Rv2825c Still unknown · low
H37Rv Rv2825c · MTBC0 - ·
215 aa · 3132892–3133539 (-) ·
RefSeq NP_217341.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical; function unknown. Structure-based hint rejected: structural ASCH hit contradicts the DUF1802 Pfam assignment; function unknown. |
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P71627
TrEMBL · unreviewed
· Predicted
|
|---|---|
| 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 | 1.879 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 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 |
|---|---|---|---|---|
DUF1802 | PF08819.18 | 1.3e-55 | 38–208 | Domain of unknown function (DUF1802) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 91.7 (very high). A confident model makes the fold comparison meaningful.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
5guq-assembly4_D |
1.00 | 0.54 | 1.2e-03 sig | 5guq-assembly4_D Crystal structure of ASCH from Zymomonas mobilis |
5y7d-assembly1_A-2 |
1.00 | 0.55 | 1.6e-03 sig | 5y7d-assembly1_A-2 Crystal structure of human Endothelial-overexpressed LPS associated factor 1 |
5y6c-assembly2_B |
1.00 | 0.49 | 4.8e-04 sig | 5y6c-assembly2_B Crystal structure of ZmASCH S128A mutant protein from Zymomonas mobilis |
5y6b-assembly4_D |
1.00 | 0.50 | 8.8e-04 sig | 5y6b-assembly4_D Crystal structure of ZmASCH Y47F mutant protein from Zymomonas mobilis |
6kit-assembly1_A |
0.99 | 0.52 | 4.2e-03 sig | 6kit-assembly1_A Structure of mouse CXorf40A, Selenomethionine derivative |
1jhd-assembly1_A-2 |
0.04 | 0.34 | 2.6e+00 | 1jhd-assembly1_A-2 Crystal Structure of Bacterial ATP Sulfurylase from the Riftia pachyptila Symbiont |
7ohq-assembly1_X |
0.02 | 0.19 | 2.3e+00 | 7ohq-assembly1_X Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae |
6ft6-assembly1_X |
0.01 | 0.21 | 6.7e+00 | 6ft6-assembly1_X Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3779 (transmembrane protein), medium confidence from genomic context alone (score 640 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) |
|---|---|---|---|---|
Rv2828c hyp |
hypothetical protein | 852 | 852 | coexpression:804 |
Rv3779 |
transmembrane protein | 640 | 640 ctx | cooccurence:640 |
Rv0048c |
membrane protein | 533 | 533 ctx | cooccurence:533 |
Rv0517 |
acyltransferase | 513 | 513 ctx | cooccurence:513 |
Rv0875c hyp |
hypothetical protein | 500 | 501 ctx | cooccurence:485 |
Rv2827c hyp |
hypothetical protein | 493 | 492 ctx | neighborhood:480 |
Rv2826c hyp |
hypothetical protein | 487 | 487 ctx | neighborhood:480 |
Rv2824c cas6 |
CRISPR-associated endoribonuclease Cas6 | 463 | 464 ctx | neighborhood:458 |
Rv2816c cas2 |
CRISPR-associated endoribonuclease Cas2 | 464 | 463 | |
Rv2823c cas10 |
CRISPR-associated protein Cas10/Csm1 | 460 | 461 ctx | neighborhood:458 |
Rv2819c csm5 |
CRISPR type III-associated RAMP protein Csm5 | 460 | 460 ctx | neighborhood:457 |
Rv2822c csm2 |
CRISPR type III-associated protein Csm2 | 459 | 460 ctx | neighborhood:458 |
Rv2820c csm4 |
CRISPR type III-associated RAMP protein Csm4 | 459 | 459 ctx | neighborhood:457 |
Rv2821c csm3 |
CRISPR type III-associated RAMP protein Csm3 | 459 | 459 ctx | neighborhood:457 |
Rv1845c blaR |
sensor-transducer protein BlaR | 422 | 423 | coexpression:423 |
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
- Structural Foldseek hit not propagated -- structural ASCH hit contradicts the DUF1802 Pfam assignment; function unknown
- Reviewed against literature (extended structural cross-check, 2026-06-02)
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_217341.1)
- 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 P71627 (TrEMBL, unreviewed; Predicted)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Model confidence: ESMFold per-residue pLDDT (mean 91.7, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
16 functional partner(s); context anchor
Rv3779 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2825c| MKLPGAKRLGDDRRPLGTLRCWRHSDIGPARGIVVTPALKEWSAAVHALLDGRQTVLLRKGGIGEKRFEVAAHEFLLFPTVAHSHAERVRPEHRDLLGPAAADSTDECVLLRAAAKVVAALPVNRPEGLDAIEDLHIWTAESVRADRLDFRPKHKLAVLVVSAIPLAEPVRLARRPEYGGCTSWVQLPVTPTLAAPVHDEAALAEVAARVREAVG