TB16.3 Family assigned · medium auto-curated
H37Rv Rv2185c · MTBC0 mtbc0_002320 ·
144 aa · 2473073–2473507 (-) ·
RefSeq NP_216701.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | SRPBCC family protein |
| Revised (this work) | SRPBCC family protein. Pfam: Polyketide_cyc2 (PF10604.16), Polyketide_cyc (PF03364.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53519
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein TB16.3 |
UniProt still lists this protein as Conserved protein TB16.3; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| eggNOG description | cyclase dehydrase |
| Orthologous group | COG2867 |
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 | 0.145 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
Polyketide_cyc2 | PF10604.16 | 1.3e-15 | 4–143 | Polyketide cyclase / dehydrase and lipid transport |
Polyketide_cyc | PF03364.26 | 2.9e-16 | 11–138 | Polyketide cyclase / dehydrase and lipid transport |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0474 (HTH-type transcriptional regulator), high confidence from genomic context alone (score 764 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) |
|---|---|---|---|---|
Rv2184c hyp |
hypothetical protein | 765 | 766 ctx | neighborhood:763 |
Rv0474 |
HTH-type transcriptional regulator | 772 | 764 ctx | cooccurence:763 |
Rv2183c hyp |
hypothetical protein | 764 | 764 ctx | neighborhood:763 |
Rv3197 |
ABC transporter ATP-binding protein | 755 | 743 ctx | cooccurence:685 |
Rv0502 hyp |
hypothetical protein | 724 | 724 ctx | cooccurence:720 |
Rv3679 |
anion transporter ATPase | 720 | 720 ctx | cooccurence:708 |
Rv0487 hyp |
hypothetical protein | 717 | 717 ctx | cooccurence:717 |
Rv2182c |
1-acylglycerol-3-phosphate O-acyltransferase | 707 | 707 ctx | neighborhood:702 |
Rv2187 fadD15 |
long-chain-fatty-acid--CoA ligase FadD15 | 679 | 679 ctx | neighborhood:669 |
Rv3680 |
anion transporter ATPase | 650 | 651 ctx | cooccurence:635 |
Rv2186c hyp |
hypothetical protein | 591 | 591 ctx | neighborhood:588 |
Rv0501 galE2 |
UDP-glucose 4-epimerase GalE | 524 | 524 ctx | cooccurence:519 |
Rv2974c hyp |
hypothetical protein | 521 | 521 ctx | cooccurence:521 |
Rv3698 hyp |
hypothetical protein | 472 | 472 ctx | cooccurence:472 |
Rv3916c hyp |
hypothetical protein | 453 | 453 ctx | cooccurence:452 |
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: SRPBCC family protein
- Pfam (hmmscan --cut_ga): Polyketide_cyc2 PF10604.16 (E=1e-15), Polyketide_cyc PF03364.26 (E=3e-16)
- (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_216701.1)
- Domains: Pfam-A via hmmscan --cut_ga — Polyketide_cyc2 (PF10604.16), Polyketide_cyc (PF03364.26)
- 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
COG2867 - Curated reference: UniProt O53519 (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 —
26 functional partner(s); context anchor
Rv0474 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002320|Rv2185c|TB16.3 MADKTTQTIYIDADPGEVMKAIADIEAYPQWISEYKEVEILEADDEGYPKRARMLMDAAIFKDTLIMSYEWPEDRQSLSWTLESSSLLKSLEGTYRLAPKGSGTEVTYELAVDLAVPMIGMLKRKAERRLIDGALKDLKKRVEG