pknA Resolved · high auto-curated
H37Rv Rv0015c · MTBC0 mtbc0_000019 ·
431 aa · 17467–18762 (-) ·
RefSeq NP_214529.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | serine/threonine-protein kinase PknA |
|---|---|
| MTBC0 PGAP re-annotation | serine/threonine protein kinase PknA |
| Revised (this work) | Serine/threonine protein kinase PknA. Pfam: Pkinase (PF00069.32), PK_Tyr_Ser-Thr (PF07714.24), Kdo (PF06293.21), ABC1 (PF03109.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WI83
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Serine/threonine-protein kinase PknA |
| EC (curated) |
EC 2.7.11.1
|
| Curated function | Protein kinase that regulates many aspects of mycobacterial physiology, and is critical for growth in vitro and survival of the pathogen in the host. Is a key component of a signal transduction pathway that regulates cell growth, cell shape and cell division via phosphorylation of target proteins such as FtsZ, Wag31, GlmU, PstP, EmbR and Rv1422. Also catalyzes the phosphorylation of the proteasome alpha-subunit (PrcA) and unprocessed proteasome beta-subunit (pre-PrcB), which results in the inhibition of processing of pre-PrcB and assembly of the proteasome complex, and thereby enhances the myc. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K TranscriptionL Replication, recombination and repairT Signal transduction mechanisms
|
|---|---|
| Preferred name | pknA |
| eggNOG description | serine threonine protein kinase |
| Orthologous group | COG0515 |
| EC number |
EC 2.7.11.1
|
| KEGG orthology |
K08884, K12132
|
| Gene Ontology (83) |
GO:0003674, GO:0003824, GO:0004672, GO:0004674, GO:0005575, GO:0005576, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006464 +71 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 | 0.148 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 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 |
|---|---|---|---|---|
Pkinase | PF00069.32 | 4.1e-46 | 13–261 | Protein kinase domain |
PK_Tyr_Ser-Thr | PF07714.24 | 1.2e-32 | 15–260 | Protein tyrosine and serine/threonine kinase |
Kdo | PF06293.21 | 2.7e-05 | 57–153 | Lipopolysaccharide kinase (Kdo/WaaP) family |
ABC1 | PF03109.23 | 2.7e-06 | 90–168 | ABC1 atypical kinase-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pknB (serine/threonine-protein kinase PknB), high confidence from genomic context alone (score 985 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0014c pknB |
serine/threonine-protein kinase PknB | 990 | 985 ctx | neighborhood:881 coexpression:829 |
Rv0018c pstP |
phosphoserine/threonine phosphatase PstP | 998 | 982 ctx | neighborhood:882 cooccurence:769 textmining:930 |
Rv0017c rodA |
cell division protein RodA | 987 | 914 ctx | neighborhood:882 textmining:858 |
Rv0019c fhaB |
FHA domain-containing protein FhaB | 979 | 901 ctx | neighborhood:780 textmining:798 |
Rv0016c pbpA |
penicillin-binding protein PbpA | 993 | 887 ctx | neighborhood:882 textmining:941 |
Rv0020c fhaA |
FHA domain-containing protein FhaA | 970 | 837 ctx | neighborhood:700 textmining:828 |
Rv0513 |
transmembrane protein | 733 | 733 | coexpression:733 |
Rv1827 garA |
glycogen accumulation regulator GarA | 960 | 701 ctx | cooccurence:467 experimental:443 textmining:873 |
Rv2031c hspX |
alpha-crystallin | 511 | 507 | experimental:500 |
Rv0440 groEL2 |
molecular chaperone GroEL | 554 | 505 | experimental:500 |
Rv0511 hemD |
uroporphyrin-III C-methyltransferase | 479 | 480 | coexpression:463 |
Rv3220c pdtaS |
two component sensor kinase | 416 | 415 | coexpression:415 |
Rv1747 |
ABC transporter ATP-binding protein/permease | 596 | 411 | |
Rv2914c pknI |
serine/threonine-protein kinase PknI | 517 | 329 | |
Rv3360 hyp |
hypothetical protein | 600 | 325 | textmining:432 |
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: serine/threonine-protein kinase PknA
- MTBC0 PGAP product: serine/threonine protein kinase PknA
- Pfam (hmmscan --cut_ga): Pkinase PF00069.32 (E=4e-46), PK_Tyr_Ser-Thr PF07714.24 (E=1e-32), Kdo PF06293.21 (E=3e-05), ABC1 PF03109.23 (E=3e-06)
- (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_214529.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pkinase (PF00069.32), PK_Tyr_Ser-Thr (PF07714.24), Kdo (PF06293.21), ABC1 (PF03109.23)
- 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
COG0515 - Curated reference: UniProt P9WI83 (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 —
42 functional partner(s); context anchor
pknB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000019|Rv0015c|pknA MSPRVGVTLSGRYRLQRLIATGGMGQVWEAVDNRLGRRVAVKVLKSEFSSDPEFIERFRAEARTTAMLNHPGIASVHDYGESQMNGEGRTAYLVMELVNGEPLNSVLKRTGRLSLRHALDMLEQTGRALQIAHAAGLVHRDVKPGNILITPTGQVKITDFGIAKAVDAAPVTQTGMVMGTAQYIAPEQALGHDASPASDVYSLGVVGYEAVSGKRPFAGDGALTVAMKHIKEPPPPLPPDLPPNVRELIEITLVKNPAMRYRSGGPFADAVAAVRAGRRPPRPSQTPPPGRAAPAAIPSGTTARVAANSAGRTAASRRSRPATGGHRPPRRTFSSGQRALLWAAGVLGALAIIIAVLLVIKAPGDNSPQQAPTPTVTTTGNPPASNTGGTDASPRLNWTERGETRHSGLQSWVVPPTPHSRASLARYEIAQ