Rv1362c Family assigned · low
H37Rv Rv1362c · MTBC0 mtbc0_001464 ·
220 aa · 1544650–1545312 (-) ·
RefSeq NP_215878.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | IcmL/VirB8-like membrane-protein fold. RefSeq leaves it 'membrane protein'. The AlphaFold model superposes on an IcmL-like type-IV-secretion protein (PDB 5cnl; Foldseek prob 1.0, E 1e-4, TM 0.75); its neighbour Rv1363c shares a VirB8-periplasmic-domain fold (7q1v) and the two are mutual STRING partners. A membrane-associated secretion-system-like fold; no classical T4SS is annotated in M. tuberculosis. |
Curated reference (UniProt)
| UniProt |
P9WM01
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv1362c |
UniProt still lists this protein as Uncharacterized protein Rv1362c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| eggNOG description | Heat shock 70 kDa protein |
| Orthologous group | COG0443 |
| KEGG orthology |
K18481
|
| KEGG modules |
M00670
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.223 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1363c (membrane protein), high confidence from genomic context alone (score 987 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1363c |
membrane protein | 986 | 987 ctx | neighborhood:800 cooccurence:773 coexpression:732 |
Rv0594 mce2F |
Mce family protein Mce2F | 774 | 774 ctx | cooccurence:765 |
Rv0172 mce1D |
Mce family protein Mce1D | 772 | 773 ctx | cooccurence:763 |
Rv0169 mce1A |
Mce family protein Mce1A | 771 | 771 ctx | cooccurence:761 |
Rv0174 mce1F |
Mce family protein Mce1F | 770 | 770 ctx | cooccurence:761 |
Rv3499c mce4A |
Mce family protein Mce4A | 765 | 765 ctx | cooccurence:754 |
Rv3495c lprN |
Mce family lipoprotein LprN | 764 | 764 ctx | cooccurence:753 |
Rv0591 mce2C |
Mce family protein Mce2C | 762 | 763 ctx | cooccurence:754 |
Rv0589 mce2A |
Mce family protein Mce2A | 762 | 762 ctx | cooccurence:753 |
Rv0592 mce2D |
Mce family protein Mce2D | 762 | 762 ctx | cooccurence:753 |
Rv0173 lprK |
Mce family lipoprotein LprK | 759 | 759 ctx | cooccurence:749 |
Rv3496c mce4D |
Mce family protein Mce4D | 755 | 756 ctx | cooccurence:744 |
Rv1972 |
Mce associated membrane protein | 752 | 753 ctx | cooccurence:719 |
Rv0593 lprL |
Mce family lipoprotein LprL | 749 | 749 ctx | cooccurence:740 |
Rv3497c mce4C |
Mce family protein Mce4C | 746 | 747 ctx | cooccurence:728 |
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
- Foldseek -> IcmL-like T4SS protein (5cnl), prob 1.0, E 1e-4, TM 0.75
- Paired with Rv1363c (VirB8-like, 7q1v); mutual STRING partners
- Structural homology: AlphaFold DB model + Foldseek vs PDB (project 'Still unknown gene function', phase5-7, 2026-06-10). A fold-level family assignment, not a demonstrated activity.
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_215878.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG0443 - Curated reference: UniProt P9WM01 (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 —
303 functional partner(s); context anchor
Rv1363c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001464|Rv1362c| MTDDVRDVNTETTDATEVAEIDSAAGEAGDSATEAFDTDSATESTAQKGQRHRDLWRMQVTLKPVPVILILLMLISGGATGWLYLEQYRPDQQTDSGAARAAVAAASDGTIALLSYSPDTLDQDFATARSHLAGDFLSYYDQFTQQIVAPAAKQKSLKTTAKVVRAAVSELHPDSAVVLVFVDQSTTSKDSPNPSMAASSVMVTLAKVDGNWLITKFTPV