Danny Rice and David Eisenberg
University of California at Los Angeles, Institute of Molecular
Biology, Los Angeles, California
The following 4 predictions were made using the Smith and Waterman
alignment algorithm with a home-made residue-residue scoring table.
The residue preference scores were derived from a database of pairs of
aligned protein structures that had the same fold, and had sequence
identity below 35%. The scoring table was used to align contest
sequences against representatives of known structural folds. The score
was determined for each alignment by randomizing the sequence 100
times, and calculating the number of standard deviations above the
random mean the true sequence scored. This score for these four
predictions varied between about 6 and 7.
1) Target Sequence to predict: (CMLE) Carboxymuconate lactonizing
enzyme. Detected protein: (6TAA) Alpha amylase.
2) Target Sequence to predict: (IPNS) isopenicillin N synthase.
Detected protein: (2PMGA) phosphoglumcomutase
3) Target Sequence to predict: (PPDK) pyruvate phosphate dikinase.
Detected protein: (2PNI) phosphatidylinositol 3-kinase (p85-Alpha
subunit SH3 Domain)
4) Target Sequence to predict: (RTP) Replication Terminator Protein.
Detected protein: (2HPDA) Cytochrome P450.
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