papA4 Resolved · medium auto-curated
H37Rv Rv1528c · MTBC0 mtbc0_001635 ·
165 aa · 1738762–1739259 (-) ·
RefSeq NP_216044.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | polyketide synthase associated protein PapA |
|---|---|
| MTBC0 PGAP re-annotation | polyketide synthase |
| Revised (this work) | Polyketide synthase. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53902
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable conserved polyketide synthase associated protein PapA4 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | papA4 |
| eggNOG description | D-alanine [D-alanyl carrier protein] ligase activity |
| Orthologous group | COG1020 |
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, 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3800c pks13 |
polyketide synthase | 855 | 827 | coexpression:648 experimental:465 |
Rv1527c pks5 |
polyketide synthase | 967 | 821 | coexpression:453 experimental:642 textmining:827 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 870 | 821 | coexpression:456 experimental:642 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 845 | 821 | coexpression:456 experimental:642 |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 844 | 821 | coexpression:455 experimental:642 |
Rv2048c pks12 |
polyketide synthase | 844 | 821 | coexpression:454 experimental:642 |
Rv3177 |
peroxidase | 732 | 733 | coexpression:732 |
Rv2946c pks1 |
polyketide synthase | 759 | 720 | coexpression:429 experimental:465 |
Rv1661 pks7 |
polyketide synthase | 740 | 713 | coexpression:435 experimental:465 |
Rv1181 pks4 |
polyketide beta-ketoacyl synthase | 738 | 710 | coexpression:430 experimental:465 |
Rv2932 ppsB |
phthiocerol synthesis polyketide synthase type I PpsB | 735 | 706 | coexpression:429 experimental:465 |
Rv2383c mbtB |
phenyloxazoline synthase | 740 | 699 | coexpression:664 |
Rv2931 ppsA |
phthiocerol synthesis polyketide synthase type I PpsA | 709 | 694 | coexpression:432 experimental:465 |
Rv0405 pks6 |
membrane bound polyketide synthase | 708 | 693 | coexpression:430 experimental:465 |
Rv2377c mbtH hyp |
hypothetical protein | 710 | 692 | coexpression:419 experimental:475 |
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: polyketide synthase associated protein PapA
- MTBC0 PGAP product: polyketide synthase
- (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_216044.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG1020 - Curated reference: UniProt O53902 (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 — 43 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001635|Rv1528c|papA4 MTQLPQPTWRWWQQRETEQVQSSHIDGEIVGALIPDLAVLHSEDASRAAVGREKHRCSLDPLGGGFRSRRASMPAGALLLSAVIAIQLDRMNARVFGDGWIGAQACMWVNKFHEESTVTALSPSSPIAQGSIARHPETMQSAYVRIAEGGSRDVAPAAQLQRRRP