Protein Info for GFF4935 in Variovorax sp. SCN45

Annotation: ABC transporter, permease protein 1 (cluster 5, nickel/peptides/opines)

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 50 100 150 200 250 300 340 signal peptide" amino acids 1 to 35 (35 residues), see Phobius details transmembrane" amino acids 106 to 125 (20 residues), see Phobius details amino acids 138 to 162 (25 residues), see Phobius details amino acids 204 to 223 (20 residues), see Phobius details amino acids 258 to 281 (24 residues), see Phobius details amino acids 306 to 331 (26 residues), see Phobius details PF19300: BPD_transp_1_N" amino acids 10 to 80 (71 residues), 41.7 bits, see alignment E=1.2e-14 PF00528: BPD_transp_1" amino acids 118 to 339 (222 residues), 135 bits, see alignment E=2.7e-43

Best Hits

Swiss-Prot: 38% identical to DPPB_HAEIN: Dipeptide transport system permease protein DppB (dppB) from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)

KEGG orthology group: K02033, peptide/nickel transport system permease protein (inferred from 62% identity to pde:Pden_1249)

Predicted SEED Role

"Dipeptide transport system permease protein DppB (TC 3.A.1.5.2)" in subsystem ABC transporter dipeptide (TC 3.A.1.5.2) (TC 3.A.1.5.2)

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 (340 amino acids)

>GFF4935 ABC transporter, permease protein 1 (cluster 5, nickel/peptides/opines) (Variovorax sp. SCN45)
MRKLVAPAALLRSGLSFALMLLVLLLVTFLIGKAAPIDPVLQVVGDRASPEAYQEARQRM
GLDQPIATQFVRYVADAAKGDLGRSTTTGRAVLEDLRQYFPATLELATLGILLGVVFGVP
LGMLAAHQHNRWIDQLLRLVGLLGYSVPVFWLGLVGLLIFYARLGWVGGPGRLDDIYQYT
VDSWSNLVLVDTLRAGNGEAFRNGLSHLVLPAALLGYFSLAYISRMTRAFFLEELGKEYV
LTARVKGASELQVLVRHVLPNVAAPLVTVIALSYAVLLEGAVLTETVFSWPGIGLYVTNA
LFSADVAAVLGGTLLVGLCFVVLNTASDVLGYLMDPRARS