Rv3415c Family assigned · low auto-curated · to review
H37Rv Rv3415c · MTBC0 mtbc0_003629 ·
275 aa · 3859133–3859960 (-) ·
RefSeq NP_217932.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | No Pfam domain above threshold; Foldseek indicates a fold similar to 8rsv-assembly1_A Rap from bacteriophage Phi3T in presence of pheromone RRGHTAS (prob 1.00, TM 0.65). Structure-based, putative. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed (flagged for human review).
Curated reference (UniProt)
| UniProt |
I6YG27
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 | 2F0NR |
|---|
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 | 2.676 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 6 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.55% of strains (801) · 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 96.8 (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 |
|---|---|---|---|---|
8rsv-assembly1_A |
1.00 | 0.65 | 6.2e-04 sig | 8rsv-assembly1_A Rap from bacteriophage Phi3T in presence of pheromone RRGHTAS |
8rte-assembly1_B |
1.00 | 0.63 | 5.7e-04 sig | 8rte-assembly1_B Rap from bacteriophage Phi105 with peptide ERPVGT |
8rsv-assembly2_B |
1.00 | 0.61 | 1.3e-03 sig | 8rsv-assembly2_B Rap from bacteriophage Phi3T in presence of pheromone RRGHTAS |
7t7t-assembly2_B |
1.00 | 0.71 | 4.0e-03 sig | 7t7t-assembly2_B Structure of TSK/BRU1 bound to histone H3.1 |
8jau-assembly1_A |
1.00 | 0.68 | 3.8e-03 sig | 8jau-assembly1_A Structure of CRL2APPBP2 bound with the C-degron of MRPL28 (dimer) |
1hz4-assembly1_A |
1.00 | 0.53 | 6.8e-04 sig | 1hz4-assembly1_A CRYSTAL STRUCTURE OF TRANSCRIPTION FACTOR MALT DOMAIN III |
8rsu-assembly1_A |
1.00 | 0.61 | 2.3e-03 sig | 8rsu-assembly1_A Rap from bacteriophage Phi3T in presence of pheromone RRGHTA |
5a7d-assembly4_D |
1.00 | 0.55 | 3.2e-03 sig | 5a7d-assembly4_D Tetrameric assembly of LGN with Inscuteable |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rsdA (anti-sigma-D factor RsdA), high confidence from genomic context alone (score 869 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) |
|---|---|---|---|---|
Rv3413c rsdA |
anti-sigma-D factor RsdA | 868 | 869 ctx | neighborhood:767 cooccurence:459 |
Rv3414c sigD |
ECF RNA polymerase sigma factor SigD | 783 | 784 ctx | neighborhood:783 |
Rv2695 hyp |
hypothetical protein | 771 | 771 ctx | cooccurence:768 |
Rv2418c octT hyp |
hypothetical protein | 771 | 771 ctx | cooccurence:770 |
Rv2186c hyp |
hypothetical protein | 763 | 763 ctx | cooccurence:762 |
Rv0383c ttfA hyp |
hypothetical protein | 758 | 758 ctx | cooccurence:758 |
Rv1111c hyp |
hypothetical protein | 743 | 743 ctx | cooccurence:743 |
Rv2091c |
membrane protein | 741 | 741 ctx | cooccurence:741 |
Rv1109c hyp |
hypothetical protein | 736 | 736 ctx | cooccurence:736 |
Rv2743c hyp |
hypothetical protein | 732 | 732 ctx | cooccurence:731 |
Rv0250c hyp |
hypothetical protein | 731 | 731 ctx | cooccurence:730 |
Rv3212 hyp |
hypothetical protein | 731 | 731 ctx | cooccurence:730 |
Rv0556 |
transmembrane protein | 721 | 721 ctx | cooccurence:721 |
Rv0481c hyp |
hypothetical protein | 718 | 719 ctx | cooccurence:717 |
Rv0996 |
transmembrane protein | 717 | 717 ctx | cooccurence:717 |
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
- Foldseek best: 8rsv-assembly1_A Rap from bacteriophage Phi3T in presence of pheromone RRGHTAS (prob 1.00, E=6e-04, TM=0.65)
- (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_217932.1)
- 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
2F0NR - Curated reference: UniProt I6YG27 (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 96.8, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
121 functional partner(s); context anchor
rsdA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003629|Rv3415c| MNETPHAPVVEQVLVAAAFGNQPGSWPLPTAITPHHLWLRAVAAGGQGRYAHAYGDLSVLRRLVPAGPLASLAHSTQGSLLRQLGWHTLARGWDGRALALAGADREAGADALIGLAADALGVGRFAAAGALLDRADPLVVSPLVADRLAVRRRWVAAELAMATGDGATAVRHAEEAVELTQAMAVASARHRVKSDVVLAAALCSAGAVARARAVGEEALDATARFGLLPLRWALACLLIDIGTVTFSAQQLRELTKIRNICAGQVRRAGGCWRTA