Rv1232c Resolved · high auto-curated
H37Rv Rv1232c · MTBC0 mtbc0_001321 ·
435 aa · 1383305–1384612 (-) ·
RefSeq NP_215748.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | magnesium transporter |
| Revised (this work) | Magnesium transporter. Pfam: SH3_actinomycetes (PF26205.1), MgtE_N (PF03448.23), CBS (PF00571.34). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O86315
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | mgtE |
| eggNOG description | CBS domain |
| Orthologous group | COG2239 |
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 | 0.308 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.34% of strains (497) · 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 |
|---|---|---|---|---|
SH3_actinomycetes | PF26205.1 | 3.3e-22 | 92–164 | Actinomycetes SH3 domain |
MgtE_N | PF03448.23 | 9.2e-23 | 186–285 | MgtE intracellular N domain |
CBS | PF00571.34 | 7.7e-08 | 356–410 | CBS domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1231c (membrane protein), high confidence from genomic context alone (score 965 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) |
|---|---|---|---|---|
Rv1231c |
membrane protein | 965 | 965 ctx | neighborhood:882 cooccurence:713 |
Rv1233c hyp |
hypothetical protein | 804 | 804 ctx | neighborhood:801 |
Rv1230c |
membrane protein | 762 | 762 ctx | neighborhood:761 |
Rv1229c mrp |
multiple resistance/pH adaptation protein | 551 | 551 ctx | neighborhood:548 |
Rv1234 |
transmembrane protein | 500 | 482 ctx | neighborhood:480 |
Rv1238 sugC |
sugar ABC transporter ATP-binding protein SugC | 433 | 411 ctx | neighborhood:404 |
Rv1235 lpqY |
trehalose ABC transporter substrate-binding lipoprotein LpqY | 412 | 411 ctx | neighborhood:404 |
Rv1237 sugB |
sugar ABC transporter permease SugB | 408 | 408 ctx | neighborhood:404 |
Rv1236 sugA |
sugar ABC transporter permease SugA | 429 | 407 ctx | neighborhood:404 |
Rv1239c corA |
magnesium and cobalt transport transmembrane protein CorA | 436 | 207 |
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: magnesium transporter
- Pfam (hmmscan --cut_ga): SH3_actinomycetes PF26205.1 (E=3e-22), MgtE_N PF03448.23 (E=9e-23), CBS PF00571.34 (E=8e-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_215748.1)
- Domains: Pfam-A via hmmscan --cut_ga — SH3_actinomycetes (PF26205.1), MgtE_N (PF03448.23), CBS (PF00571.34)
- 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
COG2239 - Curated reference: UniProt O86315 (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 —
10 functional partner(s); context anchor
Rv1231c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001321|Rv1232c| MGSVNRVYLARLSRMSVLGPLGESFGRVRDVVISISIVRQQPRVLGLVVDLATRRKIFIPILRVAAIEPHAVTLSTGNVSLHRFEQRPGEALALGQVLDTLVKVNDPALPELAGVDVVVTDLGVEQTRSRDWMVTRVAVRTQRRLRRRGPVHVVDWHNVAGLTPSALAMPGQDVAQLLDQFEGWKAVDVADAIRGLPPKRRHEVFKALHDKRLADVLQELPELDQAEVLSQLGTERAADVLEEMDPDDAADLLAVLNPTEAELLLTRMDPGDSGQVRRLLTHSPDTAGGLMTSDPVVLTPDTSIAEALARVRDPDLTPALASMVFVARPPTATPTGHYLGCVHLQRLLRDPPAELVGGVVDTDLLTLTPETPLAAVTRYFAAYNLVCGPVVDDENHLLGAVTVDDLLDHLLPHDWRVDMPELDPSGAPDRPGGPR