Protein Info for Shew_3500 in Shewanella loihica PV-4

Annotation: putative endoribonuclease L-PSP (RefSeq)

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: 68% identical to YVN1_AZOVI: RutC family protein in vnfA 5'region from Azotobacter vinelandii

KEGG orthology group: K07567, TdcF protein (inferred from 100% identity to slo:Shew_3500)

MetaCyc: 44% 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

No annotation

MetaCyc Pathways

aspartate superpathway (24/25 steps found)
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I (18/18 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 S-adenosyl-L-methionine biosynthesis (9/9 steps found)
superpathway of L-methionine biosynthesis (transsulfuration) (9/9 steps found)
superpathway of L-homoserine and L-methionine biosynthesis (8/8 steps found)
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II (13/15 steps found)
superpathway of L-threonine metabolism (15/18 steps found)
L-isoleucine biosynthesis I (from threonine) (7/7 steps found)
L-threonine degradation I (6/6 steps found)
L-methionine biosynthesis I (5/5 steps found)
L-methionine degradation II (3/3 steps found)
L-serine degradation (3/3 steps found)
glycine degradation (3/3 steps found)
L-methionine biosynthesis II (5/6 steps found)
D-serine degradation (2/3 steps found)
L-cysteine degradation II (2/3 steps found)
L-tryptophan degradation II (via pyruvate) (2/3 steps found)
seleno-amino acid detoxification and volatilization III (2/3 steps found)
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) (7/10 steps found)
L-threonine degradation V (1/2 steps found)
dimethyl sulfide biosynthesis from methionine (1/2 steps found)
seleno-amino acid detoxification and volatilization I (1/2 steps found)
seleno-amino acid biosynthesis (plants) (3/5 steps found)
homocysteine and cysteine interconversion (2/4 steps found)
L-cysteine biosynthesis VI (reverse transsulfuration) (4/7 steps found)
glycine betaine degradation III (4/7 steps found)
sulfolactate degradation III (1/3 steps found)
superpathway of L-cysteine biosynthesis (fungi) (3/6 steps found)
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis (2/5 steps found)
L-mimosine degradation (4/8 steps found)
glycine betaine degradation I (4/8 steps found)
superpathway of sulfolactate degradation (2/6 steps found)
superpathway of L-cysteine biosynthesis (mammalian) (1/5 steps found)
glutathione-mediated detoxification I (3/8 steps found)
hydrogen sulfide biosynthesis II (mammalian) (1/6 steps found)
glutathione-mediated detoxification II (1/9 steps found)
superpathway of seleno-compound metabolism (8/19 steps found)
hypoglycin biosynthesis (4/14 steps found)
purine nucleobases degradation II (anaerobic) (11/24 steps found)
superpathway of L-methionine salvage and degradation (5/16 steps found)
cyclosporin A biosynthesis (2/15 steps found)

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 4.3.1.17, 4.3.1.19, 4.4.1.11

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)

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 A3QIR8 at UniProt or InterPro

Protein Sequence (127 amino acids)

>Shew_3500 putative endoribonuclease L-PSP (RefSeq) (Shewanella loihica PV-4)
MAEKIIIATDKAPQAIGTYSQAVKVGSTVYLSGQIPLNPETMQMVSDEFEAQVVQVFDNL
TAVCEAAGGSLKDIVKLNIFMTDLANFATVNEIMGRYFEQPYPARAAIGVKQLPKDSLVE
MDGVMEL