Volume 2 Chapter 10 Search Menu PEPTIDE-SEQ

Function

PEPTIDE-SEQ is used to construct a test for amino-acids and peptide sequences using 3-letter code symbols.

Basic QUEST Procedure

The equivalent test construction in Basic QUEST is discussed under *PEPTIDE. It should be read carefully before using Graphics QUEST3D.

Graphics QUEST3D Procedure

The PEPTIDE-SEQ sub-menu is shown below.

This table summarises the buttons in the PEPTIDE-SEQ sub-menu.

When not in the middle of PDEF, the current sequence is displayed as part of the prompt in the dialog area. This diagram shows how the sequence is built up:

If no amino-acids have yet been added to the sequence, QUEST separates the left- and right-terminating bonds in the dialog area prompt with "???".

The PEPTIDE-SEQ buttons will be illustrated with some examples.

Suppose we wish to search for -,%PRO-AIB-,%

Ex.1

Select PEPTIDE-SEQ
The SEARCH menu is replaced by the PEPTIDE-SEQ sub-menu.

Select "DEFINE-SEQUENCE" to complete the sequence. The current sequence is:
-,%???-,%

Select PRO and then AIB from the displayed 3-letter code symbols

Select "DEFINE-SEQUENCE" to complete the sequence. The current sequence is:
-,%PRO-AIB-,%

Select DEFINE-SEQUENCE
QUEST returns to the SEARCH menu, and the instruction document now contains the test:
```
T1 *PEPTIDE
PSEQ    -,%PRO-AIB-,%
```
This illustrates an important difference between the Basic Version Procedure and the graphical interface: "PSEQ PRO-AIB" does not allow any connections at either end of the sequence - it can hit only di-peptides.
For safety, the graphical interface begins with all three bonding types (normal, non-standard and none) switched on. If the user does not change these options, QUEST will locate all peptides of any size containing the specified sequence.

Suppose we wish to search for -,CYS*-PRO-AIB-ALA- in cyclic peptides.

Ex.2

Select PEPTIDE-SEQ

Select "DEFINE-SEQUENCE" to complete the sequence. The current sequence is:
-,%???-,%

Select LEFT-BOND:No bond

Select "DEFINE-SEQUENCE" to complete the sequence. The current sequence is:
-,???-,%

Select RIGHT-BOND:Non-Standard and RIGHT-BOND:No bond
```
Select "DEFINE-SEQUENCE" to complete the sequence. The current sequence is:
-,???-
```
We have now selected the desired bonding patterns for the left and right ends of our sequence.
Select MODIFICATIONS:Modified

Select "DEFINE-SEQUENCE" to complete the sequence. The current sequence is:
-,???*-

Select CYS

Select "DEFINE-SEQUENCE" to complete the sequence. The current sequence is:
-,CYS*-

Select MODIFICATIONS:Unmodified and then Select PRO, then AIB, then ALA

Select "DEFINE-SEQUENCE" to complete the sequence. The current sequence is:
-,CYS*-PRO-AIB-ALA-

Select CYCLIC

Select "DEFINE-SEQUENCE" to complete the sequence. The current sequence is:
-,CYS*-PRO-AIB-ALA-  C

Select DEFINE-SEQUENCE to complete the definition.
The instruction document now contains the test:
```
T2 *PEPTIDE
PSEQ   -,CYS*-PRO-AIB-ALA-  C
```

Ex.3

Select PEPTIDE-SEQ

Select "DEFINE-SEQUENCE" to complete the sequence. The current sequence is:
-,%???-,%

Select PDEF

Type name for new residue type (three characters or less),
or press RETURN if you don't want to define a new residue.

Type ABC
```
Select the residues allowed in ABC
```
Select ILE

Select "=" to complete definition.  The current definition is:
ILE

Select LEU

Select "=" to complete definition.  The current definition is:
ILE + LEU

Select =
The newly defined amino-acid, ABC, is added to the "USER-DEFINED" area, and is now available for selection within other definitions and sequences.

Select "DEFINE-SEQUENCE" to complete the sequence. The current sequence is:
-,%???-,%

Select PDEF
Type X2
Select ANY
Select -
Select ABC

Select "=" to complete definition.  The current definition is:
ANY - ABC

Select =

Select "DEFINE-SEQUENCE" to complete the sequence. The current sequence is:
-,%???-,%

Set LEFT-BOND and RIGHT-BOND options to only Normal

Select "DEFINE-SEQUENCE" to complete the sequence. The current sequence is:
-???-

Select GLY
Select X2
Select GLY

Select "DEFINE-SEQUENCE" to complete the sequence. The current sequence is:
-GLY-X2-GLY-

Select DEFINE-SEQUENCE
The instruction document now contains the test:
```
T3 *PEPTIDE
PDEF ABC = ILE + LEU
PDEF X2  = ANY - ABC
PSEQ  -GLY-X2-GLY-
```
This would register hits for:
PEPSEQ C=6 PRO-GLY-PRO-GLY-PRO-GLY-
but not for
PEPSEQ C=6 GLY-LEU-GLY-GLY-LEU-GLY-

Related Bit Screens

The database bit screen is 67.

Ex. SCRE 67

This query registers hits for all entries having a peptide sequence record.

Related Keywords

*SYNONYM

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