Rv2052c Resolved · high auto-curated
H37Rv Rv2052c · MTBC0 mtbc0_002185 ·
534 aa · 2339526–2341130 (-) ·
RefSeq NP_216568.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | amidohydrolase |
| Revised (this work) | Amidohydrolase. Pfam: Amidohydro_3 (PF07969.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53494
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | ytcJ |
| eggNOG description | amidohydrolase |
| Orthologous group | COG1574 |
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 | 0.366 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 8 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 |
|---|---|---|---|---|
Amidohydro_3 | PF07969.18 | 9.6e-99 | 49–533 | Amidohydrolase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fxsA (transmembrane protein FxsA), high confidence from genomic context alone (score 979 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) |
|---|---|---|---|---|
Rv2053c fxsA |
transmembrane protein FxsA | 979 | 979 ctx | neighborhood:882 coexpression:831 |
Rv2051c ppm1 |
polyprenol-monophosphomannose synthase | 897 | 898 ctx | neighborhood:510 coexpression:800 |
Rv2054 hyp |
hypothetical protein | 671 | 671 ctx | neighborhood:671 |
Rv2915c hyp |
hypothetical protein | 595 | 596 ctx | cooccurence:589 |
Rv1382 hyp |
hypothetical protein | 584 | 585 ctx | cooccurence:570 |
Rv0074 hyp |
hypothetical protein | 511 | 511 ctx | cooccurence:503 |
Rv2772c |
transmembrane protein | 477 | 477 ctx | cooccurence:477 |
Rv3316 sdhC |
succinate dehydrogenase cytochrome B-556 subunit | 468 | 468 ctx | cooccurence:468 |
Rv3317 sdhD |
succinate dehydrogenase hydrophobic membrane anchor subunit | 463 | 464 ctx | cooccurence:463 |
Rv2670c zapE hyp |
hypothetical protein | 432 | 432 ctx | cooccurence:432 |
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: amidohydrolase
- Pfam (hmmscan --cut_ga): Amidohydro_3 PF07969.18 (E=1e-98)
- (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_216568.1)
- Domains: Pfam-A via hmmscan --cut_ga — Amidohydro_3 (PF07969.18)
- 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
COG1574 - Curated reference: UniProt O53494 (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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
10 functional partner(s); context anchor
fxsA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002185|Rv2052c| MSQIPVKLLVNGRVYSPTHPEATAMAVRGDVVAWLGSDDVGRDQFPDADVQDLDGRFVAPGFVDSHIHLTATGLMLSGLDLRPATSRAQCLRMVADYAADHPGQPLWGHGWDESAWPENAAPSTADLDAVLGDCPAYLARIDSHSALVSSGLRRLVPELAAATGYTAQRPLTGDAHHLARAAARYLLTDVQLADARAVALQAIAAAGVVAVHECAGPEIGGLDDWLRLRALEHGVEVIGYWGEAVATPAQARDLVTETGARGLAGDLFVDGALGSRTAWLHEPYADAPDCIGTCHLDVDGIEAHVRACTKAEVTAGFHVIGDAAVSAAVAAFERVVADLGVVAVARCGHRLEHVEMVTADQAAKLGAWGVIASVQPNFDELWGGGDGMYARRLGAQRGSELNPLALLASQGVPLALGSDAPVTGFDPWASVRAAVNHRTPGSGVSARAAFAAATRGGWRAGGVRDGRIGTLVPGAPASYAIWDAGDFDVDAPRDAVQRWSTDPRSRVPALPRLGPTDALPRCRQTVHRGAVIYG