Rv0030 Still unknown · low
H37Rv Rv0030 · MTBC0 mtbc0_000036 ·
109 aa · 33210–33539 (+) ·
RefSeq NP_214544.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF2710 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF2710 domain-containing. Function unknown. Foldseek yields only weak, near-threshold matches to uncharacterised proteins (e.g. H. pylori HP0035), with no functional assignment. |
Curated reference (UniProt)
| UniProt |
P9WM95
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv0030 |
UniProt still lists this protein as Uncharacterized protein Rv0030; 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 (DUF2710) |
| Orthologous group | 2AVE0 |
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 | 1.176 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 7 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 |
|---|---|---|---|---|
DUF2710 | PF10921.15 | 2.8e-51 | 6–106 | Protein of unknown function (DUF2710) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 64.7 (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 |
|---|---|---|---|---|
3f42-assembly1_B-2 |
1.00 | 0.70 | 4.0e-03 sig | 3f42-assembly1_B-2 Crystal structure of uncharacterized protein HP0035 from Helicobacter pylori |
7ane-assembly1_an |
1.00 | 0.67 | 3.5e-03 sig | 7ane-assembly1_an Leishmania Major mitochondrial ribosome |
3f42-assembly1_A-2 |
1.00 | 0.65 | 4.5e-03 sig | 3f42-assembly1_A-2 Crystal structure of uncharacterized protein HP0035 from Helicobacter pylori |
1pug-assembly2_D |
1.00 | 0.76 | 3.8e-02 | 1pug-assembly2_D Structure of E. coli Ybab |
1pug-assembly1_A |
1.00 | 0.73 | 5.6e-02 | 1pug-assembly1_A Structure of E. coli Ybab |
7pua-assembly1_DK |
1.00 | 0.76 | 6.7e-02 | 7pua-assembly1_DK Middle assembly intermediate of the Trypanosoma brucei mitoribosomal small subunit |
1j8b-assembly1_A-2 |
1.00 | 0.52 | 1.1e-02 | 1j8b-assembly1_A-2 Structure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function |
1pug-assembly2_C |
1.00 | 0.67 | 3.8e-02 | 1pug-assembly2_C Structure of E. coli Ybab |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0031 (Rv0031, (MTCY10H4.31), len: 70 aa. Possible remnant of a transposase, showing partial similarity to mycobacterial transposases in a short ov), medium confidence from genomic context alone (score 693 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) |
|---|---|---|---|---|
Rv0029 hyp |
hypothetical protein | 798 | 798 ctx | neighborhood:792 |
Rv0031 |
Rv0031, (MTCY10H4.31), len: 70 aa. Possible remnant of a transposase, showing partial similarity to mycobacterial transposases in a short ov | 693 | 693 ctx | neighborhood:678 |
Rv3894c eccC2 |
ESX-2 type VII secretion system protein EccC | 550 | 551 ctx | neighborhood:544 |
Rv0028 hyp |
hypothetical protein | 443 | 443 ctx | neighborhood:439 |
Rv0027 hyp |
hypothetical protein | 436 | 436 ctx | neighborhood:432 |
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
- MTBC0 PGAP product: 'DUF2710 domain-containing protein'
- Pfam: DUF2710 PF10921 (E=2.8e-51) -- a domain of unknown function
- Foldseek on the ESMFold model: only weak, near-threshold hits to uncharacterised proteins (HP0035, prob 1.0 but E~4e-3, TM 0.70); inconclusive
ESM Atlas signal (exploratory)
Ancestral protein hash c01c0c8f293e2bde8e36ce6f95f91491 ·
1 ESM-space neighbours (max similarity 0.646).
SAE features are orienting indices, not validated domains.
| # | Index | Activation | Interpretation |
|---|---|---|---|
| 1 | 16353 |
0.61 | Acidic catalytic motifs and coiled-coils |
| 2 | 14146 |
0.50 | Edge beta-hairpin interaction loops |
| 3 | 8624 |
0.47 | Presequence-to-core transition helix |
| 4 | 7936 |
0.47 | Cofactor-binding beta-loop patches |
| 5 | 14653 |
0.47 | Charged coiled-coil stalk helices |
| 6 | 13240 |
0.46 | Amphipathic core helices |
| 7 | 407 |
0.46 | Disordered pre-sequences and tails |
| 8 | 12593 |
0.46 | Disordered low-complexity regulatory tails |
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_214544.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF2710 (PF10921.15)
- 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
2AVE0 - Curated reference: UniProt P9WM95 (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 64.7, low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
5 functional partner(s); context anchor
Rv0031 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000036|Rv0030| MVSGSDSRSEPSQLSDRDLVESVLRDLSEAADKWEALVTQAETVTYSVDLGDVRAVANSDGRLLELTLHPGVMTGYAHGELADRVNLAITALRDEVEAENRARYGGRLQ