Rv0574c Family assigned · medium auto-curated
H37Rv Rv0574c · MTBC0 mtbc0_000604 ·
380 aa · 670803–671945 (-) ·
RefSeq NP_215088.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | CapA family protein |
| Revised (this work) | CapA family protein. Pfam: PGA_cap (PF09587.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WM79
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable polyglutamine synthesis accessory protein Rv0574c |
| Curated function | Could be involved in the biosynthesis, transport or localization of poly-alpha-L-glutamine (PLG), a cell wall component. Contributes to stress tolerance and virulence. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| eggNOG description | Bacterial capsule synthesis protein PGA_cap |
| Orthologous group | COG2843 |
| KEGG orthology |
K07282
|
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 | 0.619 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 missense, 1 nonsense, 3 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 0.45% of strains (659) · convergent |
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 |
|---|---|---|---|---|
PGA_cap | PF09587.16 | 2.8e-77 | 9–291 | Bacterial capsule synthesis protein PGA_cap |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pncB2 (nicotinic acid phosphoribosyltransferase PncB2), high confidence from genomic context alone (score 975 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) |
|---|---|---|---|---|
Rv0573c pncB2 |
nicotinic acid phosphoribosyltransferase PncB2 | 975 | 975 ctx | neighborhood:801 coexpression:860 |
Rv1997 ctpF |
cation transporter ATPase F | 817 | 818 | coexpression:785 |
Rv0571c hyp |
hypothetical protein | 785 | 783 ctx | cooccurence:668 |
Rv2030c hyp |
hypothetical protein | 717 | 718 ctx | cooccurence:686 |
Rv2143 hyp |
hypothetical protein | 631 | 631 ctx | cooccurence:583 |
Rv0575c |
oxidoreductase | 506 | 506 ctx | neighborhood:483 |
Rv2625c rip3 |
zinc metalloprotease Rip3 | 503 | 503 ctx | cooccurence:415 |
Rv0579 hyp |
hypothetical protein | 449 | 449 | |
Rv2624c |
universal stress protein | 430 | 418 | coexpression:415 |
Rv1734c hyp |
hypothetical protein | 409 | 410 |
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: CapA family protein
- Pfam (hmmscan --cut_ga): PGA_cap PF09587.16 (E=3e-77)
- (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_215088.1)
- Domains: Pfam-A via hmmscan --cut_ga — PGA_cap (PF09587.16)
- 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
COG2843 - Curated reference: UniProt P9WM79 (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 —
10 functional partner(s); context anchor
pncB2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000604|Rv0574c| MAGNPDVVTVLLGGDVMLGRGVDQILPHPGKPQLRERYMRDATGYVRLAERVNGRIPLPVDWRWPWGEALAVLENTATDVCLINLETTITADGEFADRKPVCYRMHPDNVPALTALRPHVCALANNHILDFGYQGLTDTVAALAGAGIQSVGAGADLLAARRSALVTVGHERRVIVGSVAAESSGVPESWAARRDRPGVWLIRDPAQRDVADDVAAQVLADKRPGDIAIVSMHWGSNWGYATAPGDVAFAHRLIDAGIDMVHGHSSHHPRPIEIYRGKPILYGCGDVVDDYEGIGGHESFRSELRLLYLTVTDPASGNLISLQMLPLRVSRMRLQRASQTDTEWLRNTIERISRRFGIRVVTRPDNLLEVVPAANLTSKE