cfp29 Resolved · high auto-curated
H37Rv Rv0798c · MTBC0 mtbc0_000847 ·
265 aa · 894539–895336 (-) ·
RefSeq NP_215313.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | family 1 encapsulin nanocompartment shell protein |
| Revised (this work) | Family 1 encapsulin nanocompartment shell protein. Pfam: Linocin_M18 (PF04454.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6WZG6
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Type 1 encapsulin shell protein |
| Curated function | Shell component of a type 1 encapsulin nanocompartment in situ; its cargo protects against oxidative stress at low pH. In situ and in E.coli assembles into proteinaceous shells about 22 nm in diameter with 2.5 nm thick walls. Cargo proteins are targeted to the interior via their C-terminal extensions; empty intact shells can be isolated in E.coli in the absence of cargo protein. There are at least 4 possible cargo proteins, DyP (encoded in the same locus), FolB, BfrB and Rv1762c; DyP and Rv1762c have been identified in vivo. Probably involved in protection against oxidative damage from the hos. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lin |
| eggNOG description | Bacteriocin |
| Orthologous group | COG1659 |
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 | 0.343 · 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 |
|---|---|---|---|---|
Linocin_M18 | PF04454.19 | 7.0e-97 | 1–251 | Encapsulating protein for peroxidase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pepC (M18 family aminopeptidase), high confidence from genomic context alone (score 794 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) |
|---|---|---|---|---|
Rv0799c hyp |
hypothetical protein | 994 | 972 ctx | neighborhood:881 cooccurence:758 textmining:803 |
Rv0800 pepC |
M18 family aminopeptidase | 794 | 794 ctx | neighborhood:788 |
Rv0801 hyp |
hypothetical protein | 668 | 668 ctx | neighborhood:663 |
Rv2350c plcB |
membrane-associated phospholipase B | 425 | 231 | |
Rv2349c plcC |
phospholipase C | 420 | 226 | |
Rv1420 uvrC |
excinuclease ABC subunit UvrC | 467 | 51 | textmining:462 |
Rv3759c proX |
glycine betaine/carnitine/choline/L-proline ABC transporter substrate-binding lipoprotein ProX | 576 | 47 | textmining:574 |
Rv3118 sseC1 hyp |
hypothetical protein | 554 | 47 | textmining:551 |
Rv3894c eccC2 |
ESX-2 type VII secretion system protein EccC | 535 | 47 | textmining:533 |
Rv3448 eccD4 |
ESX-4 secretion system protein EccD4 | 628 | 44 | textmining:627 |
Rv3904c esxE |
ESAT-6 like protein EsxE | 578 | 44 | textmining:577 |
Rv0749 vapC31 |
ribonuclease VapC31 | 441 | 44 | textmining:440 |
Rv3449 mycP4 |
membrane-anchored mycosin | 697 | 41 | textmining:698 |
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: family 1 encapsulin nanocompartment shell protein
- Pfam (hmmscan --cut_ga): Linocin_M18 PF04454.19 (E=7e-97)
- (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_215313.1)
- Domains: Pfam-A via hmmscan --cut_ga — Linocin_M18 (PF04454.19)
- 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
COG1659 - Curated reference: UniProt I6WZG6 (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 —
13 functional partner(s); context anchor
pepC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000847|Rv0798c|cfp29 MNNLYRDLAPVTEAAWAEIELEAARTFKRHIAGRRVVDVSDPGGPVTAAVSTGRLIDVKAPTNGVIAHLRASKPLVRLRVPFTLSRNEIDDVERGSKDSDWEPVKEAAKKLAFVEDRTIFEGYSAASIEGIRSASSNPALTLPEDPREIPDVISQALSELRLAGVDGPYSVLLSADVYTKVSETSDHGYPIREHLNRLVDGDIIWAPAIDGAFVLTTRGGDFDLQLGTDVAIGYASHDTDTVRLYLQETLTFLCYTAEASVALSH