Protein Info for GFF399 in Variovorax sp. SCN45

Annotation: 3'-to-5' exoribonuclease RNase R

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 773 TIGR02063: ribonuclease R" amino acids 19 to 532 (514 residues), 631.5 bits, see alignment E=1.8e-193 TIGR00358: VacB and RNase II family 3'-5' exoribonucleases" amino acids 20 to 693 (674 residues), 651.9 bits, see alignment E=1.1e-199 PF08206: OB_RNB" amino acids 25 to 82 (58 residues), 76.8 bits, see alignment 1.6e-25 PF17876: CSD2" amino acids 103 to 176 (74 residues), 78 bits, see alignment E=9.4e-26 PF00773: RNB" amino acids 198 to 529 (332 residues), 351.2 bits, see alignment E=1.2e-108 PF00575: S1" amino acids 612 to 690 (79 residues), 36.4 bits, see alignment E=1.1e-12

Best Hits

KEGG orthology group: K12573, ribonuclease R [EC: 3.1.-.-] (inferred from 96% identity to vpe:Varpa_3333)

Predicted SEED Role

"3'-to-5' exoribonuclease RNase R" in subsystem RNA processing and degradation, bacterial

Isozymes

Compare fitness of predicted isozymes for: 3.1.-.-

Use Curated BLAST to search for 3.1.-.-

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

Find the best match in UniProt

Protein Sequence (773 amino acids)

>GFF399 3'-to-5' exoribonuclease RNase R (Variovorax sp. SCN45)
LNFRKEGDHIKNNGTSSGLLDEFEGTVQGHRDGHGFVQRDDGEADIYLPPNEMRAVLHKD
RVKARVVRQDRRGRPEGRVVEIVERSEQPIIGRLLHEGGIWLVAPEDKRYGQDVLIPKGA
TGPAKVGQVVVVQLTEPPALFGQPVGRVKEVLGEIDDPGMEIEIAVRKYGVPHEFSAECL
AEAKALPEKVRPADKKGRVDLTDIPLVTIDGEDARDFDDAVYCEPAKVGRGKGWRLLVAI
ADVSAYVQTGSGIDIDAYDRATSVYFPRRVIPMLPEKLSNGLCSLNPEVERLCMVCDMLV
AADGEIYAYQFYPAVMFSHARFTYTEVAAILGNTRGPEAAKRKDRVKDLLNLADVYKALL
KQRGKRGAVDFETTETQIICDDAGRIEKIVPRTRNEAHRLIEEAMLAANVCSADFIAEGK
HPGLFRVHEGPTPEKKEILRGYLKAMGVGLSITDDPKPGEFQAIAEATKERPDAQQIHTM
LLRSMQQAIYTPINSGHFGLAYEAYTHFTSPIRRYPDLLVHRVIKAILGKTRYQLPMLPT
PGEAHAKLAKRLASRVKAPTNKPQKATVAPSKEVLAWEAAGLHCSANERRADEASRDVEA
WLKCKYMREHLGEEYGGVVTAATTFGIFVTLDAMYVEGLVHITELGGEYFKFDEMRQELR
GERTGIRYAIGTRVRVQVSRVDLDGRKIDFRLVREGEELMARAMKDKGAASSGVPVKASA
KRGTRHKAAEAGGGEPRGERGTSASAGPQSAMQAFKSAVKKAANKMKGRKPRR