Protein Info for GFF436 in Variovorax sp. SCN45

Annotation: LrgA-associated membrane protein LrgB

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 50 100 150 200 243 transmembrane" amino acids 14 to 36 (23 residues), see Phobius details amino acids 45 to 64 (20 residues), see Phobius details amino acids 76 to 94 (19 residues), see Phobius details amino acids 103 to 128 (26 residues), see Phobius details amino acids 160 to 183 (24 residues), see Phobius details amino acids 191 to 209 (19 residues), see Phobius details amino acids 216 to 238 (23 residues), see Phobius details PF04172: LrgB" amino acids 26 to 239 (214 residues), 267.9 bits, see alignment E=2.8e-84

Best Hits

Swiss-Prot: 43% identical to YOHK_SHIFL: Inner membrane protein YohK (yohK) from Shigella flexneri

KEGG orthology group: None (inferred from 93% identity to vpe:Varpa_3365)

Predicted SEED Role

"LrgA-associated membrane protein LrgB" in subsystem Murein hydrolase regulation and cell death

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 (243 amino acids)

>GFF436 LrgA-associated membrane protein LrgB (Variovorax sp. SCN45)
MMSAPARLSEIWVFLAQSPLLWLSLTLLAYLGALWLHTRSGRNPVVNPVLISVIVIVSVL
LLTRTPYDTYFEGAKFVHFLIGPATVALAVPLYGQVGRLRRLWLPIGVALLVGSVAAIVS
AIGIAWVLGGSHELMMSLAPKSATMPIAMGVAEKIGGLPSLAAVAAAIAGISGAIMATGL
LNLLRIREPAVRGFAVGMAAHGIGTARAIQVNETAGAFSALAMGLNGIATALLVPLIVKL
MGA