cut3 Family assigned · medium auto-curated
H37Rv Rv3451 · MTBC0 mtbc0_003670 ·
262 aa · 3898502–3899290 (+) ·
RefSeq NP_217968.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cutinase |
|---|---|
| MTBC0 PGAP re-annotation | cutinase family protein |
| Revised (this work) | Cutinase family protein. 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 |
P9WP39
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable carboxylesterase Culp3 |
| EC (curated) |
EC 3.1.1.-
|
| Curated function | Shows weak esterase activity with the p-nitrophenol-linked aliphatic ester pNP-butyrate. Does not exhibit cutinase activity. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | cut3 |
| 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
|
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 | 0.801 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 11 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.54% of strains (784) · 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 | 1.9e-53 | 44–226 | Cutinase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccB4 (ESX-4 secretion system protein EccB4), high confidence from genomic context alone (score 770 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3450c eccB4 |
ESX-4 secretion system protein EccB4 | 770 | 770 ctx | neighborhood:769 |
Rv3452 cut4 |
cutinase | 706 | 690 ctx | neighborhood:671 |
Rv1278 hyp |
hypothetical protein | 649 | 649 | database:544 |
Rv1747 |
ABC transporter ATP-binding protein/permease | 660 | 648 | database:530 |
Rv0153c ptbB |
phosphotyrosine protein phosphatase | 651 | 637 | experimental:629 |
Rv3157 nuoM |
NADH-quinone oxidoreductase subunit M | 647 | 629 | experimental:629 |
Rv0434 hyp |
hypothetical protein | 607 | 608 | database:561 |
Rv3036c TB22.2 hyp |
hypothetical protein | 601 | 598 | database:543 |
Rv2328 PE23 |
PE family protein PE23 | 601 | 598 | database:543 |
Rv3812 PE_PGRS62 |
PE-PGRS family protein PE_PGRS62 | 601 | 598 | database:543 |
Rv0832 PE_PGRS12 |
PE-PGRS family protein PE_PGRS12 | 601 | 598 | database:543 |
Rv0020c fhaA |
FHA domain-containing protein FhaA | 597 | 598 | database:530 |
Rv0019c fhaB |
FHA domain-containing protein FhaB | 596 | 596 | database:530 |
Rv3360 hyp |
hypothetical protein | 595 | 596 | database:530 |
Rv1827 garA |
glycogen accumulation regulator GarA | 595 | 595 | database:530 |
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 family protein
- Pfam (hmmscan --cut_ga): Cutinase PF01083.29 (E=2e-53)
- (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_217968.2)
- 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 P9WP39 (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 —
75 functional partner(s); context anchor
eccB4 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003670|Rv3451|cut3 MNNRPIRLLTSGRAGLGAGALITAVVLLIALGAVWTPVAFADGCPDAEVTFARGTGEPPGIGRVGQAFVDSLRQQTGMEIGVYPVNYAASRLQLHGGDGANDAISHIKSMASSCPNTKLVLGGYSQGATVIDIVAGVPLGSISFGSPLPAAYADNVAAVAVFGNPSNRAGGSLSSLSPLFGSKAIDLCNPTDPICHVGPGNEFSGHIDGYIPTYTTQAASFVVQRLRAGSVPHLPGSVPQLPGSVLQMPGTAAPAPESLHGR