Protein Info for PP_1167 in Pseudomonas putida KT2440

Updated annotation (from data): D-glucuronate / D-galacturonate TRAP transporter, large permease component
Rationale: Specifically important for utilization of D-glucuronate and D-galacturonate
Original annotation: putative TRAP dicarboxylate transporter, DctM subunit

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 50 100 150 200 250 300 350 400 426 signal peptide" amino acids 1 to 24 (24 residues), see Phobius details transmembrane" amino acids 47 to 68 (22 residues), see Phobius details amino acids 77 to 99 (23 residues), see Phobius details amino acids 101 to 106 (6 residues), see Phobius details amino acids 168 to 193 (26 residues), see Phobius details amino acids 214 to 236 (23 residues), see Phobius details amino acids 242 to 260 (19 residues), see Phobius details amino acids 272 to 294 (23 residues), see Phobius details amino acids 313 to 330 (18 residues), see Phobius details amino acids 336 to 353 (18 residues), see Phobius details amino acids 359 to 385 (27 residues), see Phobius details amino acids 398 to 421 (24 residues), see Phobius details PF06808: DctM" amino acids 7 to 417 (411 residues), 388.7 bits, see alignment E=1.6e-120 TIGR00786: TRAP transporter, DctM subunit" amino acids 17 to 422 (406 residues), 424.1 bits, see alignment E=2.5e-131

Best Hits

Swiss-Prot: 46% identical to YGIK_SALTY: Uncharacterized protein YgiK (ygiK) from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

KEGG orthology group: None (inferred from 99% identity to ppf:Pput_1201)

Predicted SEED Role

"TRAP-type C4-dicarboxylate transport system, large permease component"

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 Q88NP0 at UniProt or InterPro

Protein Sequence (426 amino acids)

>PP_1167 D-glucuronate / D-galacturonate TRAP transporter, large permease component (Pseudomonas putida KT2440)
MEAFILLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMIQVASGVNKFSLLAIPF
FVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSV
LIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGL
LLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATE
SAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPS
KITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGM
IMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLW
LPSVVL