Protein Info for HMPREF1078_RS05885 in Parabacteroides merdae CL09T00C40

Annotation: ribonuclease 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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 726 TIGR02063: ribonuclease R" amino acids 34 to 726 (693 residues), 810.7 bits, see alignment E=1.2e-247 TIGR00358: VacB and RNase II family 3'-5' exoribonucleases" amino acids 111 to 726 (616 residues), 564.9 bits, see alignment E=2.2e-173 PF08206: OB_RNB" amino acids 113 to 157 (45 residues), 27.9 bits, see alignment 3.7e-10 amino acids 173 to 226 (54 residues), 35.1 bits, see alignment 2.2e-12 PF17876: CSD2" amino acids 177 to 251 (75 residues), 85.3 bits, see alignment E=6.1e-28 PF17849: OB_Dis3" amino acids 178 to 245 (68 residues), 40.7 bits, see alignment E=4.9e-14 PF00773: RNB" amino acids 273 to 600 (328 residues), 385.5 bits, see alignment E=5.6e-119 PF00575: S1" amino acids 641 to 723 (83 residues), 38.5 bits, see alignment E=3.2e-13

Best Hits

KEGG orthology group: K12573, ribonuclease R [EC: 3.1.-.-] (inferred from 80% identity to pdi:BDI_3344)

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 (726 amino acids)

>HMPREF1078_RS05885 ribonuclease R (Parabacteroides merdae CL09T00C40)
MTKNKSEKKSNKPGKKKSSSKGENKRMKKEAMINAIINVFKSSPKEPFNYRQISSMIGVT
NQVQKLQVVDILYDLSSDNFISEIDRGRYRYNDWGTTAVGTFMRRQNGKNSFIPEDGGTP
IFVAERNSAHALNGDKVKIQLHAKRKGADPEGEVIEILESQRRLITGKLQVTRGFAFLIT
EDKTLANDIFIPKDKLKGGKSGDKAIVRITEWPEEAKNPLGEVVDILGTAGDNDAEMNAI
LAEFDLPYKYPANVEKAAEKISDAIPEEEIAKREDFRGVTTFTIDPKDAKDFDDALSARK
LDNGNWEVGVHIADVTYYVKPESLIDREAFSRATSVYLVDRTIPMLPERLCNQICSLRPN
EEKLCFSVIFELNKNAEIQQSHITRTIIKSDRRFTYEEAQAVIETGEGEYKEEILALNGL
AQKLRDRRFKDGAIAFDRYEVKFDIDENGKPLGTYIKESKEANKLIEEFMLLANRTVAEF
IGKSKNKTKKTFVYRIHEQPDPEKLRDFSAFISRFGYKMRTEGTKTDISKGINKLLDSVQ
GKPEENLVETLAIRSMQKAHYTTDNIGHYGLAMDYYTHFTSPIRRYPDMMVHRLLERYLA
GGRSVIKNKYEEYCKHCSEMEMVASNAERSSIKYKQVEFMKDKLGQVFDGVVSGVTEWGL
YVELNDNKCEGLVPIRDLDDDYYEFDDKNYCLLGRRTKRIYRLGDAITVKVAQANLERKQ
LDFALV