Rv2828c Family assigned · low auto-curated
H37Rv Rv2828c · MTBC0 mtbc0_003003 ·
181 aa · 3153558–3154103 (-) ·
RefSeq NP_217344.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF1802 family protein |
| Revised (this work) | DUF1802 family 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 |
I6X5G8
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DUF1802 family protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Domain of unknown function (DUF1802) |
| Orthologous group | COG4293 |
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 | 2.676 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 7 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.63% of strains (917) · 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 |
|---|---|---|---|---|
DUF1802 | PF08819.18 | 9.1e-56 | 4–174 | Domain of unknown function (DUF1802) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC22 (ribonuclease VapC22), high confidence from genomic context alone (score 754 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) |
|---|---|---|---|---|
Rv2825c hyp |
hypothetical protein | 852 | 852 | coexpression:804 |
Rv2828A hyp |
hypothetical protein | 802 | 801 ctx | neighborhood:801 |
Rv2829c vapC22 |
ribonuclease VapC22 | 755 | 754 ctx | neighborhood:751 |
Rv2830c vapB22 |
antitoxin VapB22 | 753 | 753 ctx | neighborhood:751 |
Rv3779 |
transmembrane protein | 648 | 648 ctx | cooccurence:648 |
Rv2831 echA16 |
enoyl-CoA hydratase EchA16 | 582 | 582 ctx | neighborhood:581 |
Rv0048c |
membrane protein | 544 | 544 ctx | cooccurence:544 |
Rv0517 |
acyltransferase | 526 | 526 ctx | cooccurence:526 |
Rv0875c hyp |
hypothetical protein | 517 | 517 ctx | cooccurence:495 |
Rv2826c hyp |
hypothetical protein | 437 | 437 ctx | neighborhood:421 |
Rv2827c hyp |
hypothetical protein | 432 | 432 ctx | neighborhood:421 |
Rv1353c |
HTH-type transcriptional regulator | 423 | 424 ctx | cooccurence:420 |
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: DUF1802 family protein
- Pfam (hmmscan --cut_ga): DUF1802 PF08819.18 (E=9e-56)
- (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_217344.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF1802 (PF08819.18)
- 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
COG4293 - Curated reference: UniProt I6X5G8 (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
vapC22 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003003|Rv2828c| MTPALKEWSAAVHALLDGRQTVLLRKGGIGEKRFEVAAHEFLLFPTVAHSHAERVRPEHRDLLGPAAADSTDECVLLRAAAKVVAALPVNRPEGLDAIEDLHIWTAESVRADRLDFRPKHKLAVLVVCAIPLAEPVRLARRPEYGGCTSWVQLPLTPQLAEPVHDEAALAEVAARVREAVG