_dictionary.title seqdic.s97
_dictionary.version 0.1.02
_dicdionary.datablock_id seqdic.s97
loop_
_dictionary_history.version
_dictionary_history.update
_dictionary_history.revision
0.1.01
1997-08-13
;
First production version
;
0.1.02
1997-09-04
;
Added method_list and category methods. These are pretty much a guess for
now.
;
loop_
_category_group_list.id
_category_group_list.parent_id
_category_group_list.description
'inclusive_group'
.
;
Categories that belong to the macromolecular dictionaries.
;
'general_group'
;
Categories common to all data types (sequences, structures,
enzymes, features) such as uid, citation, etc.
;
'sequence_group'
;
Categories common to protein and nucleic acid sequences.
;
loop_
_method_list.id
_method_list.description
_method_list.language
_method_list.code
'get_sequence_category'
;
Parse the items in the sequence category from a source
database file.
;
PERL
;
make_loop;
get_sequence-id;
get_sequence-type;
get_sequence-name;
get_sequence-synonym;
get_sequence-date_create;
get_sequence-update_sequence;
get_sequence-update_annotation;
get_sequence-citation;sequence_
get_sequence-length;
get_sequence-mol_weight;
get_sequence-sequence;
;
'get_feature_table_category'
;
Parse the items in the feature table category from a source
database file
;
PERL
;
get_feature_table-id;
make_loop;
while ( get_feature_table-items );
;
'get_uid_category'
;
Assign the items in the uid category for data from a source
database file
;
PERL
;
make_loop;
get_uid-_id;
get_uid-status;
get_uid-date_create;
get_uid-update;
get_uid-keyword;
get_uid-description_short;
get_uid-description_long;
;
'get_xref_category'
;
Parse the items in the xref category from a source
database file
;
PERL
;
get_xref-id;
make_loop;
while ( get_xref-item ) {
get_xref-primary;
get_xref-dbname;
get_xref-name;
get_xref-acc;
get_xref-date;
get_xref-type;
get_xref-source_db;
get_xref-source_accession;
get_xref-comments;
}
;
save_SEQUENCE
save__sequence.id
save__sequence.type
save__sequence.name
save__sequence.date_create
save__sequence.update_sequence
save__sequence.update_annotation
save__sequence.synonym
save_sequence.keyword
save__sequence.citation
save__sequence.length
save__sequence.mol_weight
save__sequence.sequence
save_LOCAL
save__local.id
save__local.synonym
save__local.keyword
save__local.description_short
save__local.description_long
save__local.comment
save_FEATURE_TABLE
save__feature_table.id
save__feature_table.feature_id
save__feature_table.feature_name
save__feature_table.feature_location
save__feature_table.feature_type
save__feature_table.feature_source
save_UID
save__uid.id
save__uid.status
save__uid.date_create
save__uid.update
save__uid.keyword
save__uid.description_short
save__uid.description_long
save_XREF
save__xref.id
save__xref.dbname
save__xref.primary
save__xref.acc
save__xref.name
save__xref.date
save__xref.type
save__xref.source_db
save__xref.source_accession
save__xref.comment
save__feature_table.feature_id.
_item_description.description ; The UID of the feature as defined in PKR. ; _item.name '_feature_table.feature_id' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code PKR_ID _item_example.case 'PKRFEAT01234' loop_ _item_linked.parent_name _item_linked.child_name '_uid.id' '_feature_table.feature_id'
save__feature_table.feature_location.
_item_description.description ; The position of the feature within the object. A comma delimited string defining the positions and/or ranges that define the location of the feature. A position is a single base or residue and specified as a single integer. A range is a contiguous segment and is specified as two integers separated by a hyphen. Any number of positions and ranges may be combined. ; _item.name '_feature_table.feature_location' _item.category_id _item.category_id _item.mandatory_code no _item_type.code line _item_example.case '149,204-265'
save__feature_table.feature_name.
_item_description.description ; The name of the feature. This is logically the name of the feature as defined in _feature.name, but there is no obvious value in trying to enforce this. ; _item.name '_feature_table.feature_name' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code line _item_example.case 'SH3'
save__feature_table.feature_source.
