Protein Info for Shewana3_0697 in Shewanella sp. ANA-3

Annotation: RNAse R (RefSeq)

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 809 TIGR02063: ribonuclease R" amino acids 19 to 725 (707 residues), 878.8 bits, see alignment E=3e-268 PF08461: WHD_RNase_R" amino acids 22 to 82 (61 residues), 36.2 bits, see alignment 1.1e-12 TIGR00358: VacB and RNase II family 3'-5' exoribonucleases" amino acids 68 to 723 (656 residues), 815.6 bits, see alignment E=3e-249 PF08206: OB_RNB" amino acids 87 to 143 (57 residues), 71.6 bits, see alignment 8.5e-24 PF17876: CSD2" amino acids 164 to 238 (75 residues), 91.9 bits, see alignment E=5.3e-30 PF00773: RNB" amino acids 260 to 586 (327 residues), 365.1 bits, see alignment E=8.9e-113 PF00575: S1" amino acids 642 to 722 (81 residues), 50.7 bits, see alignment E=4.8e-17

Best Hits

Swiss-Prot: 59% identical to RNR_VIBCH: Ribonuclease R (rnr) from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)

KEGG orthology group: K12573, ribonuclease R [EC: 3.1.-.-] (inferred from 100% identity to shn:Shewana3_0697)

MetaCyc: 60% 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)

Compare to protein 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 A0KT16 at UniProt or InterPro

Protein Sequence (809 amino acids)

>Shewana3_0697 RNAse R (RefSeq) (Shewanella sp. ANA-3)
MIKDPHFEREQDKYENPIPSREYIIEYLRSQKSPITRDSIAVALQIHDEEQLEALRRRLR
AMERDGELVFTRGQSYGLPEKMDLISGTVLGHREGYGFFKPDEGGDDLFISNRDMLMYFH
GDKVLAQKAGMDRKGRREARIVRLIQPRSAAIVGRFHVDSGMAFVIADDKRITQEILIAT
EDRNGARQGDVVVVELTRRPGRFVKAAGKVTEVLGKQMAPGMEIEIALRNYDLPHTWSAV
IEKKLRRIPDEVTEADKVGRVDLRDLPLVTIDGEDARDFDDAVYAEVKPSGGWRLWVAIA
DVSYYVRTDSALDTEARARGNSVYFPSQVIPMLPEKISNGLCSLNPHVDRLCMVAEMTIS
ARGKLSGYKFYPAVMHSHARFTYTQVAAMLEGGPIAPEHEALFPHLQCLQSLYLALDEQR
AERGAIAFETLETQFIFNDQRKIDKIVPRARNQAHKIIEECMILANVSAAKFVKKHKGEI
LYRVHESPSEQKLANFKEFLAERGLSMGGGLEPTPADYQNVMLQIADRPDAELIQVMLLR
SMRQAIYTPDNEGHFGLALEEYAHFTSPIRRYPDLVLHRVIRYLLAKEKGEANEKWTSDG
GYHYQLDELDLLGEECSNTERRADEATRDVSDWLKCEFMQDHVGDTFEAVIASVTNFGLF
VRLNDLFIDGLVHISSLGSDYYQFDPMRQRLIGEHTGQIYQVGDPVTVKVAAVNLDDRQI
DLVMLGDSGKGGRRKSAPSREKPMTARERVNREGAKMAKAAKSTGAKSKAGSDKAGASKS
KSKAGAKPKKSVKNSAKKPKAAKRSTRKK