Protein Info for PGA1_c18920 in Phaeobacter inhibens DSM 17395

Annotation: protein-export membrane protein 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 50 100 150 200 250 300 350 400 450 500 553 signal peptide" amino acids 1 to 28 (28 residues), see Phobius details transmembrane" amino acids 394 to 413 (20 residues), see Phobius details amino acids 420 to 438 (19 residues), see Phobius details amino acids 444 to 464 (21 residues), see Phobius details amino acids 487 to 509 (23 residues), see Phobius details amino acids 516 to 542 (27 residues), see Phobius details TIGR01129: protein-export membrane protein SecD" amino acids 69 to 539 (471 residues), 492.8 bits, see alignment E=8.4e-152 PF21760: SecD_1st" amino acids 185 to 242 (58 residues), 81 bits, see alignment 7e-27 PF22599: SecDF_P1_head" amino acids 259 to 370 (112 residues), 138.1 bits, see alignment E=2.3e-44 TIGR00916: protein-export membrane protein, SecD/SecF family" amino acids 302 to 532 (231 residues), 277.1 bits, see alignment E=1.2e-86 PF02355: SecD_SecF_C" amino acids 373 to 544 (172 residues), 79.6 bits, see alignment E=4e-26 PF03176: MMPL" amino acids 411 to 535 (125 residues), 33.1 bits, see alignment E=6e-12

Best Hits

Swiss-Prot: 61% identical to SECD_RHOCB: Protein translocase subunit SecD (secD) from Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)

KEGG orthology group: K03072, preprotein translocase subunit SecD (inferred from 86% identity to sit:TM1040_0996)

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

See I7EMT9 at UniProt or InterPro

Protein Sequence (553 amino acids)

>PGA1_c18920 protein-export membrane protein SecD (Phaeobacter inhibens DSM 17395)
MLQIDLWKRVLIWLVCVTGLLLALPNAFYTRVEQANDAAAEIITKGESPARLDVAGQWPS
FMPSSLVNLGLDLRGGAHLLAEVKVADVYGARMDALWPEVRDALRPERGEVGTFRRQQAP
EGQIRLKISKPEGMARALAVVRGLANPITSLTGAGATDITVSGTGDILTVELSEQEKLAS
DDRTVRQALEIIRRRIDEVGTREPTIQRQGSDRILIQVPGIGSASELKEIIGTTAQLTFN
PVVGRGTDADANAGVGNKVVPSLDEDGVFYTVEAAPVVTGEELVDAQPSFDQNGRPAVSF
RFNTTGARKFGDYTAENIGSPFAIVLDEEVVSAPVIQSHIPGGSGIITGNFTIEESTNMA
ILLRAGALPAGLEFLEERTIGPELGQDSIDAGKVATIVAFVGVLVFMALSYGLFGVFANI
ALILNIALIFGALSLIGATLTLPGIAGIVLTVGMAVDANVLIFERIREELKAGRGPARAI
DEGYSKALSAILDANITTFITAVILFAMGSGPVRGFAITLGLGIMTSVFTAIFVTRVIIV
MWFERRRPKTIEV