ACTMAP GO-record audit

Generated by analyze_actmap_go.py (standard library only). Re-run to regenerate; nothing below is hardcoded.

1. GOA rows and WITH/FROM resolution

6 GOA rows; 5 WITH/FROM tokens in total.

term	label	evidence	reference	assigned by	WITH/FROM
GO:0005737	cytoplasm	IEA	GO_REF:0000044	UniProt	UniProtKB-SubCell:SL-0086
GO:0004239	initiator methionyl aminopeptidase activity	IEA	GO_REF:0000107	Ensembl	UniProtKB:J3QPC3 \| ensembl:ENSMUSP00000137189
GO:0016485	protein processing	IEA	GO_REF:0000107	Ensembl	UniProtKB:J3QPC3 \| ensembl:ENSMUSP00000137189
GO:0070005	cysteine-type aminopeptidase activity	IDA	PMID:36173861	FlyBase	-
GO:0004239	initiator methionyl aminopeptidase activity	IDA	PMID:36173861	UniProt	-
GO:0016485	protein processing	IDA	PMID:36173861	UniProt	-

Resolved sources

UniProtKB-SubCell:SL-0086 - not a UniProt accession; not resolved here.
ensembl:ENSMUSP00000137189 - not a UniProt accession; not resolved here.
J3QPC3 -> J3QPC3 (ACTMP_MOUSE), Actin maturation protease, gene ['Actmap'], Mus musculus, 361 aa, UniProtKB reviewed (Swiss-Prot); hits returned for the query: 1; requested accession returned itself: True

Does each source carry its own evidence for the term it donated?

row term	source	source's own evidence for that term	its WITH/FROM points back at the target?
GO:0004239	`UniProtKB:J3QPC3`	ISS (GO_REF:0000024, UniProt), IEA (GO_REF:0000107, Ensembl), ISO (GO_REF:0000119, GO_Central), IDA (PMID:36173861, UniProt)	GO_REF:0000024, GO_REF:0000107, GO_REF:0000119
GO:0016485	`UniProtKB:J3QPC3`	IEA (GO_REF:0000107, Ensembl), ISO (GO_REF:0000119, GO_Central), IDA (PMID:36173861, UniProt)	GO_REF:0000107, GO_REF:0000119

2. Which peptidase branch do ACTMAP's MF terms sit in?

GO:0008238 exopeptidase activity definition:

Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain, in a reaction that requires a free N-terminal amino group, C-terminal carboxyl group or both.

definition contains the clause "free N-terminal amino group": True
GO:0004239 (initiator methionyl aminopeptidase activity) is under GO:0008238: True
GO:0070005 (cysteine-type aminopeptidase activity) is under GO:0008238: True
GO:0008242 omega peptidase activity is under GO:0008238: False

Precedent for a single-residue-releasing enzyme acting on a blocked N-terminus:
- GO:0016920 pyroglutamyl-peptidase activity under omega peptidase: True
- GO:0016920 pyroglutamyl-peptidase activity under cysteine type peptidase: True
- GO:0016920 pyroglutamyl-peptidase activity under aminopeptidase: False

Term records

GO:0004239 initiator methionyl aminopeptidase activity - EC xrefs ['3.4.11.18']; obsolete: False; comment: This term was reinstated from obsolete
def: Catalysis of the release of N-terminal initiator methionine from peptides.
GO:0070005 cysteine-type aminopeptidase activity - EC xrefs -; obsolete: False; comment: -
def: Catalysis of the hydrolysis of a single N-terminal amino acid residue from a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
GO:0004177 aminopeptidase activity - EC xrefs ['3.4.11.-', '3.4.11.1', '3.4.11.21', '3.4.11.22', '3.4.11.5', '3.4.11.6', '3.4.11.9']; obsolete: False; comment: -
def: Catalysis of the hydrolysis of a single N-terminal amino acid residue from a polypeptide chain.
GO:0008238 exopeptidase activity - EC xrefs -; obsolete: False; comment: -
def: Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain, in a reaction that requires a free N-terminal amino group, C-terminal carboxyl group or both.
GO:0008242 omega peptidase activity - EC xrefs ['3.4.19.-', '3.4.19.1', '3.4.19.2']; obsolete: False; comment: -
def: Catalysis of the cleavage of non-standard peptide bonds releasing substituted amino acids such as pyroglutamate or cleave isopeptide bonds, such as many deubiquitinating enzymes.
GO:0016920 pyroglutamyl-peptidase activity - EC xrefs ['3.4.19.3', '3.4.19.6']; obsolete: False; comment: -
def: Catalysis of the release of the N-terminal pyroglutamyl group from a peptide or protein.
GO:0008234 cysteine-type peptidase activity - EC xrefs -; obsolete: False; comment: -
def: Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
GO:0016485 protein processing - EC xrefs -; obsolete: False; comment: -
def: Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.

