Protein Info for PP_4840 in Pseudomonas putida KT2440

Annotation: D-alanine, beta-alanine, D-serine, glycine permease

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 50 100 150 200 250 300 350 400 468 transmembrane" amino acids 22 to 40 (19 residues), see Phobius details amino acids 46 to 69 (24 residues), see Phobius details amino acids 101 to 125 (25 residues), see Phobius details amino acids 131 to 149 (19 residues), see Phobius details amino acids 159 to 180 (22 residues), see Phobius details amino acids 205 to 226 (22 residues), see Phobius details amino acids 247 to 267 (21 residues), see Phobius details amino acids 281 to 303 (23 residues), see Phobius details amino acids 342 to 360 (19 residues), see Phobius details amino acids 366 to 390 (25 residues), see Phobius details amino acids 412 to 430 (19 residues), see Phobius details amino acids 436 to 455 (20 residues), see Phobius details PF00324: AA_permease" amino acids 22 to 461 (440 residues), 415.2 bits, see alignment E=3.4e-128 PF13520: AA_permease_2" amino acids 26 to 447 (422 residues), 154.7 bits, see alignment E=3.9e-49

Best Hits

Swiss-Prot: 75% identical to CYCA_ECO57: D-serine/D-alanine/glycine transporter (cycA) from Escherichia coli O157:H7

KEGG orthology group: K11737, D-serine/D-alanine/glycine transporter (inferred from 100% identity to ppf:Pput_4718)

MetaCyc: 75% identical to D-serine/alanine/glycine:H+symporter (Escherichia coli K-12 substr. MG1655)
RXN0-5130; RXN0-5201; RXN0-5202; RXN0-5203; TRANS-RXN-62A; TRANS-RXN-62B

Predicted SEED Role

"D-serine/D-alanine/glycine transporter" in subsystem Glycine and Serine Utilization or Pyruvate Alanine Serine Interconversions

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 Q88DI5 at UniProt or InterPro

Protein Sequence (468 amino acids)

>PP_4840 D-alanine, beta-alanine, D-serine, glycine permease (Pseudomonas putida KT2440)
MTQTSPIATDEPHLQRNLTNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGF
MLFFVMRAMGELLLSNLNYKSFIDFSADLLGPWAGYFTGWTYWFCWVVTGIADVVAIAAY
TQFWFPDLPQWIPALTCVGLLLSLNLVTVKMFGELEFWFALVKIVAILGLVATGLYMVIT
GFTSPSGRTAQLANLWNDGGMFPHGLMGFFAGFQIAVFAFVGIELVGTTAAEAKNPERTL
PRAINSIPIRIIVFYVLALIAIMAVTPWRDVVPGKSPFVELFVLAGLPAAASIINFVVLT
SAASSANSGVFSTSRMLYGLSQEGDAPKAFEKLSSRSVPANGLYFSCTCLLLGAVLIYLV
PNVVEAFTLVTTVSAVLFMFVWTLILLSYLKYRKDRAALHQASNYKMPGGRFMCYVCLSF
FAFILVLLSLEADTRSALVVTPIWFVVLAVTYQLVRSRRHPRTAVRNG