| http://purl.uniprot.org/unirules/MF_04057#construct | http://www.w3.org/ns/shacl#construct | "CONSTRUCT {
_:918020 up:source unirule:MF_04057 .
_:918021 up:source unirule:MF_04057 .
_:918022 up:source unirule:MF_04057 .
_:918023 up:source unirule:MF_04057 .
_:918024 up:source unirule:MF_04057 .
_:918025 up:source unirule:MF_04057 .
_:918026 up:source unirule:MF_04057 .
_:918027 up:source unirule:MF_04057 .
_:918028 up:source unirule:MF_04057 .
_:918029 up:source unirule:MF_04057 .
_:918030 up:source unirule:MF_04057 .
_:918031 up:source unirule:MF_04057 .
_:918032 up:source unirule:MF_04057 .
_:918033 up:source unirule:MF_04057 .
_:918034 up:source unirule:MF_04057 .
_:918035 up:source unirule:MF_04057 .
_:918036 up:source unirule:MF_04057 .
_:918037 up:source unirule:MF_04057 .
_:918038 up:source unirule:MF_04057 .
_:918039 up:source unirule:MF_04057 .
_:918040 up:source unirule:MF_04057 .
_:918041 up:source unirule:MF_04057 .
_:918042 up:source unirule:MF_04057 .
_:918043 up:source unirule:MF_04057 .
_:918044 up:source unirule:MF_04057 .
_:918045 up:source unirule:MF_04057 .
_:918046 up:source unirule:MF_04057 .
_:918047 up:source unirule:MF_04057 .
_:918048 up:source unirule:MF_04057 .
_:918049 up:source unirule:MF_04057 .
_:918050 up:source unirule:MF_04057 .
_:918051 up:source unirule:MF_04057 .
_:918052 up:source unirule:MF_04057 .
?this up:alternativeName ?name1 ;
up:annotation ?annotation3 ,
?annotation4 ,
?annotation5 ,
?annotation9 ,
?annotation10 ;
up:classifiedWith GO:0003677 ,
GO:0005524 ,
GO:0006351 ,
GO:0006355 ,
GO:0019073 ,
GO:0019076 ,
GO:0019083 ,
GO:0039708 ,
GO:0044095 ,
GO:0044196 ,
GO:0044423 ,
GO:0098035 ,
keyword:1048 ,
keyword:10 ,
keyword:1188 ,
keyword:231 ,
keyword:238 ,
keyword:547 ,
keyword:597 ,
keyword:67 ,
keyword:804 ,
keyword:805 ,
keyword:946 ;
up:recommendedName ?name0 .
?name0 up:fullName 'Packaging protein 1' ;
rdf:type up:Structured_Name .
?name1 up:fullName 'Packaging protein IVa2' ;
rdf:type up:Structured_Name .
?gene2 skos:prefLabel 'IVa2' .
?annotation3 a up:Function_Annotation ;
rdfs:comment "Component of the packaging machinery which encapsidates the viral DNA into preformed capsids and transcriptional activator of the viral major late promoter (MLP). Binds, along with packaging proteins 2 and 3, to the specific packaging sequence on the left end of viral genomic DNA and displays ATPase activity thereby providing the power stroke of the packaging machinery. The activity of packaging protein IVa2 is stimulated by protein 33K which acts as a terminase. May be the protein that pumps DNA into the capsid powered by ATP hydrolysis. Specifically binds to the 5'-CG-3' nucleotides of the repeats making up the packaging sequence. Component of the DEF-A and DEF-B transcription factors that bind downstream elements of the major late promoter (MLP), and stimulate transcription from the MLP after initiation of viral DNA replication. DEF-A is a heterodimer packaging proteins 1 and 2 and DEF-B is a homodimer of packaging protein 1." .
?annotation4 a up:Subunit_Annotation ;
rdfs:comment 'Homodimer. Part of a genome packaging complex composed of packaging proteins 1, 2 and 3; this complex specifically binds to the packaging sequence on the left end of viral genomic DNA and performs packaging of the viral genome. Interacts with protein 33K.' .
