Rv2683 Family assigned · medium auto-curated
H37Rv Rv2683 · MTBC0 - ·
165 aa · 3000112–3000609 (+) ·
RefSeq NP_217199.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains CBS (PF00571.34) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
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 |
I6X540
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 |
S Function unknown
|
|---|---|
| eggNOG description | CBS domain |
| Orthologous group | COG0517 |
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 | 1.413 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 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 |
|---|---|---|---|---|
CBS | PF00571.34 | 5.0e-05 | 116–162 | CBS domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: arsA (arsenic-transport integral membrane protein ArsA), high confidence from genomic context alone (score 950 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) |
|---|---|---|---|---|
Rv2684 arsA |
arsenic-transport integral membrane protein ArsA | 950 | 950 ctx | neighborhood:801 cooccurence:723 |
Rv2685 arsB1 |
arsenic-transport integral membrane protein ArsB | 898 | 899 ctx | neighborhood:606 cooccurence:728 |
Rv3396c guaA |
GMP synthase | 906 | 799 | coexpression:649 textmining:554 |
Rv2299c htpG |
chaperone protein HtpG | 757 | 725 | database:659 |
Rv1733c |
transmembrane protein | 695 | 696 ctx | cooccurence:695 |
Rv2682c dxs1 |
1-deoxy-D-xylulose 5-phosphate synthase | 644 | 645 ctx | neighborhood:645 |
Rv0018c pstP |
phosphoserine/threonine phosphatase PstP | 654 | 637 | database:626 |
Rv3887c eccD2 |
ESX-2 secretion system protein EccD | 585 | 585 ctx | cooccurence:584 |
Rv0462 lpdC |
dihydrolipoamide dehydrogenase | 583 | 583 | experimental:409 |
Rv3303c lpdA |
NAD(P)H quinone reductase LpdA | 582 | 582 | experimental:409 |
Rv2855 mtr |
mycothione reductase | 581 | 582 | experimental:409 |
Rv0794c |
oxidoreductase | 581 | 581 | experimental:409 |
Rv2713 sthA |
pyridine nucleotide transhydrogenase | 581 | 581 | experimental:409 |
Rv2390c hyp |
hypothetical protein | 572 | 572 ctx | cooccurence:476 |
Rv0853c pdc |
alpha-keto-acid decarboxylase | 512 | 512 | coexpression:453 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): CBS PF00571.34 (E=5e-05)
- (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_217199.1)
- Domains: Pfam-A via hmmscan --cut_ga — 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
COG0517 - Curated reference: UniProt I6X540 (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 —
48 functional partner(s); context anchor
arsA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2683| MKVNIDPTAPTFATYRRDMRAEQMAEDYPVVSIDSDALDAARMLAEHRLPGLLVTAGAGKQYAVLPASQVVRFIVPRYVQDDPLLAGVLNESTADRCAERLSGKKVRDVLPDHLVEVPPANADDTIIEVAAVMARLRSPLLAVVKDGSLLGVVTASRLLAAALKT