3. Census of `GO:0004239` usage

annotations to GO:0004239 across all taxa: 44884 (overwhelmingly IEA, so a full census is impractical)
restricted to taxa 9606,10090,7227,7955,559292: 86 annotations on 74 gene products
of these, 4 are ACTMAP-family (PANTHER PTHR28631) and 70 are not
non-ACTMAP symbols carrying the term: B3KWL6, CG13630, CG5188-RA, MAP1, MAP1A, MAP1B, MAP2, METAP1, METAP1D, METAP2, METAP2A, METAP2B, Q96B43, RNPEPL1, UND

ACTMAP-family product	symbol	taxon	evidence	references
B0V3H4	actmap	7955	ISS	GO_REF:0000024
J3QPC3	Actmap	10090	IDA, IEA, ISO, ISS	GO_REF:0000024, GO_REF:0000107, GO_REF:0000119, PMID:36173861
Q5BKX5	ACTMAP	9606	IDA, IEA	GO_REF:0000107, PMID:36173861
Q9VCE8	CG33108	7227	ISS	GO_REF:0000024

Family-wide usage of `GO:0004239` (not taxon-restricted)

The census above is limited to five taxa and therefore understates the family. Asking each reviewed PTHR28631 member directly: 6 of 6 carry the term.

accession	gene	carries GO:0004239	evidence	references
A6QQD2	ACTMAP	True	ISS	GO_REF:0000024
B0BM95	actmap	True	ISS	GO_REF:0000024
B0V3H4	actmap	True	ISS	GO_REF:0000024
J3QPC3	Actmap	True	IDA, IEA, ISO, ISS	GO_REF:0000024, GO_REF:0000107, GO_REF:0000119, PMID:36173861
Q5BKX5	ACTMAP	True	IDA, IEA	GO_REF:0000107, PMID:36173861
Q9VCE8	CG33108	True	ISS	GO_REF:0000024

3b. Can ACTMAP use a substrate-specific process term?

term	name	under GO:0006508	under GO:0036211	under GO:0030036	under GO:0051604
GO:0016485	protein processing	True	False	False	True
GO:0030047	actin modification	False	True	True	False
GO:0007014	actin ubiquitination	False	True	True	False

GO keeps proteolysis and protein modification in disjoint branches: True - GO:0016485 protein processing is under GO:0006508 and is NOT under GO:0036211, while GO:0030047 actin modification is NOT under GO:0006508 and is under GO:0036211.
NAA80 (Q93015) carries GO:0030047 3 time(s): IDA (PMID:29581253, UniProt), IDA (PMID:29581307, UniProt), IDA (PMID:30028079, UniProt) - but NAA80's reaction is an acetyl transfer, an additive modification, so the precedent does not extend to peptide-bond hydrolysis.
Drosophila ortholog Q9VCE8 (CG33108) carries 3 annotation(s):
GO:0004239 ISS (GO_REF:0000024) assigned by UniProt, WITH/FROM UniProtKB:Q5BKX5
GO:0070005 ISS (GO_REF:0000024) assigned by FlyBase, WITH/FROM UniProtKB:Q5BKX5
GO:0016485 ISS (GO_REF:0000024) assigned by FlyBase, WITH/FROM UniProtKB:Q5BKX5

4. Curation state of the orthologue and of the evolutionary-model pipeline

mouse orthologue J3QPC3 carries 13 GO annotations
of which 3 are root ND (no data) rows: GO:0003674 (GO_REF:0000015, MGI), GO:0008150 (GO_REF:0000015, MGI), GO:0005575 (GO_REF:0000015, MGI)
root ND present in all three aspects: True - i.e. the model organism database has not curated the gene, so the mouse knockout phenotype is unrepresented and the human record has nothing to receive by orthology beyond the UniProt annotations
human UniProt cross-reference: DR PAN-GO; Q5BKX5; 0 GO annotations based on evolutionary models.