| http://purl.uniprot.org/unirules/MF_04082#construct | http://www.w3.org/ns/shacl#construct | "CONSTRUCT {
_:937623 up:source unirule:MF_04082 .
_:937624 up:source unirule:MF_04082 .
_:937625 up:source unirule:MF_04082 .
_:937626 up:source unirule:MF_04082 .
_:937627 up:source unirule:MF_04082 .
_:937628 up:source unirule:MF_04082 .
_:937629 up:source unirule:MF_04082 .
_:937630 up:source unirule:MF_04082 .
_:937631 up:source unirule:MF_04082 .
_:937632 up:source unirule:MF_04082 .
_:937633 up:source unirule:MF_04082 .
_:937634 up:source unirule:MF_04082 .
_:937635 up:source unirule:MF_04082 .
_:937636 up:source unirule:MF_04082 .
_:937637 up:source unirule:MF_04082 .
_:937638 up:source unirule:MF_04082 .
_:937639 up:source unirule:MF_04082 .
_:937640 up:source unirule:MF_04082 .
_:937641 up:source unirule:MF_04082 .
_:937642 up:source unirule:MF_04082 .
_:937643 up:source unirule:MF_04082 .
_:937644 up:source unirule:MF_04082 .
_:937645 up:source unirule:MF_04082 .
_:937646 up:source unirule:MF_04082 .
_:937647 up:source unirule:MF_04082 .
_:937648 up:source unirule:MF_04082 .
_:937649 up:source unirule:MF_04082 .
_:937650 up:source unirule:MF_04082 .
_:937651 up:source unirule:MF_04082 .
_:937652 up:source unirule:MF_04082 .
_:937653 up:source unirule:MF_04082 .
_:937654 up:source unirule:MF_04082 .
_:937655 up:source unirule:MF_04082 .
_:937656 up:source unirule:MF_04082 .
_:937657 up:source unirule:MF_04082 .
_:937658 up:source unirule:MF_04082 .
_:937659 up:source unirule:MF_04082 .
_:937660 up:source unirule:MF_04082 .
_:937661 up:source unirule:MF_04082 .
?this up:alternativeName ?name1 ,
?name2 ;
up:annotation ?annotation4 ,
?annotation5 ,
?annotation6 ,
?annotation7 ,
?annotation9 ,
?annotation10 ,
?annotation11 ,
?annotation12 ;
up:classifiedWith GO:0005261 ,
GO:0016020 ,
GO:0019076 ,
GO:0032801 ,
GO:0033644 ,
GO:0039502 ,
GO:0039587 ,
GO:0042609 ,
keyword:1043 ,
keyword:1084 ,
keyword:1090 ,
keyword:1114 ,
keyword:1133 ,
keyword:406 ,
keyword:407 ,
keyword:472 ,
keyword:53 ,
keyword:597 ,
keyword:812 ,
keyword:813 ,
keyword:899 ,
keyword:945 ;
up:recommendedName ?name0 .
?name0 up:fullName 'Protein Vpu' ;
rdf:type up:Structured_Name .
?name1 up:fullName 'U ORF protein' ;
rdf:type up:Structured_Name .
?name2 up:fullName 'Viral protein U' ;
rdf:type up:Structured_Name .
?gene3 skos:prefLabel 'vpu' .
?annotation4 a up:Function_Annotation ;
rdfs:comment 'Enhances virion budding, by targeting human CD4 and Tetherin/BST2 to proteasome degradation. Degradation of CD4 prevents any unwanted premature interactions between viral Env and its host receptor CD4 in the endoplasmic reticulum. Degradation of antiretroviral protein Tetherin/BST2 is important for virion budding, as BST2 tethers new viral particles to the host cell membrane. Mechanistically, Vpu bridges either CD4 or BST2 to BTRC, a substrate recognition subunit of the Skp1/Cullin/F-box protein E3 ubiquitin ligase, induces their ubiquitination and subsequent proteasomal degradation. The alteration of the E3 ligase specificity by Vpu seems to promote the degradation of host IKBKB, leading to NF-kappa-B down-regulation and subsequent apoptosis. Acts as a viroporin that forms an oligomeric ion channel in membranes. Modulates the host DNA repair mechanisms to promote degradation of nuclear viral cDNA in cells that are already productively infected in order to suppress immune sensing and proviral hyper-integration (superinfection). Manipulates PML-NBs and modulates SUMOylation of host BLM protein thereby enhancing its DNA-end processing activity toward viral unintegrated linear DNA. Also inhibits RAD52-mediated homologous repair of viral cDNA, preventing the generation of dead-end circular forms of single copies of the long terminal repeat and permitting sustained nucleolytic attack.' .
