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cjfields/Data::Dumper output of example InterProTerm

Created July 22, 2010 21:34
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Data::Dumper output of example InterProTerm
$VAR1 = bless( {
'_secondary_ids' => [],
'_dblinks' => {},
'short_name' => undef,
'_ontology' => bless( {
'engine' => bless( {
'_relationship_type_store' => {
'InterPro|IS_A' => bless( {
'_secondary_ids' => [],
'_dblinks' => {},
'_ontology' => $VAR1->{'_ontology'},
'_references' => [],
'name' => 'IS_A',
'_synonyms' => [],
'definition' => undef,
'identifier' => undef,
'comment' => undef,
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::RelationshipType' ),
'InterPro|CONTAINS' => bless( {
'_secondary_ids' => [],
'_dblinks' => {},
'_ontology' => $VAR1->{'_ontology'},
'_references' => [],
'name' => 'CONTAINS',
'_synonyms' => [],
'definition' => undef,
'identifier' => undef,
'comment' => undef,
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::RelationshipType' )
},
'_inverted_relationship_store' => {
'IPR000413' => {
'Family' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'}
},
'IPR001713' => {
'IPR000010' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'}
},
'IPR000536' => {
'IPR000003' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|CONTAINS'}
},
'IPR000001' => {
'Domain' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'}
},
'IPR000003' => {
'Family' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'},
'IPR001723' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'}
},
'IPR003244' => {
'IPR000010' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'}
},
'IPR001363' => {
'IPR000010' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'}
},
'IPR000005' => {
'Domain' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'}
},
'IPR003243' => {
'IPR000010' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'}
},
'IPR003258' => {
'IPR000004' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'}
},
'IPR000010' => {
'Family' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'}
},
'IPR000004' => {
'Domain' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'}
},
'IPR000002' => {
'Domain' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'}
}
},
'_instantiated_terms_store' => {
'IPR000413' => 1,
'IPR000001' => 1,
'PTM' => 1,
'Domain' => 1,
'Family' => 1,
'IPR000003' => 1,
'IPR000005' => 1,
'Repeat' => 1,
'Active_site' => 1,
'IPR000010' => 1,
'Binding_site' => 1,
'IPR000004' => 1,
'IPR000002' => 1,
'Conserved_site' => 1,
'Region' => 1
},
'_relationship_store' => {
'IPR000010' => {
'IPR001713' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'},
'IPR003243' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'},
'IPR003244' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'},
'IPR001363' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'}
},
'IPR000004' => {
'IPR003258' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'}
},
'Family' => {
'IPR000413' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'},
'IPR000010' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'},
'IPR000003' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'}
},
'Domain' => {
'IPR000001' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'},
'IPR000004' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'},
'IPR000002' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'},
'IPR000005' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'}
},
'IPR000003' => {
'IPR000536' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|CONTAINS'}
},
'IPR001723' => {
'IPR000003' => $VAR1->{'_ontology'}{'engine'}{'_relationship_type_store'}{'InterPro|IS_A'}
}
},
'relationship_factory' => bless( {
'interface' => 'Bio::Ontology::RelationshipI',
'type' => 'Bio::Ontology::Relationship',
'_loaded_types' => {
'Bio::Ontology::Relationship' => 1
},
'_root_verbose' => 0
}, 'Bio::Ontology::RelationshipFactory' ),
'_term_store' => {
'IPR000413' => bless( {
'_secondary_ids' => [
undef
],
'_dblinks' => {
'external_doc_list' => [
bless( {
'database' => 'BLOCKS',
'primary_id' => 'IPB000413',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'PDOC',
'primary_id' => 'PDOC00215',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'PROPRO',
'primary_id' => 'integrins_alpha',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' )
],
'class_list' => [
bless( {
'database' => 'GO',
'primary_id' => 'GO:0004895',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'GO',
'primary_id' => 'GO:0007155',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'GO',
'primary_id' => 'GO:0007160',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'GO',
'primary_id' => 'GO:0008305',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' )
],
'member_list' => [
bless( {
'database' => 'PRINTS',
'primary_id' => 'PR01185',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'PREFILE',
'primary_id' => 'PS50107',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'PROSITE',
'primary_id' => 'PS00242',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'PFAM',
'primary_id' => 'PF00357',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'PFAM',
'primary_id' => 'PF01839',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'SMART',
'primary_id' => 'SM00191',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' )
]
},
'short_name' => 'Integrin_alpha',
'_ontology' => $VAR1->{'_ontology'},
'_references' => [
bless( {
'authors' => 'Hynes R.O.',
'location' => 'Cell, 549-554, 48, 1987',
'title' => 'Integrins: a family of cell surface receptors.'
