Protein Info for GFF561 in Xanthobacter sp. DMC5

Annotation: Protein translocase subunit SecD

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 50 100 150 200 250 300 350 400 450 500 535 signal peptide" amino acids 6 to 11 (6 residues), see Phobius details transmembrane" amino acids 12 to 28 (17 residues), see Phobius details amino acids 378 to 411 (34 residues), see Phobius details amino acids 422 to 444 (23 residues), see Phobius details amino acids 465 to 489 (25 residues), see Phobius details amino acids 500 to 525 (26 residues), see Phobius details PF07549: Sec_GG" amino acids 39 to 65 (27 residues), 25 bits, see alignment (E = 2.1e-09) TIGR01129: protein-export membrane protein SecD" amino acids 47 to 521 (475 residues), 470.2 bits, see alignment E=6.1e-145 PF21760: SecD_1st" amino acids 164 to 223 (60 residues), 95.1 bits, see alignment E=2.6e-31 PF22599: SecDF_P1_head" amino acids 240 to 351 (112 residues), 148.9 bits, see alignment E=1.1e-47 TIGR00916: protein-export membrane protein, SecD/SecF family" amino acids 283 to 513 (231 residues), 245.2 bits, see alignment E=6.7e-77 PF02355: SecD_SecF_C" amino acids 354 to 516 (163 residues), 56.8 bits, see alignment E=4.2e-19

Best Hits

KEGG orthology group: K03072, preprotein translocase subunit SecD (inferred from 91% identity to xau:Xaut_4309)

Predicted SEED Role

"Protein-export membrane protein SecD (TC 3.A.5.1.1)" (TC 3.A.5.1.1)

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 (535 amino acids)

>GFF561 Protein translocase subunit SecD (Xanthobacter sp. DMC5)
MLHFSRLKTTAILVTIAIGMLFAVPNVLSPGMLDHLPSWLASSRVTLGLDLQGGSHILLE
VDGPALRRERTEQLRDEVRRVLRDQKIGYSNLALRDTSVTLRLRDPNDTQKAVTELRKLA
APVTNALFGNSSGEMDLTVSSGSDGTVTLQLTDAGLTAKMRSAVDQSIEIIRRRIDQLGT
VEPNIQRQGLDRILVQVPGLQDPQRLKNLLGQTAKLSFRMVDQSMSPQQALEGRAPPESE
VLKGQDGQPYLVEKQVRVSGEDLVDAQPGFDQNSREPIVSFRFNNNGAKRFAAVSQESVG
RPFAIVLDNQVISAPVIREPILGGAGQISGSFTVQQANDLAILLRAGALPAPLKVVEERT
VGPSLGADSIQAGKTAAYVAGGLVTVFMLAVYGLFGLFALIALAVHIILMFSLQSVLGAT
LTLPGIAGVVLTIGMAVDSNVVIFERMRDEAREGRSAISAIDKGFVNALGTILDANITSL
ATAVILFLMGGSGPVRGFAVTYILGLLTTMFTAYTLTRLMIAYWVKWRRPAKLPI