
PFRMAT TS
TARGET T0110
AUTHOR 6305-9733-7289
REMARK New fold
METHOD PSI-BLAST (Altschul et al., Nucl. Acids Res. 25, 3389-3402, 1997)
METHOD (-h 0.0005 -j 20) and iterative SCANPS
METHOD (Barton et al., 2000, http://barton.ebi.ac.uk/scanps/)
METHOD were run against a combined search set comprising the SWALL, PDB and ENSEMBL
METHOD sequence databases.
METHOD Sequences hit from these runs with an E-value of less than 0.0005 were collected.
METHOD These sequences were then aligned all-against-all using AMPS
METHOD (Barton, G. J., Methods in Enzymology 183, 403-428, 1990)
METHOD and one sequence was removed from any pair sharing greater than 75%
METHOD identity. Each of the remaining sequences was then used as queries
METHOD in a second round of psiblast runs. From these runs, 1F4J (chain C)
METHOD and 1ZFJ (chain A) were the only PDB structures found with an E-value
METHOD worth investigating further. However, on inspection of their respective
METHOD alignments to T0110 within the Jalview alignment editor
METHOD (M. Clamp, URL: http://www2.ebi.ac.uk/~michele/jalview/contents.html)
METHOD and after looking at the secondary structure for T0110 by JPRED2 (Cuff and
METHOD Barton, 2000, Proteins 40, 502-511) it was decided it was unlikely that
METHOD T0110 shared structural similarity at the fold level. With no other 
METHOD reasonable candidate structures after looking at the results from the MAP
METHOD fold recognition method (Russell, et al., 1996, JMB,259,349-365) it was
METHOD concluded this was likely to be a new fold.
MODEL 1
PARENT NONE
TER
END


