Protein Info for GFF1380 in Sphingobium sp. HT1-2

Annotation: Methylsuccinyl-CoA dehydrogenase, predicted by (Erb et al, 2007)

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 50 100 150 200 250 300 350 400 450 500 560 signal peptide" amino acids 1 to 31 (31 residues), see Phobius details PF02771: Acyl-CoA_dh_N" amino acids 178 to 284 (107 residues), 95.7 bits, see alignment E=4.6e-31 PF02770: Acyl-CoA_dh_M" amino acids 292 to 393 (102 residues), 61.1 bits, see alignment E=1.8e-20 PF00441: Acyl-CoA_dh_1" amino acids 407 to 556 (150 residues), 149.4 bits, see alignment E=1.8e-47 PF08028: Acyl-CoA_dh_2" amino acids 424 to 542 (119 residues), 58.5 bits, see alignment E=1.9e-19

Best Hits

KEGG orthology group: K14448, (2S)-methylsuccinyl-CoA dehydrogenase (inferred from 92% identity to sch:Sphch_1000)

Predicted SEED Role

"Methylsuccinyl-CoA dehydrogenase, predicted by (Erb et al, 2007)"

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 (560 amino acids)

>GFF1380 Methylsuccinyl-CoA dehydrogenase, predicted by (Erb et al, 2007) (Sphingobium sp. HT1-2)
MSATMEMDKNILVLPDLPALLSGAADAAHAFVAAARPHVKARISNDGGKVDRVLADVEQH
VVHGFGWFAAYAEMLREVASWAASLDAQGSFGEIEALLAQLLFAEYGAQMLGGIPMNQGE
VIRPTDLSDDLSALDAPALRTLIRSGGGQAVKSAIANHLVDARGRATLENCGLDEMFDMV
RDQFFALSNEKVAPFAHEWHLKDELIPLPLVQELGEMGVFGMTIPEEFGGLGMGKTAMCV
VSEELSRGWIGVGSLATRSEIAAELFLTGGTAEQKAHWLPQIANAAILPTAVFTEPDTGS
DLGALRTRATLADGEYRVSGNKTWITHAARADVMTLLVRTDPDTRNYSGLSMLIAPKQRG
TVDTPFPTPGMSGGEIEVIGYRGMKEYEIGFDDFRVPAANLLGGVEGQGFKQLMATFESA
RIQTAARAIGVAQAALDIGLSYALDRKQFGRPIFDFPRVANKLAMMAAEIMGARQLTYFA
ARRKDEDKRCDLEAGMAKLIGARVAWAAADNALQIHGGNGFATEYQVSRLLADARILNIF
EGAGEIQAQVIARRLLDEAN