Protein Info for PP_0835 in Pseudomonas putida KT2440

Annotation: Sec Translocation Complex SecD subunit

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 50 100 150 200 250 300 350 400 450 500 550 620 transmembrane" amino acids 7 to 25 (19 residues), see Phobius details amino acids 462 to 480 (19 residues), see Phobius details amino acids 486 to 506 (21 residues), see Phobius details amino acids 511 to 533 (23 residues), see Phobius details amino acids 554 to 576 (23 residues), see Phobius details amino acids 583 to 606 (24 residues), see Phobius details PF13721: SecD-TM1" amino acids 2 to 105 (104 residues), 119 bits, see alignment E=3.7e-38 PF07549: Sec_GG" amino acids 118 to 142 (25 residues), 24.7 bits, see alignment (E = 3.7e-09) TIGR01129: protein-export membrane protein SecD" amino acids 125 to 606 (482 residues), 429.6 bits, see alignment E=1.4e-132 PF21760: SecD_1st" amino acids 231 to 286 (56 residues), 97 bits, see alignment 1e-31 PF22599: SecDF_P1_head" amino acids 299 to 437 (139 residues), 109.4 bits, see alignment E=2.8e-35 TIGR00916: protein-export membrane protein, SecD/SecF family" amino acids 342 to 599 (258 residues), 224.1 bits, see alignment E=1.8e-70 PF02355: SecD_SecF_C" amino acids 443 to 606 (164 residues), 60.7 bits, see alignment E=4e-20 PF03176: MMPL" amino acids 483 to 609 (127 residues), 29.8 bits, see alignment E=9.4e-11

Best Hits

Swiss-Prot: 82% identical to SECD_PSEAE: Protein translocase subunit SecD (secD) from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

KEGG orthology group: K03072, preprotein translocase subunit SecD (inferred from 100% identity to ppu:PP_0835)

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 Q88PL5 at UniProt or InterPro

Protein Sequence (620 amino acids)

>PP_0835 Sec Translocation Complex SecD subunit (Pseudomonas putida KT2440)
MLNKYPLWKYALIVLVLVVGFIYSAPNLYPDDPAVQISGASSALQVNQADLDRVSKALVD
AKIAVKGASLGEKGSGLIRLTNQEDQLPAKDVVRKALGDDYVVALNLAQTTPQWLRNLGA
SPMKLGLDLSGGVHFLLEVDMDKAMTARMKVYEGEVKTLLRKERVRYRSLPQQDGGIMLG
FADDATREQARALIRKNFNDFDLTTTDRNELAVLRLALTQAKVAEIREYSIKQNLTTVRN
RVNELGVAEPLVQRQGANRIVVELPGVQDTAEAKRILGKTANLEFRFGAEPGASKATTEV
FEFREGGRSAAVERGLIITGDQVTDAQASFDEHGRPQVNIRLDGHGGELMSRATRSNVGR
SMAVIFIEQKPVTRYVKQAVGGVEKDVAVQSFVEEKKIISLATIQSPLGSQFRITGLNGQ
GESSELALLLRAGGLAAPMYFAEERTIGPSLGADNITKGIDASLWGMLFVSLFIIAIYRA
FGVLATIALAGNMVLLLALMSLLGATLTLPGIAGIVLTMGMAVDANVLIFSRIREEIAAG
MSVQRAIHEGFNRAYSAIVDANLTTLLVGGILFAMGTGPVKGFAVTMSLGIFTSMFTAVM
VTRALVNLTCGGRDIKKLWV