Has input
Definition
- The specific molecular target of a Molecular Function. Targets correspond substrates for enzymes, interactors for binding and adaptor activities, gene for transcription factors. Can also be used the describe inputs of Biological Processes that have a high degree of molecular specificity, e.g. to specify the target gene for 'regulation of transcription'.
- Note that more than one input may be used for an annotation: this means that there are multiple substrates for a reaction. However if an enzyme can act on different substrates, or if a transcription factor has multiple targets, this should be captured as independent annotations or independent statements in Protein2GO.
- Formal definition in Relations Ontology (RO): RO:0002233 has input definition: P has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
Usage
- Use of this relation is encouraged when the molecular target of the MF/BP is more specific than what the GO term describes. A common use case is to specify the exact protein target of an MF, e.g. the target of a protein kinase activity.
- The input should represent the biologically meaningful input. Curators need to be careful in distinguishing the conclusion from an experiment from the assay conditions.
Domain
Domain refers to the GO terms that can be further specified with the relation.
- BFO:0000007 process, which corresponds to GO Biological Process and Molecular Function
(remove?? ENTITY_UNION:0000005 ! chemical, gene product, or complex
Range
Range describes the types of entities that can be used with the relation.
- Gene product
- ChemicalEntity: CHEBI:24431 - chemical entity
- ProteinContainingComplex: GO:0032991 - protein-containing complex
Note that domain and range are defined in GO Shapes.
Annotation Extension Usage Examples
1. Specifying the substrate (chemical) of a catalytic activity
Human DGKA phosphorylates 1,2-diacyl-sn-glycerol, PMID:22627129.
Annotation for DGKA | |
Gene product | UniProtKB:P23743 DGKA |
GP2term relation | enables |
GO term | GO:0004143 diacylglycerol kinase activity, has input(CHEBI:17815 1,2-diacyl-sn-glycerol) |
Evidence | IDA |
Reference | PMID:22627129 |
2. Specifying the protein target of a catalytic activity
Human CDC7 phosphorylates MCM2, PMID:15668232.
Annotation for CDC7 | |
Gene product | UniProtKB:O00311 CDC7 |
GP2term relation | enables |
GO term | GO:0004672 protein kinase activity, has input(UniProtKB:P49736 MCM2) |
Evidence | IMP |
Reference | PMID:15668232 |
3. Specifying the gene target of a DNA binding transcription factor
Human NKX6-3 regulates transcription of BAK1, PMID:26314965.
Annotation for NKX6-3 | |
Gene product | UniProtKB:A6NJ46 NKX6-3 |
GP2term relation | enables |
GO term | GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific, has input(UniProtKB:Q16611, BAK1) |
Evidence | IDA |
Reference | PMID:26314965 |
4. Specifying an interaction partner
Human DNM1L binds RAB29, PMID:25767741.
Annotation for DNM1L | |
Gene product | UniProtKB:O00429 DNM1L |
GP2term relation | enables |
GO term | GO:0031267 small GTPase binding, has input(UniProtKB:O14966, RAB29) |
Evidence | IDA |
Reference | PMID:25767741 |
5. Specifying the target(s) of a macromolecule adaptor
Human TJP2 is a molecular adaptor for tight junction proteins F11R and AFDN, PMID:23885123.
Annotation for TJP2 | |
Gene product | UniProtKB:Q9UDY2 TJP2 |
GP2term relation | enables |
GO term | GO:0030674 protein-macromolecule adaptor activity, has input(UniProtKB:Q9Y624, F11R), has input(UniProtKB:P55196, AFDN) |
Evidence | IDA |
Reference | PMID:23885123 |
Back to Annotation usage examples for each annotation extension relation