_item_description.description ; Means by which the feature was identified in the sequence. Usually the feature is listed within the original db entry. However, feature can be identified automatically/manually by PKR or even be annotated by an individual. ; _item.name '_feature_table.feature_source' _item.category_id _item.category_id _item.mandatory_code yes loop_ _item_enumeration.value _item_enumeration.description PRIMARY ; Feature is annotated in the database indicated as the primary cross-reference. ; PKR_AUTOMATIC ; Feature was identified within the PKR, for instance by searches using PKR defined features. ; COMMUNICATION ; Personal communication, hopefully from a knowlegable person... ;
save__feature_table.feature_type.
_item_description.description ; Type of the feature. The idea is to classify the features as an aid to displaying the feature table textually (e.g. limit searches to domains), or graphically, e.g. so that different kinds of features are displayed differently. A controlled vocabulary is essential to making this work so this is an enumerated type. ; _item.name '_feature_table.feature_type' _item.category_id _item.category_id _item.mandatory_code no loop_ _item_enumeration.value _item_enumeration.description DOMAIN ; A contiguous stretch of residues corresponding to a sequence or structural module. ; SIGNATURE ; A PROSITE signature. Conceptually this is similar to a domain but since it is only a tag and does not delimit the entire region, a separate type seems justified. ; SITE ; A group of residues with a specific physico-chemical function, for example, active site (residues surrounding the catalytic center) or ligand binding sites. ; 2ARY_STRUCTURE ; Secondary structural regions defined based on the three- dimensional coordinates. Typically alpha helix, beta strand, and turns. ; MODIFICATION ; Post-translational modifications, e.g. phosphorylation, acetylation, methylation, or cleavage. ; MUTATION ; Site of a known mutation. Do not use this simply for differences between reported sequences due to experimental error. ;
_item_description.description ; The UID for the internal object to which this cross-reference refers. ; _item.name '_feature_table.id' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code PKR_ID _item_example.case 'PKRFEAT01234' loop_ _item_linked.parent_name _item_linked.child_name '_uid.id' '_feature_table.id'
_item_description.description ; A text comment describing this sequence. Should be used for textual descriptions rather than as a catchall for items that have not been otherwise defined. Bite the bullet and define additional items if you need to. ; _item.name '_local.comment' _item.category_id _item.category_id _item.mandatory_code no _item_type.code text _item_example.case ; This protein has an atypical SH3 domain lacking the YDY consensus sequence. ;
_item_description.description ; Complete description of the object. This may be as long as is necessary. The local description supercedes the information in sequence.description_long. ; _item.name '_local.description_long' _item.category_id _item.category_id _item.mandatory_code no _item_type.code text _item_example.case ; DM_ABL is a member of the Abl family of proto-oncogenes. It is found in the cytoplasm and acts to initiate the cellular response to ionizing radiation. ;
save__local.description_short.
_item_description.description ; Short description of the object. Should be less than 40 characters so that it can be displayed with other information. The local description supercedes the information in sequence.description_short. ; _item.name '_local.description_short' _item.category_id _item.category_id _item.mandatory_code no _item_type.code sline _item_example.case 'TYROSINE-PROTEIN KINASE DASH/ABL'
_item_description.description ; UID (accession number) of this sequence. This is the same as uid.id ; _item.name '_local.id' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code PKR_ID loop_ _item_linked.parent_name _item_linked.child_name '_uid.id' '_local.id'
