Rv3493c Resolved · medium auto-curated
H37Rv Rv3493c · MTBC0 mtbc0_003708 ·
242 aa · 3935529–3936257 (-) ·
RefSeq NP_218010.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | Mce associated protein |
|---|---|
| MTBC0 PGAP re-annotation | mammalian cell entry protein |
| Revised (this work) | Mammalian cell entry protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X7G4
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved hypothetical Mce associated alanine and valine rich protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2ANNP |
|---|---|
| KEGG orthology |
K18481
|
| KEGG modules |
M00670
|
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 | 0.717 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 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: Rv3492c (Mce associated protein), high confidence from genomic context alone (score 973 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3492c |
Mce associated protein | 973 | 973 ctx | neighborhood:882 coexpression:780 |
Rv3496c mce4D |
Mce family protein Mce4D | 951 | 951 ctx | neighborhood:879 coexpression:615 |
Rv3494c mce4F |
Mce family protein Mce4 | 905 | 905 ctx | neighborhood:881 |
Rv3497c mce4C |
Mce family protein Mce4C | 901 | 902 ctx | neighborhood:879 |
Rv3495c lprN |
Mce family lipoprotein LprN | 900 | 901 ctx | neighborhood:879 |
Rv3498c mce4B |
Mce family protein Mce4B | 884 | 885 ctx | neighborhood:879 |
Rv3499c mce4A |
Mce family protein Mce4A | 882 | 883 ctx | neighborhood:879 |
Rv3500c yrbE4B |
integral membrane protein | 860 | 860 ctx | neighborhood:856 |
Rv3501c yrbE4A |
integral membrane protein | 815 | 816 ctx | neighborhood:813 |
Rv3299c atsB |
arylsulfatase AtsB | 730 | 730 | coexpression:730 |
Rv3502c |
3-oxoacyl-ACP reductase | 516 | 516 ctx | neighborhood:516 |
Rv2600 |
integral membrane protein | 414 | 415 | coexpression:415 |
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: Mce associated protein
- MTBC0 PGAP product: mammalian cell entry protein
- (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_218010.1)
- 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
2ANNP - Curated reference: UniProt I6X7G4 (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 —
12 functional partner(s); context anchor
Rv3492c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003708|Rv3493c| MAADTGVAGGQQSTTRRARRKASRPAGPAEGESSRPAQGAATVRAAARTESKPAKAAKPALRPVKPPPRRPAHRVLVGWLSLAAGLLAIAALAWGVTALVMQNRDADARQARNQRFVDAATQTVVNMFSYTPDTIDESVNRFVNGTSGPLRGMLNANNNVDNLKGLFRATNATSEAVVNGAALEGIDEISDNASVLVSVRVTVADIDGVNKPSMPYRLRVIVHEDENGRMTGYDLKYPDGGN