Protein Info for SMc00622 in Sinorhizobium meliloti 1021

Annotation: ribonuclease D protein

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 50 100 150 200 250 300 350 383 PF01612: DNA_pol_A_exo1" amino acids 1 to 168 (168 residues), 132.5 bits, see alignment E=1.4e-42 TIGR01388: ribonuclease D" amino acids 1 to 365 (365 residues), 456 bits, see alignment E=5.5e-141 PF00570: HRDC" amino acids 209 to 263 (55 residues), 48.3 bits, see alignment 7.8e-17

Best Hits

Swiss-Prot: 56% 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 100% identity to smk:Sinme_0987)

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)

Search 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 Q92QV7 at UniProt or InterPro

Protein Sequence (383 amino acids)

>SMc00622 ribonuclease D protein (Sinorhizobium meliloti 1021)
MIQTTADLEAACRELARSSYITIDTEFLRETTFWPVLCLIQMASPEMAVIVDPMAPGIDL
APFFALMSNPDVVKVFHAARQDIEIIHHLGNLIPHPIFDTQVAAMVCGFGDSVSYDQLVN
RIKNEQIDKSSRFTDWSRRPLTDKQLDYALADVTHLRDIYQYLTKELDREGRSSWLAEEM
AILESRETYDLHPDNAWQRLKMRVKKPIELAVLQKVAAWREREARARNVPRGRIIKDDAI
YEIAQQQPKDAEALGRLRTIPKGWERSSAGTALIEAVGEALAIPRGELPRLPRQNHAPEG
AAAASELLKVLLKLISEKEGVAAKIIANSDDLDRIAAEGEGADVAALKGWRRELFGMTAL
KLINGEVALRFVDKKVEAMEIGG