_01487 .
_:539143 up:source unirule:MF_01487 .
_:539144 up:source unirule:MF_01487 .
_:539145 up:source unirule:MF_01487 .
_:539146 up:source unirule:MF_01487 .
_:539147 up:source unirule:MF_01487 .
?this up:alternativeName ?name1 ,
?name2 ,
?name3 ;
up:annotation ?annotation5 ,
?annotation6 ,
?annotation8 ,
?annotation10 ,
?annotation11 ,
?annotation12 ;
up:classifiedWith GO:0000724 ,
GO:0003677 ,
GO:0043139 ,
keyword:227 ,
keyword:234 ,
keyword:238 ,
keyword:269 ,
keyword:347 ,
keyword:378 ,
keyword:413 ,
keyword:540 ;
up:recommendedName ?name0 .
?name0 up:ecName '5.6.2.3' ;
up:fullName 'RecBCD enzyme subunit RecD' ;
rdf:type up:Structured_Name .
?name1 up:fullName "DNA 5'-3' helicase subunit RecD" ;
rdf:type up:Structured_Name .
?name2 up:fullName 'Exonuclease V subunit RecD' ;
up:shortName 'ExoV subunit RecD' ;
rdf:type up:Structured_Name .
?name3 up:fullName 'Helicase/nuclease RecBCD subunit RecD' ;
rdf:type up:Structured_Name .
?gene4 skos:prefLabel 'recD' .
?annotation5 a up:Function_Annotation ;
rdfs:comment "A helicase/nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit has ssDNA-dependent ATPase and 5'-3' helicase activity. When added to pre-assembled RecBC greatly stimulates nuclease activity and augments holoenzyme processivity. Negatively regulates the RecA-loading ability of RecBCD." .
?annotation6 up:activity ?activity7 ;
rdf:type up:Catalytic_Activity_Annotation .
?activity7 up:enzymeClass .
?annotation8 up:activity ?activity9 ;
rdf:type up:Catalytic_Activity_Annotation .
?activity9 up:catalyticActivity ;
up:enzymeClass .
?annotation10 a up:Subunit_Annotation ;
rdfs:comment 'Heterotrimer of RecB, RecC and RecD. All subunits contribute to DNA-binding.' .
?annotation11 a up:Annotation ;
rdfs:comment "In the RecBCD complex, RecB has a slow 3'-5' helicase, an exonuclease activity and loads RecA onto ssDNA, RecD has a fast 5'-3' helicase activity, while RecC stimulates the ATPase and processivity of the RecB helicase and contributes to recognition of the Chi site." .
?annotation12 a up:Similarity_Annotation ;
rdfs:comment 'Belongs to the RecD family.' .
?case13 up:classifiedWith GO:0005524 ,
keyword:547 ,
keyword:67 .
?pfs14 up:annotation ?annotation15 .
?annotation15 faldo:begin ?pfsb16 ;
faldo:end ?pfse17 ;
up:ligand ?ligand18 ;
rdf:type up:Binding_Site_Annotation .
?pfsb16 faldo:position ?thisPositionOn19 ;
rdf:type faldo:ExactPosition .
?pfse17 faldo:position ?thisPositionOn20 ;
rdf:type faldo:ExactPosition .
?ligand18 rdfs:subClassOf chebi:30616 .
_:539148 a rdf:Statement ;
up:attribution _:539122 ;
rdf:subject ?this ;
rdf:predicate up:recommendedName ;
rdf:object ?name0 .
_:539149 a rdf:Statement ;
up:attribution _:539123 ;
rdf:subject ?this ;
rdf:predicate up:alternativeName ;
rdf:object ?name1 .
_:539150 a rdf:Statement ;
up:attribution _:539124 ;
rdf:subject ?this ;
rdf:predicate up:alternativeName ;
rdf:object ?name2 .
_:539151 a rdf:Statement ;
up:attribution _:539125 ;
rdf:subject ?this ;
rdf:predicate up:alternativeName ;
rdf:object ?name3 .
