Rv3471c Family assigned · medium auto-curated
H37Rv Rv3471c · MTBC0 - ·
177 aa · 3888808–3889341 (-) ·
RefSeq NP_217988.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Cupin_2 (PF07883.18) 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 |
O06336
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Cupin type-1 domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| eggNOG description | Cupin 2, conserved barrel domain protein |
| Orthologous group | COG0662 |
| EC number |
EC 5.3.1.9
|
| KEGG orthology |
K01810
|
| KEGG pathways |
map00010, map00030, map00500, map00520, map01100, map01110, map01120, map01130, map01200
|
| KEGG modules |
M00001, M00004, M00114
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.28% of strains (400) · 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 |
|---|---|---|---|---|
Cupin_2 | PF07883.18 | 1.0e-13 | 86–154 | Cupin domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ilvB2 (acetolactate synthase large subunit), high confidence from genomic context alone (score 883 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) |
|---|---|---|---|---|
Rv3470c ilvB2 |
acetolactate synthase large subunit | 883 | 883 ctx | neighborhood:881 |
Rv3472 hyp |
hypothetical protein | 679 | 680 ctx | neighborhood:618 |
Rv3468c |
dTDP-glucose 4,6-dehydratase | 690 | 673 ctx | neighborhood:616 |
Rv3469c mhpE |
4-hydroxy-2-oxovalerate aldolase MhpE | 649 | 649 ctx | neighborhood:646 |
Rv1525 wbbL2 |
rhamnosyl transferase WbbL | 604 | 585 ctx | cooccurence:460 |
Rv3833 |
AraC family transcriptional regulator | 575 | 514 | experimental:408 |
Rv2949c |
chorismate pyruvate-lyase | 494 | 495 ctx | cooccurence:453 |
Rv1301 |
threonylcarbamoyl-AMP synthase | 433 | 433 | coexpression:415 |
Rv2839c infB |
translation initiation factor IF-2 | 422 | 397 | |
Rv3465 rmlC |
dTDP-4-dehydrorhamnose 3,5-epimerase | 452 | 372 | |
Rv0334 rmlA |
glucose-1-phosphate thymidylyltransferase | 450 | 368 | |
Rv0322 udgA |
UDP-glucose 6-dehydrogenase UdgA | 409 | 250 |
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): Cupin_2 PF07883.18 (E=1e-13)
- (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_217988.1)
- Domains: Pfam-A via hmmscan --cut_ga — Cupin_2 (PF07883.18)
- 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
COG0662 - Curated reference: UniProt O06336 (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)
- 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
ilvB2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3471c| MSTRPERERASTSTDAVLQATVALSAGHKPAFRGFVKDPPRARAHAAAMFVSNAREAEPFVAPDLSEIRVLVDRATVGVASVSLAHATVAAGAETVWHRLQATDEIYFVLSGRGLVSVGDESGEVGPGDAVWIPAGVPQKIRALGSVPLTFLCACGPAYLPERDQRMGEAAVIGAWP