priA Family assigned · medium auto-curated
H37Rv Rv1402 · MTBC0 - ·
655 aa · 1577613–1579580 (+) ·
RefSeq NP_215918.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | primosomal protein N' |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Primosomal protein N'. Pfam: PriA_3primeBD (PF17764.7), PriA_C_2 (PF27106.1). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WMQ9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable replication restart protein PriA |
| Curated function | Initiates the restart of stalled replication forks, which reloads the replicative helicase on sites other than the origin of replication. Recognizes and binds to abandoned replication forks and remodels them to uncover a helicase loading site. Promotes assembly of the primosome at these replication forks. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | priA |
| eggNOG description | Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA |
| Orthologous group | COG1198 |
| KEGG orthology |
K04066
|
| KEGG pathways |
map03440
|
| Gene Ontology (64) |
GO:0003674, GO:0003678, GO:0003824, GO:0004003, GO:0004386, GO:0005575, GO:0005623, GO:0005886, GO:0006139, GO:0006259, GO:0006260, GO:0006261 +52 more
|
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 | 0.268 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 6 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 |
|---|---|---|---|---|
PriA_3primeBD | PF17764.7 | 2.8e-17 | 2–96 | 3'DNA-binding domain (3'BD) |
PriA_C_2 | PF27106.1 | 8.2e-18 | 556–655 | PriA, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1401 (membrane protein), high confidence from genomic context alone (score 795 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0054 ssb |
single-strand DNA-binding protein | 865 | 818 | experimental:787 |
Rv1401 |
membrane protein | 795 | 795 ctx | neighborhood:784 |
Rv2478c hyp |
hypothetical protein | 812 | 792 | experimental:787 |
Rv1406 fmt |
methionyl-tRNA formyltransferase | 762 | 762 | coexpression:613 |
Rv1391 dfp |
bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase | 716 | 717 | coexpression:648 |
Rv0051 |
transmembrane protein | 696 | 696 ctx | cooccurence:693 |
Rv1399c nlhH |
carboxylesterase NlhH | 682 | 683 ctx | neighborhood:678 |
Rv1423 whiA |
transcriptional regulator WhiA | 678 | 678 ctx | cooccurence:597 |
Rv3404c hyp |
hypothetical protein | 655 | 655 | coexpression:613 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 631 | 632 | coexpression:424 |
Rv3201c adnB |
ATP-dependent DNA helicase | 647 | 631 ctx | cooccurence:590 |
Rv0955 |
integral membrane protein | 622 | 623 ctx | cooccurence:619 |
Rv0058 dnaB |
replicative DNA helicase | 718 | 603 | |
Rv3604c |
transmembrane protein | 593 | 594 ctx | cooccurence:591 |
Rv2343c dnaG |
DNA primase | 582 | 556 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): primosomal protein N'
- Pfam (hmmscan --cut_ga): PriA_3primeBD PF17764.7 (E=3e-17), PriA_C_2 PF27106.1 (E=8e-18)
- (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_215918.1)
- Domains: Pfam-A via hmmscan --cut_ga — PriA_3primeBD (PF17764.7), PriA_C_2 (PF27106.1)
- 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
COG1198 - Curated reference: UniProt P9WMQ9 (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 —
45 functional partner(s); context anchor
Rv1401 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1402|priA MLSVPHLDRDFDYLVPAEHSDDAQPGVRVRVRFHGRLVDGFVLERRSDSDHHGKLGWLDRVVSPEPVLTTEIRRLVDAVAARYAGTRQDVLRLAVPARHARVEREITTAPGRPVVAPVDPSGWAAYGRGRQFLAALADSRAARAVWQALPGELWADRFAEAAAQTVRAGRTVLAIVPDQRDLDTLWQAATALVDEHSVVALSAGLGPEARYRRWLAALRGSARLVIGTRSAVFAPLSELGLVMVWADADDSLAEPRAPYPHAREVAMLRAHQARCAALIGGYARTAEAHALVRSGWAHDVVAPRPEVRARSPRVVALDDSGYDDARDPAARTARLPSIALRAARSALQSGAPVLVQVPRRGYIPSLACGRCRAIARCRSCTGPLSLQGAGSPGAVCRWCGRVDPTLRCVRCGSDVVRAVVVGARRTAEELGRAFPGTAVITSAGDTLVPQLDAGPALVVATPGAEPRAPGGYGAALLLDSWALLGRQDLRAAEDALWRWMTAAALVRPRGAGGVVTVVAESSIPTVQSLIRWDPVGHAEAELAARTEVGLPPSVHIAALDGPAGTVTALLEAARLPDPDRLQADLLGPVDLPPGVRRPAGIPADAPVIRMLLRVCREQGLELAASLRRGIGVLSARQTRQTRSLVRVQIDPLHIG