Protein Info for EX31_RS08785 in Rahnella sp. WP5

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 832 TIGR02063: ribonuclease R" amino acids 19 to 727 (709 residues), 913 bits, see alignment E=1.3e-278 PF08461: HTH_12" amino acids 23 to 85 (63 residues), 55.9 bits, see alignment 8.1e-19 TIGR00358: VacB and RNase II family 3'-5' exoribonucleases" amino acids 67 to 727 (661 residues), 886.8 bits, see alignment E=8.2e-271 PF08206: OB_RNB" amino acids 87 to 145 (59 residues), 77.1 bits, see alignment 1.6e-25 PF17876: CSD2" amino acids 165 to 239 (75 residues), 87.4 bits, see alignment E=1.4e-28 PF00773: RNB" amino acids 261 to 588 (328 residues), 377.2 bits, see alignment E=1.9e-116 PF00575: S1" amino acids 644 to 725 (82 residues), 52.2 bits, see alignment E=1.6e-17

Best Hits

Swiss-Prot: 78% identical to RNR_ECOLI: Ribonuclease R (rnr) from Escherichia coli (strain K12)

KEGG orthology group: K12573, ribonuclease R [EC: 3.1.-.-] (inferred from 79% identity to eca:ECA3622)

MetaCyc: 78% identical to RNase R (Escherichia coli K-12 substr. MG1655)
3.1.13.-

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 (832 amino acids)

>EX31_RS08785 ribonuclease R (Rahnella sp. WP5)
MSQDPFLEREAEKYESPIPSREFILEHLAKRETPASREEIGNELNLSGEEALEALRRRLR
AMERDGQLVFTRRQCYALPERLDLLKGTVIGHRDGYGFLRLEGVKKDDVYLSAEQMKMCI
HGDVVLAQPVGTDRKGRREARIVRVLVPKMSQIVGRYFTDAGAGFVVPDDSRLSFDILIP
ADAINGARMGYMVVVELTQRPTRRTKAVGKIVEVLGDKMGTSMAVDIALRTHEIPHVWPP
QVLKQVEDLSEQVPEEAKKGRVDLRSLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAI
ADVSYYVRHGTALDDEARSRATSVYFPSQVVPMLPEVLSNGLCSLNPQVDRLCMVCEMTI
SAQGKLTSSKFYEAVMSSHARLTYNKVWRIIEGDPELREQYSPLVKHLLELHTMYKVLDQ
ARAERGGIAFETEEAKFIFNAERRIERVEPTVRNDAHKLIEECMIMANIAAARFVEKHNE
PALFRVHDRPSDDHISALKSVLGELGLVMGGGMKPEPKDYAQIMDELADRPDREMLQTML
LRSMKQAIYDPENRGHFGLALPSYGHFTSPIRRYPDLALHRAIKYLLAKEHGTLKDRWTP
TGGWHSDYEDMLQLGEHCSMAERRADEATRNVADWLKCDFMQDHVGEVFTGIIASVTGFG
FFVRLNDLFIDGLVHVSSLDNDYYRYDNIGQRLVGESSGAVYRLGDTVEIRVEAVHMDER
KIDFALVSSTRKARGEGKTARDRAKKGGERTMRSAAPANAGRRRTAKKNVNFEPDSAFRK
DDAKPAKPKKEKAVSAVGKDGKPKKAKKPSDKTAKIAAATRAKRAKKKQSDS