Protein Info for Shew_1444 in Shewanella loihica PV-4

Updated annotation (from data): dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component
Rationale: Important for utilizing succinate, fumarate, and L-malate, as expected, and also for utilizing a-ketoglutarate
Original annotation: TRAP dicarboxylate transporter, DctM subunit (RefSeq)

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 50 100 150 200 250 300 350 400 465 signal peptide" amino acids 1 to 24 (24 residues), see Phobius details transmembrane" amino acids 25 to 26 (2 residues), see Phobius details amino acids 55 to 76 (22 residues), see Phobius details amino acids 88 to 108 (21 residues), see Phobius details amino acids 114 to 132 (19 residues), see Phobius details amino acids 139 to 162 (24 residues), see Phobius details amino acids 171 to 194 (24 residues), see Phobius details amino acids 215 to 235 (21 residues), see Phobius details amino acids 241 to 258 (18 residues), see Phobius details amino acids 278 to 295 (18 residues), see Phobius details amino acids 307 to 328 (22 residues), see Phobius details amino acids 339 to 362 (24 residues), see Phobius details amino acids 368 to 387 (20 residues), see Phobius details amino acids 393 to 419 (27 residues), see Phobius details amino acids 426 to 453 (28 residues), see Phobius details PF06808: DctM" amino acids 7 to 451 (445 residues), 356.6 bits, see alignment E=9e-111 TIGR00786: TRAP transporter, DctM subunit" amino acids 17 to 260 (244 residues), 271.1 bits, see alignment E=7.2e-85

Best Hits

KEGG orthology group: K11690, C4-dicarboxylate transporter, DctM subunit (inferred from 100% identity to slo:Shew_1444)

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 A3QCW3 at UniProt or InterPro

Protein Sequence (465 amino acids)

>Shew_1444 dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (Shewanella loihica PV-4)
MTIATLFISLFLCMLLGMPIAIALGFSSMLTILLFSDDSLASVALKLYESTSEHYTLLAI
PFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIG
SIVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGL
MMGLLLMLAIYIVARIKKLPSRPFPGFRPLAISSAKAMGGLALIVIVLGSIYGGIASPTE
AAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADKEIR
HVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNLLLLA
AGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGIT
GRSMGWVIHSCIPWLALLLFFLALITYIPQISLFLPEYIDKLNGY