Protein Info for OHPLBJKB_03863 in Escherichia coli HS(pFamp)R (ATCC 700891)

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 813 TIGR02063: ribonuclease R" amino acids 19 to 725 (707 residues), 961.9 bits, see alignment E=2.1e-293 PF08461: HTH_12" amino acids 23 to 83 (61 residues), 46.9 bits, see alignment 5.2e-16 TIGR00358: VacB and RNase II family 3'-5' exoribonucleases" amino acids 67 to 725 (659 residues), 972.1 bits, see alignment E=1.3e-296 PF08206: OB_RNB" amino acids 87 to 144 (58 residues), 78.2 bits, see alignment 7.6e-26 PF17876: CSD2" amino acids 164 to 238 (75 residues), 85.9 bits, see alignment E=4.1e-28 PF00773: RNB" amino acids 260 to 587 (328 residues), 390.6 bits, see alignment E=1.6e-120 PF00575: S1" amino acids 641 to 724 (84 residues), 66.9 bits, see alignment E=4.1e-22

Best Hits

Swiss-Prot: 100% identical to RNR_SHIFL: Ribonuclease R (rnr) from Shigella flexneri

KEGG orthology group: K12573, ribonuclease R [EC: 3.1.-.-] (inferred from 100% identity to ecx:EcHS_A4422)

MetaCyc: 100% 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 (813 amino acids)

>OHPLBJKB_03863 Ribonuclease R (Escherichia coli HS(pFamp)R (ATCC 700891))
MSQDPFQEREAEKYANPIPSREFILEHLTKREKPASRDELAVELHIEGEEQLEGLRRRLR
AMERDGQLVFTRRQCYALPERLDLVKGTVIGHRDGYGFLRVEGRKDDLYLSSEQMKTCIH
GDQVLAQPLGADRKGRREARIVRVLVPKTSQIVGRYFTEAGVGFVVPDDSRLSFDILIPP
DQIMGARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQA
VEQQVAGLKEEVPEEAKAGRVDLRDLPLVTIDGEDARDFDDAVYCEKKRGGGWRLWVAIA
DVSYYVRPPTPLDREARNRGTSVYFPSQVIPMLPEVLSNGLCSLNPQVDRLCMVCEMTVS
SKGRLTGYKFYEAVMSSHARLTYTKVWHILQGDQDLREQYAPLVKHLEELHNLYKVLDKA
REERGGISFESEEAKFIFNAERRIERIEQTQRNDAHKLIEECMILANISAARFVEKAKEP
ALFRIHDKPSTEAITSFRSVLAELGLELPGGNKPEPRDYAELLESVADRPDAEMLQTMLL
RSMKQAIYDPENRGHFGLALQSYAHFTSPIRRYPDLTLHRAIKYLLAKEQGHQGNTTETG
GYHYSMEEMLQLGQHCSMAERRADEATRDVADWLKCDFMLDQVGNVFKGVISSVTGFGFF
VRLDDLFIDGLVHVSSLDNDYYRFDQVGQRLMGESSGQTYRLGDRVEVRVEAVNMDERKI
DFSLISSERAPRNVGKTAREKAKKGDAGKKGGKRRQVGKKVNFEPDSAFRGEKKTKPKAA
KKDARKAKKPSAKTQKIAAATKAKRAAKKKVAE