Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|
| MTBC0 PGAP re-annotation | DUF5073 family protein |
|---|
| Revised (this work) | DUF5073 family protein. |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06796
TrEMBL · unreviewed
· Evidence at protein level
|
|---|
| UniProt name | Possible exported protein |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|
| eggNOG description | Domain of unknown function (DUF5073) |
|---|
| Orthologous group | 2B28X |
|---|
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 |
0.72 · relaxed/neutral
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
1 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 |
|---|
DUF5073 | PF16817.12 |
5.1e-64 | 1–120 |
Domain of unknown function (DUF5073) |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv1762c hyp |
hypothetical protein |
887 |
887 ctx |
neighborhood:881 |
Rv1754c hyp |
hypothetical protein |
555 |
55 |
textmining:549 |
Rv2212 |
adenylyl cyclase |
514 |
47 |
textmining:511 |
Rv1585c |
phage protein |
659 |
42 |
textmining:659 |
Rv1765c hyp |
hypothetical protein |
658 |
41 |
textmining:658 |
Rv0071 |
maturase |
556 |
41 |
textmining:556 |
Rv1647 |
adenylate cyclase |
511 |
41 |
textmining:511 |
Rv1318c |
adenylate cyclase |
439 |
41 |
textmining:439 |
Rv1320c |
adenylate cyclase |
436 |
41 |
textmining:436 |
Rv1319c |
adenylate cyclase |
434 |
41 |
textmining:434 |
Rv1264 |
adenylyl cyclase |
433 |
41 |
textmining:433 |
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: DUF5073 family protein
- Pfam (hmmscan --cut_ga): DUF5073 PF16817.12 (E=5e-64)
- (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_216277.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF5073 (PF16817.12)
- 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
2B28X
- Curated reference: UniProt
O06796
(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 —
11 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001876|Rv1761c|
MSDFDTERVSRAVAAALVGPGGVALVVKVFAGLPGVIHTPARRGFFRSNPERIQIGDWRYEVAHDGRLLAAHMVNGIVIAEDALIAEAVGPHLARALGQIVSRYGATVIPNINAAIEVLGTGTDYRF
Spot an error? Suggest an improvement