?annotation5 a up:Subcellular_Location_Annotation ;
rdfs:comment 'Located at a unique vertex of the capsid. Present in about 6-8 copies per virion' .
?annotation5li6 up:cellularComponent .
?annotation5li7 up:cellularComponent .
?annotation5li8 up:cellularComponent .
?annotation9 a up:Induction_Annotation ;
rdfs:comment 'Expressed in the intermediate phase of the viral replicative cycle.' .
?annotation10 a up:Similarity_Annotation ;
rdfs:comment 'Belongs to the adenoviridae packaging protein 1 family.' .
?pfs11 up:annotation ?annotation12 .
?annotation12 faldo:begin ?pfsb13 ;
faldo:end ?pfse14 ;
rdf:type up:Region_Annotation ;
rdfs:comment 'DNA-binding' .
?pfsb13 faldo:position ?thisPositionOn15 ;
rdf:type faldo:ExactPosition .
?pfse14 faldo:position ?thisPositionOn16 ;
rdf:type faldo:ExactPosition .
?pfs17 up:annotation ?annotation18 .
?annotation18 faldo:begin ?pfsb19 ;
faldo:end ?pfse20 ;
up:ligand ?ligand21 ;
rdf:type up:Binding_Site_Annotation .
?pfsb19 faldo:position ?thisPositionOn22 ;
rdf:type faldo:ExactPosition .
?pfse20 faldo:position ?thisPositionOn23 ;
rdf:type faldo:ExactPosition .
?ligand21 rdfs:subClassOf chebi:30616 .
_:918053 a rdf:Statement ;
up:attribution _:918020 ;
rdf:subject ?this ;
rdf:predicate up:recommendedName ;
rdf:object ?name0 .
_:918054 a rdf:Statement ;
up:attribution _:918021 ;
rdf:subject ?this ;
rdf:predicate up:alternativeName ;
rdf:object ?name1 .
_:918055 a rdf:Statement ;
up:attribution _:918022 ;
rdf:subject ?gene2 ;
rdf:predicate up:encodedBy ;
rdf:object ?gene2 .
_:918056 a rdf:Statement ;
up:attribution _:918023 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation3 .
_:918057 a rdf:Statement ;
up:attribution _:918024 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation4 .
_:918058 a rdf:Statement ;
up:attribution _:918025 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation5 .
_:918059 a rdf:Statement ;
up:attribution _:918026 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation9 .
_:918060 a rdf:Statement ;
up:attribution _:918027 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation10 .
_:918061 a rdf:Statement ;
up:attribution _:918028 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:10 .
_:918062 a rdf:Statement ;
up:attribution _:918029 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:67 .
_:918063 a rdf:Statement ;
up:attribution _:918030 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:238 .
_:918064 a rdf:Statement ;
up:attribution _:918031 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:1048 .
_:918065 a rdf:Statement ;
up:attribution _:918032 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:547 .
_:918066 a rdf:Statement ;
up:attribution _:918033 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:597 .
_:918067 a rdf:Statement ;
up:attribution _:918034 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:804 .
_:918068 a rdf:Statement ;
up:attribution _:918035 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:805 .
_:918069 a rdf:Statement ;
up:attribution _:918036 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:231 .
_:918070 a rdf:Statement ;
up:attribution _:918037 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:946 .
_:918071 a rdf:Statement ;
up:attribution _:918038 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:1188 .
_:918072 a rdf:Statement ;
up:attribution _:918039 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0044196 .
_:918073 a rdf:Statement ;
up:attribution _:918040 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0044095 .
_:918074 a rdf:Statement ;
up:attribution _:918041 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0044423 .
_:918075 a rdf:Statement ;
up:attribution _:918042 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0005524 .
_:918076 a rdf:Statement ;
up:attribution _:918043 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0003677 .
_:918077 a rdf:Statement ;
up:attribution _:918044 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0039708 .
_:918078 a rdf:Statement ;
up:attribution _:918045 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0006355 .
_:918079 a rdf:Statement ;
up:attribution _:918046 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0006351 .
_:918080 a rdf:Statement ;
up:attribution _:918047 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0019073 .
_:918081 a rdf:Statement ;
up:attribution _:918048 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0098035 .
