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Data Evaluation Record - Amino Acid Homology Comparison MRID NO: 44258109
Date: 1/6/98
Reviewed by: John L. Kough,
Ph.D., Biologist, BPPD
Secondary Reviewer: Doug Gurian-Sherman, Ph.D., Plant Pathologist,
BPPD
STUDY TYPE: Amino Acid Homology Comparison
MRID NO: 44258109
CHEMICAL NO: 006466
TEST MATERIAL: Truncated Cry9C delta-endotoxin
STUDY NO: none assigned
SPONSOR: Plant Genetic Systems (America) Inc., Ghent, Belgium
TITLE OF REPORT: Amino Acid Sequence Homology Search with the Corn Expressed Truncated Cry9C Protein Sequence
AUTHOR: Susan C. MacIntosh
STUDY COMPLETED: March 18, 1997
CONCLUSION: Three hundred sequences were listed as having regions of homology with the 626 amino acids of the Cry9C truncated toxin protein. The first 64 proteins in the list were all parasporal proteins from Bacillus thuringiensis otherwise known as delta-endotoxins. Other delta-endotoxins were found at 67, 76, 78, 79 and 80. These proteins had regions of homology that gave a "significant homology". The table of values indicated a matching score above 4 standard deviations would contain all the delta-endotoxins mentioned above. The algorithm for converting the matches and penalties into homology scores was not described although it was stated that "all other proteins (besides the delta-endotoxins referred to above) have less than 20% exact sequence matching and no major stretches of sequence homology could be detected, indicating that in these cases the sequence homology is not significant."
CLASSIFICATION: SUPPLEMENTAL. BPPD has not yet determined how to judge amino acid sequence homology for risk assessment purposes. No further studies need to be done at this time for analyzing homology.
STUDY DESIGN
The amino acid sequence of the Cry9C endotoxin was compared to a data base of amino acid sequences looking specifically for significant homologies with known toxins or allergens. This study has a GLP non-compliance statement.
TEST METHODS
Test Substance
The 626 amino acid sequence of the truncated version of the Cry9C delta-endotoxin as expressed in corn was used to search the data base for significant areas of sequence homology.
Test System
The system used was the Intelligenetics Fast DB software providing a fast pairwise comparison of sequences. The databases searched included all the sequence entries in the PIR, Swiss Prot and HIV AA bases. The parameters for the search were described as not stringent and based on exact matching although how these parameters are defined for the search were not described. It appears from the values presented that a positive match is given a value of +1. The homology determinations were corrected by giving a penalty value of -1 for each mismatch or gap. Gaps were also weighted for their size with an additional factor of (0.05 x gap size) being added to the penalty.
RESULTS AND DISCUSSION
There were 300 sequences listed as having regions of homology with the 626 amino acids of the Cry9C truncated toxin protein. The first 64 proteins in the list were all parasporal proteins from Bacillus thuringiensis otherwise known as delta-endotoxins. Other delta-endotoxins were found at 67, 76, 78, 79 and 80. These proteins had regions of homology that gave a "significant homology".
The table of values indicated a matching score above 4 standard deviations would contain all the delta-endotoxins mentioned above. The algorithm for converting the matches and penalties into homology scores was not described although it was stated that "all other proteins (besides the delta-endotoxins referred to above) have less than 20% exact sequence matching and no major stretches of sequence homology could be detected, indicating that in these cases the sequence homology is not significant."
Other parasporal proteins (delta-endotoxins) from Bacillus thuringiensis subspecies are found at 105 and 138 in the list. Other proteins listed within 5 standard deviations along with the first 64 delta-endotoxins and having regions of significant amino acid homology include a serine carboxypeptidase from rice; dynein, a cytosolic protein involved in chromosome movement and maintenance in Aspergillus; a transcription repair coupling factor from Haemophilus; a putative cystathionine β-lyase (EC 4.4.1.8) from Saccharomyces; a transmembrane protein from Saccharomyces; a virB4.1 protein from Agrobacterium; a glucoamylase S1/S2 precursor (EC3.2.1.3) from Saccharomyces and a transcription initiation protein SPT6 from Saccharomyces.