Rv1216c Family assigned · medium auto-curated
H37Rv Rv1216c · MTBC0 mtbc0_001304 ·
224 aa · 1367914–1368588 (-) ·
RefSeq NP_215732.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | isoprenylcysteine carboxylmethyltransferase family protein |
| Revised (this work) | Isoprenylcysteine carboxylmethyltransferase family protein. Pfam: DUF1295 (PF06966.18), PEMT (PF04191.19), ICMT (PF04140.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05317
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved integral membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| eggNOG description | PFAM Isoprenylcysteine carboxyl methyltransferase |
| Orthologous group | COG2020 |
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 | 0.249 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 3 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.17% of strains (242) · clonal |
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 |
|---|---|---|---|---|
DUF1295 | PF06966.18 | 4.0e-05 | 104–213 | Protein of unknown function (DUF1295) |
PEMT | PF04191.19 | 1.5e-10 | 111–204 | Phospholipid methyltransferase |
ICMT | PF04140.20 | 9.6e-08 | 133–202 | Isoprenylcysteine carboxyl methyltransferase (ICMT) family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1217c (tetronasin ABC transporter integral membrane protein), high confidence from genomic context alone (score 954 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1217c |
tetronasin ABC transporter integral membrane protein | 964 | 954 ctx | neighborhood:834 coexpression:735 |
Rv1218c |
tetronasin ABC transporter ATP-binding protein | 901 | 831 ctx | neighborhood:801 textmining:438 |
Rv1219c raaS |
transcriptional regulator | 916 | 812 ctx | neighborhood:801 textmining:573 |
Rv1215c hyp |
hypothetical protein | 927 | 746 ctx | neighborhood:744 textmining:724 |
Rv1220c |
methyltransferase | 653 | 537 ctx | neighborhood:536 |
Rv0701 rplC |
50S ribosomal protein L3 | 462 | 462 | |
Rv1214c PE14 |
PE family protein PE14 | 447 | 447 ctx | neighborhood:447 |
Rv3707c hyp |
hypothetical protein | 437 | 437 ctx | cooccurence:436 |
Rv0709 rpmC |
50S ribosomal protein L29 | 431 | 432 | |
Rv2120c |
integral membrane protein | 425 | 426 ctx | cooccurence:422 |
Rv3810 pirG |
cell surface protein | 415 | 416 | |
Rv1388 mihF |
integration host factor MihF | 413 | 414 | coexpression:413 |
Rv3460c rpsM |
30S ribosomal protein S13 | 412 | 413 | coexpression:412 |
Rv0538 |
membrane protein | 426 | 406 | coexpression:404 |
Rv3489 hyp |
hypothetical protein | 724 | 42 | textmining:724 |
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: integral membrane protein
- MTBC0 PGAP product: isoprenylcysteine carboxylmethyltransferase family protein
- Pfam (hmmscan --cut_ga): DUF1295 PF06966.18 (E=4e-05), PEMT PF04191.19 (E=1e-10), ICMT PF04140.20 (E=1e-07)
- (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_215732.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF1295 (PF06966.18), PEMT (PF04191.19), ICMT (PF04140.20)
- 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
COG2020 - Curated reference: UniProt O05317 (TrEMBL, unreviewed; 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 —
15 functional partner(s); context anchor
Rv1217c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001304|Rv1216c| MHIGLKIFIWGVLGLVVFGALLFGPAGTFDYWQAWVFLAAFVSTTIGPTIYLARNDPAALQRRMRSGPLAEGRTIQKFIVIGAFLGFFAMMVLSACDHRYGWSSVPAAVCVIGDVLVMTGLGIAMLVVIQNRYAASTVRVEAGQILASDGLYKIVRHPMYAGNVVMMTGIPLALGSYWAMFILVPGTLVLVFRILDEEKLLTQELSGYREYRQLVRYRLVPYVW