Rv0559c Family assigned · low
H37Rv Rv0559c · MTBC0 mtbc0_000588 ·
112 aa · 653958–654296 (-) ·
RefSeq NP_215073.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF732 domain-containing protein |
| Revised (this work) | Lipoprotein of the LprJ-like family (secreted, salicylate/rifampicin-stress-induced). RefSeq leaves it 'hypothetical protein'. |
Curated reference (UniProt)
| UniProt |
P9WKL3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0559c |
UniProt still lists this protein as Uncharacterized protein Rv0559c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF732) |
| Orthologous group | 2A2PD |
| Gene Ontology (7) |
GO:0005575, GO:0005576, GO:0005618, GO:0005623, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.321 · 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 |
|---|---|---|---|---|
DUF732 | PF05305.20 | 8.4e-11 | 29–101 | Protein of unknown function (DUF732) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 77.0 (confident). A confident model makes the fold comparison meaningful.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
6zol-assembly1_R |
0.04 | 0.37 | 9.5e+00 | 6zol-assembly1_R SARS-CoV-2-Nsp1-40S complex, focused on head |
7odt-assembly1_c |
0.01 | 0.20 | 9.5e+00 | 7odt-assembly1_c State C of the human mitoribosomal large subunit assembly intermediate |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: menJ (oxidoreductase), medium confidence from genomic context alone (score 684 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) |
|---|---|---|---|---|
Rv0561c menJ |
oxidoreductase | 849 | 684 ctx | neighborhood:684 textmining:543 |
Rv0560c |
benzoquinone methyltransferase | 951 | 668 ctx | neighborhood:668 textmining:860 |
Rv0562 grcC1 |
polyprenyl-diphosphate synthase GrcC | 520 | 520 ctx | neighborhood:520 |
Rv0455c hyp |
hypothetical protein | 665 | 73 | textmining:654 |
Rv2536 |
transmembrane protein | 805 | 41 | textmining:805 |
Rv0379 secE2 |
protein translocase subunit SecE | 751 | 41 | textmining:751 |
Rv2284 lipM |
esterase LipM | 657 | 41 | textmining:657 |
Rv1508c |
membrane protein | 651 | 41 | textmining:651 |
Rv0261c narK3 |
nitrate/nitrite transporter | 548 | 41 | textmining:548 |
Rv3707c hyp |
hypothetical protein | 433 | 41 | textmining:433 |
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
- Foldseek vs AFDB-SwissProt: lipoprotein LprJ, TM 0.59, E 3e-3
- Structural homology vs AlphaFold-Swiss-Prot (Foldseek; 542k curated SwissProt structures), project 'Still unknown gene function' phase13, 2026-06-10. Fold/family-level, not a demonstrated function.
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_215073.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF732 (PF05305.20)
- 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
2A2PD - Curated reference: UniProt P9WKL3 (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 77.0, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
10 functional partner(s); context anchor
menJ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000588|Rv0559c| MKGTKLAVVVGMTVAAVSLAAPAQADDYDAPFNNTIHRFGIYGPQDYNAWLAKISCERLSRGVDGDAYKSATFLQRNLPRGTTQGQAFQFLGAAIDHYCPEHVGVLQRAGTR