Rv0424c Still unknown · low auto-curated
H37Rv Rv0424c · MTBC0 mtbc0_000445 ·
91 aa · 513742–514017 (-) ·
RefSeq NP_214938.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. 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 |
P96270
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein |
UniProt still lists this protein as Uncharacterized protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2EKEP |
|---|
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, 2 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0426c (transmembrane protein), high confidence from genomic context alone (score 764 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) |
|---|---|---|---|---|
Rv0426c |
transmembrane protein | 764 | 764 ctx | neighborhood:761 |
Rv0425c ctpH |
metal cation transporting ATPase H | 652 | 652 ctx | neighborhood:647 |
Rv0423c thiC |
phosphomethylpyrimidine synthase | 518 | 518 ctx | neighborhood:506 |
Rv0427c xthA |
exodeoxyribonuclease III protein XthA | 496 | 497 ctx | neighborhood:494 |
Rv0421c hyp |
hypothetical protein | 489 | 489 ctx | neighborhood:466 |
Rv0422c thiD |
hydroxymethylpyrimidine/phosphomethylpyrimidine kinase | 480 | 480 ctx | neighborhood:466 |
Rv0429c def |
polypeptide deformylase | 404 | 405 | |
Rv0428c |
GCN5-like N-acetyltransferase | 402 | 402 | |
Rv3119 moaE1 |
molybdopterin synthase catalytic subunit 1 | 651 | 54 | textmining:647 |
Rv2781c |
oxidoreductase | 437 | 47 | textmining:434 |
Rv0291 mycP3 |
membrane-anchored mycosin MycP | 415 | 47 | textmining:412 |
Rv0299 |
toxin | 652 | 46 | textmining:651 |
Rv1772 hyp |
hypothetical protein | 513 | 46 | textmining:511 |
Rv0461 |
transmembrane protein | 870 | 44 | textmining:870 |
Rv0560c |
benzoquinone methyltransferase | 521 | 44 | textmining:520 |
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: hypothetical protein
- (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_214938.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
2EKEP - Curated reference: UniProt P96270 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 49.5, very low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
17 functional partner(s); context anchor
Rv0426c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000445|Rv0424c| MAEKNTRRATSQREAVAKIREAETIVMNLPICGQVKIPRPEHLAYYGGLAALAALELIDWPVALVIATGHILANNHHNRVLEELGEAMEEA