cut4 Resolved · high auto-curated
H37Rv Rv3452 · MTBC0 mtbc0_003671 ·
226 aa · 3899337–3900017 (+) ·
RefSeq NP_217969.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cutinase |
|---|---|
| MTBC0 PGAP re-annotation | cutinase Cut4 |
| Revised (this work) | Cutinase Cut4. Pfam: Cutinase (PF01083.29). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06319
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phospholipase Culp4 |
| EC (curated) |
EC 3.1.1.-
|
| Curated function | A2-type phospholipase, which is probably involved in the degradation of macrophage membrane. Hydrolyzes dipalmitoylphosphatidylcholine. Also shows moderate esterase activity and hydrolyzes the p-nitrophenol-linked aliphatic ester pNP-butyrate (C4). Does not exhibit cutinase activity. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | cut4 |
| eggNOG description | Catalyzes the hydrolysis of cutin, a polyester that forms the structure of plant cuticle |
| Orthologous group | 2A1QU |
| EC number |
EC 3.1.1.74
|
| KEGG orthology |
K08095
|
| Gene Ontology (2) |
GO:0005575, GO:0005576
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.38% of strains (556) · 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 |
|---|---|---|---|---|
Cutinase | PF01083.29 | 2.2e-51 | 47–225 | Cutinase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cut3 (cutinase), medium confidence from genomic context alone (score 690 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3451 cut3 |
cutinase | 706 | 690 ctx | neighborhood:671 |
Rv1592c hyp |
hypothetical protein | 572 | 572 ctx | cooccurence:571 |
Rv0290 eccD3 |
ESX-3 secretion system protein EccD | 503 | 503 ctx | cooccurence:503 |
Rv3450c eccB4 |
ESX-4 secretion system protein EccB4 | 473 | 473 ctx | neighborhood:472 |
Rv0283 eccB3 |
ESX-3 secretion system protein EccB3 | 469 | 470 ctx | cooccurence:469 |
Rv0888 spmT hyp |
hypothetical protein | 463 | 463 ctx | cooccurence:463 |
Rv0185 hyp |
hypothetical protein | 460 | 460 ctx | cooccurence:460 |
Rv3453 |
Rv3453, (MTCY13E12.06), len: 110 aa. Possible conserved transmembrane protein, showing weak similarity with other proteins e.g. Q9F6C3 putat | 420 | 420 ctx | neighborhood:418 |
Rv0282 eccA3 |
ESX-3 secretion system protein EccA | 404 | 404 ctx | cooccurence:404 |
Rv1270c lprA |
lipoprotein LprA | 612 | 279 | textmining:484 |
Rv2223c caeB |
carboxylesterase B | 719 | 229 | textmining:651 |
Rv3802c |
membrane protein | 890 | 193 | textmining:870 |
Rv2913c |
D-amino acid aminohydrolase | 552 | 44 | textmining:551 |
Rv1400c lipI |
lipase | 803 | 41 | textmining:803 |
Rv1399c nlhH |
carboxylesterase NlhH | 750 | 41 | textmining:750 |
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: cutinase
- MTBC0 PGAP product: cutinase Cut4
- Pfam (hmmscan --cut_ga): Cutinase PF01083.29 (E=2e-51)
- (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_217969.1)
- Domains: Pfam-A via hmmscan --cut_ga — Cutinase (PF01083.29)
- 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
2A1QU - Curated reference: UniProt O06319 (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 —
18 functional partner(s); context anchor
cut3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003671|Rv3452|cut4 MIPRPQPHSGRWRAGAARRLTSLVAAAFAAATLLLTPALAPPASAGCPDAEVVFARGTGEPPGLGRVGQAFVSSLRQQTNKSIGTYGVNYPANGDFLAAADGANDASDHIQQMASACRATRLVLGGYSQGAAVIDIVTAAPLPGLGFTQPLPPAADDHIAAIALFGNPSGRAGGLMSALTPQFGSKTINLCNNGDPICSDGNRWRAHLGYVPGMTNQAARFVASRI