Rv1146 Resolved · high auto-curated
H37Rv Rv1146 · MTBC0 - ·
470 aa · 1273355–1274767 (+) ·
RefSeq NP_215662.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane transport protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transmembrane transport protein. Pfam: MMPL (PF03176.22). |
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 |
O06546
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable conserved transmembrane transport protein MmpL13b |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | mmpL13 |
| eggNOG description | MmpL family |
| Orthologous group | COG2409 |
| KEGG orthology |
K06994, K20466, K20470
|
| Gene Ontology (38) |
GO:0005575, GO:0005576, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0005887, GO:0006810, GO:0006869, GO:0008150 +26 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 | 0.186 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.24% of strains (351) · 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 |
|---|---|---|---|---|
MMPL | PF03176.22 | 6.2e-23 | 202–422 | MMPL family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mmpL13a (transmembrane transport protein), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1145 mmpL13a |
transmembrane transport protein | 999 | 999 ctx | neighborhood:709 fusion:900 cooccurence:774 coexpression:805 textmining:650 |
Rv1147 hyp |
hypothetical protein | 857 | 857 ctx | neighborhood:490 coexpression:732 |
Rv0736 rslA |
anti-sigma-L factor RslA | 746 | 746 | coexpression:746 |
Rv2714 hyp |
hypothetical protein | 425 | 426 ctx | cooccurence:425 |
Rv0202c mmpL11 |
transmembrane transport protein MmpL11 | 443 | 307 | |
Rv1091 PE_PGRS22 |
PE-PGRS family protein PE_PGRS22 | 528 | 71 | textmining:513 |
Rv3595c PE_PGRS59 |
PE-PGRS family protein PE_PGRS59 | 525 | 71 | textmining:510 |
Rv1396c PE_PGRS25 |
PE-PGRS family protein PE_PGRS25 | 453 | 71 | textmining:436 |
Rv1089A celA2a |
Rv1089A, len: 34 aa. Probable celA2a, first part of cellulase (endoglucanase), similar to N-terminus of others. This region is a possible MT | 560 | 70 | textmining:547 |
Rv1090 celA2b |
Rv1090, (MTV017.43), len: 151 aa. Probable celA2b,second part of cellulase (endoglucanase), similar to C-terminus of others e.g. O08468 cell | 527 | 50 | textmining:523 |
Rv3566A hyp |
hypothetical protein | 549 | 47 | textmining:547 |
Rv0388c PPE9 |
Rv0388c, (MTV036.23c), len: 180 aa. PPE9, Member of the Mycobacterium tuberculosis PPE family, highly similar to others e.g. MTCY10G2_10|Z92 | 434 | 47 | textmining:431 |
Rv0304c PPE5 |
PPE family protein PPE5 | 441 | 46 | textmining:439 |
Rv3233c |
Rv3233c, (MTCY20B11.08c), len: 196 aa. Possible triacylglycerol synthase (See Daniel et al., 2004), similar to C-terminus of Q9RIU8|SCM11.13 | 436 | 46 | textmining:434 |
Rv0305c PPE6 |
PPE family protein PPE6 | 438 | 45 | textmining:436 |
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): transmembrane transport protein
- Pfam (hmmscan --cut_ga): MMPL PF03176.22 (E=6e-23)
- (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_215662.1)
- Domains: Pfam-A via hmmscan --cut_ga — MMPL (PF03176.22)
- 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
COG2409 - Curated reference: UniProt O06546 (TrEMBL, unreviewed; Inferred from homology)
- 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 —
20 functional partner(s); context anchor
mmpL13a - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1146| MATVAFVATASIVITPAAIVLLGPRLDALDVRRLVRRLLGRPDPVHKPVKQLFWYRSSKFVMRRWLPVGTAVVALLVLLGLPFLSVKWGFPDDRVLPRSASARQVGDILRDDFGHDPATQIPIVVPDARGLGPVELDSYAAELSRVPDVSAVAAPTGTFVDGSWVGTPRGATGLAEGSAFLTVSSTAPLFSRASDIQLKRLHQVAGPAGRSVVMAGVAQVNRDSVDAVTDRLPMVLGLIAAITYVLLFLLTGSVVLPAKALVCNVLSLTAAFGALVWIFQEGHFGALGTTPSGTLVANMPVLLFCIAFGLSMDYEVFLVSRIREYWLESGAARPARRSVAEVHAANDESVALGVARTGRVITAAALVMSMSFAALIAAHVSFMRMFGLGLTLAVAADATLVRMVVVPAFMHVTGRWNWWAPRPLAWLHERFGVSEAAEPVSRRRSHAGGLGKIAGRSDGQTIPASLTRNG