Rv1948c Family assigned · low
H37Rv Rv1948c · MTBC0 mtbc0_001233 ·
33 aa · 1284366–1284467 (+) ·
RefSeq NP_216464.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Suppressor-of-Fused-like fold (PDB 4KMA); fold characterised, function not established. |
Curated reference (UniProt)
| UniProt |
P95266
TrEMBL · unreviewed
· Predicted
|
|---|---|
| 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 | 2B1FN |
|---|
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 | 0.298 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 80.0 (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 |
|---|---|---|---|---|
4kma-assembly1_A |
1.00 | 0.60 | 1.1e-03 sig | 4kma-assembly1_A Crystal structure of Drosophila Suppressor of Fused |
4bkw-assembly1_A |
0.54 | 0.46 | 1.3e-01 | 4bkw-assembly1_A Crystal structure of the C-terminal region of human ZFYVE9 |
7uzy-assembly1_F |
0.04 | 0.41 | 4.9e+00 | 7uzy-assembly1_F Staphylococcus epidermidis RP62A CRISPR effector complex with non-self target RNA 2 |
8e0b-assembly2_B |
0.03 | 0.53 | 9.1e+00 | 8e0b-assembly2_B Crystal structure of human Sar1bT39N |
6rwx-assembly1_S |
0.03 | 0.22 | 3.3e+00 | 6rwx-assembly1_S Periplasmic inner membrane ring of the Shigella type 3 secretion system |
8axn-assembly1_A |
0.03 | 0.21 | 1.9e+00 | 8axn-assembly1_A Inner membrane ring and secretin N0 N1 domains of the type 3 secretion system of Shigella flexneri |
8sk7-assembly1_X |
0.02 | 0.31 | 9.7e+00 | 8sk7-assembly1_X Cryo-EM structure of designed Influenza HA binder, HA_20, bound to Influenza HA (Strain: Iowa43) |
3gr1-assembly2_F-5 |
0.02 | 0.20 | 2.6e+00 | 3gr1-assembly2_F-5 Periplasmic domain of the T3SS inner membrane protein PrgH from S.typhimurium (fragment 170-392) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1949c (Rv1949c, (MTCY09F9.15), len: 319 aa. Conserved hypothetical protein, partial ORF. Rv1949c and Rv1950c|MTCY09F9.14 are similar but frameshift), high confidence from genomic context alone (score 877 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) |
|---|---|---|---|---|
Rv1949c |
Rv1949c, (MTCY09F9.15), len: 319 aa. Conserved hypothetical protein, partial ORF. Rv1949c and Rv1950c|MTCY09F9.14 are similar but frameshift | 877 | 877 ctx | neighborhood:875 |
Rv1950c hyp |
hypothetical protein | 815 | 816 ctx | neighborhood:814 |
Rv1951c hyp |
hypothetical protein | 814 | 815 ctx | neighborhood:814 |
Rv1953 vapC14 |
ribonuclease VapC14 | 464 | 465 ctx | neighborhood:463 |
Rv1952 vapB14 |
antitoxin VapB14 | 463 | 463 ctx | neighborhood:463 |
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: 4kma-assembly1_A Crystal structure of Drosophila Suppressor of Fused (prob 1.00, E=1e-03, TM=0.60)
- (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_216464.1)
- 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
2B1FN - Curated reference: UniProt P95266 (TrEMBL, unreviewed; Predicted)
- 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 80.0, confident)
- 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
Rv1949c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001233|Rv1948c| MSPLIDGEGPGHQYIDDLNSPAPTLMISVDEYA