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## PowerPoint Slideshow about ' Dynamic Programming' - lilah-horton

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### Dynamic Programming

How to match up sequences and have the matches make sense and be quantitative

Question is

- How does a specific sequence compare to one other specific sequence?
- Is it similar?
- If so, at what level?
- Can’t compare every base to every other base--to complex

You are in the driver’s seat

- What is the most important?
- Exact nucleotide match?
- One-for-one (no gaps)?
- Length

Mathematical model

- Derive equation for each position, based on your value system
- Methodically go through each base for each sequence and calculate the value
- At the end, find the optimal path

Starting point: three possible scenarios for each position in sequences X and Y

- At a given position, the bases (Xm and Yn) are identical in X and Y
- At a given position, the base (Xm) in X is aligned with a gap in Y (and Yn appeared earlier)
- At a given position, the base in Y is aligned with a gap in X (and Xm appeared earlier)

Assign a value to each situation

- Identical: +5
- Mismatch: -2
- Insertion or deletion: -6

(Could have others; could choose different values)

- Enzymes sharing WIDMNE signature
- sequence
- alpha-glucosidase (all groups)
- alpha-xylosidase (plant, bacteria, archaea)
- Sucrase/Isomaltase (animal)
- Related sequences with broad substrate
- specificity

Aglu

Plantae

Fungi

At

XYL1

Pt Aglu

Tm

XYL

Sp Aglu

St MAL2

Anig aglA

Pp BAB3946

An AgdA

So Aglu

Ca GAM1

Bv Aglu

Soc GAM1

At Aglu-1

An agdB

Hv Aglu

Protista

Tp GAA

Hs GAA

Cj GAAII

Cj GAAI

Archaea

Ss xylS

Hs S/I-N

Hs S/I-C

Bt Aglu-III

Lv GAA

Ce AAA8317

Bh BAB0442

Aa GlcA

Lp XylQ

Sc

CAB8890

Tm

AAD3539

Animalia

Bacteria

0.1

Plant -amylases are located in different cellular compartments

- Plastids (chloroplasts, amyloplasts)
- Cytosol
- Apoplast (cell wall space)
- What is the function of the non-plastid forms?

Clade I

Secreted

421-445 aa

rice 2A

barley A

barley B

morning glory

rice 3B

dodder

maize

adzuki bean

rice 3E

rice XP_472377

Arabidopsis AMY2

apple 10

cassava

apple 9

kiwifruit

apple 8

potato

plantain

Clade II

Cytosolic

407-414 aa

Clade III

Plastidic

877-906 aa

Arabidopsis AMY3

rice NP_916641

Homologous sequences (homologues)

Share a common ancestor

Paralogs

Homologues derived by gene duplication

Functions may vary

Look for differences

Orthologs

Homologues derived by speciation

Common function

Look for similarities

- Structures important for common
- functions (orthologs)
- Structures important for unique
- functions (paralogs)
- Unusual structures

Variation in the active site loop among plant and bacterial -amylases

AtAMY1

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