_:918082 a rdf:Statement ;
up:attribution _:918049 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0019076 .
_:918083 a rdf:Statement ;
up:attribution _:918050 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0019083 .
_:918084 a rdf:Statement ;
up:source unirule:MF_04057 ;
rdf:subject ?pfs11 ;
rdf:predicate up:annotation ;
rdf:object ?annotation12 .
_:918085 a rdf:Statement ;
up:attribution _:918051 ;
rdf:subject ?pfs11 ;
rdf:predicate up:annotation ;
rdf:object ?annotation12 .
_:918086 a rdf:Statement ;
up:source unirule:MF_04057 ;
rdf:subject ?pfs17 ;
rdf:predicate up:annotation ;
rdf:object ?annotation18 .
_:918087 a rdf:Statement ;
up:attribution _:918052 ;
rdf:subject ?pfs17 ;
rdf:predicate up:annotation ;
rdf:object ?annotation18 .
}
WHERE {
#baseURI: http://purl.uniprot.org/unirule/MF_04057
#Rule MF_04057 Created by:? on:2017-03-16 Modified by:Edouard de Castro on:2022-11-19
?this up:organism ?thisOrganism ;
rdfs:seeAlso signature:MF_04057 .
?thisOrganism rdfs:subClassOf+ taxon:10508 .
BIND(URI(CONCAT(STR(?this), '#MF_04057a0')) AS ?name0) .
BIND(URI(CONCAT(STR(?this), '#MF_04057a1')) AS ?name1) .
BIND(URI(CONCAT(STR(?this), '#MF_04057a3')) AS ?annotation3) .
BIND(URI(CONCAT(STR(?this), '#MF_04057a4')) AS ?annotation4) .
BIND(URI(CONCAT(STR(?this), '#MF_04057a5')) AS ?annotation5) .
BIND(URI(CONCAT(STR(?this), '#MF_04057a9')) AS ?annotation9) .
BIND(URI(CONCAT(STR(?this), '#MF_04057a10')) AS ?annotation10) .
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch28 faldo:location ?templateMotifSequenceMatchRegionP0327229 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP0327231 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP03272MF_0405724 .
?templateMotifSequenceMatchRegionP0327229 faldo:begin ?templateMotifSequenceMatchBeginP0327230 .
?templateMotifSequenceMatchBeginP0327230 faldo:position ?templateMotifSequenceMatchBeginPositionP0327225 ;
faldo:reference isoform:P03272-1 .
?templateMotifSequenceProfileAlignmentOperationP0327231 edam:has_input signature:MF_04057 ;
rdf:type edam:operation_0300 .
?targetMotifMatch32 faldo:location ?targetMotifMatchRegionMatch33 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_0405735 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP03272MF_0405726 .
?targetMotifMatchRegionMatch33 faldo:begin ?targetMotifMatchRegionMatchBeginMF_0405734 .
?targetMotifMatchRegionMatchBeginMF_0405734 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_0405727 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_0405735 edam:has_input signature:MF_04057 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP03272MF_0405724, 1, (STRLEN(?templateMotifCigarP03272MF_0405724) - STRLEN(REPLACE(?templateMotifCigarP03272MF_0405724, CONCAT('^(?:-*[^-]){', STR(((440 - ?templateMotifSequenceMatchBeginPositionP0327225) + 1)), '}'), '')))), '[a-z]', '')) AS ?step136) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP03272MF_0405726, 1, (STRLEN(?targetMotifMatchCigarP03272MF_0405726) - STRLEN(REPLACE(?targetMotifMatchCigarP03272MF_0405726, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step136), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP03272MF_0405726, 1, (STRLEN(?targetMotifMatchCigarP03272MF_0405726) - STRLEN(REPLACE(?targetMotifMatchCigarP03272MF_0405726, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step136), '}'), '')))), '[^-]', ''))) AS ?step237) .
BIND(((?step237 + ?targetMotifMatchRegionMatchBeginPositionMF_0405727) - 1) AS ?thisPositionOn15) .
BIND(STRLEN(?thisSequenceValue) AS ?thisPositionOn16) .
