Rv2926c Family assigned · medium auto-curated
H37Rv Rv2926c · MTBC0 - ·
207 aa · 3240548–3241171 (-) ·
RefSeq NP_217442.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains YceD (PF02620.23) 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 |
P9WL17
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2926c |
UniProt still lists this protein as Uncharacterized protein Rv2926c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Uncharacterized ACR, COG1399 |
| Orthologous group | COG1399 |
| KEGG orthology |
K07040
|
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 1.064 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 6 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 |
|---|---|---|---|---|
YceD | PF02620.23 | 7.1e-29 | 84–193 | Large ribosomal RNA subunit accumulation protein YceD |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rnc (ribonuclease III), high confidence from genomic context alone (score 939 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) |
|---|---|---|---|---|
Rv2925c rnc |
ribonuclease III | 992 | 939 ctx | neighborhood:882 coexpression:505 textmining:877 |
Rv0707 rpsC |
30S ribosomal protein S3 | 931 | 932 | coexpression:763 experimental:724 |
Rv0979A rpmF |
50S ribosomal protein L32 | 882 | 868 | coexpression:857 |
Rv0640 rplK |
50S ribosomal protein L11 | 855 | 856 | coexpression:856 |
Rv0641 rplA |
50S ribosomal protein L1 | 850 | 843 | coexpression:843 |
Rv1642 rpmI |
50S ribosomal protein L35 | 835 | 835 | coexpression:795 |
Rv0053 rpsF |
30S ribosomal protein S6 | 833 | 834 | coexpression:820 |
Rv2890c rpsB |
30S ribosomal protein S2 | 832 | 833 | coexpression:821 |
Rv2909c rpsP |
30S ribosomal protein S16 | 831 | 832 | coexpression:818 |
Rv1641 infC |
initiation factor IF-3 | 831 | 832 | coexpression:820 |
Rv3443c rplM |
50S ribosomal protein L13 | 831 | 832 | coexpression:829 |
Rv0651 rplJ |
50S ribosomal protein L10 | 830 | 831 | coexpression:803 |
Rv2442c rplU |
50S ribosomal protein L21 | 829 | 830 | coexpression:824 |
Rv2927c sepIVA hyp |
hypothetical protein | 985 | 821 ctx | neighborhood:813 textmining:920 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 820 | 821 | coexpression:821 |
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): YceD PF02620.23 (E=7e-29)
- (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_217442.1)
- Domains: Pfam-A via hmmscan --cut_ga — YceD (PF02620.23)
- 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
COG1399 - Curated reference: UniProt P9WL17 (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 —
115 functional partner(s); context anchor
rnc - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2926c| MDLGGVRRRISLMARQHGPTAQRHVASPMTVDIARLGRRPGAMFELHDTVHSPARIGLELIAIDQGALLDLDLRVESVSEGVLVTGTVAAPTVGECARCLSPVRGRVQVALTELFAYPDSATDETTEEDEVGRVVDETIDLEQPIIDAVGLELPFSPVCRPDCPGLCPQCGVPLASEPGHRHEQIDPRWAKLVEMLGPESDTLRGER