Rv0477 Still unknown · low auto-curated
H37Rv Rv0477 · MTBC0 mtbc0_000502 ·
148 aa · 570141–570587 (+) ·
RefSeq NP_214991.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF2599 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF2599. Function unknown. Foldseek best (non-significant) hit: 3tgo-assembly2_D Crystal structure of the E. coli BamCD complex (prob 0.01, TM 0.15). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKV9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0477 |
UniProt still lists this protein as Uncharacterized protein Rv0477; 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 (DUF2599) |
| Orthologous group | 2EB1C |
| Gene Ontology (2) |
GO:0005575, GO:0005576
|
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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
DUF2599 | PF10783.15 | 1.5e-41 | 46–142 | Protein of unknown function (DUF2599) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 92.5 (very high). 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 |
|---|---|---|---|---|
3tgo-assembly2_D |
0.01 | 0.15 | 7.0e+00 | 3tgo-assembly2_D Crystal structure of the E. coli BamCD complex |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: deoC (2-deoxyribose-5-phosphate aldolase), 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) |
|---|---|---|---|---|
Rv0478 deoC |
2-deoxyribose-5-phosphate aldolase | 883 | 883 ctx | neighborhood:882 |
Rv0476 |
transmembrane protein | 882 | 882 ctx | neighborhood:882 |
Rv0475 hbhA |
heparin binding hemagglutinin HbhA | 835 | 829 ctx | neighborhood:766 |
Rv0474 |
HTH-type transcriptional regulator | 671 | 668 ctx | neighborhood:661 |
Rv3724B cut5b |
Rv3724B, (MTV025.072), len: 187 aa. Probable cut5b,truncated cutinase, similar to C-terminal end of others e.g. Q9XB09|RVD2-RV1758 protein ( | 592 | 592 ctx | cooccurence:587 |
Rv0283 eccB3 |
ESX-3 secretion system protein EccB3 | 583 | 583 ctx | cooccurence:511 |
Rv1758 cut1 |
cutinase | 545 | 546 ctx | cooccurence:540 |
Rv1364c |
sigma factor regulatory protein | 520 | 515 | coexpression:500 |
Rv3035 hyp |
hypothetical protein | 510 | 510 ctx | cooccurence:507 |
Rv2923c hyp |
hypothetical protein | 489 | 490 ctx | cooccurence:483 |
Rv2942 mmpL7 |
transmembrane transport protein MmpL7 | 481 | 481 ctx | cooccurence:481 |
Rv2429 ahpD |
alkyl hydroperoxide reductase AphD | 471 | 471 ctx | cooccurence:471 |
Rv0676c mmpL5 |
transmembrane transport protein MmpL5 | 470 | 470 ctx | cooccurence:470 |
Rv1874 hyp |
hypothetical protein | 459 | 459 ctx | cooccurence:459 |
Rv2608 PPE42 |
PPE family protein PPE42 | 456 | 456 ctx | cooccurence:456 |
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: DUF2599 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF2599 PF10783.15 (E=1e-41)
- Foldseek best: 3tgo-assembly2_D Crystal structure of the E. coli BamCD complex (prob 0.01, E=7e+00, TM=0.15)
- (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_214991.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF2599 (PF10783.15)
- 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
2EB1C - Curated reference: UniProt P9WKV9 (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 92.5, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
29 functional partner(s); context anchor
deoC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000502|Rv0477| MKALVAVSAVAVVALLGVSSAQADPEADPGAGEANYGGPPSSPRLVDHTEWAQWGSLPSLRVYPSQVGRTASRRLGMAAADAAWAEVLALSPEADTAGMRAQFICHWQYAEIRQPGKPSWNLEPWRPVVDDSEMLASGCNPGSPEESF