Protein Info for GFF1235 in Xanthobacter sp. DMC5

Annotation: Ribonuclease J

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 50 100 150 200 250 300 350 400 450 500 556 PF00753: Lactamase_B" amino acids 34 to 166 (133 residues), 34.6 bits, see alignment E=4.8e-12 PF12706: Lactamase_B_2" amino acids 63 to 169 (107 residues), 35.3 bits, see alignment E=2.3e-12 PF22505: RNase_J_b_CASP" amino acids 227 to 351 (125 residues), 128.6 bits, see alignment E=3e-41 PF07521: RMMBL" amino acids 356 to 410 (55 residues), 32.1 bits, see alignment 2.3e-11 PF17770: RNase_J_C" amino acids 457 to 556 (100 residues), 42.5 bits, see alignment E=2.9e-14

Best Hits

Swiss-Prot: 54% identical to RNJ_SINM2: Ribonuclease J (rnj) from Sinorhizobium meliloti (strain Sm2011 / Rm2011 / 2011)

KEGG orthology group: K07021, (no description) (inferred from 89% identity to xau:Xaut_4618)

Predicted SEED Role

"Metallo-beta-lactamase family protein, RNA-specific" in subsystem Bacterial RNA-metabolizing Zn-dependent hydrolases

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 (556 amino acids)

>GFF1235 Ribonuclease J (Xanthobacter sp. DMC5)
MAPSEELVFAPLGGVGEIGMNLGLYGFGPKKAREWLIVDLGMSFAGDEAPGVDLVLPDIR
FLETERKKIAGLVLTHGHEDHIGAVLDLWPRLKCPIYTTRFTAGLLEAKRAGEPGAPSEL
PIEVVRARQPVQIGPFSVEFVPVSHSIPDSHALAIRTAAGLVVHTGDWKLDPTPLVGEAT
DIARLKALGDEGVRAIICDSTNAIRDGISPSEADVGASLKAIVAKAKHRIAFTTFSSNVA
RIRGIAEAAYANGREVVLVGRALERVIGVAREQGLLDGIPAFRGADAYGYLPRERVVAIL
TGSQGEPRAALRRIADDDHPEIALSPGDQVVFSSRTIPGNEKVVNHIVNALIKRGVEVIT
DRTALVHVSGHPRRGELEEMYRMIRPQVAIPVHGEALHLHEHALLARRLGVPEVLNCYDG
NVIRLAPGPAERVDDVPFGRLYKDGRLLLAEGARAIPERRKLSFVGAISIAVAVNKQGGL
AGDPSVEITGVPERGEGGVDMLDHVLDTVVATLDNLPKARRRDPEALAESLERAVRSAVN
AVWGKKPVCHVHVLEV