Rv1778c Still unknown · low
H37Rv Rv1778c · MTBC0 mtbc0_001892 ·
149 aa · 2030092–2030541 (-) ·
RefSeq NP_216294.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical; Foldseek best hit (RbmA, TM 0.38) not conclusive. Function unknown. |
Curated reference (UniProt)
| UniProt |
O33181
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 | 2E3FZ |
|---|
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, 5 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.23% of strains (337) · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
DUF6941 | PF22091.3 | 7.8e-11 | 5–130 | Family of unknown function (DUF6941) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 84.5 (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 |
|---|---|---|---|---|
4be6-assembly1_A |
1.00 | 0.38 | 1.0e-03 sig | 4be6-assembly1_A V. cholera biofilm scaffolding protein RbmA |
6ru5-assembly1_A |
1.00 | 0.49 | 1.5e-02 | 6ru5-assembly1_A human complement C3 in complex with the hC3Nb1 nanobody |
8cem-assembly1_E |
1.00 | 0.45 | 8.6e-03 sig | 8cem-assembly1_E Structure of bovine native C3, re-refinement |
2wii-assembly1_A |
1.00 | 0.45 | 5.6e-03 sig | 2wii-assembly1_A Complement C3b in complex with factor H domains 1-4 |
8enu-assembly1_G |
0.99 | 0.56 | 4.7e-02 | 8enu-assembly1_G Structure of the C3bB proconvertase in complex with lufaxin |
4bei-assembly1_H |
0.99 | 0.40 | 3.5e-03 sig | 4bei-assembly1_H V. cholera biofilm scaffolding protein RbmA in complex with 18-crown- 6 |
6yo6-assembly1_A |
0.99 | 0.43 | 1.1e-02 | 6yo6-assembly1_A Structure of iC3b1 |
8ovb-assembly1_A |
0.99 | 0.48 | 2.6e-02 | 8ovb-assembly1_A Human Complement C3b in complex with Trypanosoma brucei ISG65. |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1779c (integral membrane protein), medium confidence from genomic context alone (score 540 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) |
|---|---|---|---|---|
Rv1779c |
integral membrane protein | 540 | 540 ctx | neighborhood:540 |
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: hypothetical protein
- Pfam: DUF6941 PF22091.3
- Foldseek best: 4be6-assembly1_A V. cholera biofilm scaffolding protein RbmA (prob 1.00, E=1e-03, TM=0.38)
- (structure-only promotion reviewed by hand, 2026-06-01)
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_216294.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF6941 (PF22091.3)
- 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
2E3FZ - Curated reference: UniProt O33181 (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 84.5, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
1 functional partner(s); context anchor
Rv1779c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001892|Rv1778c| MRVSLFLSDAAQADAQSGKVHALGLGWRQCQTPTPPFALVLFLDIDWDETNKQHQLKCQLLTADGDPVVVPGPHGPQRILFEAAAEAGRAPGAIHGTSVRMPLTLNIPAGIPLEPGIYEWRVEVEGYERATAVEAFIVAGGGHPPASCG