Rv3412 Still unknown · low auto-curated
H37Rv Rv3412 · MTBC0 mtbc0_003626 ·
136 aa · 3857165–3857575 (+) ·
RefSeq NP_217929.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF5319 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF5319. 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 |
P9WKY9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv3412 |
UniProt still lists this protein as Uncharacterized protein Rv3412; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Family of unknown function (DUF5319) |
| Orthologous group | 2DHRC |
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 | 0.306 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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 |
|---|---|---|---|---|
DUF5319 | PF17252.8 | 7.9e-48 | 9–122 | Family of unknown function (DUF5319) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: guaB2 (inosine-5'-monophosphate dehydrogenase), high confidence from genomic context alone (score 760 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) |
|---|---|---|---|---|
Rv3411c guaB2 |
inosine-5'-monophosphate dehydrogenase | 760 | 760 ctx | neighborhood:756 |
Rv3410c guaB3 |
oxidoreductase | 746 | 746 ctx | neighborhood:744 |
Rv2179c |
3'-5' exoribonuclease | 728 | 728 ctx | cooccurence:728 |
Rv3605c hyp |
hypothetical protein | 728 | 728 ctx | cooccurence:728 |
Rv3231c hyp |
hypothetical protein | 717 | 717 ctx | cooccurence:716 |
Rv2744c 35kd_ag hyp |
hypothetical protein | 714 | 714 ctx | cooccurence:710 |
Rv2170 |
GCN5-like N-acetyltransferase | 686 | 686 ctx | cooccurence:686 |
Rv2468c hyp |
hypothetical protein | 663 | 663 ctx | cooccurence:659 |
Rv3519 hyp |
hypothetical protein | 569 | 570 ctx | cooccurence:555 |
Rv0948c |
chorismate mutase | 524 | 525 ctx | cooccurence:518 |
Rv3221A rshA |
anti-sigma factor RshA | 524 | 524 ctx | cooccurence:498 |
Rv3205c hyp |
hypothetical protein | 504 | 505 ctx | cooccurence:486 |
Rv1638A hyp |
hypothetical protein | 497 | 497 ctx | cooccurence:492 |
Rv3409c choD |
cholesterol oxidase | 495 | 494 ctx | neighborhood:487 |
Rv1343c lprD |
lipoprotein LprD | 489 | 489 ctx | cooccurence:476 |
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: DUF5319 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF5319 PF17252.8 (E=8e-48)
- (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_217929.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF5319 (PF17252.8)
- 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
2DHRC - Curated reference: UniProt P9WKY9 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 86.6, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
47 functional partner(s); context anchor
guaB2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003626|Rv3412| MRDHLPPGLPPDPFADDPCDPSAALEAVEPGQPLDQQERMAVEADLADLAVYEALLAHKGIRGLVVCCDECQQDHYHDWDMLRSNLLQLLIDGTVRPHEPAYDPEPDSYVTWDYCRGYADASLNEAAPDADRFRRR