}, 'Bio::Annotation::Reference' ),
bless( {
'authors' => 'Albelda S.M., Buck C.A.',
'location' => 'FASEB J., 2868-2880, 4, 1990',
'title' => 'Integrins and other cell adhesion molecules.'
}, 'Bio::Annotation::Reference' ),
bless( {
'authors' => 'Springer T.A., Corbi A.L., Miller L.J., O\'Connor K., Larson R.S.',
'location' => 'EMBO J., 4023-4028, 6, 1987',
'title' => 'cDNA cloning and complete primary structure of the alpha subunit of a leukocyte adhesion glycoprotein, p150,95.'
}, 'Bio::Annotation::Reference' ),
bless( {
'authors' => 'Springer T.A.',
'location' => 'Proc. Natl. Acad. Sci. U.S.A., 65-72, 94, 1997',
'title' => 'Folding of the N-terminal, ligand-binding region of integrin alpha-subunits into a beta-propeller domain.'
}, 'Bio::Annotation::Reference' )
],
'name' => 'Integrins alpha chain',
'_synonyms' => [],
'definition' => 'Integrins , are a large family of cell surface receptors that mediate cellto cell as well as cell to matrix adhesion. Some integrins recognize the R-G-Dsequence in their extracellular matrix protein ligand. Structurally, integrinsconsist of a dimer of an alpha and a beta chain. Each subunit has a largeN-terminal extracellular domain followed by a transmembrane domain and a shortC-terminal cytoplasmic region. Some alpha subunits are cleaved post-translationally to produce a heavy and a light chain linked by a disulfidebond. Integrin alpha chains share a conserved sequence which is found atthe beginning of the cytoplasmic domain, just after the end of thetransmembrane region. The exact pairing of alpha- and beta-subunits determinesligand specificity, localisation and function. Within the N-terminal domain of alpha subunits, seven sequence repeats, eachof approximately 60 amino acids, have been found . It has been predicted that these repeats assume a beta-propeller fold. The domains contain seven four-stranded beta-sheets arranged in a torus around a pseudosymmetry axis. Integrin ligands and a putative Mg<sup>2+</sup>ion are predicted to bind to theupper face of the propeller, in a manner analogous to the way in which thetrimeric G-protein beta subunit (G beta) (which also has a beta-propellerfold) binds the G protein alpha subunit .',
'identifier' => 'IPR000413',
'comment' => undef,
'protein_count' => '126',
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' ),
'IPR001713' => bless( {
'_secondary_ids' => [],
'_dblinks' => {},
'short_name' => undef,
'_ontology' => $VAR1->{'_ontology'},
'_references' => [],
'name' => 'IPR001713',
'_synonyms' => [],
'definition' => undef,
'identifier' => 'IPR001713',
'comment' => undef,
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' ),
'PTM' => bless( {
'_secondary_ids' => [],
'_dblinks' => {},
'short_name' => undef,
'_ontology' => $VAR1->{'_ontology'},
'_references' => [],
'name' => 'post-translational modification',
'_synonyms' => [],
'definition' => undef,
'identifier' => 'PTM',
'comment' => undef,
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' ),
'Family' => bless( {
'_secondary_ids' => [],
'_dblinks' => {},
'short_name' => undef,
'_ontology' => $VAR1->{'_ontology'},
'_references' => [],
'name' => 'Family',
'_synonyms' => [],
'definition' => undef,
'identifier' => 'Family',
'comment' => undef,
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' ),
'IPR001723' => bless( {
'_secondary_ids' => [],
'_dblinks' => {},
'short_name' => undef,
'_ontology' => $VAR1->{'_ontology'},
'_references' => [],
'name' => 'IPR001723',
'_synonyms' => [],
'definition' => undef,
'identifier' => 'IPR001723',
'comment' => undef,
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' ),
'IPR001363' => bless( {
'_secondary_ids' => [],
'_dblinks' => {},
'short_name' => undef,
'_ontology' => $VAR1->{'_ontology'},
'_references' => [],
'name' => 'IPR001363',
'_synonyms' => [],
'definition' => undef,
'identifier' => 'IPR001363',
'comment' => undef,
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' ),
'Repeat' => bless( {
'_secondary_ids' => [],
'_dblinks' => {},
