pra Family assigned · medium auto-curated
H37Rv Rv1078 · MTBC0 mtbc0_001158 ·
240 aa · 1211582–1212304 (+) ·
RefSeq NP_215594.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | RDD family protein |
| Revised (this work) | RDD family protein. Pfam: RDD (PF06271.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIM7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Proline-rich antigen homolog |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | pra |
| eggNOG description | pfam rdd |
| Orthologous group | COG1714 |
| Gene Ontology (9) |
GO:0005575, GO:0005576, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.346 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
RDD | PF06271.19 | 2.0e-21 | 89–233 | RDD family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: metB (cystathionine gamma-synthase), high confidence from genomic context alone (score 861 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) |
|---|---|---|---|---|
Rv1079 metB |
cystathionine gamma-synthase | 861 | 861 ctx | neighborhood:835 |
Rv3442c rpsI |
30S ribosomal protein S9 | 800 | 801 | coexpression:800 |
Rv2220 glnA1 |
glutamine synthetase | 777 | 772 | coexpression:733 |
Rv3274c fadE25 |
acyl-CoA dehydrogenase | 746 | 746 | coexpression:746 |
Rv1077 cbs |
cystathionine beta-synthase | 759 | 741 ctx | neighborhood:735 |
Rv0733 adk |
adenylate kinase | 739 | 739 | coexpression:738 |
Rv1389 gmk |
guanylate kinase | 733 | 733 | coexpression:733 |
Rv0636 hadB |
(3R)-hydroxyacyl-ACP dehydratase subunit HadB | 732 | 732 | coexpression:732 |
Rv1076 lipU |
lipase LipU | 661 | 661 ctx | neighborhood:659 |
Rv0977 PE_PGRS16 |
PE-PGRS family protein PE_PGRS16 | 574 | 575 ctx | cooccurence:567 |
Rv0872c PE_PGRS15 |
PE-PGRS family protein PE_PGRS15 | 552 | 552 ctx | cooccurence:552 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 511 | 511 ctx | cooccurence:511 |
Rv2853 PE_PGRS48 |
PE-PGRS family protein PE_PGRS48 | 504 | 504 ctx | cooccurence:504 |
Rv0124 PE_PGRS2 |
PE-PGRS family protein PE_PGRS2 | 504 | 504 ctx | cooccurence:504 |
Rv3350c PPE56 |
PPE family protein PPE56 | 489 | 489 ctx | cooccurence:487 |
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: RDD family protein
- Pfam (hmmscan --cut_ga): RDD PF06271.19 (E=2e-21)
- (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_215594.1)
- Domains: Pfam-A via hmmscan --cut_ga — RDD (PF06271.19)
- 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
COG1714 - Curated reference: UniProt P9WIM7 (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 —
56 functional partner(s); context anchor
metB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001158|Rv1078|pra MTEQPPPGGSYPPPPPPPGPSGGHEPPPAAPPGGSGYAPPPPPSSGSGYPPPPPPPGGGAYPPPPPSAGGYAPPPPGPAIRTMPTESYTPWITRVLAAFIDWAPYVVLVGIGWVIMLVTQTSSCVTSISEYDVGQFCVSQPSMIGQLVQWLLSVGGLAYLVWNYGYRQGTTGSSIGKSVLKFKVVSETTGQPIGFGMSVVRQLAHFIDAIICFVGFLFPLWDAKRQTLADKIMTTVCVPI