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A Game Introduction to Bioinformatic Sequence Comparisons

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Figure 1. Multiple sequence alignment of class III alcohol dehydrogenase/ glutathione-dependent formaldehyde 
dehydrogenase genes from several organisms. Amino acid sequences corresponding to this class of enzymes were retrieved 
from NCBI (www.ncbi.nlm.nih.gov) for human, plant (rice), fungus (yeast), and bacteria (Rhodobacter sphaeroides), and aligned using 
ClustalW (www.ebi.ac.uk/clustalw). In the line beneath each section of sequence, an asterisk (*) indicates conservation of a specific 
amino acid residue among all sequences, a colon (:) denotes amino acid residues with highly similar chemical or structural properties, 
and a period (.) specifies lower amino acid chemical or structural similarity. Absence of any mark indicates no conservation among 
amino acids at this particular position. Gaps are noted by (-), and frequently correspond to surface loops on protein structures. Amino 
acid residues in bold-faced type are involved in substrate binding.
360 THE AMERICAN BIOLOGY TEACHER, VOLUME 69, NO. 6, AUGUST 2007 
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Table I. PAM30 Scoring Matrix
BIOINFORMATIC SEQUENCE COMPARISONS 361
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Table II. Card Descriptions
Amino Acid Chemical characteristics AbbreviatedNames
Occurrence 
in Deck
Alanine Non-polar, short side chain Ala; A 7
Arginine Positively charged, large side chain Arg; R 5
Asparagine Polar, uncharged side chain Asn; N 4
Aspartate Negatively charged, side chain Asp; D 5
Cysteine Polar, uncharged side chain Cys; C 3
Glutamine Polar, uncharged side chain Gln, Q 4
Glutamate Negatively charged side chain Glu; E 6
Glycine Non-polar, short side chain Gly; G 7
Histidine Positively charged side chain His; H 3
Isoleucine Non-polar side chain Ile; I 6
Leucine Non-polar side chain Leu; L 9
Lysine Positively charged side chain Lys; K 6
Methionine Non-polar side chain Met; M 2
Phenylalanine Aromatic, Non-polar side chain Phe, F 4
Proline Non-polar side chain Pro; P 5
Serine Polar, uncharged side chain Ser; S 7
Threonine Polar, uncharged side chain Thr; T 6
Tryptophan Aromatic, Non-polar side chain Trp; W 2
Tyrosine Aromatic, polar side chain Tyr; Y 4
Valine Non-polar side chain Val; V 7
Figure 2. A sample player ’s hand in the four player game. All eight cards are dealt to the player face-
down. The cards are arranged in two rows aligned with each other. The player then chooses to turn over one-half 
of those cards dealt, as shown in the figure. Play begins as cards are drawn or picked-up from the discard pile and 
substituted for any of their original cards. 
362 THE AMERICAN BIOLOGY TEACHER, VOLUME 69, NO. 6, AUGUST 2007 
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ATLANTA!
See page 378 for more info.
Visit Piedmont Park while in
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