Protein Info for PP_4489 in Pseudomonas putida KT2440

Annotation: sigma-54 dependent transcriptional regulator

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 50 100 150 200 250 300 350 400 450 519 PF01842: ACT" amino acids 2 to 38 (37 residues), 29 bits, see alignment 2.3e-10 PF00989: PAS" amino acids 84 to 134 (51 residues), 25.3 bits, see alignment 3.9e-09 PF00158: Sigma54_activat" amino acids 208 to 374 (167 residues), 201.1 bits, see alignment E=3.1e-63 PF14532: Sigma54_activ_2" amino acids 210 to 379 (170 residues), 60.4 bits, see alignment E=6.9e-20 PF18024: HTH_50" amino acids 466 to 515 (50 residues), 50.7 bits, see alignment 3.5e-17 TIGR04381: TyrR family helix-turn-helix domain" amino acids 469 to 516 (48 residues), 73.2 bits, see alignment 6.6e-25

Best Hits

Swiss-Prot: 43% identical to TYRR_ENTAG: Transcriptional regulatory protein TyrR (tyrR) from Enterobacter agglomerans

KEGG orthology group: K03721, transcriptional regulator of aroF, aroG, tyrA and aromatic amino acid transport (inferred from 100% identity to ppf:Pput_1425)

Predicted SEED Role

"Phenylalanine hydroxylase transcriptional activator PhhR" in subsystem Aromatic amino acid degradation

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 Q88EH4 at UniProt or InterPro

Protein Sequence (519 amino acids)

>PP_4489 sigma-54 dependent transcriptional regulator (Pseudomonas putida KT2440)
MRIKVHCQNRIGILRDILNLLVEYGINVLRGEVGGDHGNAIYLHCPNLINLQFQALRPKF
EAIAGVFGVKRVGLMPSERRHMELNALLGALDFPVLSIDMGGSIVAANRAAAQLLGVRVD
EVPGMPLARYVEDFDLPELVRANKSRINGLRIKVKGDVFLADIAPLQSEHDDSEALAGAV
LTLHRADRIGERIYNVRKQELRGFDSIFQSSRVMAAVVREARRMAPLDAPLLIEGETGTG
KELLARACHLASPRGQSPLMALNCAGLPESMAETELFGYGPGAFEGARAEGKLGLLELTA
GGTLFLDGVGEMSPRLQVKLLRFLQDGCFRRVGSDEEVYLDVRVICATQVDLSELCARGE
FRQDLYHRLNVLSLHIPPLRECMDGLEGLVQHFLDQASRQIGCAMPRLAPAAMDKLGQYH
WPGNVRQLENVLFQAVSLCDGGVVKSEHIRLPDYGVRQPLGEFSLEGDLSQIVGRFEKAV
LESLMGEFPSSRALGKRLGVSHTTIANKLRDYSLNKSAD