_item_description.description ; A list of locally defined keywords. Keywords can be any terms that a user would want to use to lookup this entry, such as, enzymatic activity, function, cellular location, etc. ; _item.name '_local.keyword' _item.category_id _item.category_id _item.mandatory_code no _item_type.code line _item_example.case 'inactive mutant, transmembrane protein'
_item_description.description ; A list of locally defined synonyms (in addition to those defined in the primary database entry. ; _item.name '_local.synonym' _item.category_id _item.category_id _item.mandatory_code no _item_type.code line _item_example.case 'abl, d-abl, dm_abl'
_item_description.description ; Unparsed citations - just as they appear in the database. We anticipate great difficulty in parsing references consistently from disparate databases. This item is a placeholder for citation information until sufficient parsing routines are available. ; _item.name '_sequence.citation' _item.category_id _item.category_id _item.mandatory_code no _item_type.code text _item_examples.case ; RP SEQUENCE FROM N.A. RX MEDLINE; 88174728. RA HENKEMEYER M.J., BENNETT R.L., GERTLER F.B., HOFFMANN F.M.; RL MOL. CELL. BIOL. 8:843-853(1988). RN [2] RP SEQUENCE OF 374-648 FROM N.A. RX MEDLINE; 84082064. RA HOFFMANN F.M., FRESCO L.D., HOFFMAN-FALK H., SHILO B.-Z.; RL CELL 35:393-401(1983). ;
_item_description.description ; Creation date for the entry in the source database. We suppose that not all databases have this so we make it optional. ; _item.name '_sequence.date_create' _item.category_id _item.category_id _item.mandatory_code no _item_type.code YYYY-MM-DD _item_examples.case '1995-11-01'
_item_description.description ; UID (accession number) of this sequence. This is the same as uid.id ; _item.name '_sequence.id' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code PKR_ID loop_ _item_linked.parent_name _item_linked.child_name '_uid.id' '_sequence.id'
_item_description.description ; The length of the sequence in residues or bases. ; _item.name '_sequence.length' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code int _item_example.case '1520'
_item_description.description ; The molecular weight of the unmodified sequence in daltons. ; _item.name '_sequence.mol_weight' _item.category_id _item.category_id _item.mandatory_code no _item_type.code int _item_example.case '161836'
_item_description.description ; Trivial name of this entry in the source database. Trivial names are subject to change without notice by the database mantainer. ; _item.name '_sequence.name' _item.category_id _item.category_id _item.mandatory_code no _item_type.code line _item_examples.case 'ABL_DROME'
_item_description.description
;
The base or residue sequence. The allowable alphabet is determined
by _sequence.type.
;
_item.name '_sequence.sequence'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code residue
_item_example.case
;
MGAQQGKDRG AHSGGGGSGA PVSCIGLSSS PVASVSPHCI SSSSGVSSAP LGGGSTLRGS
RIKSSSSGVA SGSGSGGGGG GSGSGLSQRS GGHKDARCNP TVGLNIFTEH NGTKHSSFRG
HPGKYHMNLE ALLQSRPLPH IPAGSTRPLF WRIAELQQHQ QDSGGLGLQG SSLGGGHSST
TSVFESAHRW TSKENLLAPG PEEDDPQLFV ALYDFQAGGE NQLSLKKGEQ VRILSYNKSG
EWCEAHSDSG NVGWVPSNYV TPLNSLEKHS WYHGPISRNA AEYLLSSGIN GSFLVRESES
SPGQRSISLR YEGRVYHYRI SEDPDGKVFV TQEAKFNTLA ELVHHHSVPH EGHGLITPLL
YPAPKQNKPT VFPLSPEPDE WEICRTDIMM KHKLGGGQYG EVYEAVWKRY GNTVAVKTLK
EDTMALKDFL EEAAIMKEMK HPNLVQLIGV CTREPPFYII TEFMSHGNLL DFLRSAGRET
LDAVALLYMA TQIASGMSYL ESRNYIHRDL AARNCLVGDN KLVKVADFGL ARLMRDDTYT
AHAGAKFPIK WTAPEGLAYN KFSTKSDVWA FGVLLWEIAT YGMSPYPAID LTDVYHKLDK
GYRMERPPGC PPEVYDLMRQ CWQWDATDRP TFKSIHHALE HMFQESSITE AVEKQLNANA
TSASSSAPST SGVATGGGAT TTTAASGCAS SSSATASLSL TPQMVKKGLP GGQALTPNAH
HNDPHQQQAS TPMSETGSTS TKLSTFSSQG KGNVQMRRTT NKQGKQAPAP PKRTSLLSSS
RDSTYREEDP ANARCNFIDD LSTNGLARDI NSLTQRYDSE TDPAADPDTD ATGDSLEQSL
SQVIAAPVTN KMQHSLHSGG GGGGIGPRSS QQHSSFKRPT GTPVMGNRGL ETRQSKRSQL
HSQAPGPGPP STQPHHGNNG VVTSAHPITV GALDVMNVKQ VVNRYGTLPK GARIGAYLDS
LEDSSEAAPA LPATAPSLPP ANGHATPPAA RLNPKASPIP PQQMIRSNSS GGVTMQNNAA
ASLNKLQRHR TTTEGTMMTF SSFRAGGSSS SPKRSASGVA SGVQPALANL EFPPPPLDLP
