Rv2082 Still unknown · low auto-curated
H37Rv Rv2082 · MTBC0 mtbc0_002215 ·
54 aa · 2366550–2366711 (+) ·
RefSeq NP_216598.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF5631 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF5632, DUF5631. Function unknown. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
Q10690
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2082 |
UniProt still lists this protein as Uncharacterized protein Rv2082; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2A1TI |
|---|---|
| Gene Ontology (33) |
GO:0002682, GO:0002684, GO:0008150, GO:0009605, GO:0009607, GO:0035821, GO:0043207, GO:0044003, GO:0044403, GO:0044419, GO:0048518, GO:0048583 +21 more
|
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) pseudogene candidate
| pN/pS | 1.138 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 18 missense, 0 nonsense, 3 frameshift |
| Disruption | 3 distinct premature-stop/frameshift site(s); most common in 4.14% of strains (6015) · 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 |
|---|---|---|---|---|
DUF5632 | PF18646.7 | 1.0e-30 | 511–593 | Family of unknown function (DUF5632) |
DUF5631 | PF18645.7 | 6.4e-40 | 619–713 | Family of unknown function (DUF5631) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: PE_PGRS16 (PE-PGRS family protein PE_PGRS16), high confidence from genomic context alone (score 833 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) |
|---|---|---|---|---|
Rv2086 hyp |
hypothetical protein | 841 | 840 ctx | neighborhood:552 cooccurence:655 |
Rv0977 PE_PGRS16 |
PE-PGRS family protein PE_PGRS16 | 838 | 833 ctx | cooccurence:773 |
Rv3448 eccD4 |
ESX-4 secretion system protein EccD4 | 831 | 832 ctx | cooccurence:715 coexpression:432 |
Rv2083 hyp |
hypothetical protein | 827 | 827 ctx | neighborhood:785 |
Rv2305 hyp |
hypothetical protein | 818 | 818 ctx | cooccurence:718 |
Rv2084 hyp |
hypothetical protein | 807 | 807 ctx | neighborhood:801 |
Rv2085 hyp |
hypothetical protein | 795 | 796 ctx | neighborhood:552 cooccurence:559 |
Rv0124 PE_PGRS2 |
PE-PGRS family protein PE_PGRS2 | 790 | 782 ctx | cooccurence:774 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 790 | 782 ctx | cooccurence:774 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 790 | 782 ctx | cooccurence:774 |
Rv0872c PE_PGRS15 |
PE-PGRS family protein PE_PGRS15 | 790 | 782 ctx | cooccurence:774 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 790 | 782 ctx | cooccurence:774 |
Rv2853 PE_PGRS48 |
PE-PGRS family protein PE_PGRS48 | 789 | 781 ctx | cooccurence:773 |
Rv1243c PE_PGRS23 |
PE-PGRS family protein PE_PGRS23 | 786 | 779 ctx | cooccurence:770 |
Rv1917c PPE34 |
PPE family protein PPE34 | 777 | 777 ctx | cooccurence:774 |
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: DUF5631 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF5632 PF18646.7 (E=1e-30), DUF5631 PF18645.7 (E=6e-40)
- (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_216598.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF5632 (PF18646.7), DUF5631 (PF18645.7)
- 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
2A1TI - Curated reference: UniProt Q10690 (SwissProt, reviewed; 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 —
179 functional partner(s); context anchor
PE_PGRS16 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002215|Rv2082| MGDRRARIAPGIEELGPTLVETVRRRDALPRIAQAVVVAATRNYGVPDNETDLL