Protein Info for PP_5264 in Pseudomonas putida KT2440

Annotation: helicase a single-stranded DNA dependent ATPase

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 50 100 150 200 250 300 350 400 450 500 550 600 669 TIGR01074: ATP-dependent DNA helicase Rep" amino acids 3 to 668 (666 residues), 1080.4 bits, see alignment E=0 PF00580: UvrD-helicase" amino acids 4 to 266 (263 residues), 297.6 bits, see alignment E=2.7e-92 PF13245: AAA_19" amino acids 17 to 249 (233 residues), 82 bits, see alignment E=1.1e-26 PF13361: UvrD_C" amino acids 271 to 613 (343 residues), 250.4 bits, see alignment E=9.4e-78 PF13538: UvrD_C_2" amino acids 555 to 608 (54 residues), 28.7 bits, see alignment 2.4e-10

Best Hits

Swiss-Prot: 51% identical to REP_HAEIN: ATP-dependent DNA helicase Rep (rep) from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)

KEGG orthology group: K03656, ATP-dependent DNA helicase Rep [EC: 3.6.4.12] (inferred from 100% identity to ppu:PP_5264)

Predicted SEED Role

"ATP-dependent DNA helicase Rep" in subsystem DNA repair, bacterial UvrD and related helicases

Isozymes

Compare fitness of predicted isozymes for: 3.6.4.12

Use Curated BLAST to search for 3.6.4.12

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 Q88CB7 at UniProt or InterPro

Protein Sequence (669 amino acids)

>PP_5264 helicase a single-stranded DNA dependent ATPase (Pseudomonas putida KT2440)
MSRLNPRQQEARDYVGGPLLVLAGAGSGKTSVITRKIAHLIQNCGIRAQYIVAMTFTNKA
AREMKERVATLLRPGEGRGLTVCTFHNLGLNIIRKEHERLGYKPGFSIFDESDIKALLSD
IMQKEYSGDDGIDEIKNMIGAWKNDLVLPPEALEKARNPREQTAAIVYTHYQRTLKAFNA
VDFDDLILQPVKLFQEHPEVLERWQNRVRYLLVDEYQDTNASQYLLVKMLIGMRNQFTVV
GDDDQSIYAWRGARPENLMLLKEDYPSLKIVMLEQNYRSTSRILRCANVLIANNPHAFEK
QLWSEMGVGDEIRVIRCKNEEAEAERVAMEILTLHLRTNRPYSDFAILYRGNYQAKLIEL
KLQHHQVPYRLSGGNSFFGRQEVKDLMAYLRLLVNPDDDNAYLRVINVPRREIGSTTLEK
LGNYATERGISMYAASEELGLGEHLDARYTERLQRFKHWLDGVRHKVALEDPIAALHEMI
RDIDYENWIRQQTASDKAAEFRISNVWFLVEALKNTLEKDEEGDMTIEDAIGKLVLRDML
ERQQEEEENAEGVQMMTLHASKGLEFPYVFIMGMEEEILPHRSSIEADTIEEERRLAYVG
ITRARQTLAFTFAAKRKQYGEIIDCTPSRFLDELPPDDLAWEGLDDAPVEVKAARGNNAL
ADIRAMLKR