Protein Info for PP_0200 in Pseudomonas putida KT2440

Annotation: putative membrane bound peptidase, nefD

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 50 100 150 200 250 300 350 400 448 signal peptide" amino acids 1 to 24 (24 residues), see Phobius details transmembrane" amino acids 242 to 264 (23 residues), see Phobius details amino acids 271 to 290 (20 residues), see Phobius details amino acids 295 to 312 (18 residues), see Phobius details amino acids 319 to 338 (20 residues), see Phobius details amino acids 345 to 370 (26 residues), see Phobius details PF25145: NfeD1b_N" amino acids 28 to 214 (187 residues), 68.1 bits, see alignment E=1.2e-22 PF24961: NfeD_membrane" amino acids 251 to 363 (113 residues), 84.5 bits, see alignment E=9.1e-28 PF01957: NfeD" amino acids 384 to 438 (55 residues), 32 bits, see alignment 1.8e-11

Best Hits

KEGG orthology group: K07403, membrane-bound serine protease (ClpP class) (inferred from 100% identity to ppu:PP_0200)

Predicted SEED Role

"Putative membrane-bound ClpP-class protease associated with aq_911" in subsystem YbbK

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 Q88RD2 at UniProt or InterPro

Protein Sequence (448 amino acids)

>PP_0200 putative membrane bound peptidase, nefD (Pseudomonas putida KT2440)
MIARCWRWLLLLLLLGITPGGQAAPGAVWVLNIDDAIGPASADYLVRSLGQAQAQGAQLV
VIRMDTPGGLDSAMRQMIKAILSSTVPVASYVAPSGARAASAGTYILYASHIAAMAPGTN
LGAATPVRIGGAPGTPSDDKAKGGDDETLARKQVNDAAAYIRGLAQMRGRNADWAEKAVR
EAVSLSASEALRLNVIDQVADDLPDLLRKLDGKTLQVAGQPRQLQTAGASVVEHLPDWRT
RFLAVITNPSVALILIMIGVYGLLFEFMNPGSAVGGVVGGICLLLALYALQLLPVSFAGV
ALILLGITFMIAEAFLPSFGVVGFGGIVAFVVGALILIDTDAPGFGIPLALIGTLALLSA
LLIGGVLGMALKARQRALVSGDAGLVGSLVTVTQVMASDPFCGVVLAQGEQWQVQCATPL
QTGQNVRVTARHGVMLEVSAAAPATQGE