Rv1154c Family assigned · low auto-curated · to review
H37Rv Rv1154c · MTBC0 - ·
213 aa · 1280843–1281484 (-) ·
RefSeq NP_215670.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | No Pfam domain above threshold; Foldseek indicates a fold similar to 2hiy-assembly1_B The structure of conserved bacterial protein SP0830 from Strept (prob 1.00, TM 0.79). 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).
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 |
O06552
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DUF1697 domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF1697) |
| Orthologous group | COG3797 |
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, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.15% of strains (225) · 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 |
|---|---|---|---|---|
DUF1697 | PF08002.17 | 3.0e-32 | 38–164 | Protein of unknown function (DUF1697) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 91.3 (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 |
|---|---|---|---|---|
2hiy-assembly1_B |
1.00 | 0.79 | 2.5e-10 sig | 2hiy-assembly1_B The structure of conserved bacterial protein SP0830 from Streptococcus pneumoniae. |
2hiy-assembly1_A |
1.00 | 0.80 | 1.4e-09 sig | 2hiy-assembly1_A The structure of conserved bacterial protein SP0830 from Streptococcus pneumoniae. |
2nyi-assembly1_B |
0.94 | 0.29 | 8.0e-04 sig | 2nyi-assembly1_B Crystal Structure of an Unknown Protein from Galdieria sulphuraria |
2crl-assembly1_A |
0.92 | 0.51 | 5.0e-02 | 2crl-assembly1_A The apo form of HMA domain of copper chaperone for superoxide dismutase |
6wue-assembly1_A-2 |
0.90 | 0.50 | 3.7e-02 | 6wue-assembly1_A-2 Tetragonal crystal form of SbtB from Synechocystis PCC6803 |
3dfe-assembly1_F |
0.80 | 0.47 | 7.7e-02 | 3dfe-assembly1_F Crystal structure of a Putative Pii-Like Signaling Protein (YP_323533.1) from ANABAENA VARIABILIS ATCC 29413 at 2.35 A resolution |
5dih-assembly1_E |
0.69 | 0.31 | 9.4e-03 sig | 5dih-assembly1_E Structure of Haliangium ochraceum BMC-T HO-5812 |
8b2r-assembly1_A |
0.63 | 0.58 | 4.6e-01 | 8b2r-assembly1_A Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikF with a rice (Oryza sativa) RGA5 HMA domain mutant. |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: omt (O-methyltransferase), 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) |
|---|---|---|---|---|
Rv1153c omt |
O-methyltransferase | 883 | 883 ctx | neighborhood:882 |
Rv1155 |
pyridoxine/pyridoxamine 5'-phosphate oxidase | 589 | 589 ctx | neighborhood:585 |
Rv0806c cpsY |
exopolysaccharide phosphotransferase CpsY | 419 | 420 ctx | cooccurence:418 |
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
- Pfam (hmmscan --cut_ga): DUF1697 PF08002.17 (E=3e-32)
- Foldseek best: 2hiy-assembly1_B The structure of conserved bacterial protein SP0830 from Strept (prob 1.00, E=2e-10, TM=0.79)
- (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_215670.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF1697 (PF08002.17)
- 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
COG3797 - Curated reference: UniProt O06552 (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 91.3, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
3 functional partner(s); context anchor
omt - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1154c| MEFPLITANSLSSKTWRAMPRAYVAVASFSGGLVQSGMAKFAAFLRGVNVGGVNLKMAEVATALTDAGFCNVRTILASGNVLLESTCGAAEVREKTEATLRERFGYDAWALIYDVDTVRTIVTAYPFECELEGYQSYVTFVADAAILDELSALADTAGPDENISRGPDPLGVLYWQVPKGSTLDSTIGQTMGKKRYKSSTTTRNLRTLAKVLR