?annotation5 a up:Activity_Regulation_Annotation ;
rdfs:comment 'Ion channel activity is inhibited by hexamethylene amiloride in vitro.' .
?annotation6 a up:Subunit_Annotation ;
rdfs:comment 'Homopentamer. Interacts with host CD4 and BRTC; these interactions induce proteasomal degradation of CD4. Interacts with host BST2; this interaction leads to the degradation of host BST2. Interacts with host FBXW11. Interacts with host AP1M1; this interaction plays a role in the mistrafficking and subsequent degradation of host BST2. Interacts with host RANBP2; this interaction allows Vpu to down-regulate host BLM sumoylation.' .
?annotation7 a up:Subcellular_Location_Annotation .
?annotation7li8 up:cellularComponent .
?annotation9 a up:Domain_Annotation ;
rdfs:comment 'The N-terminus and transmembrane domains are required for self-oligomerization and proper virion budding, whereas the cytoplasmic domain is required for CD4 degradation. The cytoplasmic domain is composed of 2 amphipathic alpha helix that form a U-shape.' .
?annotation10 a up:PTM_Annotation ;
rdfs:comment 'Phosphorylated by host CK2. This phosphorylation is necessary for interaction with human BTRC and degradation of CD4.' .
?annotation11 a up:Annotation ;
rdfs:comment 'HIV-1 lineages are divided in three main groups, M (for Major), O (for Outlier), and N (for New, or Non-M, Non-O). The vast majority of strains found worldwide belong to the group M. Group O seems to be endemic to and largely confined to Cameroon and neighboring countries in West Central Africa, where these viruses represent a small minority of HIV-1 strains. The group N is represented by a limited number of isolates from Cameroonian persons. The group M is further subdivided in 9 clades or subtypes (A to D, F to H, J and K).' .
?annotation12 a up:Similarity_Annotation ;
rdfs:comment 'Belongs to the HIV-1 VPU protein family.' .
?pfs13 up:annotation ?annotation14 .
?annotation14 faldo:begin ?pfsb15 ;
faldo:end ?pfse16 ;
rdf:type up:Topological_Domain_Annotation ;
rdfs:comment 'Extracellular' .
?pfsb15 faldo:position ?thisPositionOn17 ;
rdf:type faldo:ExactPosition .
?pfse16 faldo:position ?thisPositionOn18 ;
rdf:type faldo:ExactPosition .
?pfs19 up:annotation ?annotation20 .
?annotation20 faldo:begin ?pfsb21 ;
faldo:end ?pfse22 ;
rdf:type up:Transmembrane_Annotation ;
rdfs:comment 'Helical' .
?pfsb21 faldo:position ?thisPositionOn23 ;
rdf:type faldo:ExactPosition .
?pfse22 faldo:position ?thisPositionOn24 ;
rdf:type faldo:ExactPosition .
?pfs25 up:annotation ?annotation26 .
?annotation26 faldo:begin ?pfsb27 ;
faldo:end ?pfse28 ;
rdf:type up:Topological_Domain_Annotation ;
rdfs:comment 'Cytoplasmic' .
?pfsb27 faldo:position ?thisPositionOn29 ;
rdf:type faldo:ExactPosition .
?pfse28 faldo:position ?thisPositionOn30 ;
rdf:type faldo:ExactPosition .
?pfs31 up:annotation ?annotation32 .
?annotation32 faldo:begin ?pfsb33 ;
faldo:end ?pfse34 ;
rdf:type up:Modified_Residue_Annotation ;
rdfs:comment 'Phosphoserine; by host CK2' .
