Protein Info for Sama_1933 in Shewanella amazonensis SB2B

Annotation: ribonuclease D (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

1 50 100 150 200 250 300 371 PF01612: DNA_pol_A_exo1" amino acids 5 to 171 (167 residues), 144 bits, see alignment E=6.3e-46 TIGR01388: ribonuclease D" amino acids 7 to 369 (363 residues), 380 bits, see alignment E=6.6e-118 PF00570: HRDC" amino acids 214 to 281 (68 residues), 55.2 bits, see alignment E=8.4e-19 PF21293: RNAseD_HRDC_C" amino acids 300 to 362 (63 residues), 77 bits, see alignment E=1.2e-25

Best Hits

Swiss-Prot: 71% identical to RND_SHESA: Ribonuclease D (rnd) from Shewanella sp. (strain ANA-3)

KEGG orthology group: K03684, ribonuclease D [EC: 3.1.13.5] (inferred from 100% identity to saz:Sama_1933)

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: 3.1.26.3

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 A1S6Y2 at UniProt or InterPro

Protein Sequence (371 amino acids)

>Sama_1933 ribonuclease D (RefSeq) (Shewanella amazonensis SB2B)
MLEFHYVKDDEALTALVDQYSQSRLLVLDTEFVRTRTYYAKLGLIQVYDGNTLALIDPLD
IQDLSGFWALLTNPNILKLVHSCSEDLEVFARYGKVQPTPLFDSQIAAALSGMGHGLGYA
KLVEECLGQTLDKGESRTDWIKRPLTDAQLQYAANDVFYLYQLYPQLEQKLKTLGRFDWV
LEEGARLTEGRLQRPEAATAYLKVKNAFQLTPKQLAYLKVLAAWRLERALDRDLALGFVI
KDHALIALAKKPPRSISDLLKINDLSEHEKRIHGKDILKVLQKADVENPPAAIDVIALKP
AYKQAFKNIKAALTEICEREGLPSELFCSKRHIHEYLEYRWQGDAEDTPLLLQGWRGKLA
TDVLQALVLEP