fmt Resolved · high auto-curated
H37Rv Rv1406 · MTBC0 mtbc0_001507 ·
312 aa · 1591510–1592448 (+) ·
RefSeq NP_215922.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | methionyl-tRNA formyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | methionyl-tRNA formyltransferase |
| Revised (this work) | Methionyl-tRNA formyltransferase. Pfam: Formyl_trans_N (PF00551.25), Formyl_trans_C (PF02911.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WND3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Methionyl-tRNA formyltransferase |
| EC (curated) |
EC 2.1.2.9
|
| Curated function | Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | fmt |
| eggNOG description | Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus |
| Orthologous group | COG0223 |
| EC number |
EC 2.1.2.9
|
| KEGG orthology |
K00604
|
| KEGG pathways |
map00670, map00970
|
| Gene Ontology (54) |
GO:0003674, GO:0003824, GO:0004479, GO:0006139, GO:0006396, GO:0006399, GO:0006400, GO:0006412, GO:0006413, GO:0006464, GO:0006518, GO:0006725 +42 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 | 0.597 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 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 |
|---|---|---|---|---|
Formyl_trans_N | PF00551.25 | 1.9e-32 | 2–179 | Formyl transferase |
Formyl_trans_C | PF02911.24 | 1.0e-21 | 204–303 | Formyl transferase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fmu (16S rRNA m5C967 methyltransferase), high confidence from genomic context alone (score 997 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 998 | 997 ctx | neighborhood:881 coexpression:973 |
Rv3356c folD |
bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase | 961 | 947 | coexpression:461 database:900 |
Rv2763c dfrA |
dihydrofolate reductase | 935 | 907 | database:900 |
Rv2211c gcvT |
aminomethyltransferase | 933 | 906 | database:900 |
Rv2124c metH |
methionine synthase | 922 | 905 | database:900 |
Rv0956 purN |
phosphoribosylglycinamide formyltransferase PurN | 935 | 903 | database:900 |
Rv2754c thyX |
thymidylate synthase ThyX | 944 | 902 | database:900 textmining:463 |
Rv1093 glyA1 |
serine hydroxymethyltransferase | 927 | 901 | database:900 |
Rv0389 purT |
phosphoribosylglycinamide formyltransferase PurT | 900 | 901 | database:900 |
Rv0070c glyA2 |
serine hydroxymethyltransferase | 926 | 900 | database:900 |
Rv1007c metS |
methionine--tRNA ligase | 912 | 900 | database:900 |
Rv1408 rpe |
ribulose-phosphate 3-epimerase | 898 | 888 ctx | neighborhood:846 |
Rv1409 ribG |
bifunctional riboflavin biosynthesis diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino) uracil reductas | 866 | 846 ctx | neighborhood:846 |
Rv1402 priA |
primosomal protein N' | 762 | 762 | coexpression:613 |
Rv1405c |
methyltransferase | 758 | 759 ctx | neighborhood:757 |
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: methionyl-tRNA formyltransferase
- MTBC0 PGAP product: methionyl-tRNA formyltransferase
- Pfam (hmmscan --cut_ga): Formyl_trans_N PF00551.25 (E=2e-32), Formyl_trans_C PF02911.24 (E=1e-21)
- (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_215922.1)
- Domains: Pfam-A via hmmscan --cut_ga — Formyl_trans_N (PF00551.25), Formyl_trans_C (PF02911.24)
- 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
COG0223 - Curated reference: UniProt P9WND3 (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 —
81 functional partner(s); context anchor
fmu - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001507|Rv1406|fmt MRLVFAGTPEPALASLRRLIESPSHDVIAVLTRPDAASGRRGKPQPSPVAREAAERGIPVLRPSRPNSAEFVAELSDLAPECCAVVAYGALLGGPLLAVPPHGWVNLHFSLLPAWRGAAPVQAAIAAGDTITGATTFQIEPSLDSGPIYGVVTEVIQPTDTAGDLLKRLAVSGAALLSTTLDGIADQRLTPRPQPADGVSVAPKITVANARVRWDLPAAVVERRIRAVTPNPGAWTLIGDLRVKLGPVHLDAAHRPSKPLPPGGIHVERTSVWIGTGSEPVRLGQIQPPGKKLMNAADWARGARLDLAARAT