Rv1139c Family assigned · medium auto-curated
H37Rv Rv1139c · MTBC0 mtbc0_001224 ·
166 aa · 1274925–1275425 (-) ·
RefSeq NP_215655.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | isoprenylcysteine carboxyl methyltransferase family protein |
| Revised (this work) | Isoprenylcysteine carboxyl methyltransferase family protein. Pfam: ICMT (PF04140.20), PEMT (PF04191.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06539
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved hypothetical membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Isoprenylcysteine carboxyl methyltransferase |
| Orthologous group | COG1755 |
| KEGG orthology |
K16168
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 |
|---|---|---|---|---|
ICMT | PF04140.20 | 1.0e-26 | 73–163 | Isoprenylcysteine carboxyl methyltransferase (ICMT) family |
PEMT | PF04191.19 | 8.8e-08 | 75–163 | Phospholipid methyltransferase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1138c (oxidoreductase), high confidence from genomic context alone (score 979 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1138c |
oxidoreductase | 988 | 979 ctx | neighborhood:881 cooccurence:767 textmining:489 |
Rv1660 pks10 |
chalcone synthase | 926 | 901 ctx | cooccurence:774 coexpression:532 |
Rv1665 pks11 |
chalcone synthase | 904 | 871 ctx | cooccurence:774 |
Rv1372 pks18 |
alpha-pyrone synthesis polyketide synthase-like protein | 875 | 832 ctx | cooccurence:702 coexpression:400 |
Rv1137c |
Hypothetical protein; Rv1137c, (MTCI65.04c), len: 122 aa. Hypothetical unknown protein. | 767 | 767 ctx | neighborhood:737 |
Rv2638 hyp |
hypothetical protein | 606 | 215 | textmining:519 |
Rv2161c hyp |
hypothetical protein | 805 | 55 | textmining:803 |
Rv2781c |
oxidoreductase | 815 | 54 | textmining:813 |
Rv0952 sucD |
succinyl-CoA ligase subunit alpha | 437 | 50 | textmining:432 |
Rv3224 |
iron-regulated short-chain dehydrogenase/reductase | 657 | 47 | textmining:655 |
Rv3572 hyp |
hypothetical protein | 656 | 47 | textmining:654 |
Rv2192c trpD |
anthranilate phosphoribosyltransferase | 523 | 47 | textmining:520 |
Rv2643 arsC |
arsenic-transport integral membrane protein ArsC | 480 | 46 | textmining:478 |
Rv3089 fadD13 |
long chain-fatty-acid--CoA ligase FadD13 | 431 | 44 | textmining:430 |
Rv0820 phoT |
phosphate ABC transporter ATP-binding protein PhoT | 514 | 42 | textmining:514 |
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: hypothetical protein
- MTBC0 PGAP product: isoprenylcysteine carboxyl methyltransferase family protein
- Pfam (hmmscan --cut_ga): ICMT PF04140.20 (E=1e-26), PEMT PF04191.19 (E=9e-08)
- (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_215655.1)
- Domains: Pfam-A via hmmscan --cut_ga — ICMT (PF04140.20), PEMT (PF04191.19)
- 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
COG1755 - Curated reference: UniProt O06539 (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 —
18 functional partner(s); context anchor
Rv1138c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001224|Rv1139c| MYYLLILAVVFERLAELVVAQRNARWSFAQGGKEFGRPHYVVMVILHTALLLGCVVEPWALHRPFIPWLGWPMLAVVVASQGLRWWCVKSLGKRWNTRVIVLPHATLVRRGPYRWMRHPNYVAVVAEGFALPLVHTAWLTALVFTLANATLLTVRLRVENSVLGYI