_:539152 a rdf:Statement ;
up:attribution _:539126 ;
rdf:subject ?gene4 ;
rdf:predicate up:encodedBy ;
rdf:object ?gene4 .
_:539153 a rdf:Statement ;
up:attribution _:539127 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation5 .
_:539154 a rdf:Statement ;
up:attribution _:539128 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation6 .
_:539155 a rdf:Statement ;
up:attribution _:539129 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation8 .
_:539156 a rdf:Statement ;
up:attribution _:539130 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation10 .
_:539157 a rdf:Statement ;
up:attribution _:539131 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation11 .
_:539158 a rdf:Statement ;
up:attribution _:539132 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation12 .
_:539159 a rdf:Statement ;
up:attribution _:539133 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:227 .
_:539160 a rdf:Statement ;
up:attribution _:539134 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:234 .
_:539161 a rdf:Statement ;
up:attribution _:539135 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:238 .
_:539162 a rdf:Statement ;
up:attribution _:539136 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:269 .
_:539163 a rdf:Statement ;
up:attribution _:539137 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:347 .
_:539164 a rdf:Statement ;
up:attribution _:539138 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:378 .
_:539165 a rdf:Statement ;
up:attribution _:539139 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:413 .
_:539166 a rdf:Statement ;
up:attribution _:539140 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:540 .
_:539167 a rdf:Statement ;
up:attribution _:539141 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0043139 .
_:539168 a rdf:Statement ;
up:attribution _:539142 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0003677 .
_:539169 a rdf:Statement ;
up:attribution _:539143 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0000724 .
_:539170 a rdf:Statement ;
up:attribution _:539144 ;
rdf:subject ?case13 ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:67 .
_:539171 a rdf:Statement ;
up:attribution _:539145 ;
rdf:subject ?case13 ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:547 .
_:539172 a rdf:Statement ;
up:attribution _:539146 ;
rdf:subject ?case13 ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0005524 .
_:539173 a rdf:Statement ;
up:source unirule:MF_01487 ;
rdf:subject ?pfs14 ;
rdf:predicate up:annotation ;
rdf:object ?annotation15 .
_:539174 a rdf:Statement ;
up:attribution _:539147 ;
rdf:subject ?pfs14 ;
rdf:predicate up:annotation ;
rdf:object ?annotation15 .
}
WHERE {
#baseURI: http://purl.uniprot.org/unirule/MF_01487
#Rule MF_01487 Created by:? on:2013-12-17 Modified by:Elisabeth Coudert on:2025-05-19
VALUES ?supertaxon21 {taxon:201174 taxon:976 taxon:204428 taxon:1090 taxon:68337 taxon:1224 taxon:203691}
?this up:organism ?thisOrganism ;
rdfs:seeAlso signature:MF_01487 .
?thisOrganism rdfs:subClassOf+ ?supertaxon21 .
FILTER (! (EXISTS {
?this rdfs:seeAlso signature:MF_01488 .
})) .
BIND(URI(CONCAT(STR(?this), '#MF_01487a0')) AS ?name0) .
BIND(URI(CONCAT(STR(?this), '#MF_01487a1')) AS ?name1) .
BIND(URI(CONCAT(STR(?this), '#MF_01487a2')) AS ?name2) .
BIND(URI(CONCAT(STR(?this), '#MF_01487a3')) AS ?name3) .
BIND(URI(CONCAT(STR(?this), '#MF_01487a5')) AS ?annotation5) .
BIND(URI(CONCAT(STR(?this), '#MF_01487a6')) AS ?annotation6) .
BIND(URI(CONCAT(STR(?this), '#MF_01487a8')) AS ?annotation8) .
BIND(URI(CONCAT(STR(?this), '#MF_01487a10')) AS ?annotation10) .
BIND(URI(CONCAT(STR(?this), '#MF_01487a11')) AS ?annotation11) .
