Protein Info for HSERO_RS05680 in Herbaspirillum seropedicae SmR1

Annotation: DNA-directed RNA polymerase subunit alpha

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 50 100 150 200 250 293 transmembrane" amino acids 32 to 53 (22 residues), see Phobius details amino acids 59 to 76 (18 residues), see Phobius details amino acids 97 to 123 (27 residues), see Phobius details amino acids 144 to 168 (25 residues), see Phobius details amino acids 219 to 240 (22 residues), see Phobius details amino acids 260 to 282 (23 residues), see Phobius details PF12911: OppC_N" amino acids 28 to 59 (32 residues), 31.8 bits, see alignment 1e-11 PF00528: BPD_transp_1" amino acids 111 to 287 (177 residues), 92.1 bits, see alignment E=3.7e-30

Best Hits

KEGG orthology group: K02034, peptide/nickel transport system permease protein (inferred from 100% identity to hse:Hsero_1132)

Predicted SEED Role

"Dipeptide transport system permease protein dppC"

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

See D8J1M8 at UniProt or InterPro

Protein Sequence (293 amino acids)

>HSERO_RS05680 DNA-directed RNA polymerase subunit alpha (Herbaspirillum seropedicae SmR1)
MKALHDSTGSQAGAPAPAASAPAKRVRRHSTMAWIGMAIVGFWILMAILGPSISPYDATA
IVDTDVFSGMSHKFLLGSDYLGRDMLSRILFGTRATIGLALAATVLASATGTAIALFAAF
SGGWRDAVISRALDALISIPSKMFALMMVATFGSSMLLLVLTAAITYMPGAYRIARSLAV
NVQAMEYVQAARARGEGVWYIMTVEMLPNMIRPVLADFGLRFVYVVLLLSGLSFLSLGVQ
PPDADWGSLVRENISGLGEGALAVIMPALAIASLTIGVNLLIDNLRSKRAAKE