pcnA Resolved · high auto-curated
H37Rv Rv3907c · MTBC0 - ·
480 aa · 4391631–4393073 (-) ·
RefSeq YP_178026.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | poly(A) polymerase PcnA |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Poly(A) polymerase PcnA. Pfam: PolyA_pol (PF01743.27), PolyA_pol_RNAbd (PF12627.13), HD (PF01966.29). |
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 |
L7N672
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable poly(A) polymerase PcnA |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | pcnA |
| eggNOG description | poly(A) polymerase |
| Orthologous group | COG0617 |
| EC number |
EC 2.7.7.19, EC 2.7.7.72
|
| KEGG orthology |
K00970, K00974
|
| KEGG pathways |
map03013, map03018
|
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 | 0.231 · 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 |
|---|---|---|---|---|
PolyA_pol | PF01743.27 | 4.6e-33 | 39–165 | Poly A polymerase head domain |
PolyA_pol_RNAbd | PF12627.13 | 6.3e-18 | 193–252 | Probable RNA and SrmB- binding site of polymerase A |
HD | PF01966.29 | 4.6e-15 | 268–366 | HD domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mutT4 (mutator protein MutT), medium confidence from genomic context alone (score 689 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3906c hyp |
hypothetical protein | 851 | 851 ctx | neighborhood:849 |
Rv2773c dapB |
4-hydroxy-tetrahydrodipicolinate reductase | 779 | 779 | coexpression:761 |
Rv3908 mutT4 |
mutator protein MutT | 689 | 689 ctx | neighborhood:679 |
Rv3909 hyp |
hypothetical protein | 682 | 682 ctx | neighborhood:679 |
Rv3910 murJ |
peptidoglycan biosynthesis protein | 680 | 680 ctx | neighborhood:679 |
Rv3219 whiB1 |
transcriptional regulator WhiB1 | 640 | 640 ctx | cooccurence:640 |
Rv3905c esxF |
ESAT-6 like protein EsxF | 588 | 589 ctx | neighborhood:586 |
Rv3904c esxE |
ESAT-6 like protein EsxE | 585 | 585 ctx | neighborhood:582 |
Rv3903c cpnT hyp |
hypothetical protein | 584 | 584 ctx | neighborhood:583 |
Rv3902c ift hyp |
hypothetical protein | 583 | 583 ctx | neighborhood:582 |
Rv3441c mrsA |
phosphoglucosamine mutase | 590 | 571 ctx | fusion:552 |
Rv2783c gpsI |
bifunctional guanosine pentaphosphate synthetase/polyribonucleotide nucleotidyltransferase | 826 | 570 | experimental:462 textmining:614 |
Rv3260c whiB2 |
transcriptional regulator WhiB2 | 556 | 556 ctx | cooccurence:555 |
Rv1409 ribG |
bifunctional riboflavin biosynthesis diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino) uracil reductas | 526 | 526 | coexpression:511 |
Rv1547 dnaE1 |
DNA polymerase III subunit alpha | 514 | 512 ctx | cooccurence:496 |
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): poly(A) polymerase PcnA
- Pfam (hmmscan --cut_ga): PolyA_pol PF01743.27 (E=5e-33), PolyA_pol_RNAbd PF12627.13 (E=6e-18), HD PF01966.29 (E=5e-15)
- (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 YP_178026.1)
- Domains: Pfam-A via hmmscan --cut_ga — PolyA_pol (PF01743.27), PolyA_pol_RNAbd (PF12627.13), HD (PF01966.29)
- 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
COG0617 - Curated reference: UniProt L7N672 (TrEMBL, unreviewed; 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
mutT4 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3907c|pcnA MPEAVQEADLLTAAAVALNRHAALLRELGSVFAAAGHELYLVGGSVRDALLGRLSPDLDFTTDARPERVQEIVRPWADAVWDTGIEFGTVGVGKSDHRMEITTFRADSYDRVSRHPEVRFGDCLEGDLVRRDFTTNAMAVRVTATGPGEFLDPLGGLAALRAKVLDTPAAPSGSFGDDPLRMLRAARFVSQLGFAVAPRVRAAIEEMAPQLARISAERVAAELDKLLVGEDPAAGIDLMVQSGMGAVVLPEIGGMRMAIDEHHQHKDVYQHSLTVLRQAIALEDDGPDLVLRWAALLHDIGKPATRRHEPDGGVSFHHHEVVGAKMVRKRMRALKYSKQMIDDISQLVYLHLRFHGYGDGKWTDSAVRRYVTDAGALLPRLHKLVRADCTTRNKRRAARLQASYDRLEERIAELAAQEDLDRVRPDLDGNQIMAVLDIPAGPQVGEAWRYLKELRLERGPLSTEEATTELLSWWKSRGNR