chp1 Resolved · high auto-curated
H37Rv Rv3822 · MTBC0 mtbc0_004051 ·
404 aa · 4310831–4312045 (+) ·
RefSeq NP_218339.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | sulfolipid-1 biosynthesis membrane-anchored acyltransferase Chp1 |
| Revised (this work) | Sulfolipid-1 biosynthesis membrane-anchored acyltransferase Chp1. Pfam: PE-PPE (PF08237.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07801
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | SL1278 acyltransferase Chp1 |
| EC (curated) |
EC 2.3.1.284
|
| Curated function | Involved in the final steps of the cell wall sulfolipid-1 (SL-1) biosynthesis. Catalyzes two successive acylations of the precursor 2-palmitoyl-3-(C43)-phthioceranyl-alpha, alpha'-D-trehalose-2'-sulfate (SL1278) to yield the tetraacylated sulfolipid SL-1. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
N Cell motility
|
|---|---|
| eggNOG description | PE-PPE domain |
| Orthologous group | COG5651 |
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) pseudogene candidate
| pN/pS | 1.012 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 17 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 1.23% of strains (1781) · clonal |
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 |
|---|---|---|---|---|
PE-PPE | PF08237.18 | 3.3e-76 | 104–325 | PE-PPE domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sap (integral membrane protein), high confidence from genomic context alone (score 707 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) |
|---|---|---|---|---|
Rv1184c chp2 hyp |
hypothetical protein | 783 | 740 | coexpression:740 |
Rv3821 sap |
integral membrane protein | 850 | 707 ctx | neighborhood:703 textmining:511 |
Rv3849 espR |
ESX-1 transcriptional regulator EspR | 580 | 580 | coexpression:580 |
Rv3820c papA2 |
trehalose-2-sulfate acyltransferase | 475 | 475 ctx | neighborhood:472 |
Rv3823c mmpL8 |
integral membrane transport protein MmpL8 | 402 | 148 | |
Rv2214c ephD |
oxidoreductase EphD | 437 | 47 | textmining:434 |
Rv1901 cinA |
competence damage-inducible protein CinA | 435 | 45 | 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: sulfolipid-1 biosynthesis membrane-anchored acyltransferase Chp1
- Pfam (hmmscan --cut_ga): PE-PPE PF08237.18 (E=3e-76)
- (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_218339.1)
- Domains: Pfam-A via hmmscan --cut_ga — PE-PPE (PF08237.18)
- 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
COG5651 - Curated reference: UniProt O07801 (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 —
7 functional partner(s); context anchor
sap - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004051|Rv3822|chp1 MKCPGVSDCVATVRHDNVFAIAAGLRWSAAVPPLHKGDAVTKLLVGAIAGGMLACAAILGDGIASADTALIVPGTAPSPYGPLRSLYHFNPAMQPQIGANYYNPTATRHVVSYPGSFWPVTGLNSPTVGSSVSAGTNNLDAAIRSTDGPIFVAGLSQGTLVLDREQARLANDPTAPPPGQLTFIKAGDPNNLLWRAFRPGTHVPIIDYTVPAPVESQYDTINIVGQYDIFSDPPNRPGNLLADLNAIAAGGYYGHSATAFSDPARVAPRDITTTTNSLGATTTTYFIRTDQLPLVRALVDMAGLPPQAAGTVDAALRPIIDRAYQPGPAPAVNPRDLVQGIRGIPAIAPAIAIPIGSTTGASAATSTAAATAAATNALRGANVGPGANKALSMVRGLLPKGKKH