Latest revision as of 19:00, 2 July 2008

Additional (or Modified) Documentation for Specific Categories of Basic 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) (1)

* E-2 Kyoto Encyclopedia of Genes and Genomes (KEGG ) reaction number (if assigned) (1)

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

ADD:

* RA-1 Repressor? ______ (yes/no). Activator?______ (yes/no). Both?______ (yes/no) (1)

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

* RA-2 Regulatory ligands/effectors: _____________________ (list in a box?) (1)

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

ADD:

*R-1 Fluorescent? ______ (yes/no). Luminescent? ______(yes/no). c. Other? __________ (1)

*R-2 Spectroscopic data: (2)

1. absorption max. ______ nm
2. emission max. ______ nm
3. luminescent max. ______ nm
4. other notable spectroscopic features: _____________

________________________________________________________

Annotation to the IP-issue entry: VERY IMPORTANT FOR REPORTERS! (1)

E.C. number (if applicable) (1)

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. (2)

Feature annotation of the linker spanning the two fused segments (1)

Sources of both sequences. (3 + 3 = 6) [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.) (2)

•Under dependencies, be sure to include chassis type, growth conditions and any other key factors that relate to the promoter function. (2)

OMIT: nothing

RNA

(suggestions needed!)

ADD: nothing OMIT: nothing

DNA

(suggestions needed!)

ADD: nothing OMIT: nothing

Conjugation

(suggestions needed!)

ADD: nothing OMIT: nothing

SCM (7/2/08)