pknE Resolved · high auto-curated
H37Rv Rv1743 · MTBC0 mtbc0_001856 ·
566 aa · 1981076–1982776 (+) ·
RefSeq NP_216259.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | serine/threonine-protein kinase PknE |
|---|---|
| MTBC0 PGAP re-annotation | serine/threonine protein kinase PknE |
| Revised (this work) | Serine/threonine protein kinase PknE. Pfam: Pkinase (PF00069.32), PK_Tyr_Ser-Thr (PF07714.24), Thioredoxin_4 (PF13462.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WI77
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Serine/threonine-protein kinase PknE |
| EC (curated) |
EC 2.7.11.1
|
| Curated function | Important for survival of the bacterium in the host during infection. Promotes the survival of infected macrophages by activating multiple signaling responses and suppressing apoptosis of macrophages during nitrate stress. May contribute to the adaptation of M.tuberculosis during stress conditions by maintaining the cellular integrity. Can phosphorylate the FHA domain of Rv1747. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K TranscriptionL Replication, recombination and repairT Signal transduction mechanisms
|
|---|---|
| Preferred name | pknE |
| eggNOG description | serine threonine protein kinase |
| Orthologous group | COG0515 |
| EC number |
EC 2.7.11.1
|
| KEGG orthology |
K08884, K12132
|
| Gene Ontology (65) |
GO:0003674, GO:0003824, GO:0004672, GO:0004674, GO:0005575, GO:0005576, GO:0006464, GO:0006468, GO:0006793, GO:0006796, GO:0006807, GO:0006950 +53 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 | 1.194 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 7 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 | 1.1e-42 | 16–229 | Protein kinase domain |
PK_Tyr_Ser-Thr | PF07714.24 | 4.3e-27 | 18–260 | Protein tyrosine and serine/threonine kinase |
Thioredoxin_4 | PF13462.13 | 1.2e-06 | 389–544 | Thioredoxin |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pstP (phosphoserine/threonine phosphatase PstP), high confidence from genomic context alone (score 855 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0018c pstP |
phosphoserine/threonine phosphatase PstP | 902 | 855 ctx | cooccurence:762 |
Rv1827 garA |
glycogen accumulation regulator GarA | 833 | 637 ctx | cooccurence:460 textmining:561 |
Rv0019c fhaB |
FHA domain-containing protein FhaB | 601 | 557 | |
Rv1740 vapB34 |
antitoxin VapB34 | 540 | 540 ctx | neighborhood:533 |
Rv1742 hyp |
hypothetical protein | 540 | 539 ctx | neighborhood:535 |
Rv1741 vapC34 |
ribonuclease VapC34 | 536 | 536 ctx | neighborhood:533 |
Rv1747 |
ABC transporter ATP-binding protein/permease | 692 | 524 | |
Rv2031c hspX |
alpha-crystallin | 523 | 521 | experimental:500 |
Rv0020c fhaA |
FHA domain-containing protein FhaA | 777 | 510 | textmining:564 |
Rv0440 groEL2 |
molecular chaperone GroEL | 567 | 507 | experimental:500 |
Rv1364c |
sigma factor regulatory protein | 567 | 435 | |
Rv1739c |
sulfate ABC transporter permease | 419 | 419 ctx | neighborhood:415 |
Rv0014c pknB |
serine/threonine-protein kinase PknB | 641 | 416 | textmining:411 |
Rv1712 cmk |
cytidylate kinase | 416 | 416 | coexpression:409 |
Rv2874 dipZ |
integral membrane C-type cytochrome biogenesis protein DipZ | 457 | 346 |
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 PknE
- MTBC0 PGAP product: serine/threonine protein kinase PknE
- Pfam (hmmscan --cut_ga): Pkinase PF00069.32 (E=1e-42), PK_Tyr_Ser-Thr PF07714.24 (E=4e-27), Thioredoxin_4 PF13462.13 (E=1e-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_216259.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pkinase (PF00069.32), PK_Tyr_Ser-Thr (PF07714.24), Thioredoxin_4 (PF13462.13)
- 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 P9WI77 (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 —
34 functional partner(s); context anchor
pstP - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001856|Rv1743|pknE MDGTAESREGTQFGPYRLRRLVGRGGMGDVYEAEDTVRERIVALKLMSETLSSDPVFRTRMQREARTAGRLQEPHVVPIHDFGEIDGQLYVDMRLINGVDLAAMLRRQGPLAPPRAVAIVRQIGSALDAAHAAGATHRDVKPENILVSADDFAYLVDFGIASATTDEKLTQLGNTVGTLYYMAPERFSESHATYRADIYALTCVLYECLTGSPPYQGDQLSVMGAHINQAIPRPSTVRPGIPVAFDAVIARGMAKNPEDRYVTCGDLSAAAHAALATADQDRATDILRRSQVAKLPVPSTHPVSPGTRWPQPTPWAGGAPPWGPPSSPLPRSARQPWLWVGVAVAVVVALAGGLGIALAHPWRSSGPRTSAPPPPPPADAVELRVLNDGVFVGSSVAPTTIDIFNEPICPPCGSFIRSYASDIDTAVADKQLAVRYHLLNFLDDQSHSKNYSTRAVAASYCVAGQNDPKLYASFYSALFGSDFQPQENAASDRTDAELAHLAQTVGAEPTAISCIKSGADLGTAQTKATNASETLAGFNASGTPFVWDGSMVVNYQDPSWLARLIG