?pfsb33 faldo:position ?thisPositionOn35 ;
rdf:type faldo:ExactPosition .
?pfse34 faldo:position ?thisPositionOn36 ;
rdf:type faldo:ExactPosition .
?pfs37 up:annotation ?annotation38 .
?annotation38 faldo:begin ?pfsb39 ;
faldo:end ?pfse40 ;
rdf:type up:Modified_Residue_Annotation ;
rdfs:comment 'Phosphoserine; by host CK2' .
?pfsb39 faldo:position ?thisPositionOn41 ;
rdf:type faldo:ExactPosition .
?pfse40 faldo:position ?thisPositionOn42 ;
rdf:type faldo:ExactPosition .
_:937662 a rdf:Statement ;
up:attribution _:937623 ;
rdf:subject ?this ;
rdf:predicate up:recommendedName ;
rdf:object ?name0 .
_:937663 a rdf:Statement ;
up:attribution _:937624 ;
rdf:subject ?this ;
rdf:predicate up:alternativeName ;
rdf:object ?name1 .
_:937664 a rdf:Statement ;
up:attribution _:937625 ;
rdf:subject ?this ;
rdf:predicate up:alternativeName ;
rdf:object ?name2 .
_:937665 a rdf:Statement ;
up:attribution _:937626 ;
rdf:subject ?gene3 ;
rdf:predicate up:encodedBy ;
rdf:object ?gene3 .
_:937666 a rdf:Statement ;
up:attribution _:937627 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation4 .
_:937667 a rdf:Statement ;
up:attribution _:937628 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation5 .
_:937668 a rdf:Statement ;
up:attribution _:937629 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation6 .
_:937669 a rdf:Statement ;
up:attribution _:937630 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation7 .
_:937670 a rdf:Statement ;
up:attribution _:937631 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation9 .
_:937671 a rdf:Statement ;
up:attribution _:937632 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation10 .
_:937672 a rdf:Statement ;
up:attribution _:937633 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation11 .
_:937673 a rdf:Statement ;
up:attribution _:937634 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation12 .
_:937674 a rdf:Statement ;
up:attribution _:937635 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:53 .
_:937675 a rdf:Statement ;
up:attribution _:937636 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:1043 .
_:937676 a rdf:Statement ;
up:attribution _:937637 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:945 .
_:937677 a rdf:Statement ;
up:attribution _:937638 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:1090 .
_:937678 a rdf:Statement ;
up:attribution _:937639 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:1114 .
_:937679 a rdf:Statement ;
up:attribution _:937640 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:1084 .
_:937680 a rdf:Statement ;
up:attribution _:937641 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:407 .
_:937681 a rdf:Statement ;
up:attribution _:937642 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:406 .
_:937682 a rdf:Statement ;
up:attribution _:937643 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:472 .
_:937683 a rdf:Statement ;
up:attribution _:937644 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:597 .
_:937684 a rdf:Statement ;
up:attribution _:937645 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:812 .
_:937685 a rdf:Statement ;
up:attribution _:937646 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:1133 .
_:937686 a rdf:Statement ;
up:attribution _:937647 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:813 .
_:937687 a rdf:Statement ;
up:attribution _:937648 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:899 .
_:937688 a rdf:Statement ;
up:attribution _:937649 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0033644 .
_:937689 a rdf:Statement ;
up:attribution _:937650 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0016020 .
_:937690 a rdf:Statement ;
up:attribution _:937651 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0005261 .
_:937691 a rdf:Statement ;
up:attribution _:937652 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0042609 .
_:937692 a rdf:Statement ;
up:attribution _:937653 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0032801 .
_:937693 a rdf:Statement ;
up:attribution _:937654 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0039587 .
_:937694 a rdf:Statement ;
up:attribution _:937655 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0039502 .
_:937695 a rdf:Statement ;
up:attribution _:937656 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0019076 .
_:937696 a rdf:Statement ;
up:source unirule:MF_04082 ;
rdf:subject ?pfs13 ;
rdf:predicate up:annotation ;
rdf:object ?annotation14 .
