Rv2271 Still unknown · low auto-curated
H37Rv Rv2271 · MTBC0 mtbc0_002413 ·
99 aa · 2571437–2571736 (+) ·
RefSeq NP_216787.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF2695 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF2695. Function unknown. Foldseek best (non-significant) hit: 7kuw-assembly1_A High-throughput design and refinement of stable prote (prob 0.04, TM 0.37). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLF7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2271 |
UniProt still lists this protein as Uncharacterized protein Rv2271; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF2695) |
| Orthologous group | 2B2YH |
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, 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
DUF2695 | PF10905.14 | 4.7e-27 | 39–91 | Protein of unknown function (DUF2695) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 50.2 (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 |
|---|---|---|---|---|
7kuw-assembly1_A |
0.04 | 0.37 | 5.2e+00 | 7kuw-assembly1_A High-throughput design and refinement of stable proteins using sequence-only models |
8pv2-assembly1_CQ |
0.01 | 0.24 | 9.6e+00 | 8pv2-assembly1_CQ Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lppN (lipoprotein LppN), medium confidence from genomic context alone (score 577 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) |
|---|---|---|---|---|
Rv2270 lppN |
lipoprotein LppN | 577 | 577 ctx | neighborhood:576 |
Rv2272 |
transmembrane protein | 546 | 546 ctx | neighborhood:534 |
Rv2273 |
transmembrane protein | 539 | 538 ctx | neighborhood:534 |
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: DUF2695 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF2695 PF10905.14 (E=5e-27)
- Foldseek best: 7kuw-assembly1_A High-throughput design and refinement of stable proteins using (prob 0.04, E=5e+00, TM=0.37)
- (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_216787.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF2695 (PF10905.14)
- 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
2B2YH - Curated reference: UniProt P9WLF7 (SwissProt, reviewed; 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 50.2, low)
- 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
lppN - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002413|Rv2271| MTTPPDKARRRFLRDAYKNAERVARTALLTIDQDQLEQLLDYVDERLGEQPCDHTARHAQRWAQSHRIEWETLAEGLQEFGGYCDCEIVMNVEPEAIFG