'short_name' => undef,
'_ontology' => $VAR1->{'_ontology'},
'_references' => [],
'name' => 'Repeat',
'_synonyms' => [],
'definition' => undef,
'identifier' => 'Repeat',
'comment' => undef,
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' ),
'IPR003243' => bless( {
'_secondary_ids' => [],
'_dblinks' => {},
'short_name' => undef,
'_ontology' => $VAR1->{'_ontology'},
'_references' => [],
'name' => 'IPR003243',
'_synonyms' => [],
'definition' => undef,
'identifier' => 'IPR003243',
'comment' => undef,
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' ),
'IPR000010' => bless( {
'_secondary_ids' => [
undef
],
'_dblinks' => {
'external_doc_list' => [
bless( {
'database' => 'BLOCKS',
'primary_id' => 'IPB000010',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'PDOC',
'primary_id' => 'PDOC00259',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' )
],
'class_list' => [
bless( {
'database' => 'GO',
'primary_id' => 'GO:0004869',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' )
],
'member_list' => [
bless( {
'database' => 'PROSITE',
'primary_id' => 'PS00287',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'PFAM',
'primary_id' => 'PF00031',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'SMART',
'primary_id' => 'SM00043',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' )
]
},
'short_name' => 'Cystatin',
'_ontology' => $VAR1->{'_ontology'},
'_references' => [
bless( {
'authors' => 'Barrett A.J.',
'location' => 'Trends Biochem. Sci., 193-196, 12, 1987'
}, 'Bio::Annotation::Reference' ),
bless( {
'authors' => 'Rawlings N.D., Barrett A.J.',
'location' => 'J. Mol. Evol., 60-71, 30, 1990',
'title' => 'Evolution of proteins of the cystatin superfamily.'
}, 'Bio::Annotation::Reference' ),
bless( {
'authors' => 'Bode W., Turk V.',
'location' => 'FEBS Lett., 213-219, 285, 1991',
'title' => 'The cystatins: protein inhibitors of cysteine proteinases.'
}, 'Bio::Annotation::Reference' )
],
'name' => 'Cysteine proteases inhibitor',
'_synonyms' => [],
'definition' => 'Members of this family are inhibitors of cysteine proteases , , , which are found in the tissues and body fluids of animals, as well as in plants. They can be grouped into three distinct but related families. These are the type 1 cystatins (or stefins), type 2 cystatins, and the kininogens.Kininogen is the precursor of the active peptide bradykinin that plays a role in blood coagulation by helping to position optimally prekallikrein and factor XI next to factor XII. They are also inhibitors of cysteine proteases. Structurally, kininogens are made of three contiguous type-2 cystatin domains, followed by an additional domain (of variable length) which contains the sequence of bradykinin. The first of the three cystatin domains seems to have lost its inhibitory activity.',
'identifier' => 'IPR000010',
'comment' => undef,
'protein_count' => '219',
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' ),
'Binding_site' => $VAR1,
'IPR000004' => bless( {
'_secondary_ids' => [],
'_dblinks' => {
'external_doc_list' => [
bless( {
'database' => 'QDOC',
'primary_id' => 'QDOC50015',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' )
],
'member_list' => [
bless( {
'database' => 'PREFILE',
'primary_id' => 'PS50015',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'PRODOM',
'primary_id' => 'PD001732',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'SMART',
'primary_id' => 'SM00118',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' )
]
},
'short_name' => 'SapB',
'_ontology' => $VAR1->{'_ontology'},
'_references' => [
bless( {
'authors' => 'O\'Hara P.J., Munford R.S., Sheppard P.O.',
'location' => 'J. Lipid Res., 1653-1663, 36, 1995',
'title' => 'Saposin-like proteins (SAPLIP) carry out diverse functions on a common backbone structure.'
}, 'Bio::Annotation::Reference' ),
bless( {
'authors' => 'Ponting C.P.',
'location' => 'Protein Sci., 359-361, 3, 1994',
'title' => 'Acid sphingomyelinase possesses a domain homologous to its activator proteins: saposins B and D.'
