Rv1097c Family assigned · low
H37Rv Rv1097c · MTBC0 mtbc0_001180 ·
293 aa · 1233703–1234584 (-) ·
RefSeq NP_215613.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Apa-like fold (fibronectin-binding protein Apa, PDB 5ZX9); putative adhesin / secreted protein. |
Curated reference (UniProt)
| UniProt |
O53445
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable membrane glycine and proline rich protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2EAJ3 |
|---|
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 | 2.489 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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)
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 91.1 (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 |
|---|---|---|---|---|
5zx9-assembly1_A |
1.00 | 0.61 | 3.2e-05 sig | 5zx9-assembly1_A Crystal structure of apo form fibronectin-binding protein Apa from Mycobacterium tuberculosis |
3bhd-assembly2_B |
0.06 | 0.21 | 3.3e-01 | 3bhd-assembly2_B Crystal structure of human thiamine triphosphatase (THTPA) |
6sc2-assembly1_D |
0.04 | 0.15 | 1.8e+00 | 6sc2-assembly1_D Structure of the dynein-2 complex; IFT-train bound model |
8bwy-assembly1_e |
0.01 | 0.11 | 3.4e+00 | 8bwy-assembly1_e In situ outer dynein arm from Chlamydomonas reinhardtii in a pre-power stroke state |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fum (fumarate hydratase), high confidence from genomic context alone (score 888 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) |
|---|---|---|---|---|
Rv1098c fum |
fumarate hydratase | 888 | 888 ctx | neighborhood:882 |
Rv1099c glpX |
fructose 1,6-bisphosphatase | 821 | 821 ctx | neighborhood:816 |
Rv1100 hyp |
hypothetical protein | 510 | 510 ctx | neighborhood:507 |
Rv3286c sigF |
RNA polymerase sigma factor SigF | 470 | 437 | coexpression: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
- MTBC0 PGAP product: hypothetical protein
- Foldseek best: 5zx9-assembly1_A Crystal structure of apo form fibronectin-binding protein Apa f (prob 1.00, E=3e-05, TM=0.61)
- (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_215613.1)
- 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
2EAJ3 - Curated reference: UniProt O53445 (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 91.1, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
4 functional partner(s); context anchor
fum - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001180|Rv1097c| MTVPPAGPYGNYPYGPNTYGQDPYWGGQPQGGSYPPAYPPQQYPPGWPAGPYPPGPPPPGPGSKTPWLILAGLAVLGVILLVVILVIGLRGDNKSTTATSPATSAPTSQPFSQQTATGCTPNVSGGVQPIGDSISAGKLSFPTSAAPGWSAFSDDQNPNLIDAVGVGHEVAGADQWMMQAEVAITNFVTTMDVAAQASKLMQCVADGPGYAGSSPTLGPTKTSSITVDGVRAARVDADITIADSSRNVKGDSVTIIAVDTKPVTVFLGATPIGDATSRATVERVIEALKVNKS