pfkB Family assigned · medium auto-curated
H37Rv Rv2029c · MTBC0 mtbc0_002162 ·
339 aa · 2304018–2305037 (-) ·
RefSeq NP_216545.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 6-phosphofructokinase PfkB |
|---|---|
| MTBC0 PGAP re-annotation | 1-phosphofructokinase family hexose kinase |
| Revised (this work) | 1-phosphofructokinase family hexose kinase. Pfam: PfkB (PF00294.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WID3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ATP-dependent 6-phosphofructokinase isozyme 2 |
| EC (curated) |
EC 2.7.1.11, EC 2.7.1.144
|
| Curated function | Catalyzes the phosphorylation of D-fructose 6-phosphate to fructose 1,6-bisphosphate by ATP, the first committing step of glycolysis. Can also catalyze the phosphorylation of tagatose-6-phosphate. The catalytic efficiency with tagatose-6-phosphate is about 1.8 times lower than that with fructose 6-phosphate. Can use phosphate donors other than ATP (GTP and ITP), with lower efficiency. In addition, can catalyze the reverse gluconeogenic reaction, albeit with low efficiency. May support and maintain basic glycolysis and metabolic fluxes during conditions inhibiting PfkA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | pfkB |
| eggNOG description | belongs to the carbohydrate kinase PfkB family |
| Orthologous group | COG1105 |
| EC number |
EC 2.7.1.11, EC 2.7.1.144, EC 2.7.1.56
|
| KEGG orthology |
K00882, K00917, K16370
|
| KEGG pathways |
map00010, map00030, map00051, map00052, map00680, map01100, map01110, map01120, map01130, map01200, map01230
|
| KEGG modules |
M00001, M00345
|
| Gene Ontology (26) |
GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005975, GO:0006793, GO:0006796, GO:0008150, GO:0008152 +14 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 | 0.432 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 5 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.34% of strains (497) · 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 |
|---|---|---|---|---|
PfkB | PF00294.30 | 4.3e-61 | 18–306 | pfkB family carbohydrate kinase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2028c (universal stress protein), high confidence from genomic context alone (score 983 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2030c hyp |
hypothetical protein | 996 | 984 ctx | neighborhood:865 coexpression:860 textmining:800 |
Rv2028c |
universal stress protein | 993 | 983 ctx | neighborhood:882 coexpression:860 textmining:630 |
Rv1448c tal |
transaldolase | 954 | 940 | coexpression:427 database:900 |
Rv0363c fba |
fructose-bisphosphate aldolase | 967 | 939 | database:900 textmining:481 |
Rv3010c pfkA |
6-phosphofructokinase | 972 | 920 | database:900 textmining:675 |
Rv0946c pgi |
glucose-6-phosphate isomerase | 954 | 909 | database:900 textmining:518 |
Rv1449c tkt |
transketolase | 935 | 907 | database:900 |
Rv3255c manA |
mannose-6-phosphate isomerase | 917 | 906 | database:900 |
Rv2032 acg |
NAD(P)H nitroreductase | 922 | 900 ctx | neighborhood:470 coexpression:819 |
Rv1099c glpX |
fructose 1,6-bisphosphatase | 906 | 900 | database:900 |
Rv2006 otsB1 |
trehalose-6-phosphate phosphatase OtsB | 898 | 896 ctx | neighborhood:460 coexpression:781 |
Rv1997 ctpF |
cation transporter ATPase F | 908 | 889 | coexpression:860 |
Rv2625c rip3 |
zinc metalloprotease Rip3 | 880 | 866 | coexpression:860 |
Rv1736c narX |
nitrate reductase-like protein NarX | 888 | 860 | coexpression:860 |
Rv2624c |
universal stress protein | 857 | 857 | coexpression:855 |
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: 6-phosphofructokinase PfkB
- MTBC0 PGAP product: 1-phosphofructokinase family hexose kinase
- Pfam (hmmscan --cut_ga): PfkB PF00294.30 (E=4e-61)
- (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_216545.1)
- Domains: Pfam-A via hmmscan --cut_ga — PfkB (PF00294.30)
- 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
COG1105 - Curated reference: UniProt P9WID3 (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 —
101 functional partner(s); context anchor
Rv2028c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002162|Rv2029c|pfkB MTEPAAWDEGKPRIITLTMNPALDITTSVDVVRPTEKMRCGAPRYDPGGGGINVARIVHVLGGCSTALFPAGGSTGSLLMALLGDAGVPFRVIPIAASTRESFTVNESRTAKQYRFVLPGPSLTVAEQEQCLDELRGAAASAAFVVASGSLPPGVAADYYQRVADICRRSSTPLILDTSGGGLQHISSGVFLLKASVRELRECVGSELLTEPEQLAAAHELIDRGRAEVVVVSLGSQGALLATRHASHRFSSIPMTAVSGVGAGDAMVAAITVGLSRGWSLIKSVRLGNAAGAAMLLTPGTAACNRDDVERFFELAAEPTEVGQDQYVWHPIVNPEASP