}, 'Bio::Annotation::Reference' ),
bless( {
'authors' => 'Hofmann K., Tschopp J.',
'location' => 'Trends Microbiol., 91-94, 4, 1996',
'title' => 'Cytotoxic T cells: more weapons for new targets?'
}, 'Bio::Annotation::Reference' ),
bless( {
'authors' => 'Liepinsh E., Otting G., Andersson M., Ruysschaert J.M.',
'location' => 'Nat. Struct. Biol., 793-795, 4, 1997',
'title' => 'Saposin fold revealed by the NMR structure of NK-lysin.'
}, 'Bio::Annotation::Reference' ),
bless( {
'authors' => 'Ponting C.P., Russell R.B.',
'location' => 'Trends Biochem. Sci., 179-180, 20, 1995',
'title' => 'Swaposins: circular permutations within genes encoding saposin homologues.'
}, 'Bio::Annotation::Reference' )
],
'name' => 'Saposin type B',
'_synonyms' => [],
'definition' => 'Saposins are small lysosomal proteins that serve as activators of variouslysosomal lipid-degrading enzymes . They probably act by isolating thelipid substrate from the membrane surroundings, thus making it more accessible to the soluble degradative enzymes. All mammaliansaposinsare synthesized as a single precursor molecule (prosaposin) which containsfour Saposin-B domains, yielding the active saposins after proteolyticcleavage, and two Saposin-A domains that are removed in the activationreaction. The Saposin-B domains also occur in other proteins, many of them active in the lysis of membranes , . The 3D-structure of NK-lysin has recently been determined and found tobe very different from the one predicted in .A group of plantaspartic proteases related to cyprosin. These proteinshave a peculiar SAP-B domain where the two halves are \'swapped\' .',
'identifier' => 'IPR000004',
'comment' => undef,
'protein_count' => '135',
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' ),
'IPR000002' => bless( {
'_secondary_ids' => [],
'_dblinks' => {
'external_doc_list' => [
bless( {
'database' => 'QDOC',
'primary_id' => 'QDOC50218',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' )
],
'member_list' => [
bless( {
'database' => 'PREFILE',
'primary_id' => 'PS50218',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'PRODOM',
'primary_id' => 'PD004563',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' )
]
},
'short_name' => 'Fizzy',
'_ontology' => $VAR1->{'_ontology'},
'_references' => [
bless( {
'authors' => 'Shirayama M., Toth A., Galova M., Nasmyth K.',
'location' => 'Nature, 203-207, 402, 1999',
'title' => 'APC(Cdc20) promotes exit from mitosis by destroying the anaphase inhibitor Pds1 and cyclin Clb5.'
}, 'Bio::Annotation::Reference' )
],
'name' => 'Cdc20/Fizzy',
'_synonyms' => [],
'definition' => 'The Cdc20/Fizzy region is almost always associated with the G-protein beta WD-40 repeat (). Ubiquitin-mediated proteolysis due to the anaphase-promoting complex/cyclosome(APC/C) is essential for separation of sister chromatids, requiring degradation of the anaphase inhibitor Pds1, and for exit from mitosis, requiring inactivation of cyclin B Cdk1 kinases . In yeastCdc20 is required for two microtubule-dependent processes, nuclear movements prior to anaphase and chromosome separation. APC(Cdc20) allows activation of Cdc14 and promotes exit from mitosis by mediating proteolysis of Pds1 and the S phase cyclin Clb5 in the yeast Saccharomyces cerevisiae. This domain is also found in a number of, as yet, uncharacterised proteins. These include a mammalianprotein, p55CDC, that is present in dividing cells and isassociated with protein kinase activity.',
'identifier' => 'IPR000002',
'comment' => undef,
'protein_count' => '57',
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' ),
'Conserved_site' => bless( {
'_secondary_ids' => [],
'_dblinks' => {},
'short_name' => undef,
'_ontology' => $VAR1->{'_ontology'},
'_references' => [],
'name' => 'Conserved Site',
'_synonyms' => [],
'definition' => undef,
'identifier' => 'Conserved_site',
'comment' => undef,
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' ),
'Region' => bless( {
'_secondary_ids' => [],
'_dblinks' => {},
'short_name' => undef,
'_ontology' => $VAR1->{'_ontology'},
'_references' => [],
'name' => 'Region',
'_synonyms' => [],
'definition' => undef,
'identifier' => 'Region',
'comment' => undef,
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' ),
'IPR000001' => bless( {
'_secondary_ids' => [],
'_dblinks' => {
'external_doc_list' => [
bless( {
'database' => 'BLOCKS',
'primary_id' => 'IPB000001',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'PDOC',
'primary_id' => 'PDOC00020',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' )
],
'member_list' => [
bless( {
'database' => 'PRINTS',
'primary_id' => 'PR00018',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'PROFILE',
'primary_id' => 'PS50070',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'PROSITE',
'primary_id' => 'PS00021',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'PFAM',
'primary_id' => 'PF00051',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'PRODOM',
'primary_id' => 'PD000395',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'SMART',
'primary_id' => 'SM00130',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' )
]
},
'short_name' => 'Kringle',
'_ontology' => $VAR1->{'_ontology'},
'_references' => [
bless( {
'authors' => 'Fujikawa K., McMullen B.A.',
'location' => 'J. Biol. Chem., 5328-5341, 260, 1985',
'title' => 'Primary structure of the heavy chain of human factor XIIa.'
