Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|
| MTBC0 PGAP re-annotation | PDZ-interacting protease regulator Ppr1 |
|---|
| Revised (this work) | PDZ-interacting protease regulator Ppr1. |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53383
TrEMBL · unreviewed
· Predicted
|
|---|
| UniProt name | Hypothetical proline rich protein |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|
| eggNOG description | Protein of unknown function (DUF732) |
|---|
| Orthologous group | 2ANQM |
|---|
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 |
0.361 · purifying
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
3 synonymous, 3 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 |
|---|
DUF732 | PF05305.20 |
4.6e-12 | 36–118 |
Protein of unknown function (DUF732) |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv2524c fas |
fatty acid synthase |
815 |
788 |
coexpression:644 |
Rv1135A |
Rv1135A, len: 80 aa. Possible acetyl-CoA acetyltransferase (possible gene fragment), highly similar to other acetyl-CoA acetyltransferases e |
752 |
751 |
coexpression:405 database:447 |
Rv3546 fadA5 |
acetyl-CoA acetyltransferase FadA |
747 |
747 |
database:447 |
Rv3556c fadA6 |
acetyl-CoA acetyltransferase FadA |
746 |
746 |
database:447 |
Rv3540c ltp2 |
lipid transfer protein |
746 |
746 |
database:447 |
Rv3523 ltp3 |
lipid carrier protein |
746 |
745 |
database:447 |
Rv1627c |
nonspecific lipid-transfer protein |
746 |
745 |
database:447 |
Rv0243 fadA2 |
acetyl-CoA acetyltransferase FadA |
746 |
745 |
database:447 |
Rv3522 ltp4 |
lipid transfer protein |
745 |
745 |
database:447 |
Rv2790c ltp1 |
lipid-transfer protein |
745 |
745 |
database:447 |
Rv0859 fadA |
acyltransferase |
745 |
745 |
database:447 |
Rv1867 hyp |
hypothetical protein |
745 |
745 |
database:447 |
Rv1074c fadA3 |
beta-ketoacyl CoA thiolase FadA |
745 |
745 |
database:447 |
Rv0914c |
lipid carrier protein or keto acyl-CoA thiolase |
745 |
745 |
database:447 |
Rv1323 fadA4 |
acetyl-CoA acetyltransferase |
745 |
745 |
database:447 |
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: PDZ-interacting protease regulator Ppr1
- Pfam (hmmscan --cut_ga): DUF732 PF05305.20 (E=5e-12)
- (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_217850.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF732 (PF05305.20)
- 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
2ANQM
- Curated reference: UniProt
O53383
(TrEMBL, unreviewed; Predicted)
- 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 —
124 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003546|Rv3333c|prp1
MFTGIASHAGALGAALVVLIGAAILHDGPAAADPNQDDRFLALLEKKEIPAVANVPRVIDAAHKVCRKLDGGMPVNDIVDGLRNDAYNIDPVMRLYPVRLTTTMTRFISAAVEIYCPNHHSKMAFAMANFEPGSNEPTHRVAASTRSAVNSGSDLRASVSDMTIMSPGWREPTGAMLASVLGAVRAGDPLIPNPPPIPVPPPAAQTLIPPPPIVAPPPPRPAPPQQPPPPPPEVEPPAGVPQSGGAAGSGGAGSGGGGGGDGPVEPSPARPMPPGFIRLAP
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