Protein Info for GFF1516 in Variovorax sp. SCN45

Annotation: TRAP-type C4-dicarboxylate transport system, large permease component

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 66 (20 residues), see Phobius details amino acids 78 to 99 (22 residues), see Phobius details amino acids 104 to 127 (24 residues), see Phobius details amino acids 139 to 163 (25 residues), see Phobius details amino acids 170 to 193 (24 residues), see Phobius details amino acids 213 to 234 (22 residues), see Phobius details amino acids 240 to 256 (17 residues), see Phobius details amino acids 271 to 293 (23 residues), see Phobius details amino acids 312 to 329 (18 residues), see Phobius details amino acids 336 to 384 (49 residues), see Phobius details amino acids 396 to 417 (22 residues), see Phobius details PF06808: DctM" amino acids 7 to 416 (410 residues), 411.6 bits, see alignment E=1.8e-127 TIGR00786: TRAP transporter, DctM subunit" amino acids 17 to 419 (403 residues), 482.3 bits, see alignment E=5.2e-149

Best Hits

Swiss-Prot: 49% identical to Y050_HAEIN: Putative TRAP transporter large permease protein HI_0050 (HI_0050) from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)

KEGG orthology group: None (inferred from 88% identity to vpe:Varpa_0715)

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)

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

Find the best match in UniProt

Protein Sequence (426 amino acids)

>GFF1516 TRAP-type C4-dicarboxylate transport system, large permease component (Variovorax sp. SCN45)
MTILVFVGSLLVAMAMGIPIAFSLLACGVALMWHLDLFDAQILAQNVIGGADSFPLLAVP
FFMLAGEIMNVGGLSKRIVDLALALVGHVKGGLGYVTIMAGCLLSALSGSAVADAAALTA
LLLPMMVKAGHDKARAGGLIAATGIIGPVIPPSIGLVIFGVAANVSISKLFMAAIVPGLL
IGGALWVTWAWLVRHEKIQPPPRKPAREVMKAARDAGWALLLPVIILVGLRMGVFTPTEA
AVVAAVYAFFVATFIYRELSFDALYKVFVSAAKTSAVVMFLIAAAMVSAWLITVADLPSK
VVGLLEPFMGNKILLMIMVMLLVMAVGTAMDMTPTILILTPVLMPVVIAAGIDPVYFGVM
FIINNSIGLITPPVGVVLNVVAGVGKMKMDDVTRGVLPFMAAEFAIMFVMVIFPQLVTVP
ARWFGG