BIND(URI(CONCAT(STR(?this), '#MF_01487a12')) AS ?annotation12) .
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch26 faldo:location ?templateMotifSequenceMatchRegionP0499327 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP0499329 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP04993MF_0148722 .
?templateMotifSequenceMatchRegionP0499327 faldo:begin ?templateMotifSequenceMatchBeginP0499328 .
?templateMotifSequenceMatchBeginP0499328 faldo:position ?templateMotifSequenceMatchBeginPositionP0499323 ;
faldo:reference isoform:P04993-1 .
?templateMotifSequenceProfileAlignmentOperationP0499329 edam:has_input signature:MF_01487 ;
rdf:type edam:operation_0300 .
?targetMotifMatch30 faldo:location ?targetMotifMatchRegionMatch31 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_0148733 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP04993MF_0148724 .
?targetMotifMatchRegionMatch31 faldo:begin ?targetMotifMatchRegionMatchBeginMF_0148732 .
?targetMotifMatchRegionMatchBeginMF_0148732 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_0148725 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_0148733 edam:has_input signature:MF_01487 ;
rdf:type edam:operation_0300 .
BIND(?this AS ?tagFT_1) .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP04993MF_0148722, 1, (STRLEN(?templateMotifCigarP04993MF_0148722) - STRLEN(REPLACE(?templateMotifCigarP04993MF_0148722, CONCAT('^(?:-*[^-]){', STR(((171 - ?templateMotifSequenceMatchBeginPositionP0499323) + 1)), '}'), '')))), '[a-z]', '')) AS ?step134) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP04993MF_0148724, 1, (STRLEN(?targetMotifMatchCigarP04993MF_0148724) - STRLEN(REPLACE(?targetMotifMatchCigarP04993MF_0148724, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step134), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP04993MF_0148724, 1, (STRLEN(?targetMotifMatchCigarP04993MF_0148724) - STRLEN(REPLACE(?targetMotifMatchCigarP04993MF_0148724, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step134), '}'), '')))), '[^-]', ''))) AS ?step235) .
BIND(((?step235 + ?targetMotifMatchRegionMatchBeginPositionMF_0148725) - 1) AS ?thisPositionOn19) .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP04993MF_0148722, 1, (STRLEN(?templateMotifCigarP04993MF_0148722) - STRLEN(REPLACE(?templateMotifCigarP04993MF_0148722, CONCAT('^(?:-*[^-]){', STR(((178 - ?templateMotifSequenceMatchBeginPositionP0499323) + 1)), '}'), '')))), '[a-z]', '')) AS ?step136) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP04993MF_0148724, 1, (STRLEN(?targetMotifMatchCigarP04993MF_0148724) - STRLEN(REPLACE(?targetMotifMatchCigarP04993MF_0148724, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step136), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP04993MF_0148724, 1, (STRLEN(?targetMotifMatchCigarP04993MF_0148724) - STRLEN(REPLACE(?targetMotifMatchCigarP04993MF_0148724, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step136), '}'), '')))), '[^-]', ''))) AS ?step237) .
BIND(((?step237 + ?targetMotifMatchRegionMatchBeginPositionMF_0148725) - 1) AS ?thisPositionOn20) .
BIND(?this AS ?pfs1t38) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn19))) AS ?pfsb16) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn20))) AS ?pfse17) .
FILTER ((SUBSTR(?thisSequenceValue, ?thisPositionOn19, (?thisPositionOn20 - ?thisPositionOn19)) = 'GGPGTGKT')) .
BIND(URI(CONCAT(STR(?this), '#MF_01487a15')) AS ?annotation15) .
BIND(?this AS ?pfs14) .
}
OPTIONAL {
?this a up:Protein .
BIND(?this AS ?caseWithTag39) .
}
BIND(IF(BOUND(?tagFT_1), ?caseWithTag39, ?UNBOUND_VARIABLE) AS ?case13) .
}
"xsd:string |
