Rv2077A Still unknown · low auto-curated
H37Rv Rv2077A · MTBC0 - ·
99 aa · 2334295–2334594 (-) ·
RefSeq YP_177658.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. Foldseek best (non-significant) hit: 6uuj-assembly2_E Structure of PE5-PPE4-EspG3 complex from the type VII (prob 0.90, TM 0.69). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
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 |
L7N6B8
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | PE family protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2B0F7 |
|---|
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, 0 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.32% of strains (468) · 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)
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 81.0 (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 |
|---|---|---|---|---|
6uuj-assembly2_E |
0.90 | 0.69 | 1.0e+00 | 6uuj-assembly2_E Structure of PE5-PPE4-EspG3 complex from the type VII (ESX-3) secretion system, space group P212121 |
6s1k-assembly1_I |
0.16 | 0.53 | 5.3e+00 | 6s1k-assembly1_I E. coli Core Signaling Unit, carrying QQQQ receptor mutation |
2f1m-assembly1_A |
0.15 | 0.61 | 9.0e+00 | 2f1m-assembly1_A Conformational flexibility in the multidrug efflux system protein AcrA |
6s1k-assembly1_E |
0.14 | 0.50 | 5.3e+00 | 6s1k-assembly1_E E. coli Core Signaling Unit, carrying QQQQ receptor mutation |
2f1m-assembly2_D |
0.14 | 0.62 | 9.6e+00 | 2f1m-assembly2_D Conformational flexibility in the multidrug efflux system protein AcrA |
6s1k-assembly1_K |
0.13 | 0.52 | 7.5e+00 | 6s1k-assembly1_K E. coli Core Signaling Unit, carrying QQQQ receptor mutation |
3zx6-assembly1_B |
0.12 | 0.54 | 7.5e+00 | 3zx6-assembly1_B Structure of Hamp(AF1503)-Tsr fusion - Hamp (A291V) mutant |
9had-assembly1_A |
0.11 | 0.51 | 7.1e+00 | 9had-assembly1_A Der f 21 dust mite allergen with computationally designed DerF21_b10 binder |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2077c (transmembrane protein), high confidence from genomic context alone (score 782 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) |
|---|---|---|---|---|
Rv2077c |
transmembrane protein | 782 | 782 ctx | neighborhood:781 |
Rv2076c hyp |
hypothetical protein | 676 | 677 ctx | neighborhood:675 |
Rv2078 hyp |
hypothetical protein | 651 | 651 | coexpression:651 |
Rv2075c hyp |
hypothetical protein | 415 | 416 ctx | neighborhood:414 |
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
- Foldseek best: 6uuj-assembly2_E Structure of PE5-PPE4-EspG3 complex from the type VII (ESX-3) s (prob 0.90, E=1e+00, TM=0.69)
- (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 YP_177658.1)
- 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
2B0F7 - Curated reference: UniProt L7N6B8 (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 81.0, confident)
- 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
Rv2077c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2077A| MGSNELQVVLGQLEVAASQSQGLGAQFAASATPPESGQPFQATTVAVSGINAAICCAAAEFATRTQATATGVAAAAAAYAHQEATAASEMAAVTQVTVV