Rv2473 Still unknown · low auto-curated
H37Rv Rv2473 · MTBC0 mtbc0_002635 ·
238 aa · 2799816–2800532 (+) ·
RefSeq NP_216989.1
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: 5xsj-assembly1_L XylFII-LytSN complex (prob 0.97, TM 0.45). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53200
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible alanine and proline rich membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2ATIH |
|---|
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 | 0.94 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 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 83.1 (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 |
|---|---|---|---|---|
5xsj-assembly1_L |
0.97 | 0.45 | 8.7e-02 | 5xsj-assembly1_L XylFII-LytSN complex |
1y4c-assembly1_A |
0.97 | 0.56 | 2.7e-01 | 1y4c-assembly1_A Designed Helical Protein fusion MBP |
5jsn-assembly2_D |
0.54 | 0.43 | 6.7e-01 | 5jsn-assembly2_D Bcl2-inhibitor complex |
8eup-assembly1_b |
0.41 | 0.50 | 1.9e+00 | 8eup-assembly1_b Ytm1 associated 60S nascent ribosome State 1A |
1xzp-assembly1_A |
0.35 | 0.55 | 2.1e+00 | 1xzp-assembly1_A Structure of the GTP-binding protein TrmE from Thermotoga maritima |
7xgf-assembly2_D |
0.33 | 0.40 | 1.4e+00 | 7xgf-assembly2_D Crystal structure of BCL-xL in complex with computationally designed inhibitor protein |
8eja-assembly1_B |
0.28 | 0.40 | 1.3e+00 | 8eja-assembly1_B Computational design of potent and selective inhibitors of Bak and Bax |
3fyq-assembly1_A |
0.20 | 0.36 | 1.4e+00 | 3fyq-assembly1_A Structure of Drosophila melanogaster talin IBS2 domain (residues 1981-2168) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: aglA (alpha-glucosidase AglA), medium confidence from genomic context alone (score 586 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) |
|---|---|---|---|---|
Rv2472 hyp |
hypothetical protein | 786 | 786 ctx | neighborhood:781 |
Rv2471 aglA |
alpha-glucosidase AglA | 585 | 586 ctx | neighborhood:586 |
Rv2470 glbO |
hemoglobin GlbO | 577 | 578 ctx | neighborhood:578 |
Rv2469c hyp |
hypothetical protein | 412 | 413 ctx | neighborhood:407 |
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: 5xsj-assembly1_L XylFII-LytSN complex (prob 0.97, E=9e-02, TM=0.45)
- (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_216989.1)
- 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
2ATIH - Curated reference: UniProt O53200 (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 83.1, 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
aglA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002635|Rv2473| MAPTSSSVASELLMPWPSAAASGVVGWRTTATASQRYHRPMSDTPFAEPYPEQRPPWGVPPPGWDGSSRPAPSTTPRSPGRWSLVAALALAVVSLGVGIVGWFHRQPHDKPSPAPSAPTFTSQQISDAKENVCAAHRIVRQAAVLNTNQANPVPGDPTGDLAVAANARLALYSGGDYLLRRLTAEPATPAELRDAVRSLANALQELAVNYLAGAPDSVVTPLRLALERDTRAVDPLCV