Protein Info for SO3935 in Shewanella oneidensis MR-1

Name: vacB
Annotation: ribonuclease R (NCBI ptt file)

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 808 TIGR02063: ribonuclease R" amino acids 19 to 725 (707 residues), 879.3 bits, see alignment E=2e-268 PF08461: HTH_12" amino acids 22 to 82 (61 residues), 37.2 bits, see alignment 5.6e-13 TIGR00358: VacB and RNase II family 3'-5' exoribonucleases" amino acids 68 to 724 (657 residues), 814.8 bits, see alignment E=5.1e-249 PF08206: OB_RNB" amino acids 87 to 143 (57 residues), 73.1 bits, see alignment 3e-24 PF17876: CSD2" amino acids 164 to 238 (75 residues), 90.8 bits, see alignment E=1.2e-29 PF00773: RNB" amino acids 260 to 586 (327 residues), 371.5 bits, see alignment E=1e-114 PF00575: S1" amino acids 642 to 722 (81 residues), 53.9 bits, see alignment E=4.7e-18

Best Hits

Swiss-Prot: 57% 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 son:SO_3935)

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)

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 Q8EAG7 at UniProt or InterPro

Protein Sequence (808 amino acids)

>SO3935 ribonuclease R (NCBI ptt file) (Shewanella oneidensis MR-1)
MIKDPHFEREQDKYENPIPSREYIIEYLRSQKSPITRDSIAAALQIHDEEQLEALRRRLR
AMERDGELVFTRGQSYGLPEKMDLISGTVLGHKEGYGFFKPDEGGDDLFISNRDMLMYFH
GDKVLAQKVGMDRKGRREARIVRLIQPRSAAIVGRFHVDSGMAFVIADDKRITQEILIAS
EDRNGARQGDVVVVELTRRPGRFVKAAGKVTEVLGKQMAPGMEIEIALRNYDLPHTWSAA
IEKKLRRIPDEVTESDKVGRVDLRSLPLVTIDGEDARDFDDAVYAEVKPSGGWRLWVAIA
DVSYYVRTDSALDTEARARGNSVYFPSQVIPMLPEKISNGLCSLNPHVDRLCMVAEMTIS
ARGKLSGYKFYPAVMHSHARFTYTQVAAMLEGGPIAPEHEALFVHLQCLQSLYLALDEQR
AERGAIAFETIETQFIFNDQRKIDKIVPRARNQAHKIIEECMILANVSAAKFVKKHKGEI
LYRVHESPSEQKLANFKEFLAERGLSMGGGLEPTPADYQNVMLQIADRPDAELIQVMLLR
SMRQAIYTPDNEGHFGLALEEYAHFTSPIRRYPDLVLHRVIRYLLAKEKGEANEKWTPDG
GYHYQLDELDQLGEECSTTERRADEATRDVSDWLKCEFMQDHVGDTFEAVIASVTNFGLF
VRLNDLFIDGLVHISSLGSDYYQFDPMRQRLIGEHTGQVYQVGDPVTVKVAAVNLDDRQI
DLMMLGDSGKGGRRKAAPSRDKPMTARERVNREGAKMAKTAKSSGAKSKAGSGKAASKSK
SKAGTKPKKSVKDTAKKPKAAKRSTRKK