Protein Info for PGA1_c13290 in Phaeobacter inhibens DSM 17395

Annotation: putative 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 50 100 150 200 250 300 350 385 PF01612: DNA_pol_A_exo1" amino acids 3 to 173 (171 residues), 133 bits, see alignment E=1e-42 TIGR01388: ribonuclease D" amino acids 5 to 367 (363 residues), 375.3 bits, see alignment E=1.8e-116 PF00570: HRDC" amino acids 216 to 268 (53 residues), 40.3 bits, see alignment 2.5e-14

Best Hits

Swiss-Prot: 69% identical to RND_JANSC: Ribonuclease D (rnd) from Jannaschia sp. (strain CCS1)

KEGG orthology group: K03684, ribonuclease D [EC: 3.1.13.5] (inferred from 84% identity to sit:TM1040_1474)

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

See I7DZX5 at UniProt or InterPro

Protein Sequence (385 amino acids)

>PGA1_c13290 putative ribonuclease D (Phaeobacter inhibens DSM 17395)
MKTLTSTEDLQAFCEAAAQHDYVTVDTEFLRERTYYSKLCLVQLAYPGAGDENAVLVDPL
ADGLSLEPLYDLFRNETVVKVFHAARQDLEIFWVDAQVFPKPLFDTQVAAMVCGFGEQVG
YETLVRKIVKQGLDKTSRFTDWSRRPLSDAQKTYALADVTHLRQIYEYLAAELKRTGRAR
WVEEELQVLTDPATYDVDPQEAWRRVKTRTNSGKFLAVVRELAAFRETYAKTNNVPRNRV
FKDDALVELASTKPKNASDLGNSRLLLREARKGAIAEGILQAVARGVDCPAGSQPQPDRS
REKLQVNPALADLLRVLLKAKTEASGVAAKLIAPSSDLDAIAAGQRNVPALKGWRLEVFG
ADALRLCNGEIALAAKGQDVKVVTL