}, 'Bio::Annotation::Reference' ),
bless( {
'authors' => 'Patthy L., Trexler M., Vali V., Banyai L., Varadi A.',
'location' => 'FEBS Lett., 131-136, 171, 1984',
'title' => 'Kringles: Modules specialized for protein binding.'
}, 'Bio::Annotation::Reference' ),
bless( {
'authors' => 'Atkinson R.A., Williams R.J.P.',
'location' => 'J. Mol. Biol., 541-552, 212, 1990',
'title' => 'Solution structure of the kringle 4 domain from human plasminogen by 1H nuclear magnetic resonance spectroscopy and distance geometry.'
}, 'Bio::Annotation::Reference' ),
bless( {
'authors' => 'Castellino F.J., Beals J.M.',
'location' => 'J. Mol. Evol., 358-369, 26, 1987',
'title' => 'The genetic relationships between the kringle domains of human plasminogen, prothrombin, tissue plasminogen activator, urokinase, and coagulation factor XII.'
}, 'Bio::Annotation::Reference' ),
bless( {
'authors' => 'Patthy L.',
'location' => 'Cell, 657-663, 41, 1985',
'title' => 'Evolution of the proteases of blood coagulation and fibrinolysis by assembly from modules.'
}, 'Bio::Annotation::Reference' ),
bless( {
'authors' => 'Takahashi K., Ikeo K., Gojobori T.',
'location' => 'FEBS Lett., 146-148, 287, 1991',
'title' => 'Evolutionary origin of numerous kringles in human and simian apolipoprotein(a).'
}, 'Bio::Annotation::Reference' ),
bless( {
'authors' => 'Friezner Degen S.J., Stuart L.A., Han S., Jamison C.S.',
'location' => 'Biochemistry, 9781-9791, 30, 1991',
'title' => 'Characterization of the mouse cDNA and gene coding for a hepatocyte growth factor-like protein: expression during development.'
}, 'Bio::Annotation::Reference' ),
bless( {
'authors' => 'Miyazawa K., Shimomura T., Kitamura A., Kondo J., Morimoto Y., Kitamura N.',
'location' => 'J. Biol. Chem., 10024-10028, 268, 1993',
'title' => 'Molecular cloning and sequence analysis of the cDNA for a human serine protease reponsible for activation of hepatocyte growth factor. Structural similarity of the protease precursor to blood coagulation factor XII.'
