infA Resolved · high auto-curated
H37Rv Rv3462c · MTBC0 - ·
73 aa · 3880432–3880653 (-) ·
RefSeq NP_217979.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | translation initiation factor IF-1 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Translation initiation factor IF-1. Pfam: eIF-1a (PF01176.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WKK3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Translation initiation factor IF-1 |
| Curated function | One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre-initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initiation complex. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | infA |
| eggNOG description | One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre- initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initation complex |
| Orthologous group | COG0361 |
| KEGG orthology |
K02518
|
| Gene Ontology (20) |
GO:0003674, GO:0005488, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0008150, GO:0016020, GO:0030312 +8 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 0 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 |
|---|---|---|---|---|
eIF-1a | PF01176.26 | 9.6e-30 | 8–71 | Translation initiation factor 1A / IF-1 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rpsK (30S ribosomal protein S11), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3459c rpsK |
30S ribosomal protein S11 | 999 | 1000 ctx | neighborhood:547 cooccurence:653 coexpression:923 experimental:928 database:547 textmining:452 |
Rv0682 rpsL |
30S ribosomal protein S12 | 999 | 999 | coexpression:967 experimental:928 database:655 |
Rv3460c rpsM |
30S ribosomal protein S13 | 999 | 999 ctx | neighborhood:547 cooccurence:493 coexpression:927 experimental:829 database:629 textmining:441 |
Rv0718 rpsH |
30S ribosomal protein S8 | 999 | 999 ctx | cooccurence:639 coexpression:863 experimental:928 database:659 |
Rv0702 rplD |
50S ribosomal protein L4 | 998 | 999 | coexpression:865 experimental:928 database:844 |
Rv0707 rpsC |
30S ribosomal protein S3 | 998 | 999 ctx | cooccurence:656 coexpression:860 experimental:928 database:659 |
Rv0705 rpsS |
30S ribosomal protein S19 | 998 | 999 ctx | cooccurence:447 coexpression:891 experimental:928 database:659 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 998 | 998 | coexpression:890 experimental:928 database:652 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 998 | 998 ctx | cooccurence:527 coexpression:864 experimental:928 database:659 |
Rv0721 rpsE |
30S ribosomal protein S5 | 998 | 998 | coexpression:864 experimental:928 database:652 |
Rv3458c rpsD |
30S ribosomal protein S4 | 998 | 998 ctx | neighborhood:508 cooccurence:496 coexpression:767 experimental:928 database:652 |
Rv0683 rpsG |
30S ribosomal protein S7 | 997 | 997 | coexpression:858 experimental:928 database:652 |
Rv3461c rpmJ |
50S ribosomal protein L36 | 996 | 995 ctx | neighborhood:812 coexpression:975 |
Rv2785c rpsO |
30S ribosomal protein S15 | 994 | 994 | coexpression:693 experimental:928 database:652 |
Rv2890c rpsB |
30S ribosomal protein S2 | 994 | 993 | coexpression:702 experimental:928 database:611 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): translation initiation factor IF-1
- Pfam (hmmscan --cut_ga): eIF-1a PF01176.26 (E=1e-29)
- (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_217979.1)
- Domains: Pfam-A via hmmscan --cut_ga — eIF-1a (PF01176.26)
- 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
COG0361 - Curated reference: UniProt P9WKK3 (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 —
139 functional partner(s); context anchor
rpsK - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3462c|infA MAKKDGAIEVEGRVVEPLPNAMFRIELENGHKVLAHISGKMRQHYIRILPEDRVVVELSPYDLSRGRIVYRYK