BIND(?this AS ?pfs1t38) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn15))) AS ?pfsb13) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn16))) AS ?pfse14) .
FILTER ((BOUND(?thisPositionOn15) && BOUND(?thisPositionOn16))) .
BIND(URI(CONCAT(STR(?this), '#MF_04057a12')) AS ?annotation12) .
BIND(?this AS ?pfs11) .
}
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch43 faldo:location ?templateMotifSequenceMatchRegionP0327244 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP0327246 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP03272MF_0405739 .
?templateMotifSequenceMatchRegionP0327244 faldo:begin ?templateMotifSequenceMatchBeginP0327245 .
?templateMotifSequenceMatchBeginP0327245 faldo:position ?templateMotifSequenceMatchBeginPositionP0327240 ;
faldo:reference isoform:P03272-1 .
?templateMotifSequenceProfileAlignmentOperationP0327246 edam:has_input signature:MF_04057 ;
rdf:type edam:operation_0300 .
?targetMotifMatch47 faldo:location ?targetMotifMatchRegionMatch48 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_0405750 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP03272MF_0405741 .
?targetMotifMatchRegionMatch48 faldo:begin ?targetMotifMatchRegionMatchBeginMF_0405749 .
?targetMotifMatchRegionMatchBeginMF_0405749 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_0405742 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_0405750 edam:has_input signature:MF_04057 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP03272MF_0405739, 1, (STRLEN(?templateMotifCigarP03272MF_0405739) - STRLEN(REPLACE(?templateMotifCigarP03272MF_0405739, CONCAT('^(?:-*[^-]){', STR(((171 - ?templateMotifSequenceMatchBeginPositionP0327240) + 1)), '}'), '')))), '[a-z]', '')) AS ?step151) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP03272MF_0405741, 1, (STRLEN(?targetMotifMatchCigarP03272MF_0405741) - STRLEN(REPLACE(?targetMotifMatchCigarP03272MF_0405741, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step151), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP03272MF_0405741, 1, (STRLEN(?targetMotifMatchCigarP03272MF_0405741) - STRLEN(REPLACE(?targetMotifMatchCigarP03272MF_0405741, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step151), '}'), '')))), '[^-]', ''))) AS ?step252) .
BIND(((?step252 + ?targetMotifMatchRegionMatchBeginPositionMF_0405742) - 1) AS ?thisPositionOn22) .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP03272MF_0405739, 1, (STRLEN(?templateMotifCigarP03272MF_0405739) - STRLEN(REPLACE(?templateMotifCigarP03272MF_0405739, CONCAT('^(?:-*[^-]){', STR(((178 - ?templateMotifSequenceMatchBeginPositionP0327240) + 1)), '}'), '')))), '[a-z]', '')) AS ?step153) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP03272MF_0405741, 1, (STRLEN(?targetMotifMatchCigarP03272MF_0405741) - STRLEN(REPLACE(?targetMotifMatchCigarP03272MF_0405741, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step153), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP03272MF_0405741, 1, (STRLEN(?targetMotifMatchCigarP03272MF_0405741) - STRLEN(REPLACE(?targetMotifMatchCigarP03272MF_0405741, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step153), '}'), '')))), '[^-]', ''))) AS ?step254) .
BIND(((?step254 + ?targetMotifMatchRegionMatchBeginPositionMF_0405742) - 1) AS ?thisPositionOn23) .
BIND(?this AS ?pfs1t55) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn22))) AS ?pfsb19) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn23))) AS ?pfse20) .
FILTER (REGEX('GP[ARNDCQEGHILKMFPSTWYVBZJUOX][ARNDCQEGHILKMFPSTWYVBZJUOX][ARNDCQEGHILKMFPSTWYVBZJUOX][ARNDCQEGHILKMFPSTWYVBZJUOX]KS', SUBSTR(?thisSequenceValue, ?thisPositionOn22, (?thisPositionOn23 - ?thisPositionOn22)))) .
BIND(URI(CONCAT(STR(?this), '#MF_04057a18')) AS ?annotation18) .
BIND(?this AS ?pfs17) .
}
}
"xsd:string |
