Rv0857 Family assigned · medium auto-curated
H37Rv Rv0857 · MTBC0 - ·
157 aa · 953257–953730 (+) ·
RefSeq NP_215372.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Polyketide_cyc2 (PF10604.16), Polyketide_cyc (PF03364.26) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
I6Y4Z9
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Cyclase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | cyclase dehydrase |
| Orthologous group | COG3832 |
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 | 1.346 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 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 | 4.2e-11 | 10–145 | Polyketide cyclase / dehydrase and lipid transport |
Polyketide_cyc | PF03364.26 | 5.5e-07 | 18–142 | 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 753 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) |
|---|---|---|---|---|
Rv0856 hyp |
hypothetical protein | 846 | 846 ctx | neighborhood:841 |
Rv0474 |
HTH-type transcriptional regulator | 752 | 753 ctx | cooccurence:749 |
Rv0855 far |
fatty-acid-CoA racemase | 741 | 741 ctx | neighborhood:741 |
Rv3679 |
anion transporter ATPase | 715 | 716 ctx | cooccurence:715 |
Rv0487 hyp |
hypothetical protein | 709 | 709 ctx | cooccurence:696 |
Rv3197 |
ABC transporter ATP-binding protein | 674 | 675 ctx | cooccurence:670 |
Rv0502 hyp |
hypothetical protein | 668 | 668 ctx | cooccurence:667 |
Rv3916c hyp |
hypothetical protein | 587 | 587 ctx | cooccurence:576 |
Rv3680 |
anion transporter ATPase | 584 | 585 ctx | cooccurence:582 |
Rv0854 hyp |
hypothetical protein | 561 | 560 ctx | neighborhood:516 |
Rv0501 galE2 |
UDP-glucose 4-epimerase GalE | 556 | 557 ctx | cooccurence:554 |
Rv3662c hyp |
hypothetical protein | 536 | 536 ctx | cooccurence:534 |
Rv2974c hyp |
hypothetical protein | 499 | 499 ctx | cooccurence:496 |
Rv3698 hyp |
hypothetical protein | 498 | 498 ctx | cooccurence:486 |
Rv2712c hyp |
hypothetical protein | 495 | 496 ctx | cooccurence:493 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): Polyketide_cyc2 PF10604.16 (E=4e-11), Polyketide_cyc PF03364.26 (E=6e-07)
- (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_215372.2)
- 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
COG3832 - Curated reference: UniProt I6Y4Z9 (TrEMBL, unreviewed; Predicted)
- 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 —
22 functional partner(s); context anchor
Rv0474 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0857| MIANLVAVAIRASREVVIEAPPEVIVEALADMDAVPSWSSVHKRVEVVDTYSDGRPHHVKVTIKVAGIVDTELLEYHWGPDWVVWDAAKTAQQHGQHGEYNLRREDNDKTRVRFTLTVEPSAPLPAFWVNIARKKILHAATEGLRKQVVGRRRFTSG