Protein Info for Pf6N2E2_1668 in Pseudomonas fluorescens FW300-N2E2
Updated annotation (from data): Xylonate dehydratase (EC 4.2.1.82)
Rationale: Specifically important for utilizing D-Xylose. Automated validation from mutant phenotype: the predicted function (XYLONATE-DEHYDRATASE-RXN) was linked to the condition via a MetaCyc pathway. This annotation was also checked manually.
Original annotation: Xylonate dehydratase (EC 4.2.1.82)
These analyses and tools can help you predict a protein's function, but be skeptical. For enzymes, over 10% of annotations from KEGG or SEED are probably incorrect. For other types of proteins, the error rates may be much higher. MetaCyc and Swiss-Prot have low error rates, but the best hits in these databases are often quite distant, so this protein's function may not be the same. TIGRFam has low error rates. Finally, many experimentally-characterized proteins are not in any of these databases. To find relevant papers, use PaperBLAST.
Protein Families and Features
Best Hits
KEGG orthology group: K01687, dihydroxy-acid dehydratase [EC: 4.2.1.9] (inferred from 98% identity to pba:PSEBR_a2329)MetaCyc: 64% identical to xylonate dehydratase monomer (Caulobacter vibrioides CB15)
Xylonate dehydratase. [EC: 4.2.1.82]
Predicted SEED Role
"Xylonate dehydratase (EC 4.2.1.82)" in subsystem Xylose utilization (EC 4.2.1.82)
MetaCyc Pathways
- superpathway of branched chain amino acid biosynthesis (17/17 steps found)
- superpathway of L-isoleucine biosynthesis I (13/13 steps found)
- L-isoleucine biosynthesis I (from threonine) (7/7 steps found)
- L-valine biosynthesis (4/4 steps found)
- pyruvate fermentation to isobutanol (engineered) (4/5 steps found)
- superpathway of L-threonine metabolism (13/18 steps found)
- L-isoleucine biosynthesis IV (4/6 steps found)
- D-xylose degradation VI (3/5 steps found)
- L-isoleucine biosynthesis III (4/7 steps found)
- D-xylose degradation III (2/5 steps found)
- D-xylose degradation V (2/5 steps found)
- L-isoleucine biosynthesis II (4/8 steps found)
- D-xylose degradation to ethylene glycol (engineered) (1/4 steps found)
- D-xylose degradation IV (3/7 steps found)
- superpathway of pentose and pentitol degradation (15/42 steps found)
KEGG Metabolic Maps
- Biosynthesis of alkaloids derived from histidine and purine
- Pantothenate and CoA biosynthesis
- Pentose and glucuronate interconversions
- Valine, leucine and isoleucine biosynthesis
Isozymes
Compare fitness of predicted isozymes for: 4.2.1.9
Use Curated BLAST to search for 4.2.1.82 or 4.2.1.9
Sequence Analysis Tools
PaperBLAST (search for papers about homologs of this protein)
Search CDD (the Conserved Domains Database, which includes COG and superfam)
Compare to protein structures
Predict protein localization: PSORTb (Gram-negative bacteria)
Predict transmembrane helices and signal peptides: Phobius
Check the current SEED with FIGfam search
Find homologs in fast.genomics or the ENIGMA genome browser
See A0A159ZXT5 at UniProt or InterPro
Protein Sequence (594 amino acids)
>Pf6N2E2_1668 Xylonate dehydratase (EC 4.2.1.82) (Pseudomonas fluorescens FW300-N2E2) MSDTPKHRLRSEQWFNDPAHADMTALYVERYMNYGMTREELQSGRPIIGIAQTGSDLTPC NRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPLD GVVLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAG EIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYA TGKRICDLVRQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLEDW QRIGEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRLHEDCATVSGKTIGEIVS NSLTSNTDVIHPFDTPLKHRAGFIVLSGNFFDSAIMKMSVVGEAFRKTYLSEPGAENSFE ARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGID SLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLKTNDRLKVDLNTRTVNLLIDDAEMA QRRREWIPNIPPSQTPWQELYRQLVGQLSTGGCLEPATLHLRVIARSGEPRHSH