Protein Info for BPHYT_RS29300 in Burkholderia phytofirmans PsJN

Annotation: endoribonuclease L-PSP

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

Best Hits

Swiss-Prot: 40% identical to RIDA_PYRFU: 2-iminobutanoate/2-iminopropanoate deaminase (yjgF) from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

KEGG orthology group: None (inferred from 100% identity to bpy:Bphyt_5909)

MetaCyc: 34% identical to enamine/imine deaminase, redox-regulated chaperone (Escherichia coli K-12 substr. MG1655)
Tryptophanase. [EC: 3.5.99.10, 4.1.99.1, 4.1.99.2, 4.3.1.13, 4.3.1.17, 4.3.1.18, 4.3.3.8, 4.4.1.1, 4.4.1.13, 4.4.1.15, 4.4.1.25, 4.4.1.28, 4.4.1.35, 4.5.1.2]; 3.5.99.10,4.3.1.-,4.3.1.19,4.4.1.1,4.4.1.1,4.4.1.2,3.5.99.7,4.4.1.11 [EC: 3.5.99.10, 4.1.99.1, 4.1.99.2, 4.3.1.13, 4.3.1.17, 4.3.1.18, 4.3.3.8, 4.4.1.1, 4.4.1.13, 4.4.1.15, 4.4.1.25, 4.4.1.28, 4.4.1.35, 4.5.1.2, 3.5.99.7, 4.3.1.19, 4.4.1.11, 4.4.1.2]

Predicted SEED Role

"Bona fide RidA/YjgF/TdcF/RutC subgroup"

MetaCyc Pathways

aspartate superpathway (23/25 steps found)
superpathway of branched chain amino acid biosynthesis (17/17 steps found)
superpathway of L-isoleucine biosynthesis I (13/13 steps found)
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I (16/18 steps found)
superpathway of L-threonine metabolism (16/18 steps found)
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II (13/15 steps found)
L-isoleucine biosynthesis I (from threonine) (7/7 steps found)
glycine betaine degradation III (6/7 steps found)
D-serine degradation (3/3 steps found)
L-serine degradation (3/3 steps found)
L-methionine biosynthesis II (5/6 steps found)
L-threonine degradation I (5/6 steps found)
superpathway of S-adenosyl-L-methionine biosynthesis (7/9 steps found)
superpathway of L-methionine biosynthesis (transsulfuration) (7/9 steps found)
glycine betaine degradation I (6/8 steps found)
superpathway of L-homoserine and L-methionine biosynthesis (6/8 steps found)
L-cysteine degradation II (2/3 steps found)
L-methionine degradation II (2/3 steps found)
L-tryptophan degradation II (via pyruvate) (2/3 steps found)
glycine degradation (2/3 steps found)
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) (7/10 steps found)
L-threonine degradation V (1/2 steps found)
L-methionine biosynthesis I (3/5 steps found)
seleno-amino acid biosynthesis (plants) (3/5 steps found)
sulfolactate degradation III (1/3 steps found)
purine nucleobases degradation II (anaerobic) (16/24 steps found)
superpathway of L-cysteine biosynthesis (fungi) (3/6 steps found)
superpathway of sulfolactate degradation (3/6 steps found)
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis (2/5 steps found)
superpathway of L-cysteine biosynthesis (mammalian) (2/5 steps found)
L-mimosine degradation (4/8 steps found)
homocysteine and cysteine interconversion (1/4 steps found)
L-cysteine biosynthesis VI (reverse transsulfuration) (3/7 steps found)
glutathione-mediated detoxification I (3/8 steps found)
hydrogen sulfide biosynthesis II (mammalian) (1/6 steps found)
superpathway of L-methionine salvage and degradation (7/16 steps found)
glutathione-mediated detoxification II (1/9 steps found)
hypoglycin biosynthesis (4/14 steps found)
superpathway of seleno-compound metabolism (6/19 steps found)
cyclosporin A biosynthesis (2/15 steps found)

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 3.5.99.7, 4.3.1.17, 4.3.1.18, 4.3.1.19

Use Curated BLAST to search for 3.5.99.10 or 3.5.99.7 or 4.1.99.1 or 4.1.99.2 or 4.3.1.13 or 4.3.1.17 or 4.3.1.18 or 4.3.1.19 or 4.3.3.8 or 4.4.1.1 or 4.4.1.11 or 4.4.1.13 or 4.4.1.15 or 4.4.1.2 or 4.4.1.25 or 4.4.1.28 or 4.4.1.35 or 4.5.1.2

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 B2TFY8 at UniProt or InterPro

Protein Sequence (134 amino acids)

>BPHYT_RS29300 endoribonuclease L-PSP (Burkholderia phytofirmans PsJN)
MDKRERSEQCPRTINPEGLAPPGGHYSHVSIANGMVFVSGQLPIDPTGRKLTDQPFEAQA
EQVLANLATALAGAGSDVTKLVQVRVYIVDIEYWATFNEIYARWTGAAKPARAVVPVPAL
HFGLKIEVEAVACV