Rv0552 Resolved · high auto-curated
H37Rv Rv0552 · MTBC0 mtbc0_000581 ·
534 aa · 646440–648044 (+) ·
RefSeq NP_215066.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | amidohydrolase |
| Revised (this work) | Amidohydrolase. Pfam: Amidohydro_3 (PF07969.18), Amidohydro_1 (PF01979.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06418
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
|
|---|---|
| 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 | 0.268 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 6 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 | 3.1e-83 | 50–532 | Amidohydrolase family |
Amidohydro_1 | PF01979.27 | 5.6e-09 | 208–531 | Amidohydrolase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: menC (muconate cycloisomerase), high confidence from genomic context alone (score 902 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) |
|---|---|---|---|---|
Rv0553 menC |
muconate cycloisomerase | 902 | 902 ctx | neighborhood:881 |
Rv0554 bpoC |
non-heme bromoperoxidase BpoC | 878 | 878 ctx | neighborhood:878 |
Rv0551c fadD8 |
fatty-acid--CoA ligase FadD8 | 792 | 793 ctx | neighborhood:784 |
Rv0557 mgtA |
GDP-mannose-dependent alpha-mannosyltransferase | 761 | 749 ctx | neighborhood:749 |
Rv0555 menD |
bifunctional 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase/2-oxoglutarate decarboxylase | 683 | 683 ctx | neighborhood:682 |
Rv0556 |
transmembrane protein | 669 | 669 ctx | neighborhood:669 |
Rv0548c menB |
1,4-dihydroxy-2-naphthoyl-CoA synthase | 614 | 615 ctx | neighborhood:615 |
Rv0074 hyp |
hypothetical protein | 572 | 572 ctx | cooccurence:570 |
Rv0558 menH |
demethylmenaquinone methyltransferase | 492 | 492 ctx | neighborhood:492 |
Rv0547c |
oxidoreductase | 405 | 405 ctx | neighborhood:405 |
Rv2672 |
protease | 688 | 174 | textmining:638 |
Rv3829c |
dehydrogenase | 401 | 152 | |
Rv1898 hyp |
hypothetical protein | 808 | 67 | textmining:803 |
Rv0842 |
integral membrane protein | 715 | 47 | textmining:714 |
Rv0874c hyp |
hypothetical protein | 806 | 45 | textmining:806 |
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=3e-83), Amidohydro_1 PF01979.27 (E=6e-09)
- (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_215066.1)
- Domains: Pfam-A via hmmscan --cut_ga — Amidohydro_3 (PF07969.18), Amidohydro_1 (PF01979.27)
- 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 O06418 (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 —
16 functional partner(s); context anchor
menC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000581|Rv0552| MADADLVMTGTVLTVDDARPTAEAIAVADGRVIAVGDRSEVAGLVGANTRVIDLGAGCVMPGFVEAHGHPLLEAVVLSDRFVDIRPVTMRDADDVVAAIRGEVARRGPAGAYLVGWDPLLQSGLGEPTLTWLDSLAPNGPLVIIHNSGHKAYFNSHAAWLNGLTRDTADPKGAKYGRDGNGELDGTAEEIGAILPLLAGVADPSNFGAMLRAECARLNRAGLTTCSEMAFDPGYRPMVEAVRAELTVRLCTYEISNARMCTDATPGQGDDMLRQVGIKIWVDGSPWVGNIDLTFPYLDTPATRAIGVPPGSRGCANYTREQLAEIVGAYFPRGWQIACHVHGDGGVDTILDVYEEALRRNPRDDHRLRLEHVGAIRPDQLRRAAELGVTCSIFVDQIHYWGDVIVDDLFGAQRGSRWMPAGSAVAAGMRISLHNDPPVTPEEPLRNISVAATRVAPSGRVLAPEERLTVEQAIRAQTIDAAWQLFAEDAIGSLQVGKYADMVVLSADPRTVPPEQIADLAVRATFLAGRQVYRR