PPPEEFEGGP PPPPPAPESA VQAIQQHLHA QLPNNGNISN GNGTNNNDSS HNDVSNIAPS
VEEASSRFGV SLRKREPSTD SCSSLGSPPE DLKEKLITEI KAAGKDTAPA SHLANGSGIA
VVDPVSLLVT ELAESMNLPK PPPQQQQKLT NGNSTGSGFK AQLKKVEPKK MSAPMPKRTA
NTIIDFKAHL RRVDKEKEPA TPAPAPATVA VANNANCNTT GTLNRKEDGS KKFSQAMQKT
EIKIDVTNSN VEADAGAAGE GDLGKRRSTD DEEQSHTEGL GSGGQGSADM TQSLYEQKPQ
IQQKPAVPHK PTKLTIYATP IAKLTEPASS ASSTQISRES ILELVGLLEG SLKHPVNAIA
GSQWLQLSDK LNILHNSCVI FAENGAMPPH SKFQFRELVT RVEAQSQHLR SAGSKNVQDN
ERLVAEVGQS LRQISNALNR'
;
_item_description.description ; This item contains a list of synonymous names for the sequence - if such exist. The list is a comma delimited string. ; _item.name '_sequence.synonym' _item.category_id _item.category_id _item.mandatory_code no _item_type.code line _item_example.case ' abl, d-abl, dm_abl'
_item_description.description ; Describes the type of molecule in this sequence entry. Allowed types are PROTEIN, RNA, and DNA. ; _item.name '_sequence.type' _item.category_id _item.category_id _item.mandatory_code yes loop_ _item_enumeration.value _item_enumeration.detail DNA ; DNA sequence ; RNA ; RNA sequence ; PROTEIN ; protein sequence ;
save__sequence.update_annotation.
_item_description.description ; Last annotation update for the entry in the source database. We suppose that not all databases have this so we make it optional. ; _item.name '_sequence.update_annotation' _item.category_id _item.category_id _item.mandatory_code no _item_type.code YYYY-MM-DD _item_examples.case '1995-11-01'
save__sequence.update_sequence.
_item_description.description ; Last sequence update date for the entry in the source database. We suppose that not all databases have this so we make it optional. ; _item.name '_sequence.update_sequence' _item.category_id _item.category_id _item.mandatory_code no _item_type.code YYYY-MM-DD _item_examples.case '1995-11-01'
_item_description.description ; Date this uid was assigned. Note the date the information was created in a source database. ; _item.name '_uid.date_create' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code YYYY-MM-DD _item_examples.case '1997-05-05'
_item_description.description ; Complete description of the object. This may be as long as is necessary. ; _item.name '_uid.description_long' _item.category_id _item.category_id _item.mandatory_code no _item_type.code text _item_example.case ; CC -!- CATALYTIC ACTIVITY: ATP + A PROTEIN TYROSINE = ADP + CC PROTEIN TYROSINE PHOSPHATE. CC -!- SUBCELLULAR LOCATION: CYTOPLASMIC. ;
_item_description.description ; Short description of the object. Should be less than 40 characters so that it can be displayed with other information. For sequences, this is typically taken from the description line. ; _item.name '_uid.description_short' _item.category_id _item.category_id _item.mandatory_code no _item_type.code sline _item_example.case 'TYROSINE-PROTEIN KINASE DASH/ABL'
_item_description.description ; This is the accession number, each object in the database must have one. The _uid.id provides the mechanism for associating information in various categories with a single object. ; _item.name '_uid.id' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code code
_item_description.description ; Keywords describing this object, comma delimited. ; _item.name '_uid.keyword' _item.category_id _item.category_id _item.mandatory_code no _item_type.code line _item_example.case 'leukemia, tyrosine-protein kinase'
_item_description.description ; Indicates whether this object is currently active, and should therefore be reported in response to queries, or inactive and present merely for archival purposes. This field could also be used for placing objects on hold, e.g. until after publication. ; _item.name '_uid.status' _item.category_id _item.category_id _item.mandatory_code yes loop_ _item_enumeration.value _item_enumeration.description ACTIVE 'Object is currently active' REPLACED 'Object has been replace by new data' HOLD 'Object is on hold'
_item_description.description
;
Date the content of the corresponding object was checked against
external data source or updated.
