Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | polypeptide deformylase |
|---|
| MTBC0 PGAP re-annotation | peptide deformylase |
|---|
| Revised (this work) | Peptide deformylase. Pfam: Pep_deformylase (PF01327.27). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIJ3
SwissProt · reviewed
· Evidence at protein level
|
|---|
| UniProt name | Peptide deformylase |
|---|
| EC (curated) |
EC 3.5.1.88
|
|---|
| Curated function | Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions. |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|
| Preferred name | def |
|---|
| eggNOG description | Removes the formyl group from the N-terminal Met of newly synthesized proteins. Requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions |
|---|
| Orthologous group | COG0242 |
|---|
| EC number |
EC 3.5.1.88
|
|---|
| KEGG orthology |
K01462
|
|---|
| Gene Ontology (28) |
GO:0003674, GO:0003824, GO:0006464, GO:0006807, GO:0008150, GO:0008152, GO:0009987, GO:0016787, GO:0016810, GO:0016811, GO:0018193, GO:0018206 +16 more
|
|---|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are
computed annotations, not manual curation; cross-check against the primary literature
before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS |
1.396 · diversifying/relaxed
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
1 synonymous, 4 missense, 0 nonsense, 0 frameshift
|
|---|
pN/pS from segregating SNPs (singletons removed) normalised by possible sites.
Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene).
A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic
variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A
clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a
convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|
Pep_deformylase | PF01327.27 |
1.7e-38 | 5–163 |
Polypeptide deformylase |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv2442c rplU |
50S ribosomal protein L21 |
927 |
924 |
experimental:888 |
Rv2462c tig |
trigger factor |
934 |
923 |
experimental:888 |
Rv0706 rplV |
50S ribosomal protein L22 |
924 |
921 |
experimental:921 |
Rv0056 rplI |
50S ribosomal protein L9 |
920 |
921 |
experimental:888 |
Rv3456c rplQ |
50S ribosomal protein L17 |
915 |
915 |
experimental:914 |
Rv0702 rplD |
50S ribosomal protein L4 |
914 |
915 |
experimental:895 |
Rv0715 rplX |
50S ribosomal protein L24 |
912 |
913 |
experimental:888 |
Rv1643 rplT |
50S ribosomal protein L20 |
914 |
911 |
experimental:888 |
Rv0053 rpsF |
30S ribosomal protein S6 |
906 |
906 |
experimental:901 |
Rv3443c rplM |
50S ribosomal protein L13 |
902 |
902 |
experimental:888 |
Rv2909c rpsP |
30S ribosomal protein S16 |
901 |
902 |
experimental:888 |
Rv3442c rpsI |
30S ribosomal protein S9 |
901 |
902 |
experimental:888 |
Rv2412 rpsT |
30S ribosomal protein S20 |
924 |
901 |
experimental:888 |
Rv2890c rpsB |
30S ribosomal protein S2 |
900 |
900 |
experimental:888 |
Rv2441c rpmA |
50S ribosomal protein L27 |
898 |
899 |
experimental:888 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression,
experimental, database, text-mining) into a 0–1000 score. The ctx
badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion,
phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an
unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not
depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with
the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: polypeptide deformylase
- MTBC0 PGAP product: peptide deformylase
- Pfam (hmmscan --cut_ga): Pep_deformylase PF01327.27 (E=2e-38)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024),
An imputed ancestral reference genome for the MTBC,
doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_214943.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pep_deformylase (PF01327.27)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG0242
- Curated reference: UniProt
P9WIJ3
(SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of
145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
98 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000451|Rv0429c|def
MAVVPIRIVGDPVLHTATTPVTVAADGSLPADLAQLIATMYDTMDAANGVGLAANQIGCSLRLFVYDCAADRAMTARRRGVVINPVLETSEIPETMPDPDTDDEGCLSVPGESFPTGRAKWARVTGLDADGSPVSIEGTGLFARMLQHETGHLDGFLYLDRLIGRYARNAKRAVKSHGWGVPGLSWLPGEDPDPFGH
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