Protein Info for EX31_RS03765 in Rahnella sp. WP5

Annotation: LPS assembly protein LptD

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 791 signal peptide" amino acids 1 to 30 (30 residues), see Phobius details PF03968: LptD_N" amino acids 57 to 198 (142 residues), 79.6 bits, see alignment E=2.2e-26 PF04453: LptD" amino acids 316 to 704 (389 residues), 356.9 bits, see alignment E=1.8e-110

Best Hits

Swiss-Prot: 68% identical to LPTD_YERE8: LPS-assembly protein LptD (lptD) from Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)

KEGG orthology group: K04744, LPS-assembly protein (inferred from 100% identity to rah:Rahaq_3763)

MetaCyc: 65% identical to lipopolysaccharide assembly protein LptD (Escherichia coli K-12 substr. MG1655)
TRANS-RXN-237 [EC: 7.5.2.5]

Predicted SEED Role

"Outer membrane protein Imp, required for envelope biogenesis / Organic solvent tolerance protein precursor"

MetaCyc Pathways

Isozymes

No predicted isozymes

Use Curated BLAST to search for 7.5.2.5

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 (791 amino acids)

>EX31_RS03765 LPS assembly protein LptD (Rahnella sp. WP5)
MKNRRLKTRLPTMLAATIWSVLYSHGAMADLAAQCMLGVPTYDKPLVQGDPNSLPVTINA
DKATGNYPDSALFSGNVNVVQGNSTLDADQVQLNQIANPNQPTPTRTATATGNVRYNDNQ
IKLNGPKGFANLTTKDTDVQDGDYQMVGRQGRGQADKMKQRDNNRYTIMDNGTFTTCLPG
DNSWSVVGSEVIQDRQEEVAEIWNARFHIGPVPVFYSPYMQLPIGNKRRSGFLIPNANYS
SNNGVGVTVPYYWNIAPNYDATITPNYMSNRGLQLQNEFRYLTVAGAGLMEFDYLGNDKK
IDQQYVEDENRTSDKTKRWMYYWRHAGVYDQVWRFNVDYTKVSDPYYFTDFDSKYGSSTD
GYSTQKFSVGYANQNWDVTLASKQFQVFSDFGNANAYRAQPQLDINYYKNDVGPFDLHLY
GQAVKFTSVNPDNPEAVRTHFEPTISLPLSNGWGSLDNEVKLMTTHYQQDIPDAYYDSNP
NTKLRSSVNRTMPEFKSDGKMVFDRTMDWNSDYTQTLEPRVQYLYIPYRNQSSINTYDST
LLQSDYTGLFRDKSYSGLDRIASANQVASGLTTRIYDENLEERFNASAGQIYYFQPPRTG
DVDSVLDKNDDTGSLVWAGDSYYKINNFWGIRGGVQYDTRLDALALGDAVLEYRADSERM
IQLSYRYASPEYIQATLPNVTNPGYQDGISQVGGIASWPIADRWAIVGAYYYDTKAQQPA
DQLIGLQYNTCCWAINVGYERKITSYDTVKSESKYDNKIGFNIELRGLGNNQTLGTKEML
ASGILPYQRAF