;
_item.name '_uid.update'
_item.category_id _item.category_id
_item.mandatory_code yes
_item_type.code YYYY-MM-DD
_item_examples.case '1997-05-05'
_item_description.description ; Accession number for this entry in the cross-referenced database. The accession number should be the most stable identifier for the entry. ; _item.name '_xref.acc' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code line _item_examples.case 'P00522'
_item_description.description ; A comment (when necessary) about the source or content of the cross reference. ; _item.name '_xref.comment' _item.category_id _item.category_id _item.mandatory_code no _item_type.code text _item_examples.case 'S.S. Taylor, personal communication'
_item_description.description ; Date at which this cross-reference was updated in its source. For primary references it is the update date. For indirect references it is the update date for the source entry. the update dates are prioritized as follows: overall update > annotation update > sequence update. The highest priority date is used. Do all database provide dates - we think so ; _item.name '_xref.date' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code yyyy-mm-dd _item_examples.case '1997-01-01'
_item_description.description ; Name of the database being referenced. This item uses a controlled vocabulary. ; _item.name '_xref.dbname' _item.category_id _item.category_id _item.mandatory_code yes _item_type.code line loop_ _item_enumeration.value _item_enumeration.detail PDB ; Protein Data Bank - Brookhaven National Laboratory ; SWISS ; SWISS-PROT Protein Sequence Database - European Molecular Biology Laboratory ; GENBANK ; Genbank Nucleic Acid Sequence Database - National Center for Biotechnology Information ; EMBL ; EMBL Nucleic Acid Sequence Database - European Molecular Biology Laboratory ; PIR ; Protein Information Resource - National Biomedical Research Foundation ; OMIM ; Online Mendeleian Inheritance in Man ; GDB ; Genome Database - Johns Hopkins University ; PKR ; Protein Kinase Resource - San Diego Supercomputer Center, The University of California, San Diego ;
_item_description.description ; Value in _xref.id associates this cross-reference with a database entry. _xref.id is the same as _uid.id. ; _item.name '_xref.id' _item.categoty.id xref _item.mandatory_code yes _item_type.code line _item_examples.case 'PKRPSEQ012345' loop_ _item_linked.parent_name _item_linked.child_name '_uid.id' '_xref.id'
_item_description.description ; Trivial name of this entry in the cross-referenced database. Trivial names are subject to change without notice by the database mantainer. ; _item.name '_xref.name' _item.category_id _item.category_id _item.mandatory_code no _item_type.code line _item_examples.case 'ABL_DROME'
_item_description.description ; Flags the primary reference for the entry. The primary entry is the source of the data in the sequence whose _sequence.id is the same as the _xref.id. ; _item.name '_xref.primary' _item.category_id _item.category_id _item.mandatory_code yes loop_ _item_enumeration.value _item_enumeration.detail yes ; The entry is the primary source of data in this object ; no ; The entry is not a primary source, but a cross-reference listed in the primary source ;
_item_description.description ; If the cross reference is made based on some database entry that is not the original source - the accession number of the entry should be provided here. This item complements the xref.source_db item above. ; _item.name '_xref.source_accession' _item.category_id _item.category_id _item.mandatory_code no _item_type.code code