_:937697 a rdf:Statement ;
up:attribution _:937657 ;
rdf:subject ?pfs13 ;
rdf:predicate up:annotation ;
rdf:object ?annotation14 .
_:937698 a rdf:Statement ;
up:source unirule:MF_04082 ;
rdf:subject ?pfs19 ;
rdf:predicate up:annotation ;
rdf:object ?annotation20 .
_:937699 a rdf:Statement ;
up:attribution _:937658 ;
rdf:subject ?pfs19 ;
rdf:predicate up:annotation ;
rdf:object ?annotation20 .
_:937700 a rdf:Statement ;
up:source unirule:MF_04082 ;
rdf:subject ?pfs25 ;
rdf:predicate up:annotation ;
rdf:object ?annotation26 .
_:937701 a rdf:Statement ;
up:attribution _:937659 ;
rdf:subject ?pfs25 ;
rdf:predicate up:annotation ;
rdf:object ?annotation26 .
_:937702 a rdf:Statement ;
up:source unirule:MF_04082 ;
rdf:subject ?pfs31 ;
rdf:predicate up:annotation ;
rdf:object ?annotation32 .
_:937703 a rdf:Statement ;
up:attribution _:937660 ;
rdf:subject ?pfs31 ;
rdf:predicate up:annotation ;
rdf:object ?annotation32 .
_:937704 a rdf:Statement ;
up:source unirule:MF_04082 ;
rdf:subject ?pfs37 ;
rdf:predicate up:annotation ;
rdf:object ?annotation38 .
_:937705 a rdf:Statement ;
up:attribution _:937661 ;
rdf:subject ?pfs37 ;
rdf:predicate up:annotation ;
rdf:object ?annotation38 .
}
WHERE {
#baseURI: http://purl.uniprot.org/unirule/MF_04082
#Rule MF_04082 Created by:? on:2017-06-06 Modified by:Catherine Rivoire on:2025-01-14
?this up:organism ?thisOrganism ;
rdfs:seeAlso signature:MF_04082 .
?thisOrganism rdfs:subClassOf+ taxon:11646 .
BIND(URI(CONCAT(STR(?this), '#MF_04082a0')) AS ?name0) .
BIND(URI(CONCAT(STR(?this), '#MF_04082a1')) AS ?name1) .
BIND(URI(CONCAT(STR(?this), '#MF_04082a2')) AS ?name2) .
BIND(URI(CONCAT(STR(?this), '#MF_04082a4')) AS ?annotation4) .
BIND(URI(CONCAT(STR(?this), '#MF_04082a5')) AS ?annotation5) .
BIND(URI(CONCAT(STR(?this), '#MF_04082a6')) AS ?annotation6) .
BIND(URI(CONCAT(STR(?this), '#MF_04082a7')) AS ?annotation7) .
BIND(URI(CONCAT(STR(?this), '#MF_04082a9')) AS ?annotation9) .
BIND(URI(CONCAT(STR(?this), '#MF_04082a10')) AS ?annotation10) .
BIND(URI(CONCAT(STR(?this), '#MF_04082a11')) AS ?annotation11) .
BIND(URI(CONCAT(STR(?this), '#MF_04082a12')) AS ?annotation12) .
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch47 faldo:location ?templateMotifSequenceMatchRegionP0591948 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP0591950 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP05919MF_0408243 .
?templateMotifSequenceMatchRegionP0591948 faldo:begin ?templateMotifSequenceMatchBeginP0591949 .
?templateMotifSequenceMatchBeginP0591949 faldo:position ?templateMotifSequenceMatchBeginPositionP0591944 ;
faldo:reference isoform:P05919-1 .
?templateMotifSequenceProfileAlignmentOperationP0591950 edam:has_input signature:MF_04082 ;
rdf:type edam:operation_0300 .
?targetMotifMatch51 faldo:location ?targetMotifMatchRegionMatch52 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_0408254 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP05919MF_0408245 .
?targetMotifMatchRegionMatch52 faldo:begin ?targetMotifMatchRegionMatchBeginMF_0408253 .
