Protein Info for LRK54_RS00090 in Rhodanobacter denitrificans FW104-10B01

Annotation: outer membrane protein assembly factor BamB

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 50 100 150 200 250 300 350 399 signal peptide" amino acids 1 to 22 (22 residues), see Phobius details TIGR03300: outer membrane assembly lipoprotein YfgL" amino acids 6 to 394 (389 residues), 396.1 bits, see alignment E=6.3e-123 PF13570: PQQ_3" amino acids 45 to 87 (43 residues), 30.6 bits, see alignment 4.9e-11 amino acids 111 to 141 (31 residues), 23 bits, see alignment (E = 1.3e-08) amino acids 142 to 181 (40 residues), 39.5 bits, see alignment 7.6e-14 amino acids 182 to 224 (43 residues), 19 bits, see alignment 2.3e-07 PF13360: PQQ_2" amino acids 45 to 96 (52 residues), 26 bits, see alignment 1e-09 amino acids 113 to 323 (211 residues), 173.3 bits, see alignment E=1e-54 amino acids 307 to 394 (88 residues), 37.6 bits, see alignment E=3e-13 PF01011: PQQ" amino acids 69 to 94 (26 residues), 20.6 bits, see alignment (E = 4.4e-08) amino acids 126 to 159 (34 residues), 30.8 bits, see alignment 2.6e-11 amino acids 164 to 193 (30 residues), 32.2 bits, see alignment (E = 9e-12)

Best Hits

Swiss-Prot: 33% identical to BAMB_SALTY: Outer membrane protein assembly factor BamB (bamB) from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

KEGG orthology group: None (inferred from 40% identity to sml:Smlt2059)

Predicted SEED Role

"Outer membrane protein YfgL, lipoprotein component of the protein assembly complex (forms a complex with YaeT, YfiO, and NlpB)"

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search 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 (399 amino acids)

>LRK54_RS00090 outer membrane protein assembly factor BamB (Rhodanobacter denitrificans FW104-10B01)
MIKRALLIALASLVTLAGCHSFKKENVQPPTPLAKDFKPTLQVTRLWRTSVGDGAGTSGA
RLRPTVVDGVLYAASTNGKLVAIDATSGKSLWSKSSRTHGWFGWGDKKRKDAQYAGGPAV
NGDLLAVGTLDGHVYAVNAKDGSPRWDVEVSSEVLASPVIVGDMVVVRTGDGRVYALDAA
TGQRRWVYDQGTVPLLSLRGNGALLAANGVLFFGSDDGKLVALRQDNGAKLWEQKLASGE
GRTEIDRLNDADGAILLDGSTLYGTAYHGNVAAVDGPSGRPLWTHPFSSFESLAVNDHAV
FGVNDASVVWAFDKNGGADMWKNDALKYRWLSGPAVQGNYVVVGDLEGYVHWLQTGDGAL
AARERLSKKAIRAQPLVVGDIVYVEDVEGRIGAYRLSAH