Protein Info for SO3660 in Shewanella oneidensis MR-1

Annotation: sigma-54 dependent transcriptional regulator/sensory box protein (NCBI ptt file)

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 50 100 150 200 250 300 350 400 450 488 PF00989: PAS" amino acids 20 to 133 (114 residues), 46.4 bits, see alignment E=1.7e-15 TIGR00229: PAS domain S-box protein" amino acids 22 to 143 (122 residues), 67.7 bits, see alignment E=5.4e-23 PF08448: PAS_4" amino acids 23 to 137 (115 residues), 27.8 bits, see alignment E=1.1e-09 PF13426: PAS_9" amino acids 34 to 134 (101 residues), 46.8 bits, see alignment E=1.4e-15 PF00158: Sigma54_activat" amino acids 178 to 344 (167 residues), 238.2 bits, see alignment E=1.8e-74 PF14532: Sigma54_activ_2" amino acids 179 to 348 (170 residues), 71.6 bits, see alignment E=3.8e-23 PF01078: Mg_chelatase" amino acids 190 to 293 (104 residues), 25.4 bits, see alignment E=4e-09 PF07728: AAA_5" amino acids 201 to 318 (118 residues), 28.2 bits, see alignment E=7.5e-10 PF25601: AAA_lid_14" amino acids 349 to 431 (83 residues), 77.5 bits, see alignment E=2.7e-25 PF02954: HTH_8" amino acids 434 to 478 (45 residues), 29.7 bits, see alignment 2e-10

Best Hits

KEGG orthology group: None (inferred from 100% identity to son:SO_3660)

Predicted SEED Role

"Formate hydrogenlyase transcriptional activator" in subsystem Formate hydrogenase

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

See Q8EB72 at UniProt or InterPro

Protein Sequence (488 amino acids)

>SO3660 sigma-54 dependent transcriptional regulator/sensory box protein (NCBI ptt file) (Shewanella oneidensis MR-1)
MATKIPATMPLDKHFLPENQLLLNAVGEGIYGFDLNGNAVFINPAAERMTGWKNEELLGK
NIHNCHHHSHADGSHYPQEDCPIYNTLKDGIAREITHDVFWRKDGSSFPVYYSSTPVYRD
NKLIGVVAIFRDISIQKQTEQSLRHALAQVQALSEQLASENHYLQAELADKTGDVDISGG
SAVIRHMIQQLHMVANTDSTVLICGENGTGKELVARNLHQLSRRKDKPMISVNCAAFSAS
LLESELFGHEKGAFTGATSQRKGRFELAHQGTLFLDEVAELSLEAQSKLLRVIQEQSFER
LGGSETIKVDIRLVAASHHDLLKRVEQGLFRMDLYYRLNVFPIQVPPLRARLGDMPELVS
HILHTLNRKLGKKIRGVSQKGLKKLMTYSWPGNVRELQNILEREAILSQTDILHIHAMPT
HHLQTQTAASPLQTLAEAEAQHIEQTLKQLNWRISGANGAANVLGVPPSTLRSRMKKLGI
TRQITRAC