Protein Info for PP_4952 in Pseudomonas putida KT2440

Annotation: ATP-dependent RNA helicase, specific for 23S rRNA

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 50 100 150 200 250 300 350 400 461 signal peptide" amino acids 1 to 28 (28 residues), see Phobius details PF00270: DEAD" amino acids 30 to 196 (167 residues), 156.6 bits, see alignment E=9.8e-50 PF04851: ResIII" amino acids 44 to 190 (147 residues), 31 bits, see alignment E=4.7e-11 PF00271: Helicase_C" amino acids 232 to 339 (108 residues), 87.5 bits, see alignment E=1.5e-28 PF03880: DbpA" amino acids 389 to 459 (71 residues), 90.7 bits, see alignment E=1e-29

Best Hits

Swiss-Prot: 40% identical to CSHE_BACCR: DEAD-box ATP-dependent RNA helicase CshE (cshE) from Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)

KEGG orthology group: K05591, ATP-independent RNA helicase DbpA [EC: 3.6.4.13] (inferred from 100% identity to ppu:PP_4952)

Predicted SEED Role

"ATP-dependent 23S rRNA helicase DbpA"

Isozymes

Compare fitness of predicted isozymes for: 3.6.4.13

Use Curated BLAST to search for 3.6.4.13

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 Q88D75 at UniProt or InterPro

Protein Sequence (461 amino acids)

>PP_4952 ATP-dependent RNA helicase, specific for 23S rRNA (Pseudomonas putida KT2440)
MTTESTAFATLPLSTAMLANLEALGYASMTPIQAQSLPVILKGQDLIAQAKTGSGKTAAF
GIGLLNPINPRYFGCQALVLCPTRELADQVAKELRRLARAEDNIKILTLCGGVSLGPQIA
SLEHGAHIIVGTPGRIQQHLDKGTLVLDGLNTLVLDEADRMLDMGFFDAIASIIGKTPSR
RQTLLFSATYPAGIKQLAADFMRNPQQVKVESLHTDNQIEQRFIEIDPQQRLEAVTRVLG
HYRPQSCVAFCFTKQQCEDVVAHLTAKGIVAQALHGDLEQRDRDQVLTMFANRSSSVLVA
TDVAARGLDIDGLDMVINVELARDAEIHVHRVGRTGRAGEKGVAVSLVAPAEGHRAQAIE
ALQNSPLRWDQLDSLKNKGGEPLLPVMTTLCIAAGRKDKLRPGDILGALTGDAGIPGKQV
GKIAIFDFQAFVAVERALAKQAMQRLNSGKIKGRALKVRII