Rv0854 Family assigned · medium auto-curated
H37Rv Rv0854 · MTBC0 mtbc0_000909 ·
147 aa · 954334–954777 (+) ·
RefSeq NP_215369.1
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 |
I6X9Y7
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 | 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 | 8.7e-20 | 6–139 | Polyketide cyclase / dehydrase and lipid transport |
Polyketide_cyc | PF03364.26 | 1.1e-16 | 11–137 | Polyketide cyclase / dehydrase and lipid transport |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: far (fatty-acid-CoA racemase), high confidence from genomic context alone (score 823 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) |
|---|---|---|---|---|
Rv0855 far |
fatty-acid-CoA racemase | 822 | 823 ctx | neighborhood:817 |
Rv0474 |
HTH-type transcriptional regulator | 763 | 755 ctx | cooccurence:754 |
Rv3197 |
ABC transporter ATP-binding protein | 718 | 705 ctx | cooccurence:639 |
Rv3679 |
anion transporter ATPase | 697 | 697 ctx | cooccurence:686 |
Rv0487 hyp |
hypothetical protein | 691 | 691 ctx | cooccurence:691 |
Rv0502 hyp |
hypothetical protein | 677 | 678 ctx | cooccurence:675 |
Rv0164 TB18.5 hyp |
hypothetical protein | 658 | 659 ctx | cooccurence:655 |
Rv0853c pdc |
alpha-keto-acid decarboxylase | 624 | 624 ctx | neighborhood:618 |
Rv3680 |
anion transporter ATPase | 605 | 605 ctx | cooccurence:591 |
Rv0856 hyp |
hypothetical protein | 596 | 596 ctx | neighborhood:571 |
Rv0876c |
transmembrane protein | 583 | 583 ctx | cooccurence:583 |
Rv0857 hyp |
hypothetical protein | 561 | 560 ctx | neighborhood:516 |
Rv3916c hyp |
hypothetical protein | 558 | 558 ctx | cooccurence:558 |
Rv0501 galE2 |
UDP-glucose 4-epimerase GalE | 536 | 536 ctx | cooccurence:536 |
Rv2974c hyp |
hypothetical protein | 515 | 515 ctx | cooccurence:515 |
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=9e-20), Polyketide_cyc PF03364.26 (E=1e-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_215369.1)
- 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
COG3832 - Curated reference: UniProt I6X9Y7 (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 —
23 functional partner(s); context anchor
far - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000909|Rv0854| MAIKESRDIVIEASPEEILDVIADFEAMTEWSPAHQSVEILETGDDGRPSKVKMKVKTAGITDEQVVAYSWTDRSVRWTLVSSTQQRSQDGKYELTPKGDNTLVQFEITVDPQVPLPGFVLKRAIKGTIDTATEALRSQVLKVKKGQ