Protein Info for Sama_3067 in Shewanella amazonensis SB2B

Annotation: exoribonuclease II (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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 808 TIGR02063: ribonuclease R" amino acids 19 to 724 (706 residues), 875.2 bits, see alignment E=3.5e-267 PF08461: HTH_12" amino acids 23 to 83 (61 residues), 34.8 bits, see alignment 3.2e-12 TIGR00358: VacB and RNase II family 3'-5' exoribonucleases" amino acids 68 to 723 (656 residues), 808.7 bits, see alignment E=3.6e-247 PF08206: OB_RNB" amino acids 87 to 143 (57 residues), 68.9 bits, see alignment 5.8e-23 PF17876: CSD2" amino acids 164 to 238 (75 residues), 89.2 bits, see alignment E=3.7e-29 PF00773: RNB" amino acids 260 to 586 (327 residues), 377.3 bits, see alignment E=1.8e-116 PF00575: S1" amino acids 642 to 724 (83 residues), 52.9 bits, see alignment E=1e-17

Best Hits

Swiss-Prot: 61% 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 saz:Sama_3067)

MetaCyc: 57% 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 A1SA63 at UniProt or InterPro

Protein Sequence (808 amino acids)

>Sama_3067 exoribonuclease II (RefSeq) (Shewanella amazonensis SB2B)
MINDPHFEREQEKYDNPIPSREFILEYLRSQTSPQPRDSIAEALKIHDEERLEALRRRLR
AMERDGELVFTRGQCYGLPERMDLMSGTVLGHKDGFGFFRPDNGGDDLFINERDMQLYFH
GDKVLAQKAGVDRRGRRDARIVRLLSERSAALVGRFYVDAGMAFVVADDKRIPHEILIAN
EDKNGARHGDVVVIELTRRPGRYVRAGGKVTEVLGKQMAPGMEIEIALRNYDLPHQWSAV
IEKKLRRIPDYVTDEDKEGRVDLRELPLVTIDGEDARDFDDAVYAERKRGGGWRLWVAIA
DVSHYVRTDSALDKEARARGNSVYFPSQVIPMLPEKLSNGLCSLNPGVDRLCMVAEMTIS
AKGGLSGYKFYPAVMHSHARFTYTQVAAMLEGGEVKDEHKALFPHLKVLQELYLCLDEQR
AERGAIAFETLETQFIFNEQRKIDRIVPRARNQAHKIIEECMILANVAAAKFVIKHKGHV
LYRVHEKPSEQKLTQFKDFLAERGLSMTGGLEPEPADYLALMAQLAGRPDAELIQVMLLR
SMRQAVYTPDNEGHFGLALEAYSHFTSPIRRYPDLVLHRVIRYLLAKERGEASEKWTADG
GYHYQLEELDLLGEECSNTERRADEATRDVSDWLKCEFMQDHVGDSFSGVIASVTSFGLF
VRLDELFIDGLVHISSLGSDYFQYDPQRQRLIGENSGQIYQIGDPVAVKVASVNLDDRQI
DLQMEGERPGRKKAGKKPTTARDRANLEGARTGNGKPGKGGSVRSQLAGGKLGGSETKKR
DAKAKDGKKPKKAAEAKPKAAKRVKRKK