}, 'Bio::Annotation::Reference' )
],
'name' => 'Kringle',
'_synonyms' => [],
'definition' => 'Kringles are autonomous structural domains, found throughout the blood clotting and fibrinolytic proteins.Kringle domains are believed to play a role in binding mediators (e.g., membranes,other proteins or phospholipids), and in the regulation of proteolytic activity, , . Kringle domains , , are characterised by a triple loop, 3-disulphide bridge structure, whose conformation is defined by a number of hydrogen bonds and small pieces of anti-parallel beta-sheet. They are found in a varying number of copies, in some serine proteases andplasma proteins.',
'identifier' => 'IPR000001',
'comment' => undef,
'protein_count' => '129',
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' ),
'IPR000536' => bless( {
'_secondary_ids' => [],
'_dblinks' => {},
'short_name' => undef,
'_ontology' => $VAR1->{'_ontology'},
'_references' => [],
'name' => 'IPR000536',
'_synonyms' => [],
'definition' => undef,
'identifier' => 'IPR000536',
'comment' => undef,
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' ),
'Domain' => bless( {
'_secondary_ids' => [],
'_dblinks' => {},
'short_name' => undef,
'_ontology' => $VAR1->{'_ontology'},
'_references' => [],
'name' => 'Domain',
'_synonyms' => [],
'definition' => undef,
'identifier' => 'Domain',
'comment' => undef,
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' ),
'IPR000003' => bless( {
'_secondary_ids' => [],
'_dblinks' => {
'class_list' => [
bless( {
'database' => 'GO',
'primary_id' => 'GO:0003677',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'GO',
'primary_id' => 'GO:0004879',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'GO',
'primary_id' => 'GO:0005496',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'GO',
'primary_id' => 'GO:0005634',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'GO',
'primary_id' => 'GO:0006355',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' )
],
'member_list' => [
bless( {
'database' => 'PRINTS',
'primary_id' => 'PR00545',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' )
]
},
'short_name' => 'RtnoidX_receptor',
'_ontology' => $VAR1->{'_ontology'},
'_references' => [
bless( {
'authors' => 'Nishihara T., Nishikawa J.-I., Kitaura M., Imagawa M.',
'location' => 'Nucleic Acids Res., 606-611, 23, 1995',
'title' => 'Vitamin D receptor contains multiple dimerisation interfaces that are functionally different.'
}, 'Bio::Annotation::Reference' ),
bless( {
'authors' => 'Schmitt J., De Vos P., Verhoeven G., Stunnenberg H.G.',
'location' => 'Nucleic Acids Res., 1161-1166, 22, 1994',
'title' => 'Human androgen receptor expressed in HeLa cells activates transcription in vitro.'
}, 'Bio::Annotation::Reference' )
],
'name' => 'Retinoid X receptor',
'_synonyms' => [],
'definition' => 'Steroid or nuclear hormone receptors (4A nuclear receptor, NRs) constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. Members of the superfamily include the steroid hormone receptors and receptors for thyroid hormone, retinoids, 1,25-dihydroxy-vitamin D3 and a variety of other ligands. The proteins function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner , . In addition to C-terminal ligand-binding domains, these nuclear receptors contain a highly-conserved, N-terminal zinc-finger that mediates specific binding to target DNA sequences, termed ligand-responsive elements. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components; hormone binding greatly increases receptor affinity.NRs are extremely important in medical research, a large number of them being implicated in diseases such as cancer, diabetes, hormone resistance syndromes, etc. While several NRs act as ligand-inducible transcription factors, many do not yet have a defined ligand and are accordingly termed "orphan" receptors. During the last decade, more than 300 NRs have been described, many of which are orphans, which cannot easily be named due to current nomenclature confusions in the literature. However, a new system has recently been introduced in an attempt to rationalise the increasingly complex set of names used to describe superfamily members.The retinoic acid (retinoid X) receptor consists of 3 functional and structural domains: an N-terminal (modulatory) domain; a DNA binding domainthat mediates specific binding to target DNA sequences (ligand-responsiveelements); and a hormone binding domain. The N-terminal domain differs between retinoic acid isoforms; the small highly-conserved DNA-bindingdomain (~65 residues) occupies the central portion of the protein; and the ligand binding domain lies at the receptor C-terminus.Synonym(s): 2B nuclear receptor',
'identifier' => 'IPR000003',
'comment' => undef,
'protein_count' => '75',
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' ),
'IPR003244' => bless( {
'_secondary_ids' => [],
'_dblinks' => {},
'short_name' => undef,
'_ontology' => $VAR1->{'_ontology'},
'_references' => [],
'name' => 'IPR003244',
'_synonyms' => [],
'definition' => undef,
'identifier' => 'IPR003244',
'comment' => undef,
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' ),
'IPR000005' => bless( {
'_secondary_ids' => [],
'_dblinks' => {
'external_doc_list' => [
bless( {
'database' => 'BLOCKS',
'primary_id' => 'IPB000005',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'PDOC',
'primary_id' => 'PDOC00040',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' )
],
'class_list' => [
bless( {
'database' => 'GO',
'primary_id' => 'GO:0003700',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'GO',
'primary_id' => 'GO:0005622',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'GO',
'primary_id' => 'GO:0006355',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' )
],
'member_list' => [
bless( {
'database' => 'PRINTS',
'primary_id' => 'PR00032',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'PROFILE',
'primary_id' => 'PS01124',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'PROSITE',
'primary_id' => 'PS00041',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'PFAM',
'primary_id' => 'PF00165',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' ),
bless( {
'database' => 'SMART',
'primary_id' => 'SM00342',
'_root_verbose' => 0
}, 'Bio::Annotation::DBLink' )
]
},
'short_name' => 'HTHAraC',
'_ontology' => $VAR1->{'_ontology'},
'_references' => [
bless( {
'authors' => 'Gallegos M.-T., Michan C., Ramos J.L.',
'location' => 'Nucleic Acids Res., 807-810, 21, 1993',
'title' => 'The XylS/AraC family of regulators.'
