Protein Info for GFF2866 in Sphingobium sp. HT1-2

Annotation: Protocatechuate 4,5-dioxygenase beta chain (EC 1.13.11.8)

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 PCYB_SPHSK: Protocatechuate 4,5-dioxygenase beta chain (ligB) from Sphingobium sp. (strain NBRC 103272 / SYK-6)

KEGG orthology group: K04101, protocatechuate 4,5-dioxygenase, beta chain [EC: 1.13.11.8] (inferred from 81% identity to sch:Sphch_3899)

MetaCyc: 68% identical to protocatechuate 4,5-dioxygenase beta chain (Sphingomonas sp. SYK6)
Protocatechuate 4,5-dioxygenase. [EC: 1.13.11.8]; 1.13.11.- [EC: 1.13.11.8]; RXN-10889 [EC: 1.13.11.8]

Predicted SEED Role

"Protocatechuate 4,5-dioxygenase beta chain (EC 1.13.11.8)" in subsystem Central meta-cleavage pathway of aromatic compound degradation (EC 1.13.11.8)

MetaCyc Pathways

protocatechuate degradation I (meta-cleavage pathway) (8/8 steps found)
superpathway of vanillin and vanillate degradation (9/10 steps found)
methylgallate degradation (6/6 steps found)
3,4-dichlorobenzoate degradation (3/4 steps found)
syringate degradation (8/12 steps found)
3-chlorobenzoate degradation II (via protocatechuate) (3/6 steps found)

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 1.13.11.8

Use Curated BLAST to search for 1.13.11.8

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

Find the best match in UniProt

Protein Sequence (282 amino acids)

>GFF2866 Protocatechuate 4,5-dioxygenase beta chain (EC 1.13.11.8) (Sphingobium sp. HT1-2)
MARITAGVATSHVPAIGAAMDLKKTAEPYWQPLFAGYDWSRQWIAQEKPDVVILVYNDHA
SAFDMKIIPTFAIGCGERYKPADEGWGPRPVPDVIGEPDLAWHIAQSLILDEFDMTIINE
MDVDHGLTVPLSLMFGQPDAWPCRVIPVAVNVVTYPPPSGNRCWRLGEAIARAVESFPED
LNVQIWGTGGMSHQLQGPRAGLINAEWDNRFLDLMSQSDDGEALRAIEHIEYLRETGSEG
IEMVMWLIMRGALGDKVQPLHRHYHVPASNTAVGHLVLEPTD