Protein Info for GFF4851 in Variovorax sp. SCN45

Annotation: Coupling protein VirD4, ATPase required for T-DNA transfer

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 50 100 150 200 250 300 350 400 450 500 550 600 672 transmembrane" amino acids 6 to 31 (26 residues), see Phobius details amino acids 45 to 62 (18 residues), see Phobius details amino acids 74 to 96 (23 residues), see Phobius details PF02534: T4SS-DNA_transf" amino acids 111 to 558 (448 residues), 340.7 bits, see alignment E=2.3e-105 PF10412: TrwB_AAD_bind" amino acids 173 to 539 (367 residues), 101.1 bits, see alignment E=1e-32 PF12696: TraG-D_C" amino acids 404 to 524 (121 residues), 99.4 bits, see alignment E=2.3e-32

Best Hits

KEGG orthology group: K03205, type IV secretion system protein VirD4 (inferred from 100% identity to rpi:Rpic_2643)

Predicted SEED Role

"Type IV secretion system protein VirD4" in subsystem Type 4 secretion and conjugative transfer or pVir Plasmid of Campylobacter

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 (672 amino acids)

>GFF4851 Coupling protein VirD4, ATPase required for T-DNA transfer (Variovorax sp. SCN45)
MQGTNVLFGQIAVVFGIVIAGVWSATQWTAAALGYQLRLGSPWFDFFGTPVYHPWGLFEW
WFFFDAYAPHIFDAGGAIAAGSGLIAMVVAIGMSIWRSRQSKLVTTYGSARWANAEDIHK
AGLDQPAGVFLGLHRQQYLRHEGPEHVLTFAPTRSGKGVGLVVPTLLSWPASAVIHDIKG
ENWSITAGWRSRFSHCLLFNPTDAKSSAYNPLLEVRRGAHEVRDVQNIADILVDPEGALE
RRNHWEKTSHALLVGAILHVLYAGEDKTLRGVANFLSDPACPFELTLHRMMTTPHIGGGP
HLVVASAAREVLNKSDNERSGVLSTAMSFLGLYRDPTVAEVTSRCDWRIADLIAAEHPVS
LYLVVPPSDISRTKPLIRLILNQIGRRLTESLDGSDGIARRHKLLLMLDEFPALGRLDFF
ETALAFMAGYGIRSFLIAQSLNQIDKAYGQNHSILDNCHVRVTFATNDERTAKRISETLG
TATELRAQRNYAGHRLAPWLGHLMVSRQETARPLLTPGEVMQLPPDEAVVMVSSVAPIKA
KKLRYYADSNFKRRVLPPPVLATLSMQGRYADVPPERADDWSGLAIPAMPVAPTADAADG
LENLGSADDSGPRRQPELSEAVTYDPDLVAPAADLGLLDDDDMPHPLPRQLDPALQRTAR
LASLDPDDGIDL