Protein Info for PGA1_c06040 in Phaeobacter inhibens DSM 17395

Updated annotation (from data): DNA damage response helicase, ligase-associated
Rationale: Conserved and specific phenotype: important for resisting cisplatin. Related to Lhr, which is either a DNA:DNA or DNA:RNA helicase, but lacks the long C-terminal extension that might have a regulatory role (see putative winged helix domain in E. coli lhr). This is also related to the archael protein saci_1500, which has also been linked to DNA damage response, as a mutant is sensitive to UV (PMID: 26148716)
Original annotation: putative DEAD/DEAH box helicase

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 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 811 TIGR04121: DEXH box helicase, DNA ligase-associated" amino acids 8 to 795 (788 residues), 1028.4 bits, see alignment E=0 PF04851: ResIII" amino acids 19 to 186 (168 residues), 26 bits, see alignment E=2.1e-09 PF00270: DEAD" amino acids 21 to 187 (167 residues), 93.8 bits, see alignment E=2.5e-30 PF00271: Helicase_C" amino acids 240 to 340 (101 residues), 58.9 bits, see alignment E=1.4e-19 PF19306: WH_Lhr" amino acids 369 to 536 (168 residues), 129.6 bits, see alignment E=2e-41 PF08494: DEAD_assoc" amino acids 585 to 766 (182 residues), 159.8 bits, see alignment E=1.8e-50

Best Hits

KEGG orthology group: K03724, ATP-dependent helicase Lhr and Lhr-like helicase [EC: 3.6.4.-] (inferred from 79% identity to sil:SPO3098)

Predicted SEED Role

"ATP-dependent helicase, DEAD/DEAH box family, associated with Flp pilus assembly" in subsystem Widespread colonization island

Isozymes

Compare fitness of predicted isozymes for: 3.6.4.-

Use Curated BLAST to search for 3.6.4.-

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 I7DY23 at UniProt or InterPro

Protein Sequence (811 amino acids)

>PGA1_c06040 DNA damage response helicase, ligase-associated (Phaeobacter inhibens DSM 17395)
MSRLPDVITDWFSTRGWTIHPHQQEMLARVDDPATLLIAPTGGGKTMAGFLPTLADLATG
DHQGLHTLYVSPLKALAADIKRNLRTPVEDMGLPIRIDDRTGDTPASRKRSQRADPPHIL
LTTPESLALLTSYEDAPRMFAGLKRVVLDEIHALAESKRGDQLMLALTRLQAICPDMRRV
GLSATVDDPAAIAQYLARHPAPCDIVLADPGPAPDIRMLHTDAAPPWAGGGAAHAIPAVL
EQIKAHRTTLIFHNTRAQAEIFFRNLWLANDDALPIGIHHGSLDRVQRDRVEAAMVRGEL
RAVVCTGSLDLGIDWGDVDLVIQIGAPKNVKRLVQRIGRANHRYNAPSKALLVPANRFEV
VECRAALEAVEAGTLDGSPRSPGPRDVLCQHILIRACAGPFAADDLFAEVTGAGAYASLT
RAEFDACLDFCATGGYALRVYDQWQRLLQRPDGLWQLRDPRAARRIRMNIGTIQDADLLK
VRLKRSRGGKPLGEIEEAFAATLTPGDTFLIGGQVVRYESLREMTVEVSRNASKTPKVAV
FSGTKFATSTQLSTRILDILQRDSWPDLPSHTADWLALQRQVSEMPRRGQLLLESFPFRG
REYLCVYGFAGRNAMQTLGLLLTKRMEELSLDPLGFVATDYATLIWGLSPVADPAPLFDP
DKLRAGLDGWLADNAVMKRSFRAVANIAGLIERNTPGQRKSGRQATFSSDILYDTLRKYD
PDHLLLDITRQEALGGLVDFGRIEEMLTRINGNITLNRLSQISPLAAPLLLEVGKVPVKG
AAQEKLLQRETEDLMRLAGLAALEAPAAPEL