Protein Info for GFF3821 in Variovorax sp. SCN45

Annotation: RND efflux system, inner membrane transporter

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

1 100 200 300 400 500 600 700 800 900 1000 1056 signal peptide" amino acids 9 to 11 (3 residues), see Phobius details transmembrane" amino acids 12 to 27 (16 residues), see Phobius details amino acids 340 to 359 (20 residues), see Phobius details amino acids 366 to 388 (23 residues), see Phobius details amino acids 394 to 414 (21 residues), see Phobius details amino acids 438 to 459 (22 residues), see Phobius details amino acids 470 to 495 (26 residues), see Phobius details amino acids 549 to 567 (19 residues), see Phobius details amino acids 875 to 893 (19 residues), see Phobius details amino acids 900 to 920 (21 residues), see Phobius details amino acids 926 to 949 (24 residues), see Phobius details amino acids 975 to 996 (22 residues), see Phobius details amino acids 1005 to 1029 (25 residues), see Phobius details PF00873: ACR_tran" amino acids 1 to 1030 (1030 residues), 1240.3 bits, see alignment E=0 TIGR00915: RND transporter, hydrophobe/amphiphile efflux-1 (HAE1) family" amino acids 1 to 1041 (1041 residues), 1554.6 bits, see alignment E=0 PF03176: MMPL" amino acids 331 to 496 (166 residues), 26.7 bits, see alignment E=4.1e-10 PF02355: SecD_SecF_C" amino acids 873 to 1022 (150 residues), 21.3 bits, see alignment E=2.3e-08

Best Hits

Swiss-Prot: 55% identical to TTGB_PSEPK: Probable efflux pump membrane transporter TtgB (ttgB) from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)

KEGG orthology group: K03296, hydrophobic/amphiphilic exporter-1 (mainly G- bacteria), HAE1 family (inferred from 79% identity to aav:Aave_2111)

Predicted SEED Role

"RND efflux system, inner membrane transporter CmeB" in subsystem Multidrug Resistance Efflux Pumps or Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)

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 (1056 amino acids)

>GFF3821 RND efflux system, inner membrane transporter (Variovorax sp. SCN45)
MAQFFIDRPIFAWVLSIVVMLAGLMAIRTLPLEQYPDIAPPRVSINATYTGASAKTVEDS
VTQVIEQQMKGLDNLLYMQSTSNSSGVARLSLTFDAGTNIDVAQMQVQNKLQQAMSRLPQ
QVQSRGVTVTKGGNDFLMIVSMYSGDGSASAVDVGDYISSNLVDVISRIDGVGEVQTLGT
GYAMRLWLDPDKLRKYALIPSDVSAAITAQNAQVSAGQLGALPAAAGQQLNATITARSKL
QTAEQFENVVLRSTPDGAVVRLKDVARVELGAENLTVRSQLGGRPGAGLGVVLADGANAV
QVAEAVKARIEELKPLFPNQLQTFVSYDTTPFVSASIDEVVKALLEAMLLVVLVMYVFLQ
NMRATLIPAIAVPVVLLGTFGVLSLAGYSINTLTMFGMVLAIGLLVDDAIVVVENVERVM
HEEGLSPKEATRKSMAEITPALVGIALVLSAVFIPMAFFGGSTGVIYRQFSITIVSAMAL
SVFVALTLTPALCATLLKPVHKGEHPVPRRGLLGRVDRFFAAFNRGFDKSANRYEGIVGG
IVRRGKRSLVVYLLIAGVMALLFMRLPTSFLPDEDQAFLQVQVTLPPGASNARLQPVVEQ
VQQYFGKQAEVLSVNVITGQNGDQSSARAFVKLKDWSERTGAGQSAAELARRANKELSTV
RDARIFVLLPPAVRGLGANAGFNFHLKDINGLGHDALVKARDQAIELLGQRPEVANVRSN
NLDDTPEFAVDIDDARAGALSLATSDIDSTLSSAMGGTYINDFLDKGRVKRVYMQGDTDF
RMLPADIDRWSVRNSLGQMVPFPSFSSSRWSYGSPQLQRYNGSPSYEFVGDAAPGVSSGD
AMAAVDAVMKQMPPGIGYEWTGASLQERLSGAQAPLLYAISILFVFLCLAALYESWSVPF
SVILVVPLGIVGALLFTSLRGLSNDVYFQVGLLTTVGLSSKNAILIVEFAKQLQEQGKGV
VEATLQAVRLRLRPILMTSLAFGFGVLPLAIGTGAGAGGRQSIGTAVLGGMVVGTALGIF
FVPLFFALIRGWLAGRRKAKPVQEISSGTTAGQGGH