Protein Info for PP_5352 in Pseudomonas putida KT2440

Annotation: DNA-dependent ATPase I and helicase II, nucleotide Excision Repair Complex

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 728 PF00580: UvrD-helicase" amino acids 13 to 275 (263 residues), 295.9 bits, see alignment E=8.9e-92 PF13245: AAA_19" amino acids 17 to 258 (242 residues), 80.1 bits, see alignment E=4.4e-26 PF13361: UvrD_C" amino acids 280 to 619 (340 residues), 281 bits, see alignment E=4.5e-87 PF13538: UvrD_C_2" amino acids 559 to 615 (57 residues), 31.2 bits, see alignment 4e-11 PF21196: PcrA_UvrD_tudor" amino acids 682 to 723 (42 residues), 24.4 bits, see alignment 5.4e-09

Best Hits

Swiss-Prot: 64% identical to UVRD_ECOLI: DNA helicase II (uvrD) from Escherichia coli (strain K12)

KEGG orthology group: K03657, DNA helicase II / ATP-dependent DNA helicase PcrA [EC: 3.6.4.12] (inferred from 100% identity to ppu:PP_5352)

MetaCyc: 64% identical to DNA helicase II (Escherichia coli K-12 substr. MG1655)
RXN-11135 [EC: 5.6.2.4]

Predicted SEED Role

"ATP-dependent DNA helicase UvrD/PcrA" in subsystem DNA repair, bacterial UvrD and related helicases

Isozymes

Compare fitness of predicted isozymes for: 3.6.4.12

Use Curated BLAST to search for 3.6.4.12 or 5.6.2.4

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 Q88C31 at UniProt or InterPro

Protein Sequence (728 amino acids)

>PP_5352 DNA-dependent ATPase I and helicase II, nucleotide Excision Repair Complex (Pseudomonas putida KT2440)
MRTDDLSLLLNSLNDAQRQAVAATLGRQLVLAGAGSGKTRVLVHRIAWLIQVEQASPHSI
LSVTFTNKAAAEMRQRIEQLLGINPAGMWVGTFHGLAHRLLRAHWQEARLVQNFQILDSD
DQQRLIKRVMRELGLDEQKWPARQAQWFINGQKDEGLRPQHIQAGGDLFLATMREVYTAY
EQACERAGVIDFSELLLRALDLWRDHPGLLEHYQRRFRHVLVDEFQDTNAVQYAWLRLLA
RGGDSLMAVGDDDQSIYGWRGAKIENIHQYTADFPDAEMIRLEQNYRSTGGILKAANALI
ANNSGRLGKELWTDMGEGEPLTLYAAYNEHDEARYVVETIESLVKQGNARNEIAILYRSN
AQSRVLEEALLRERIPYRIYGGQRFFERAEIKNAMAYLRLIEGRGNDAALERVINVPPRG
IGEKTVEAIREHARHSQLSMWEAMCQLIAAKALKGRAASALGAFIELIEGLAAKVVDMPL
HTMTQTTIEQSGLITYHQEEKGEKGQARVENLEELVSAARNFESTDEDADLSPLSAFLGH
ASLEAGDTQADEHEDSIQLMTLHSAKGLEFPYVFLVGMEEGLFPHKMSLEEPGRLEEERR
LAYVGITRAMRQLVMTYAETRRLYGSETYNKVSRFVREIPAGLVQEVRLSNSVSRPFGGA
KTATNSNLFANASIPQTAFNLGQRVQHAVFGEGVILNFEGSGAQARVQVNFAEGSKWLML
GYAKLEAV