Protein Info for PP_3601 in Pseudomonas putida KT2440

Annotation: galactarate dehydratase

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

1 50 100 150 200 250 300 350 400 450 517 TIGR03248: galactarate dehydratase" amino acids 12 to 517 (506 residues), 939.4 bits, see alignment E=2.1e-287 PF08666: SAF" amino acids 19 to 88 (70 residues), 32.1 bits, see alignment E=2.1e-11 PF04295: GD_AH_second" amino acids 119 to 263 (145 residues), 124.4 bits, see alignment E=5.3e-40 PF20629: GD_AH_C" amino acids 273 to 513 (241 residues), 309 bits, see alignment E=3.1e-96

Best Hits

Swiss-Prot: 64% identical to GARD_BACSU: Probable galactarate dehydratase (L-threo-forming) (garD) from Bacillus subtilis (strain 168)

KEGG orthology group: K01708, galactarate dehydratase [EC: 4.2.1.42] (inferred from 99% identity to ppf:Pput_3100)

MetaCyc: 59% identical to GarD (Escherichia coli K-12 substr. MG1655)
Galactarate dehydratase. [EC: 4.2.1.42]

Predicted SEED Role

"D-galactarate dehydratase (EC 4.2.1.42)" in subsystem D-Galacturonate and D-Glucuronate Utilization or D-galactarate, D-glucarate and D-glycerate catabolism (EC 4.2.1.42)

MetaCyc Pathways

KEGG Metabolic Maps

Isozymes

No predicted isozymes

Use Curated BLAST to search for 4.2.1.42

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search 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 Q88GW6 at UniProt or InterPro

Protein Sequence (517 amino acids)

>PP_3601 galactarate dehydratase (Pseudomonas putida KT2440)
MQLIEHSDSPRYVRLHDDDNVVVVVNDGGLGEGARFADGLTLIEGVPQSHKVATVSIAKG
EPVRRYGQIIGYALEDLRQGSWVQESQLAMPAAPELDSLPRCDAVPQPLPPLEGFTFEGY
RNADGTVGTRNILGITTTVQCVTGVLEHAVKRIRNELLPKYPNVDDVVAITHSYGCGVAI
NARDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQASQVMHDNDPSVDLSDPWLYRLQD
ASLGFVEMIEQIMDLAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA
ADLLVRAGATVLFSEVTEVRDAIYMLTSRAENQDVADALVREMDWYDRYLQQGAADRSAN
TTPGNKKGGLSNIVEKSLGSIVKSGSGAIQGVLGPGERANRKGLIFCATPASDFVCGTLQ
LAAGMNLHVFTTGRGTPYGLAMAPVVKVCTRSELAQRWPDLIDIDAGRIASGRSTIEELG
WELFHYYLDVASGRKQTWAEQHRLHNDITLFNPAPIT