}, 'Bio::Annotation::Reference' ),
bless( {
'authors' => 'Henikoff S., Wallace J.C., Brown J.P.',
'location' => 'Meth. Enzymol., 111-132, 183, 1990',
'title' => 'Finding protein similarities with nucleotide sequence databases.'
}, 'Bio::Annotation::Reference' ),
bless( {
'authors' => 'Parker L.L., Hall B.G.',
'location' => 'Genetics, 455-471, 124, 1990',
'title' => 'Characterisation and nucleotide sequence of the cryptic cel operon of Escherichia coli K12.'
}, 'Bio::Annotation::Reference' ),
bless( {
'authors' => 'Bustos S.A., Schleif R.F.',
'location' => 'Proc. Natl. Acad. Sci. U.S.A., 5638-5642, 90, 1993',
'title' => 'Functional domains of the AraC protein.'
}, 'Bio::Annotation::Reference' )
],
'name' => 'Helix-turn-helix, AraC type ',
'_synonyms' => [],
'definition' => 'Many bacterial transcription regulation proteins bind DNA through a\'helix-turn-helix\' (HTH) motif. One major subfamily of these proteins , is related to the arabinose operon regulatory protein AraC , .Except for celD , all of these proteins seem to be positive transcriptional factors.Although the sequences belonging to this family differ somewhat in length, in nearly every case the HTH motif is situated towards the C-terminus in the third quarter of most of the sequences. The minimal DNA binding domain spans roughly 100 residues and comprises two HTH subdomains; the classical HTH domain and another HTH subdomain with similarity to the classical HTH domain but with an insertion of one residue in the turn-region. The N-terminal and central regions of these proteins are presumedto interact with effector molecules and may be involved in dimerization .The known structure of MarA () shows that the AraC domain is alpha helical and shows the two HTH subdomains both bind the major groove of the DNA. The two HTH subdomains are separated by only 27angstroms, which causes the cognate DNA to bend.',
'identifier' => 'IPR000005',
'comment' => undef,
'protein_count' => '765',
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' ),
'Active_site' => bless( {
'_secondary_ids' => [],
'_dblinks' => {},
'short_name' => undef,
'_ontology' => $VAR1->{'_ontology'},
'_references' => [],
'name' => 'Active Site',
'_synonyms' => [],
'definition' => undef,
'identifier' => 'Active_site',
'comment' => undef,
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' ),
'IPR003258' => bless( {
'_secondary_ids' => [],
'_dblinks' => {},
'short_name' => undef,
'_ontology' => $VAR1->{'_ontology'},
'_references' => [],
'name' => 'IPR003258',
'_synonyms' => [],
'definition' => undef,
'identifier' => 'IPR003258',
'comment' => undef,
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' )
}
}, 'Bio::Ontology::SimpleOntologyEngine' ),
'name' => 'InterPro',
'_root_verbose' => 0
}, 'Bio::Ontology::Ontology' ),
'_references' => [],
'name' => 'Binding Site',
'_synonyms' => [],
'definition' => undef,
'identifier' => 'Binding_site',
'comment' => undef,
'_root_verbose' => 0,
'is_obsolete' => 0
}, 'Bio::Ontology::InterProTerm' );
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