Protein Info for GFF294 in Variovorax sp. SCN45

Annotation: Lipid A export permease/ATP-binding protein MsbA

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 50 100 150 200 250 300 350 400 450 500 555 transmembrane" amino acids 29 to 50 (22 residues), see Phobius details amino acids 100 to 149 (50 residues), see Phobius details amino acids 216 to 237 (22 residues), see Phobius details amino acids 243 to 263 (21 residues), see Phobius details TIGR02203: lipid A export permease/ATP-binding protein MsbA" amino acids 2 to 544 (543 residues), 666.2 bits, see alignment E=1.9e-204 PF00664: ABC_membrane" amino acids 2 to 262 (261 residues), 120.6 bits, see alignment E=1.6e-38 PF00005: ABC_tran" amino acids 325 to 473 (149 residues), 121.2 bits, see alignment E=7.4e-39 PF09818: ABC_ATPase" amino acids 417 to 517 (101 residues), 27 bits, see alignment E=3.4e-10

Best Hits

Swiss-Prot: 59% identical to MSBA_POLSJ: Lipid A export ATP-binding/permease protein MsbA (msbA) from Polaromonas sp. (strain JS666 / ATCC BAA-500)

KEGG orthology group: K11085, ATP-binding cassette, subfamily B, bacterial MsbA [EC: 3.6.3.-] (inferred from 95% identity to vpe:Varpa_2716)

MetaCyc: 37% identical to ATP-binding lipopolysaccharide transport protein (Escherichia coli K-12 substr. MG1655)
TRANS-RXN-236 [EC: 7.5.2.6]; 7.5.2.6 [EC: 7.5.2.6]

Predicted SEED Role

"Lipid A export ATP-binding/permease protein MsbA" in subsystem ZZ gjo need homes

Isozymes

Compare fitness of predicted isozymes for: 3.6.3.-

Use Curated BLAST to search for 3.6.3.- or 7.5.2.6

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 (555 amino acids)

>GFF294 Lipid A export permease/ATP-binding protein MsbA (Variovorax sp. SCN45)
MLAAITEPLMAALLKPLLDRGFTRGEMPLWFVPAAVLLLFAVRGIAQFISQYALSRIANE
GMQKLRRVMFERLLGAELALFTRQSASALSNTVVYEVQTGAMLLVQALLGLSRDGFTLIA
LLGYLVYLNWKLTLIVAFLVPSISWIMKVFSKRLYRLTQQGQQATDELAYVVEENVLAHR
VVRLHGAEGAQGRRFEQLSQRLNRLAVKSTIAQAATTPLTQMMASLALSVVVMIALWQSG
KQGFTVGGFVAYITAMLMLIAPIRRLAEVAGPITRGLAALERGLVLIDEVAPESQGTFRI
EHAEGRIELRNVQVSYRGDDEQRALDGVNLTIEPGQVVAFVGPSGSGKTTLVNLLPRFVQ
PSSGQVLLDGHDTSEWELKSLRAQFAMVSQDVVMLNETLAANVALGSEIDRERVLQCIDA
ANLSSHVENLPQGIDTVLGHNATQLSGGQRQRLAIARALYKNAPVLLLDEATSALDTESE
RLVQDALQRLMQNRTTLIVAHRLSTIQHADRIIVMEQGRIAEQGSHEQLMQLDGLYARLQ
TLAVRSAPPGQDPTL