infC Resolved · high auto-curated
H37Rv Rv1641 · MTBC0 mtbc0_001750 ·
201 aa · 1864294–1864899 (+) ·
RefSeq NP_216157.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | initiation factor IF-3 |
|---|---|
| MTBC0 PGAP re-annotation | translation initiation factor IF-3 |
| Revised (this work) | Translation initiation factor IF-3. Pfam: IF3_N (PF05198.22), IF3_C (PF00707.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKJ9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Translation initiation factor IF-3 |
| Curated function | IF-3 binds to the 30S ribosomal subunit and shifts the equilibrium between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | infC |
| eggNOG description | IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins |
| Orthologous group | COG0290 |
| KEGG orthology |
K02520
|
| Gene Ontology (60) |
GO:0003674, GO:0003676, GO:0003723, GO:0003743, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006412 +48 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 | 0.961 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 6 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 |
|---|---|---|---|---|
IF3_N | PF05198.22 | 1.0e-32 | 7–75 | Translation initiation factor IF-3, N-terminal domain |
IF3_C | PF00707.28 | 3.1e-32 | 84–168 | Translation initiation factor IF-3, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplT (50S ribosomal protein L20), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1643 rplT |
50S ribosomal protein L20 | 998 | 996 ctx | neighborhood:750 cooccurence:578 coexpression:967 textmining:606 |
Rv1642 rpmI |
50S ribosomal protein L35 | 997 | 994 ctx | neighborhood:811 coexpression:968 textmining:622 |
Rv3460c rpsM |
30S ribosomal protein S13 | 996 | 988 | coexpression:942 experimental:765 textmining:731 |
Rv0683 rpsG |
30S ribosomal protein S7 | 989 | 988 | coexpression:888 experimental:882 |
Rv3459c rpsK |
30S ribosomal protein S11 | 992 | 982 | coexpression:859 experimental:878 textmining:588 |
Rv0705 rpsS |
30S ribosomal protein S19 | 989 | 976 | coexpression:849 experimental:849 textmining:587 |
Rv3462c infA |
translation initiation factor IF-1 | 992 | 953 | coexpression:785 experimental:790 textmining:850 |
Rv1388 mihF |
integration host factor MihF | 958 | 952 | coexpression:731 experimental:765 |
Rv0682 rpsL |
30S ribosomal protein S12 | 955 | 948 | coexpression:906 experimental:474 |
Rv0640 rplK |
50S ribosomal protein L11 | 972 | 946 | coexpression:946 textmining:519 |
Rv2890c rpsB |
30S ribosomal protein S2 | 972 | 935 | coexpression:839 experimental:474 textmining:590 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 970 | 933 | coexpression:877 experimental:474 textmining:585 |
Rv0053 rpsF |
30S ribosomal protein S6 | 941 | 923 | coexpression:852 experimental:474 |
Rv3458c rpsD |
30S ribosomal protein S4 | 935 | 923 | coexpression:859 experimental:474 |
Rv2785c rpsO |
30S ribosomal protein S15 | 940 | 922 ctx | cooccurence:403 coexpression:674 experimental:615 |
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: initiation factor IF-3
- MTBC0 PGAP product: translation initiation factor IF-3
- Pfam (hmmscan --cut_ga): IF3_N PF05198.22 (E=1e-32), IF3_C PF00707.28 (E=3e-32)
- (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_216157.1)
- Domains: Pfam-A via hmmscan --cut_ga — IF3_N (PF05198.22), IF3_C (PF00707.28)
- 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
COG0290 - Curated reference: UniProt P9WKJ9 (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 —
143 functional partner(s); context anchor
rplT - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001750|Rv1641|infC MSTETRVNERIRVPEVRLIGPGGEQVGIVRIEDALRVAADADLDLVEVAPNARPPVCKIMDYGKYKYEAAQKARESRRNQQQTVVKEQKLRPKIDDHDYETKKGHVVRFLEAGSKVKVTIMFRGREQSRPELGYRLLQRLGADVADYGFIETSAKQDGRNMTMVLAPHRGAKTRARARHPGEPAGGPPPKPTAGDSKAAPN