_item_description.description ; Source based upon which the the cross-reference is made - this is in cases where cross-reference comes not from the source data base, but internally from PKR, from personal communications, etc. ; _item.name '_xref.source_db' _item.category_id _item.category_id _item.mandatory_code no _item_type.code line
_item_description.description ; List the type of the database the xref is. ; _item.name '_xref.type' _item.category_id _item.category_id _item.mandatory_code yes loop_ _item_enumeration.value _item_enumeration.detail PROTEIN ; xref is to a protein sequence database ; NUCLEIC ; xref is to DNA or RNA sequence database ; STRUCTURE ; xref is to a three-dimensional structure database ; ENZYME ; xref is an enzyme DB ;
_category.description ; The feature_table category is a list of all the features contained in a sequence or structure. ; _category.id _category.id _category.mandatory_code yes loop_ _category_key.name '_feature_table.id' '_feature_table.feature_name' loop_ _category_group.id 'inclusive_group' 'sequence_group' loop_ _category_methods.method_id _category_methods.category_id 'get_feature_table_category' feature_table loop_ _category_example.case _category_example.details 'Example 1' ; _feature_table.id PKRPSEQ012345 loop_ _feature_table.feature_id _feature_table.feature_name _feature_table.feature_location _feature_table.feature_source PKRFEAT00344 SP-SH3 204-265 PRIMARY PKRFEAT00343 SP-SH2 271-363 PRIMARY PKRFEAT00011 SP-PROTEIN_KINASE 388-644 PRIMARY PKRFEAT01010 SP-ATP 394-402 PRIMARY PKRFEAT06060 KINASE_CAT_RES 509 PKR ;
_category.description ; The sequence category contains only the information publically available - local enhancements are entered in the "local" category. While the local category could in principal duplicate all items of sequence, in fact this is not necessary. ; _category.id _category.id _category.mandatory_code no loop_ _category_key.name '_local.id' loop_ _category_group.id 'inclusive_group' 'sequence_group' loop_ _category_example.case _category_example.details 'Example 1' ; loop_ _local.id _local.synonym _local.keyword _local.comment PKRPSEQ012345 'abl, d-abl, dm_abl' 'inactive mutant, transmembrane protein' ; This protein has an atypical SH3 domain lacking the YDY consensus sequence. ; ;
_category.description ; Protein/DNA sequence and other relevant information parsed from the database entry (cross-references, 'domains' name and location, etc). The sequence category contains only the information publically available - local enhancements are entered in the "local" category. ; _category.id _category.id _category.mandatory_code yes loop_ _category_key.name '_sequence.id' '_sequence.sequence' loop_ _category_group.id 'inclusive_group' ` 'sequence_group' loop_ _category_methods.method_id _category_methods.category_id 'get_sequence_category' sequence loop_ _category_example.case _category_example.details 'Example - Tyrosine_protein kinase DASH/ABL' ; loop_ _sequence.id _sequence.type _sequence.name _sequence.synonym _sequence.date_create _sequence.update_sequence _sequence.update_annotation _sequence.citation _sequence.length _sequence.mol_weight _sequence.sequence PKRPSEQ012345 PROTEIN ABL_DROME abl, d-abl, dm_abl 1986-07-21 1990-01-01 1995-11-01 ; RX MEDLINE; 88174728. RA HENKEMEYER M.J., BENNETT R.L., GERTLER F.B., HOFFMANN F.M.; RN [1] RP SEQUENCE FROM N.A. RX MEDLINE; 88174728. [NCBI, Geneva] RA HENKEMEYER M.J., BENNETT R.L., GERTLER F.B., HOFFMANN F.M.; RL MOL. CELL. BIOL. 8:843-853(1988). RN [2] RP SEQUENCE OF 374-648 FROM N.A. RX MEDLINE; 84082064. RA HOFFMANN F.M., FRESCO L.D., HOFFMAN-FALK H., SHILO B.