Rv0395 Still unknown · low auto-curated
H37Rv Rv0395 · MTBC0 mtbc0_000414 ·
134 aa · 478304–478708 (+) ·
RefSeq NP_214909.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. Foldseek best (non-significant) hit: 8csp-assembly1_5 Human mitochondrial small subunit assembly intermedia (prob 0.57, TM 0.50). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95203
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 | 2BWWP |
|---|
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 | 0.65 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 63.7 (low). Low-confidence model: the fold may be unreliable, so treat these structural hits with caution.
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 |
|---|---|---|---|---|
8csp-assembly1_5 |
0.57 | 0.50 | 2.1e-01 | 8csp-assembly1_5 Human mitochondrial small subunit assembly intermediate (State A) |
5twb-assembly1_A |
0.57 | 0.57 | 3.8e-01 | 5twb-assembly1_A Oxidoreductase IruO in the reduced form |
5che-assembly1_B |
0.51 | 0.43 | 1.5e-01 | 5che-assembly1_B Crystal structure of Arabidopsis glutamyl-tRNA reductase in complex with its regulatory proteins |
9jxu-assembly1_A |
0.44 | 0.42 | 1.5e-01 | 9jxu-assembly1_A Crystal structure of cysteine synthase A from Limosilactobacillus reuteri LR1 in its apo form |
5jjc-assembly2_D |
0.44 | 0.42 | 1.4e-01 | 5jjc-assembly2_D Crystal Structure of double mutant (Q96A-Y125A) O-Acetyl Serine Sulfhydralase from Brucella abortus |
4gc5-assembly1_A |
0.41 | 0.50 | 4.3e-01 | 4gc5-assembly1_A Crystal structure of murine TFB1M |
6dnz-assembly1_D |
0.28 | 0.38 | 3.1e-01 | 6dnz-assembly1_D Trypanosoma brucei PRMT1 enzyme-prozyme heterotetrameric complex with AdoHcy |
4zem-assembly1_A |
0.28 | 0.39 | 2.1e-01 | 4zem-assembly1_A Crystal structure of eIF2B beta from Chaetomium thermophilum |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0396 hyp |
hypothetical protein | 889 | 889 ctx | neighborhood:882 |
Rv0397 hyp |
hypothetical protein | 619 | 619 ctx | neighborhood:615 |
Rv0394c hyp |
hypothetical protein | 598 | 599 ctx | neighborhood:596 |
Rv3327 |
transposase fusion protein | 503 | 93 | textmining:475 |
Rv1371 |
membrane protein | 668 | 87 | textmining:652 |
Rv0894 |
transcriptional regulator | 462 | 82 | textmining:438 |
Rv3845 hyp |
hypothetical protein | 871 | 55 | textmining:870 |
Rv2283 hyp |
hypothetical protein | 524 | 55 | textmining:517 |
Rv3383c idsB |
polyprenyl synthetase IdsB | 656 | 46 | textmining:655 |
Rv1504c |
Rv1504c, (MTCY277.26c), len: 199 aa. Conserved hypothetical protein, similar to N-terminal region of P27833|RFFA_ECOLI lipopolysaccharide bi | 810 | 45 | textmining:810 |
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: 8csp-assembly1_5 Human mitochondrial small subunit assembly intermediate (State (prob 0.57, E=2e-01, TM=0.50)
- (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_214909.1)
- 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
2BWWP - Curated reference: UniProt P95203 (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 63.7, low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 10 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000414|Rv0395| MDWMPLGDYETFRHWSGKPRAWGPQESGWRAWFGGKIVDGLCEVLDEHLAVRRRGVPAAIGCVPWLSSEAVAETLLALSAFCVVIDKGTSFPSRLRNPDKGFPNVALLRLRDMAPSEHGSRCSSARGRLCLSMS