Rv0470A Still unknown · low auto-curated
H37Rv Rv0470A · MTBC0 - ·
146 aa · 561854–562294 (-) ·
RefSeq YP_177622.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. Foldseek best (non-significant) hit: 6b87-assembly1_A-2 Crystal structure of transmembrane protein TMHC2_E (prob 0.13, TM 0.62). |
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 |
L7N651
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | 1,4-dihydroxy-2-naphthoate prenyltransferase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| eggNOG description | Belongs to the MenA family. Type 1 subfamily |
| Orthologous group | COG1575 |
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) pseudogene candidate
| pN/pS | 0.517 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 5.77% of strains (8381) · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 54.5 (low). Low-confidence model: the fold may be unreliable, so treat these structural hits with caution.
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 |
|---|---|---|---|---|
6b87-assembly1_A-2 |
0.13 | 0.62 | 9.5e+00 | 6b87-assembly1_A-2 Crystal structure of transmembrane protein TMHC2_E |
2dnx-assembly1_A |
0.06 | 0.39 | 7.6e+00 | 2dnx-assembly1_A Solution structure of RSGI RUH-063, an N-terminal domain of Syntaxin 12 from human cDNA |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0472c (HTH-type transcriptional regulator), high confidence from genomic context alone (score 801 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) |
|---|---|---|---|---|
Rv0471c hyp |
hypothetical protein | 834 | 834 ctx | neighborhood:781 |
Rv0472c |
HTH-type transcriptional regulator | 801 | 801 ctx | neighborhood:800 |
Rv0355c PPE8 |
PPE family protein PPE8 | 712 | 713 ctx | cooccurence:708 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 706 | 706 ctx | cooccurence:706 |
Rv3347c PPE55 |
PPE family protein PPE55 | 705 | 705 ctx | cooccurence:702 |
Rv3350c PPE56 |
PPE family protein PPE56 | 704 | 704 ctx | cooccurence:702 |
Rv2209 |
integral membrane protein | 703 | 703 ctx | cooccurence:699 |
Rv1004c |
membrane protein | 701 | 701 ctx | cooccurence:696 |
Rv0341 iniB |
isoniazid inducible protein IniB | 694 | 695 ctx | cooccurence:685 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 690 | 690 ctx | cooccurence:690 |
Rv0304c PPE5 |
PPE family protein PPE5 | 684 | 685 ctx | cooccurence:681 |
Rv2819c csm5 |
CRISPR type III-associated RAMP protein Csm5 | 683 | 684 ctx | cooccurence:682 |
Rv3343c PPE54 |
PPE family protein PPE54 | 683 | 683 ctx | cooccurence:679 |
Rv1917c PPE34 |
PPE family protein PPE34 | 678 | 678 ctx | cooccurence:674 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 676 | 676 ctx | cooccurence:676 |
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
- Foldseek best: 6b87-assembly1_A-2 Crystal structure of transmembrane protein TMHC2_E (prob 0.13, E=1e+01, TM=0.62)
- (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 YP_177622.1)
- 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
COG1575 - Curated reference: UniProt L7N651 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 54.5, low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
74 functional partner(s); context anchor
Rv0472c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0470A| MGAGGWEVVLASLPYGLLCTTVLMGKHIDKIGYDEPLGIRTLPVLLGETCARTVTLAMMVGFYLLIAVNVMLAAMPWPRCWSPGRCPGWRKCGPISCDGGPSSRHRRFRCGRCGMPRWPGCTCVRPVRCWLWAWRSVPGGAPGDFR