-Z.; RL CELL 35:393-401(1983). ; 1520 161836 ; MGAQQGKDRGAHSGGGGSGAPVSCIGLSSSPVASVSPHCISSSSGVSSAPLGGGSTLRGS RIKSSSSGVASGSGSGGGGGGSGSGLSQRSGGHKDARCNPTVGLNIFTEHNGTKHSSFRG HPGKYHMNLEALLQSRPLPHIPAGSTRPLFWRIAELQQHQQDSGGLGLQGSSLGGGHSST TSVFESAHRWTSKENLLAPGPEEDDPQLFVALYDFQAGGENQLSLKKGEQVRILSYNKSG EWCEAHSDSGNVGWVPSNYVTPLNSLEKHSWYHGPISRNAAEYLLSSGINGSFLVRESES SPGQRSISLRYEGRVYHYRISEDPDGKVFVTQEAKFNTLAELVHHHSVPHEGHGLITPLL YPAPKQNKPTVFPLSPEPDEWEICRTDIMMKHKLGGGQYGEVYEAVWKRYGNTVAVKTLK EDTMALKDFLEEAAIMKEMKHPNLVQLIGVCTREPPFYIITEFMSHGNLLDFLRSAGRET LDAVALLYMATQIASGMSYLESRNYIHRDLAARNCLVGDNKLVKVADFGLARLMRDDTYT AHAGAKFPIKWTAPEGLAYNKFSTKSDVWAFGVLLWEIATYGMSPYPAIDLTDVYHKLDK GYRMERPPGCPPEVYDLMRQCWQWDATDRPTFKSIHHALEHMFQESSITEAVEKQLNANA TSASSSAPSTSGVATGGGATTTTAASGCASSSSATASLSLTPQMVKKGLPGGQALTPNAH HNDPHQQQASTPMSETGSTSTKLSTFSSQGKGNVQMRRTTNKQGKQAPAPPKRTSLLSSS RDSTYREEDPANARCNFIDDLSTNGLARDINSLTQRYDSETDPAADPDTDATGDSLEQSL SQVIAAPVTNKMQHSLHSGGGGGGIGPRSSQQHSSFKRPTGTPVMGNRGLETRQSKRSQL HSQAPGPGPPSTQPHHGNNGVVTSAHPITVGALDVMNVKQVVNRYGTLPKGARIGAYLDS LEDSSEAAPALPATAPSLPPANGHATPPAARLNPKASPIPPQQMIRSNSSGGVTMQNNAA ASLNKLQRHRTTTEGTMMTFSSFRAGGSSSSPKRSASGVASGVQPALANLEFPPPPLDLP PPPEEFEGGPPPPPPAPESAVQAIQQHLHAQLPNNGNISNGNGTNNNDSSHNDVSNIAPS VEEASSRFGVSLRKREPSTDSCSSLGSPPEDLKEKLITEIKAAGKDTAPASHLANGSGIA VVDPVSLLVTELAESMNLPKPPPQQQQKLTNGNSTGSGFKAQLKKVEPKKMSAPMPKRTA NTIIDFKAHLRRVDKEKEPATPAPAPATVAVANNANCNTTGTLNRKEDGSKKFSQAMQKT EIKIDVTNSNVEADAGAAGEGDLGKRRSTDDEEQSHTEGLGSGGQGSADMTQSLYEQKPQ IQQKPAVPHKPTKLTIYATPIAKLTEPASSASSTQISRESILELVGLLEGSLKHPVNAIA GSQWLQLSDKLNILHNSCVIFAENGAMPPHSKFQFRELVTRVEAQSQHLRSAGSKNVQDN ERLVAEVGQSLRQISNALNR ; ;
_item_description.description ; A list of keywords. Keywords can be any terms that a user would want to use to lookup this entry, such as, enzymatic activity, function, cellular location, etc. ; _item.name '_sequence.keyword' _item.category_id _item.category_id _item.mandatory_code no _item_type.code line _item_example.case 'inactive mutant, transmembrane protein'
_category.description ; The Universal IDentifier is the primary key for each object, e.g. sequences, structures, features, enzymological data. The UID defines the acession number of an object in the database. The UID provides the unique ID for all categories via parent-child linking. UID are composed as follows: char 1-3: PKR char 4-7: object type, e.g. PSEQ, FEAT, STRC, ENZM char 8-13: number 000001 - 999999 ; _category.id _category.id _category.mandatory_code yes loop_ _category_key.name '_uid.id' loop_ _category_group.id 'inclusive_group' 'general_group' loop_ _category_methods.method_id _category_methods.category_id 'get_uid_category' uid loop_ _category_example.case _category_example.details 'Example 1' ; loop_ _uid.id _uid.status _uid.date_create _uid.update _uid.keyword _uid.description_short _uid.description_long PKRPSEQ000321 ACTIVE 1986-07-21 1995-11-01 Ableson, leukemia, SH2 domain, SH3 domain, tyrosine-protein kinase ; CC -!- CATALYTIC ACTIVITY: ATP + A PROTEIN TYROSINE = ADP + CC PROTEIN TYROSINE PHOSPHATE. CC -!- SUBCELLULAR LOCATION: CYTOPLASMIC. CC -!- SIMILARITY: TO OTHER PROTEIN-TYROSINE KINASES IN THE CATALYTIC CC DOMAIN. BELONGS TO THE ABL SUBFAMILY. CC -!- SIMILARITY: CONTAINS A COPY EACH OF THE SH2 AND SH3 DOMAINS. ; ;
_category.description ; Cross-references to external data ; _category.id _category.id _category.mandatory_code no _category_key.name '_xref.id' loop_ _category_group.id 'inclusive_group' 'xref_group' loop_ _category_methods.method_id _category_methods.category_id 'get_xref_category' xref loop_ _category_examples.case _category_examples.details 'Example Case 1' ; _xref.id loop_ _xref.primary _xref.dbname _xref.name _xref.acc _xref.date _xref.type _xref.source_db _xref.source_accession _xref.comments PKRPSEQ012345 yes SWISS ABL_DROME P00522 1995-11-01 protein . . . no EMBL . M19692 1995-11-01 nucleic SWISS P00522 . no PIR TVFFA A28128 1995-11-01 protein . . . ;