Rv1861 Family assigned · medium auto-curated
H37Rv Rv1861 · MTBC0 mtbc0_001974 ·
101 aa · 2127203–2127508 (+) ·
RefSeq NP_216377.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | GlsB/YeaQ/YmgE family stress response membrane protein |
| Revised (this work) | GlsB/YeaQ/YmgE family stress response membrane protein. Pfam: Transgly_assoc (PF04226.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95154
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable conserved transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Transglycosylase associated protein |
| Orthologous group | COG2261 |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 3 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 |
|---|---|---|---|---|
Transgly_assoc | PF04226.19 | 1.6e-12 | 51–100 | Transglycosylase associated protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: adhA (alcohol dehydrogenase A), high confidence from genomic context alone (score 797 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1862 adhA |
alcohol dehydrogenase A | 796 | 797 ctx | neighborhood:790 |
Rv1364c |
sigma factor regulatory protein | 680 | 662 | coexpression:656 |
Rv3701c egtD |
histidine-specific methyltransferase EtgD | 645 | 645 | coexpression:645 |
Rv1860 apa hyp |
hypothetical protein | 550 | 551 ctx | neighborhood:544 |
Rv1859 modC |
molybdenum ABC transporter ATP-binding protein ModC | 546 | 546 ctx | neighborhood:544 |
Rv1954A |
Rv1954A, len: 100 aa. Hypothetical unknown protein. | 543 | 517 | coexpression:508 |
Rv1234 |
transmembrane protein | 444 | 437 | coexpression:418 |
Rv0204c |
transmembrane protein | 455 | 434 ctx | cooccurence:415 |
Rv1876 bfrA |
bacterioferritin BfrA | 423 | 423 | coexpression:406 |
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: GlsB/YeaQ/YmgE family stress response membrane protein
- Pfam (hmmscan --cut_ga): Transgly_assoc PF04226.19 (E=2e-12)
- (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_216377.1)
- Domains: Pfam-A via hmmscan --cut_ga — Transgly_assoc (PF04226.19)
- 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
COG2261 - Curated reference: UniProt P95154 (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 —
9 functional partner(s); context anchor
adhA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001974|Rv1861| MDITATTEFSAMNLDGKTGIGWLGYIVIGGIAGWLASKIVKGGGSGILMNVVIGVVGAFGAGLVLNALGVDVNHGGYWFTFFVALGGAVVLLWIVGMVRKT