?targetMotifMatchRegionMatchBeginMF_0408253 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_0408246 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_0408254 edam:has_input signature:MF_04082 ;
rdf:type edam:operation_0300 .
BIND(1 AS ?thisPositionOn17) .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP05919MF_0408243, 1, (STRLEN(?templateMotifCigarP05919MF_0408243) - STRLEN(REPLACE(?templateMotifCigarP05919MF_0408243, CONCAT('^(?:-*[^-]){', STR(((6 - ?templateMotifSequenceMatchBeginPositionP0591944) + 1)), '}'), '')))), '[a-z]', '')) AS ?step155) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP05919MF_0408245, 1, (STRLEN(?targetMotifMatchCigarP05919MF_0408245) - STRLEN(REPLACE(?targetMotifMatchCigarP05919MF_0408245, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step155), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP05919MF_0408245, 1, (STRLEN(?targetMotifMatchCigarP05919MF_0408245) - STRLEN(REPLACE(?targetMotifMatchCigarP05919MF_0408245, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step155), '}'), '')))), '[^-]', ''))) AS ?step256) .
BIND(((?step256 + ?targetMotifMatchRegionMatchBeginPositionMF_0408246) - 1) AS ?thisPositionOn18) .
BIND(?this AS ?pfs1t57) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn17))) AS ?pfsb15) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn18))) AS ?pfse16) .
FILTER ((BOUND(?thisPositionOn17) && BOUND(?thisPositionOn18))) .
BIND(URI(CONCAT(STR(?this), '#MF_04082a14')) AS ?annotation14) .
BIND(?this AS ?pfs13) .
}
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch62 faldo:location ?templateMotifSequenceMatchRegionP0591963 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP0591965 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP05919MF_0408258 .
?templateMotifSequenceMatchRegionP0591963 faldo:begin ?templateMotifSequenceMatchBeginP0591964 .
?templateMotifSequenceMatchBeginP0591964 faldo:position ?templateMotifSequenceMatchBeginPositionP0591959 ;
faldo:reference isoform:P05919-1 .
?templateMotifSequenceProfileAlignmentOperationP0591965 edam:has_input signature:MF_04082 ;
rdf:type edam:operation_0300 .
?targetMotifMatch66 faldo:location ?targetMotifMatchRegionMatch67 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_0408269 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP05919MF_0408260 .
?targetMotifMatchRegionMatch67 faldo:begin ?targetMotifMatchRegionMatchBeginMF_0408268 .
?targetMotifMatchRegionMatchBeginMF_0408268 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_0408261 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_0408269 edam:has_input signature:MF_04082 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP05919MF_0408258, 1, (STRLEN(?templateMotifCigarP05919MF_0408258) - STRLEN(REPLACE(?templateMotifCigarP05919MF_0408258, CONCAT('^(?:-*[^-]){', STR(((7 - ?templateMotifSequenceMatchBeginPositionP0591959) + 1)), '}'), '')))), '[a-z]', '')) AS ?step170) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP05919MF_0408260, 1, (STRLEN(?targetMotifMatchCigarP05919MF_0408260) - STRLEN(REPLACE(?targetMotifMatchCigarP05919MF_0408260, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step170), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP05919MF_0408260, 1, (STRLEN(?targetMotifMatchCigarP05919MF_0408260) - STRLEN(REPLACE(?targetMotifMatchCigarP05919MF_0408260, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step170), '}'), '')))), '[^-]', ''))) AS ?step271) .
BIND(((?step271 + ?targetMotifMatchRegionMatchBeginPositionMF_0408261) - 1) AS ?thisPositionOn23) .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP05919MF_0408258, 1, (STRLEN(?templateMotifCigarP05919MF_0408258) - STRLEN(REPLACE(?templateMotifCigarP05919MF_0408258, CONCAT('^(?:-*[^-]){', STR(((27 - ?templateMotifSequenceMatchBeginPositionP0591959) + 1)), '}'), '')))), '[a-z]', '')) AS ?step172) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP05919MF_0408260, 1, (STRLEN(?targetMotifMatchCigarP05919MF_0408260) - STRLEN(REPLACE(?targetMotifMatchCigarP05919MF_0408260, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step172), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP05919MF_0408260, 1, (STRLEN(?targetMotifMatchCigarP05919MF_0408260) - STRLEN(REPLACE(?targetMotifMatchCigarP05919MF_0408260, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step172), '}'), '')))), '[^-]', ''))) AS ?step273) .
