pknB Family assigned · medium auto-curated
H37Rv Rv0014c · MTBC0 mtbc0_000018 ·
626 aa · 15590–17470 (-) ·
RefSeq NP_214528.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | serine/threonine-protein kinase PknB |
|---|---|
| MTBC0 PGAP re-annotation | Stk1 family PASTA domain-containing Ser/Thr kinase |
| Revised (this work) | Stk1 family PASTA domain-containing Ser/Thr kinase. Pfam: Pkinase (PF00069.32), PK_Tyr_Ser-Thr (PF07714.24), ABC1 (PF03109.23), Pkinase_fungal (PF17667.8), PASTA (PF03793.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WI81
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Serine/threonine-protein kinase PknB |
| 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 GarA, GlmU, PapA5, FhaB (Rv0019c), FhaA (Rv0020c), MviN, PstP, EmbR, Rv1422, Rv1747, RseA and RmlA. Also catalyzes the phosphorylation of the core proteasome alpha-subunit (PrcA), and thereby regulates the proteolytic activity of the proteasome. Is a major regulator of the oxygen-dependent rep. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K TranscriptionL Replication, recombination and repairT Signal transduction mechanisms
|
|---|---|
| Preferred name | pknB |
| eggNOG description | serine threonine protein kinase |
| Orthologous group | COG0515 |
| EC number |
EC 2.7.11.1
|
| KEGG orthology |
K08884, K12132
|
| Gene Ontology (128) |
GO:0000270, GO:0003674, GO:0003824, GO:0004672, GO:0004674, GO:0005488, GO:0005515, GO:0005575, GO:0005618, GO:0005623, GO:0006022, GO:0006023 +116 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 | 0.306 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 8 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 | 9.1e-50 | 11–265 | Protein kinase domain |
PK_Tyr_Ser-Thr | PF07714.24 | 7.4e-35 | 13–264 | Protein tyrosine and serine/threonine kinase |
ABC1 | PF03109.23 | 2.2e-07 | 89–165 | ABC1 atypical kinase-like domain |
Pkinase_fungal | PF17667.8 | 1.9e-05 | 111–202 | Fungal protein kinase |
PASTA | PF03793.25 | 1.9e-15 | 360–422 | PASTA 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 997 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0018c pstP |
phosphoserine/threonine phosphatase PstP | 999 | 997 ctx | neighborhood:881 cooccurence:770 coexpression:667 experimental:693 textmining:920 |
Rv0015c pknA |
serine/threonine-protein kinase PknA | 990 | 985 ctx | neighborhood:881 coexpression:829 |
Rv1827 garA |
glycogen accumulation regulator GarA | 999 | 982 ctx | cooccurence:471 experimental:964 textmining:949 |
Rv0020c fhaA |
FHA domain-containing protein FhaA | 996 | 968 ctx | neighborhood:700 experimental:870 textmining:882 |
Rv0019c fhaB |
FHA domain-containing protein FhaB | 991 | 959 ctx | neighborhood:780 experimental:711 textmining:798 |
Rv0017c rodA |
cell division protein RodA | 993 | 940 ctx | neighborhood:881 textmining:894 |
Rv0016c pbpA |
penicillin-binding protein PbpA | 993 | 888 ctx | neighborhood:881 textmining:945 |
Rv0178 |
Mce associated membrane protein | 804 | 805 | coexpression:798 |
Rv1747 |
ABC transporter ATP-binding protein/permease | 945 | 801 | experimental:711 textmining:736 |
Rv1614 lgt |
prolipoprotein diacylglyceryl transferase | 770 | 762 | coexpression:732 |
Rv3783 rfbD |
O-antigen/lipopolysaccharide ABC transporter permease RfbD | 741 | 741 | coexpression:733 |
Rv3360 hyp |
hypothetical protein | 937 | 732 | experimental:711 textmining:775 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 719 | 701 ctx | neighborhood:544 |
Rv2927c sepIVA hyp |
hypothetical protein | 712 | 624 | coexpression:408 |
Rv1901 cinA |
competence damage-inducible protein CinA | 592 | 578 ctx | neighborhood:544 |
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 PknB
- MTBC0 PGAP product: Stk1 family PASTA domain-containing Ser/Thr kinase
- Pfam (hmmscan --cut_ga): Pkinase PF00069.32 (E=9e-50), PK_Tyr_Ser-Thr PF07714.24 (E=7e-35), ABC1 PF03109.23 (E=2e-07), Pkinase_fungal PF17667.8 (E=2e-05), PASTA PF03793.25 (E=2e-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 NP_214528.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pkinase (PF00069.32), PK_Tyr_Ser-Thr (PF07714.24), ABC1 (PF03109.23), Pkinase_fungal (PF17667.8), PASTA (PF03793.25)
- 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 P9WI81 (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 —
78 functional partner(s); context anchor
pstP - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000018|Rv0014c|pknB MTTPSHLSDRYELGEILGFGGMSEVHLARDLRLHRDVAVKVLRADLARDPSFYLRFRREAQNAAALNHPAIVAVYDTGEAETPAGPLPYIVMEYVDGVTLRDIVHTEGPMTPKRAIEVIADACQALNFSHQNGIIHRDVKPANIMISATNAVKVMDFGIARAIADSGNSVTQTAAVIGTAQYLSPEQARGDSVDARSDVYSLGCVLYEVLTGEPPFTGDSPVSVAYQHVREDPIPPSARHEGLSADLDAVVLKALAKNPENRYQTAAEMRADLVRVHNGEPPEAPKVLTDAERTSLLSSAAGNLSGPRTDPLPRQDLDDTDRDRSIGSVGRWVAVVAVLAVLTVVVTIAINTFGGITRDVQVPDVRGQSSADAIATLQNRGFKIRTLQKPDSTIPPDHVIGTDPAANTSVSAGDEITVNVSTGPEQREIPDVSTLTYAEAVKKLTAAGFGRFKQANSPSTPELVGKVIGTNPPANQTSAITNVVIIIVGSGPATKDIPDVAGQTVDVAQKNLNVYGFTKFSQASVDSPRPAGEVTGTNPPAGTTVPVDSVIELQVSKGNQFVMPDLSGMFWVDAEPRLRALGWTGMLDKGADVDAGGSQHNRVVYQNPPAGTGVNRDGIITLRFGQ