Rv0566c Family assigned · medium auto-curated
H37Rv Rv0566c · MTBC0 mtbc0_000595 ·
163 aa · 661099–661590 (-) ·
RefSeq NP_215080.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | YajQ family cyclic di-GMP-binding protein |
| Revised (this work) | YajQ family cyclic di-GMP-binding protein. Pfam: YajQ (PF04461.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFK9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Nucleotide-binding protein Rv0566c |
| Curated function | Nucleotide-binding protein. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | trpF |
| eggNOG description | Belongs to the UPF0234 family |
| Orthologous group | COG1666 |
| KEGG orthology |
K09767
|
| Gene Ontology (11) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0016020, GO:0044424, GO:0044444, GO:0044464, GO:0071944
|
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 | 0.296 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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 |
|---|---|---|---|---|
YajQ | PF04461.19 | 1.4e-62 | 4–163 | Nucleotide-binding protein YajQ-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0565c (monooxygenase), high confidence from genomic context alone (score 934 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) |
|---|---|---|---|---|
Rv0565c |
monooxygenase | 934 | 934 ctx | neighborhood:788 coexpression:703 |
Rv0564c gpdA1 |
glycerol-3-phosphate dehydrogenase | 735 | 735 ctx | neighborhood:734 |
Rv1392 metK |
S-adenosylmethionine synthetase | 432 | 433 | coexpression:423 |
Rv0567 |
methyltransferase/methylase | 429 | 429 ctx | neighborhood:423 |
Rv2033c hyp |
hypothetical protein | 435 | 78 | textmining:413 |
Rv0360c hyp |
hypothetical protein | 418 | 50 | textmining:413 |
Rv0421c hyp |
hypothetical protein | 414 | 44 | textmining:413 |
Rv2676c hemQ hyp |
hypothetical protein | 412 | 41 | textmining:413 |
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: YajQ family cyclic di-GMP-binding protein
- Pfam (hmmscan --cut_ga): YajQ PF04461.19 (E=1e-62)
- (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_215080.1)
- Domains: Pfam-A via hmmscan --cut_ga — YajQ (PF04461.19)
- 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
COG1666 - Curated reference: UniProt P9WFK9 (SwissProt, reviewed; 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 —
8 functional partner(s); context anchor
Rv0565c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000595|Rv0566c| MADSSFDIVSKVDRQEVDNALNQAAKELATRFDFRGTDTKIAWKGDEAVELTSSTEERVKAAVDVFKEKLIRRDISLKAFEAGEPQASGKTYKVTGALKQGISSENAKKITKLIRDAGPKNVKTQIQGDEVRVTSKKRDDLQAVIAMLKKADLDVALQFVNYR