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=Additional (or Modified) Documentation for Specific  Categories of Simple Parts=
(Relative to All Parts List of 8/20/07)

Scott C. Mohr
(8/21/07; updated 7/2/08)

==Protein coding sequences (CDS’s) / Enzymes (CDS-E)==

	ADD:

	* E-1 Enzyme Commission (EC) number (if assigned) <SPAN style= 'color:red'>'''(1)'''</span> 

	* E-2 Kyoto Encyclopedia of Genes and Genomes (KEGG ) reaction number (if assigned) <SPAN style= 'color:blue'>'''(1)'''</span>

==Protein coding sequences (CDS’s) / Repressors and Activators (CDS-RA)==

	ADD:

	* RA-1 Repressor?  ______ (yes/no).  Activator?______ (yes/no).  Both?______ (yes/no) <SPAN style= 'color:red'>'''(1)'''</span>

	''N.B.,'' Some proteins are repressors under some circumstances and activators under other circumstances.

	* RA-2 Regulatory ligands/effectors: _____________________ (list in a box?) <SPAN style= 'color:red'>'''(1)'''</span>

==Protein coding sequences (CDS’s) / Reporters (CDS-R)==

	ADD:

	*R-1 Fluorescent?  ______ (yes/no).  Luminescent?  ______(yes/no).	c. Other? __________ <SPAN style= 'color:red'>'''(1)'''</span>

	*R-2 Spectroscopic data:  <SPAN style= 'color:blue'>'''(2)'''</span>

# absorption max. ______ nm   
# emission max. ______ nm
# luminescent max. ______ nm
# other notable spectroscopic features:  _____________


		________________________________________________________

	Annotation to the IP-issue entry: VERY IMPORTANT FOR REPORTERS!  <SPAN style= 'color:red'>'''(1)'''</span>

	E.C. number (if applicable) <SPAN style= 'color:blue'>'''(1)'''</span>

==Protein coding sequences (CDS’s) / Uncategorized (CDS-U)==

	ADD:
	nothing
	OMIT:
	nothing

==Protein coding sequences (CDS’s) / (Binary!) Fusion Proteins (CDS-F, new category)==

	ADD:

	Method used to fuse the two components.  <SPAN style= 'color:red'>'''(2)'''</span>

	Feature annotation of the linker spanning the two fused segments  <SPAN style= 'color:red'>'''(1)'''</span>

	Sources of ''both'' sequences. <SPAN style= 'color:red'>'''(3 + 3 = 6)'''</span>  [Note the high point value!]

	OMIT:

	E.C. number(s) – if inappropriate

==Ribosome binding Sites (RBS’s)==

	ADD:
	nothing
	OMIT:
	Nothing

==Terminators==

	ADD:
	nothing (best mFold structure?)
	OMIT:
	nothing

==Promoters (suggested renaming of “Regulatory regions”)==

	ADD:
•In the part “long description,” INDICATE SPECIFICALLY IF THIS IS A COMPOSITE PART (i.e. whether or not it encodes a repressor/activator binding site, and if so, the identity of the repressor/activator and co-repressor/inducer.)
<SPAN style= 'color:red'>'''(2)'''</span>

•Under dependencies, be sure to include chassis type, growth conditions and any other key factors that relate to the promoter function. <SPAN style= 'color:red'>'''(2)'''</span>

	OMIT:
	nothing
 
==RNA==
(suggestions needed!)

	ADD:
	nothing
	OMIT:
	nothing

==DNA==
(suggestions needed!)

	ADD:
	nothing
	OMIT:
	nothing

==Conjugation==
(suggestions needed!)

	ADD:
	nothing
	OMIT:
	nothing