Protein Info for SO3748 in Shewanella oneidensis MR-1

Annotation: LysM domain protein (NCBI ptt file)

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 50 100 150 200 250 304 signal peptide" amino acids 1 to 23 (23 residues), see Phobius details PF01476: LysM" amino acids 49 to 85 (37 residues), 21.7 bits, see alignment 2.5e-08 PF03734: YkuD" amino acids 97 to 229 (133 residues), 71.9 bits, see alignment E=1.3e-23 PF17969: Ldt_C" amino acids 234 to 300 (67 residues), 71.8 bits, see alignment E=9.2e-24

Best Hits

Swiss-Prot: 63% identical to YBIS_ECOLI: Probable L,D-transpeptidase YbiS (ybiS) from Escherichia coli (strain K12)

KEGG orthology group: None (inferred from 100% identity to son:SO_3748)

MetaCyc: 63% identical to L,D-transpeptidase LdtB (Escherichia coli K-12 substr. MG1655)
RXN0-5401

Predicted SEED Role

"LysM domain protein"

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 Q8EAY9 at UniProt or InterPro

Protein Sequence (304 amino acids)

>SO3748 LysM domain protein (NCBI ptt file) (Shewanella oneidensis MR-1)
MSMLRTTALLLTLVFPSLSALATEYPLPSPKSRLVGENLYYTVPEGKHTLEDIAAQFQLG
LSNLLEANPGVDPFLPKPGSKLLIPKQLILPNAPREGIVINVAEMRLYYYPKGKKTVEVL
PIGIGQIGKDTPENWVTSVQRKRANPTWTPTPRIRKEYAARGEILPAVWPAGPDNPMGLY
ALYIGNLYAIHGTNASFGIGLRVSQGCVRLRHDDIEHLFKTVPIGTRVQFVNQPIKATEE
PDGKRYLAVHQPLSRTIAEFESNEPVALSLPKDIAKFIAKADTDSSMIKKLLDERTGVPA
IINQ