BIND(((?step273 + ?targetMotifMatchRegionMatchBeginPositionMF_0408261) - 1) AS ?thisPositionOn24) .
BIND(?this AS ?pfs1t74) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn23))) AS ?pfsb21) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn24))) AS ?pfse22) .
FILTER ((BOUND(?thisPositionOn23) && BOUND(?thisPositionOn24))) .
BIND(URI(CONCAT(STR(?this), '#MF_04082a20')) AS ?annotation20) .
BIND(?this AS ?pfs19) .
}
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch79 faldo:location ?templateMotifSequenceMatchRegionP0591980 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP0591982 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP05919MF_0408275 .
?templateMotifSequenceMatchRegionP0591980 faldo:begin ?templateMotifSequenceMatchBeginP0591981 .
?templateMotifSequenceMatchBeginP0591981 faldo:position ?templateMotifSequenceMatchBeginPositionP0591976 ;
faldo:reference isoform:P05919-1 .
?templateMotifSequenceProfileAlignmentOperationP0591982 edam:has_input signature:MF_04082 ;
rdf:type edam:operation_0300 .
?targetMotifMatch83 faldo:location ?targetMotifMatchRegionMatch84 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_0408286 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP05919MF_0408277 .
?targetMotifMatchRegionMatch84 faldo:begin ?targetMotifMatchRegionMatchBeginMF_0408285 .
?targetMotifMatchRegionMatchBeginMF_0408285 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_0408278 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_0408286 edam:has_input signature:MF_04082 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP05919MF_0408275, 1, (STRLEN(?templateMotifCigarP05919MF_0408275) - STRLEN(REPLACE(?templateMotifCigarP05919MF_0408275, CONCAT('^(?:-*[^-]){', STR(((28 - ?templateMotifSequenceMatchBeginPositionP0591976) + 1)), '}'), '')))), '[a-z]', '')) AS ?step187) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP05919MF_0408277, 1, (STRLEN(?targetMotifMatchCigarP05919MF_0408277) - STRLEN(REPLACE(?targetMotifMatchCigarP05919MF_0408277, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step187), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP05919MF_0408277, 1, (STRLEN(?targetMotifMatchCigarP05919MF_0408277) - STRLEN(REPLACE(?targetMotifMatchCigarP05919MF_0408277, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step187), '}'), '')))), '[^-]', ''))) AS ?step288) .
BIND(((?step288 + ?targetMotifMatchRegionMatchBeginPositionMF_0408278) - 1) AS ?thisPositionOn29) .
BIND(STRLEN(?thisSequenceValue) AS ?thisPositionOn30) .
BIND(?this AS ?pfs1t89) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn29))) AS ?pfsb27) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn30))) AS ?pfse28) .
FILTER ((BOUND(?thisPositionOn29) && BOUND(?thisPositionOn30))) .
BIND(URI(CONCAT(STR(?this), '#MF_04082a26')) AS ?annotation26) .
BIND(?this AS ?pfs25) .
}
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch94 faldo:location ?templateMotifSequenceMatchRegionP0591995 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP0591997 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP05919MF_0408290 .
?templateMotifSequenceMatchRegionP0591995 faldo:begin ?templateMotifSequenceMatchBeginP0591996 .
?templateMotifSequenceMatchBeginP0591996 faldo:position ?templateMotifSequenceMatchBeginPositionP0591991 ;
faldo:reference isoform:P05919-1 .
?templateMotifSequenceProfileAlignmentOperationP0591997 edam:has_input signature:MF_04082 ;
rdf:type edam:operation_0300 .
?targetMotifMatch98 faldo:location ?targetMotifMatchRegionMatch99 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_04082101 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP05919MF_0408292 .
?targetMotifMatchRegionMatch99 faldo:begin ?targetMotifMatchRegionMatchBeginMF_04082100 .
