Protein Info for GFF2103 in Sphingobium sp. HT1-2

Annotation: Ribonuclease J (endonuclease and 5

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 50 100 150 200 250 300 350 400 450 500 545 PF00753: Lactamase_B" amino acids 28 to 162 (135 residues), 40.3 bits, see alignment E=8.8e-14 PF12706: Lactamase_B_2" amino acids 60 to 164 (105 residues), 42 bits, see alignment E=2e-14 PF22505: RNase_J_b_CASP" amino acids 222 to 345 (124 residues), 125.8 bits, see alignment E=2.3e-40 PF07521: RMMBL" amino acids 360 to 404 (45 residues), 38.2 bits, see alignment 2.9e-13 PF17770: RNase_J_C" amino acids 450 to 543 (94 residues), 41 bits, see alignment E=8.2e-14

Best Hits

Swiss-Prot: 43% identical to RNJ_SINM2: Ribonuclease J (rnj) from Sinorhizobium meliloti (strain Sm2011 / Rm2011 / 2011)

KEGG orthology group: None (inferred from 87% identity to sch:Sphch_1170)

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 (545 amino acids)

>GFF2103 Ribonuclease J (endonuclease and 5 (Sphingobium sp. HT1-2)
MTPKDELLFLALGGSGEIGMNVNLYGCQGKWVMVDLGLTFADPLYPGVELVLPDLAFIEE
RKDDLLGIVLTHGHEDHIGAIPYLAADLGVPLYATPFTAGLIRLKLEEEGLTKEVKLHVI
ENEGSFNLGPFGFRYVPLAHSIPEGNAVLIDTPHGRIFHTGDWKLDAAPLLGQPSTPEEL
TAIGDEGVLALVCDSTNVFNPEPSGSESTVRDGLMQTVAAAKGRVLVTTFASNAARVQTL
GEVAAATGRKLCVAGRSLDRIISTAKAAGYLKDFPPLVDWDDAMDLPRSEVMFIATGGQG
EARAALSRIAFDSHPIKLAEGDTVVFSSKQIPGNEIAIGRIQNALATKGIIMVTDRQAEV
HVSGHPGRPELESMYRWIRPAILLPVHGERRHMAEQARLGLATGIPDAVVQSNGDLLRLA
PGKPTIIGHEDTGRLVLDGDVILPADGATMNERRKLGLHGQISVAVALDAKNRLIGEPVL
RTQGVPVEEDKDAFLAEAAEEAAAAVAKGSMEQEALRERLRLAVRRTATRWTGKKPIVDV
LLIRA