Protein Info for PP_4880 in Pseudomonas putida KT2440

Annotation: exoribonuclease 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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 857 TIGR02063: ribonuclease R" amino acids 23 to 745 (723 residues), 877.1 bits, see alignment E=9.1e-268 PF08461: HTH_12" amino acids 27 to 81 (55 residues), 31.8 bits, see alignment 2.7e-11 TIGR00358: VacB and RNase II family 3'-5' exoribonucleases" amino acids 78 to 745 (668 residues), 756.6 bits, see alignment E=2.2e-231 PF08206: OB_RNB" amino acids 91 to 148 (58 residues), 75.5 bits, see alignment 5.1e-25 PF17876: CSD2" amino acids 168 to 242 (75 residues), 83.2 bits, see alignment E=2.9e-27 PF00773: RNB" amino acids 264 to 601 (338 residues), 380.7 bits, see alignment E=1.6e-117 PF00575: S1" amino acids 661 to 745 (85 residues), 49.5 bits, see alignment E=1.1e-16

Best Hits

KEGG orthology group: K12573, ribonuclease R [EC: 3.1.-.-] (inferred from 100% identity to ppf:Pput_4760)

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

See Q88DE6 at UniProt or InterPro

Protein Sequence (857 amino acids)

>PP_4880 exoribonuclease R (Pseudomonas putida KT2440)
MADWQSLDPEAAREAEKYDNPIPSRELILQRLADRGEPAAREELAKEFGLYEEDQIEALR
RRLRAMERDGQLIYTRRGTYAPVDKLDLICGRVSGHRDGFGFLIPDDGSEDLFLSPSQMR
LVFDGDRGLARVSGVDRRGRREGVLVEVISRAHESVVGRYFEEGGIGYVTPDNPKIQQEV
LVTAGRNGGAKIGQFVEIKITHWPTPRFQPQGDVVEVIGNYMAPGMEIDVALRSYDIPHV
WPNDVVKEARKFRSEVEEKDKEKRVDLRHLPFVTIDGEDARDFDDAVYCEPLGKLRLFSG
GWRLYVAIADVSSYVRLGSALDVEAQQRGNSVYFPERVVPMLPEELSNGLCSLNPHVDRL
AMVCEMTMNKAGQMVDYQFYEGVIHSHARLTYNKVSSMLEHSRTREGKALREEYKEVVPD
LKNLYNLYKVLVEARHTRGAIDFETQETRIIFGEERKIAEIRPTVRNDAHKLIEECMLAA
NVATAEFLQKHGVPALYRVHDGPPPERLEKLRAFLGELGLSLHKGKDPSPKDYQALLASI
AGRPDFHLIQTVMLRSLSQAVYSTENNGHFGLNYEAYTHFTSPIRRYPDLLVHRAIRSII
RSKVDTPHVKRAGAMSIPKARIYPYDENTLEQLGEQCSMTERRADEATRDVVNWLKCEFM
KDRVGETFPGVITAVTGFGLFVELTDIYVEGLVHVSALPGDYYHFDPVHHRLAGERTGRS
FRLGDTIEVKVMRVDLDERKIDFEVSEKTLAAPIGRKQRGAAPVAEKAEQQPATEAKATP
KPRSRKSEASEAYFPKDAVQRNAEVRKSREMKKALMTDARSSAGSKSEKGGKPSGKPTKH
RKGPPKSGAPRKNKSNS