?targetMotifMatchRegionMatchBeginMF_04082100 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_0408293 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_04082101 edam:has_input signature:MF_04082 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP05919MF_0408290, 1, (STRLEN(?templateMotifCigarP05919MF_0408290) - STRLEN(REPLACE(?templateMotifCigarP05919MF_0408290, CONCAT('^(?:-*[^-]){', STR(((52 - ?templateMotifSequenceMatchBeginPositionP0591991) + 1)), '}'), '')))), '[a-z]', '')) AS ?step1102) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP05919MF_0408292, 1, (STRLEN(?targetMotifMatchCigarP05919MF_0408292) - STRLEN(REPLACE(?targetMotifMatchCigarP05919MF_0408292, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1102), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP05919MF_0408292, 1, (STRLEN(?targetMotifMatchCigarP05919MF_0408292) - STRLEN(REPLACE(?targetMotifMatchCigarP05919MF_0408292, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1102), '}'), '')))), '[^-]', ''))) AS ?step2103) .
BIND(((?step2103 + ?targetMotifMatchRegionMatchBeginPositionMF_0408293) - 1) AS ?thisPositionOn35) .
BIND(?thisPositionOn35 AS ?thisPositionOn36) .
BIND(?this AS ?pfs1t104) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn35))) AS ?pfsb33) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn36))) AS ?pfse34) .
FILTER ((SUBSTR(?thisSequenceValue, ?thisPositionOn35, 1) = 'S')) .
BIND(URI(CONCAT(STR(?this), '#MF_04082a32')) AS ?annotation32) .
BIND(?this AS ?pfs31) .
}
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch109 faldo:location ?templateMotifSequenceMatchRegionP05919110 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP05919112 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP05919MF_04082105 .
?templateMotifSequenceMatchRegionP05919110 faldo:begin ?templateMotifSequenceMatchBeginP05919111 .
?templateMotifSequenceMatchBeginP05919111 faldo:position ?templateMotifSequenceMatchBeginPositionP05919106 ;
faldo:reference isoform:P05919-1 .
?templateMotifSequenceProfileAlignmentOperationP05919112 edam:has_input signature:MF_04082 ;
rdf:type edam:operation_0300 .
?targetMotifMatch113 faldo:location ?targetMotifMatchRegionMatch114 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_04082116 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP05919MF_04082107 .
?targetMotifMatchRegionMatch114 faldo:begin ?targetMotifMatchRegionMatchBeginMF_04082115 .
?targetMotifMatchRegionMatchBeginMF_04082115 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_04082108 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_04082116 edam:has_input signature:MF_04082 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP05919MF_04082105, 1, (STRLEN(?templateMotifCigarP05919MF_04082105) - STRLEN(REPLACE(?templateMotifCigarP05919MF_04082105, CONCAT('^(?:-*[^-]){', STR(((56 - ?templateMotifSequenceMatchBeginPositionP05919106) + 1)), '}'), '')))), '[a-z]', '')) AS ?step1117) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP05919MF_04082107, 1, (STRLEN(?targetMotifMatchCigarP05919MF_04082107) - STRLEN(REPLACE(?targetMotifMatchCigarP05919MF_04082107, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1117), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP05919MF_04082107, 1, (STRLEN(?targetMotifMatchCigarP05919MF_04082107) - STRLEN(REPLACE(?targetMotifMatchCigarP05919MF_04082107, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1117), '}'), '')))), '[^-]', ''))) AS ?step2118) .
BIND(((?step2118 + ?targetMotifMatchRegionMatchBeginPositionMF_04082108) - 1) AS ?thisPositionOn41) .
BIND(?thisPositionOn41 AS ?thisPositionOn42) .
BIND(?this AS ?pfs1t119) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn41))) AS ?pfsb39) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn42))) AS ?pfse40) .
FILTER ((SUBSTR(?thisSequenceValue, ?thisPositionOn41, 1) = 'S')) .
BIND(URI(CONCAT(STR(?this), '#MF_04082a38')) AS ?annotation38) .
BIND(?this AS ?pfs37) .
}
}
"xsd:string |
