Rv1234 Resolved · high auto-curated
H37Rv Rv1234 · MTBC0 mtbc0_001323 ·
175 aa · 1385420–1385947 (+) ·
RefSeq NP_215750.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | general stress protein |
| Revised (this work) | General stress protein. Pfam: YflT (PF11181.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O50451
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2CAW2 |
|---|
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 | 0.122 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 1 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 |
|---|---|---|---|---|
YflT | PF11181.14 | 2.6e-23 | 37–114 | Heat induced stress protein YflT domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lpqY (trehalose ABC transporter substrate-binding lipoprotein LpqY), high confidence from genomic context alone (score 855 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1235 lpqY |
trehalose ABC transporter substrate-binding lipoprotein LpqY | 855 | 855 ctx | neighborhood:853 |
Rv1236 sugA |
sugar ABC transporter permease SugA | 850 | 849 ctx | neighborhood:847 |
Rv1238 sugC |
sugar ABC transporter ATP-binding protein SugC | 846 | 846 ctx | neighborhood:845 |
Rv1237 sugB |
sugar ABC transporter permease SugB | 846 | 846 ctx | neighborhood:844 |
Rv1364c |
sigma factor regulatory protein | 842 | 834 | coexpression:831 |
Rv1244 lpqZ |
lipoprotein LpqZ | 790 | 791 | coexpression:705 |
Rv3759c proX |
glycine betaine/carnitine/choline/L-proline ABC transporter substrate-binding lipoprotein ProX | 739 | 740 | coexpression:706 |
Rv3470c ilvB2 |
acetolactate synthase large subunit | 735 | 725 | coexpression:724 |
Rv1876 bfrA |
bacterioferritin BfrA | 664 | 646 | coexpression:646 |
Rv1231c |
membrane protein | 640 | 640 ctx | neighborhood:527 |
Rv3278c |
transmembrane protein | 585 | 584 | coexpression:498 |
Rv1233c hyp |
hypothetical protein | 538 | 538 ctx | neighborhood:533 |
Rv1209 hyp |
hypothetical protein | 536 | 536 ctx | cooccurence:534 |
Rv1226c |
transmembrane protein | 529 | 528 | coexpression:501 |
Rv0862c hyp |
hypothetical protein | 524 | 524 ctx | cooccurence:504 |
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: transmembrane protein
- MTBC0 PGAP product: general stress protein
- Pfam (hmmscan --cut_ga): YflT PF11181.14 (E=3e-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_215750.1)
- Domains: Pfam-A via hmmscan --cut_ga — YflT (PF11181.14)
- 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
2CAW2 - Curated reference: UniProt O50451 (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 —
47 functional partner(s); context anchor
lpqY - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001323|Rv1234| MTSPFQPRQVPGSTPAAAGAGRRGVPALPTPPKGWPVGSYPTYAEAQRAVDYLSEQQFPVQQVTIVGVDLMQVERVTGRLTWPKVLGGGVLSGAWLGLFIGLVLGFFSPNPWSALVTGLVAGVFFGLITSAVPYAMARGTRDFSSTMQLVAGRYDVLCDPQNAEKARDLLARLAI