Protein Info for GFF1081 in Xanthobacter sp. DMC5

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 61 to 770 (710 residues), 695.3 bits, see alignment E=9.6e-213 TIGR00358: VacB and RNase II family 3'-5' exoribonucleases" amino acids 194 to 758 (565 residues), 494.9 bits, see alignment E=3.4e-152 PF17876: CSD2" amino acids 225 to 295 (71 residues), 39.3 bits, see alignment E=8.2e-14 PF00773: RNB" amino acids 313 to 638 (326 residues), 327.4 bits, see alignment E=1.6e-101 PF00575: S1" amino acids 687 to 757 (71 residues), 33.7 bits, see alignment E=6e-12

Best Hits

KEGG orthology group: K12573, ribonuclease R [EC: 3.1.-.-] (inferred from 86% identity to xau:Xaut_3864)

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

Find the best match in UniProt

Protein Sequence (832 amino acids)

>GFF1081 Ribonuclease R (Xanthobacter sp. DMC5)
LPKRPTKPPTRTHASKDGRAAKPSHAERPARATKSRAARKQAAAAHEAAALAVAPLATGE
MPTKAQVLAFIATQNGEVGKREIARAFGLSAAQKVELKQLLRDLSAEGTVSRERRRLHVP
GALPAEVLADIVSRDGDGELVAVPVEWDSEAQGEAPHILVQVPRRASGPAPGLSDRVLLR
IVEGSIEHAVPHVGRVIKVLEKARKQTMGIFRAAPQGGGGRIIPIDKKQLGRELQVPPGA
EHEAEDGDLVTVELMRQRVFGLPTARVKEKLGSLKSEKAVSLIAIHAHGIPNAFPDVVLK
EAEAAKQITVRGREDWRDLPLVTIDPPDAKDHDDAVHAAADEDGGFIVTVAIADVSAYVR
PGTALDREALIRGNSVYFPDRVVPMLPERISNDLCSLRPDEDRPALAVRLVIGGDGRKRS
HSFHRILMRSAGKLAYAQAQNAIEGRTDDITDPLVEGVLKPLYAAYACVKKARDARQPLD
LDLPERKIILKPDGTVDRVVVPERLDAHRLIEEFMILANVAAAETLEEKKTPLIYRVHDG
PTLAKLSALRDFLKTLDIGLPKTDQVRPSHFNRILEEVKDTDAAPLVNQVILRSQSQAEY
ASENYGHFGLNLRRYAHFTSPIRRYADLIVHRGLVRALGVGKDGLPDDATVESLGEVAAA
ISVTERRAMAAERETVDRLIAHHLADQIGATFNGRITGATKAGLFVALDITGADGFIPAS
TLGQDYYRYDEVRQALVGDRTGEMHRIGDRVEVKLVEAAPVAGALRFELLSEGSYVKGPR
GGGPQRRGAPSGFAGRPGKSLPGRAKPGKSGSGKSGSGKASPGKAKPGGGRR