Protein Info for GFF220 in Variovorax sp. SCN45

Annotation: tRNA pseudouridine(55) synthase (EC 5.4.99.25)

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 50 100 150 200 250 321 TIGR00431: tRNA pseudouridine(55) synthase" amino acids 14 to 224 (211 residues), 233.4 bits, see alignment E=1.1e-73 PF01509: TruB_N" amino acids 35 to 185 (151 residues), 172.9 bits, see alignment E=8.5e-55 PF16198: TruB_C_2" amino acids 186 to 243 (58 residues), 60 bits, see alignment E=3e-20 PF09157: TruB-C_2" amino acids 248 to 302 (55 residues), 23.5 bits, see alignment E=6.5e-09

Best Hits

Swiss-Prot: 66% identical to TRUB_VEREI: tRNA pseudouridine synthase B (truB) from Verminephrobacter eiseniae (strain EF01-2)

KEGG orthology group: K03177, tRNA pseudouridine synthase B [EC: 5.4.99.12] (inferred from 89% identity to vap:Vapar_2750)

Predicted SEED Role

"tRNA pseudouridine synthase B (EC 4.2.1.70)" in subsystem tRNA processing (EC 4.2.1.70)

MetaCyc Pathways

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 4.2.1.70, 5.4.99.12

Use Curated BLAST to search for 4.2.1.70 or 5.4.99.12

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

Find the best match in UniProt

Protein Sequence (321 amino acids)

>GFF220 tRNA pseudouridine(55) synthase (EC 5.4.99.25) (Variovorax sp. SCN45)
MNAPRTRVQRRPVHGVLLLDKPLGLSSNQALQKAKWLLRAEKAGHTGTLDPLATGVLPLC
FGAATKFSQLHLDADKTYEATARLGVKTATGDAEGDVIAERSVQVTPEDLARVEAQFTGP
IRQVPPMHSALKKDGKALYEYAREGIEIERAPRDVVIHKLAIDTVGAIGDNVIRILATVS
KGTYIRTLGEDIGEALGCGAHLTSLRRVATGDFVEAQCVTLEALEAMDEDERLARLLPAE
ALVDGHSRVTLGAEDAARFLSGLRRRGSWVDAGEVAVFGAEPAAFLGTAHVTAGELIPGR
LLNPIEIQQILLNAQQTEATP