Protein Info for GFF3531 in Xanthobacter sp. DMC5

Annotation: Ribonuclease D

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 50 100 150 200 250 300 350 382 PF01612: DNA_pol_A_exo1" amino acids 3 to 169 (167 residues), 122.4 bits, see alignment E=1.8e-39 TIGR01388: ribonuclease D" amino acids 4 to 364 (361 residues), 405.6 bits, see alignment E=1.1e-125 PF00570: HRDC" amino acids 212 to 279 (68 residues), 49.8 bits, see alignment E=2.7e-17

Best Hits

Swiss-Prot: 69% identical to RND_NITHX: Ribonuclease D (rnd) from Nitrobacter hamburgensis (strain DSM 10229 / NCIMB 13809 / X14)

KEGG orthology group: K03684, ribonuclease D [EC: 3.1.13.5] (inferred from 92% identity to xau:Xaut_3138)

Predicted SEED Role

"Ribonuclease D (EC 3.1.26.3)" in subsystem Experimental tye or tRNA processing (EC 3.1.26.3)

MetaCyc Pathways

Isozymes

Compare fitness of predicted isozymes for: 3.1.13.5, 3.1.26.3

Use Curated BLAST to search for 3.1.13.5 or 3.1.26.3

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 (382 amino acids)

>GFF3531 Ribonuclease D (Xanthobacter sp. DMC5)
MDPITSTEALAAACERLARHPFVTVDTEFLRESTFWPKLCVVQVASPDEAILIDALSEGL
DLAPFYRLMGNERVMKVFHAGRQDIEIIWHQARLIPHPVFDTQVAAMVLGYGDSISYDQL
VQRTVGHSLDKSSRFTDWSRRPLSQAQITYAIADVTHLRDIYIKLTADLDARGRGEWVGE
EMHVLTSPATYEQHPEQAWERLKSRVRKPRELAVLVEVAAWREREAQTRDLPRGRVIKDE
VIGEIAVQQPQTPERLAELRSLPKGFERSRYGEAVLEAVKRGVARDPKTLPRIERDKPLP
NGASATVELLKVLLRMTAEQNAVAAKVIATTEDLERIAVSDEADVPALKGWRRELFGVHA
LALKAGQLALAVDKGKVVAVQK