pknJ Resolved · high auto-curated
H37Rv Rv2088 · MTBC0 mtbc0_002222 ·
589 aa · 2373035–2374804 (+) ·
RefSeq NP_216604.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane serine/threonine-protein kinase PknJ |
|---|---|
| MTBC0 PGAP re-annotation | serine/threonine protein kinase PknJ |
| Revised (this work) | Serine/threonine protein kinase PknJ. Pfam: Pkinase (PF00069.32), PK_Tyr_Ser-Thr (PF07714.24), PknH_C (PF14032.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WI67
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Serine/threonine-protein kinase PknJ |
| EC (curated) |
EC 2.7.11.1
|
| Curated function | In vitro, phosphorylates various substrates such as EmbR, PepE, MmaA4, Pyk, LldD and GroEL2. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K TranscriptionL Replication, recombination and repairT Signal transduction mechanisms
|
|---|---|
| Preferred name | pknJ |
| eggNOG description | serine threonine protein kinase |
| Orthologous group | COG0515 |
| EC number |
EC 2.7.11.1
|
| KEGG orthology |
K08884, K12132
|
| Gene Ontology (42) |
GO:0003674, GO:0003824, GO:0004672, GO:0004674, GO:0005488, GO:0006464, GO:0006468, GO:0006793, GO:0006796, GO:0006807, GO:0008150, GO:0008152 +30 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 | 0.511 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 7 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.72% of strains (1052) · clonal |
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 | 5.7e-44 | 14–268 | Protein kinase domain |
PK_Tyr_Ser-Thr | PF07714.24 | 5.8e-28 | 16–228 | Protein tyrosine and serine/threonine kinase |
PknH_C | PF14032.13 | 6.6e-42 | 394–586 | PknH-like extracellular domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pstP (phosphoserine/threonine phosphatase PstP), high confidence from genomic context alone (score 847 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0018c pstP |
phosphoserine/threonine phosphatase PstP | 897 | 847 ctx | cooccurence:770 |
Rv1827 garA |
glycogen accumulation regulator GarA | 707 | 603 ctx | cooccurence:437 |
Rv0019c fhaB |
FHA domain-containing protein FhaB | 576 | 508 | |
Rv2087 |
Rv2087, (MTCY49.27), len: 76 aa. Conserved hypothetical protein, similar to but shorter than transposases, but we can find no sequence error | 458 | 459 ctx | neighborhood:454 |
Rv0020c fhaA |
FHA domain-containing protein FhaA | 587 | 425 | |
Rv0014c pknB |
serine/threonine-protein kinase PknB | 571 | 404 | |
Rv1747 |
ABC transporter ATP-binding protein/permease | 532 | 388 | |
Rv3080c pknK |
serine/threonine-protein kinase PknK | 534 | 326 | |
Rv2914c pknI |
serine/threonine-protein kinase PknI | 507 | 296 | |
Rv2176 pknL |
serine/threonine-protein kinase PknL | 495 | 296 | |
Rv0015c pknA |
serine/threonine-protein kinase PknA | 483 | 293 | |
Rv1743 pknE |
serine/threonine-protein kinase PknE | 472 | 293 | |
Rv0931c pknD |
serine/threonine-protein kinase PknD | 481 | 290 | |
Rv1266c pknH |
serine/threonine-protein kinase PknH | 485 | 284 | |
Rv0410c pknG |
serine/threonine-protein kinase PknG | 496 | 263 |
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: transmembrane serine/threonine-protein kinase PknJ
- MTBC0 PGAP product: serine/threonine protein kinase PknJ
- Pfam (hmmscan --cut_ga): Pkinase PF00069.32 (E=6e-44), PK_Tyr_Ser-Thr PF07714.24 (E=6e-28), PknH_C PF14032.13 (E=7e-42)
- (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_216604.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pkinase (PF00069.32), PK_Tyr_Ser-Thr (PF07714.24), PknH_C (PF14032.13)
- 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 P9WI67 (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 —
18 functional partner(s); context anchor
pstP - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002222|Rv2088|pknJ MAHELSAGSVFAGYRIERMLGAGGMGTVYLARNPDLPRSEALKVLAAELSRDLDFRARFVREADVAAGLDHPNIVAVHQRGQFEGRLWIAMQFVDGGNAEDALRAATMTTARAVYVIGEVAKALDYAHQQGVIHRDIKPANFLLSRAAGGDERVLLSDFGIARALGDTGLTSTGSVLATLAYAAPEVLAGQGFDGRADLYSLGCALFRLLTGEAPFAAGAGAAVAVVAGHLHQPPPTVSDRVPGLSAAMDAVIATAMAKDPMRRFTSAGEFAHAAAAALYGGATDGWVPPSPAPHVISQGAVPGSPWWQHPVGSVTALATPPGHGWPPGLPPLPRRPRRYRRGVAAVAAVMVVAAAAVTAVTMTSHQPRTATPPSAAALSPTSSSTTPPQPPIVTRSRLPGLLPPLDDVKNFVGIQNLVAHEPMLQPQTPNGSINPAECWPAVGGGVPSAYDLGTVIGFYGLTIDEPPTGTAPNQVGQLIVAFRDAATAQRHLADLASIWRRCGGRTVTLFRSEWRRPVELSTSVPEVVDGITTMVLTAQGPVLRVREDHAIAAKNNVLVDVDIMTPDTSRGQQAVIGITNYILAKIPG