Difference between revisions of "Part:BBa K404300"

Revision as of 19:28, 5 August 2013

SEG-Linker

Amino acid sequence:
GGSGGGSEGGGSEGGGSEGGGSEGGGSEGGGSGGGS

This part is a peptide linker, it can be used to connect two protein parts / domains and add additional space between them. This can be necessary to avoid interactions between the different parts when fusion proteins are created. The SEG linker was created to connect our protein domains to a fusion construct. Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
COMPATIBLE WITH RFC[1000]

<td width="100%" colspan="2" style="background-color: rgb(221, 221, 221);">Parameters for BioBrick <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_K404300">BBa_K404300</a> automatically created by the <a href="http://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator">BioBrick-AutoAnnotator</a> version 1.0</td></tr><tr><td width="100%" colspan="2">Nucleotide sequence in RFC 25, so ATGGCCGGC and ACCGGT were added (in italics) to the 5' and 3' ends: (underlined part encodes the protein)
ATGGCCGGCGGTGGTTCT ... GGCGGTAGCACCGGT
ORF from -8 to 114 (excluding stop-codon)</td></tr><tr><td width="100%" colspan="2">Amino acid sequence: (RFC25 scars in shown in bold, other sequence features underlined; both given below)

1	MAGGGSGGGSEGGGSEGGGSEGGGSEGGGSEGGGSGGGSTG*

</td></tr><tr><td colspan="2" width="100%">Sequence features: (with their position in the amino acid sequence, also underlined or shown bold above)

</td></tr><tr><td width="100%" colspan="2">Amino acid composition:

A (Ala)	1 (2.4%)
R (Arg)	0 (0.0%)
N (Asn)	0 (0.0%)
D (Asp)	0 (0.0%)

C (Cys)	0 (0.0%)
Q (Gln)	0 (0.0%)
E (Glu)	5 (12.2%)
G (Gly)	25 (61.0%)

H (His)	0 (0.0%)
I (Ile)	0 (0.0%)
L (Leu)	0 (0.0%)
K (Lys)	0 (0.0%)

M (Met)	1 (2.4%)
F (Phe)	0 (0.0%)
P (Pro)	0 (0.0%)
S (Ser)	8 (19.5%)

T (Thr)	1 (2.4%)
W (Trp)	0 (0.0%)
Y (Tyr)	0 (0.0%)
V (Val)	0 (0.0%)

</td></tr><tr><td width="40%">Amino acid counting

	Total number:	41
	Positively charged (Arg+Lys):	0 (0.0%)
	Negatively charged (Asp+Glu):	5 (12.2%)

</td><td width="60%">Biochemical parameters

	Molecular mass [Da]:	3089.9
	Theoretical pI:	3.51
	Extinction coefficient at 280 nm [M^-1 cm^-1]:	0 / 0 (all Cys red/ox)

</td></tr><tr><td colspan="2" width="100%">Codon usage

	Organism:	E. coli	B. subtilis	S. cerevisiae	A. thaliana	Mammals
	Codon quality (CAI):	excellent (0.89)	good (0.75)	good (0.63)	good (0.61)	good (0.80)

</td></tr><tr><td colspan="2" width="100%"> The BioBrick-AutoAnnotator was created by <a href="http://2013.igem.org/Team:TU-Munich">TU-Munich 2013</a> iGEM team. For more information please see the <a href="http://2013.igem.org/Team:TU-Munich/Results/Software">documentation</a>.
If you have any questions, comments or suggestions, please email us at <a href="mailto:igem@wzw.tum.de?Subject=AutoAnnotator" target="_top">igem@wzw.tum.de</a>.</td></tr></table>
</html>

@@ Line 20: / Line 20: @@
 ===Functional Parameters===
 <partinfo>BBa_K404300 parameters</partinfo>
-<!-- -->
+<html><table border="1" cellspacing="0" width="100%" !important><tr><!-- Time stamp in ms since 1/1/1970 1375730849949 --><td width="100%" colspan="2" style="background-color: rgb(221, 221, 221);"><strong>Parameters for BioBrick <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_K404300">BBa_K404300</a> automatically created by the <a href="http://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator">BioBrick-AutoAnnotator</a> version 1.0</strong></td></tr><tr><td width="100%" colspan="2"><strong>Nucleotide sequence</strong> in <strong>RFC 25</strong>, so ATGGCCGGC and ACCGGT were added (in italics) to the 5' and 3' ends: (underlined part encodes the protein)<br><span style="font-family:'Courier New', Arial;">&nbsp;<u><i>ATGGCCGGC</i>GGTGGTTCT&nbsp;...&nbsp;GGCGGTAGC<i>ACCGGT</i></u></span><br>&nbsp;<strong>ORF</strong> from -8 to 114 (excluding stop-codon)</td></tr><tr><td width="100%" colspan="2"><strong>Amino acid sequence:</strong> (RFC25 scars in shown in bold, other sequence features underlined; both given below)<br><span style="font-family:'Courier New', Arial;"><table border="0" cellspacing="0" width="100%" !important><tr><td align="right" width="2%">1&nbsp;</td><td width="98%">MAGGGSGGGSEGGGSEGGGSEGGGSEGGGSEGGGSGGGSTG*</td></tr></table></span></td></tr><tr><td colspan="2" width="100%"><strong>Sequence features:</strong> (with their position in the amino acid sequence, also underlined or shown bold above)<table border="0" cellspacing="0" width="60%" !important></table></td></tr><tr><td width="100%" colspan="2"><strong>Amino acid composition:</strong><table border="0" cellspacing="0" width="100%"><tr><td width="20%"><table border="1" cellspacing="0" width="100%"><tr><td width="50%">A (Ala)</td><td width="50%">1 (2.4%)</td></tr><tr><td width="50%">R (Arg)</td><td width="50%">0 (0.0%)</td></tr><tr><td width="50%">N (Asn)</td><td width="50%">0 (0.0%)</td></tr><tr><td width="50%">D (Asp)</td><td width="50%">0 (0.0%)</td></tr></table></td><td width="20%"><table border="1" cellspacing="0" width="100%"><tr><td width="50%">C (Cys)</td><td width="50%">0 (0.0%)</td></tr><tr><td width="50%">Q (Gln)</td><td width="50%">0 (0.0%)</td></tr><tr><td width="50%">E (Glu)</td><td width="50%">5 (12.2%)</td></tr><tr><td width="50%">G (Gly)</td><td width="50%">25 (61.0%)</td></tr></table></td><td width="20%"><table border="1" cellspacing="0" width="100%"><tr><td width="50%">H (His)</td><td width="50%">0 (0.0%)</td></tr><tr><td width="50%">I (Ile)</td><td width="50%">0 (0.0%)</td></tr><tr><td width="50%">L (Leu)</td><td width="50%">0 (0.0%)</td></tr><tr><td width="50%">K (Lys)</td><td width="50%">0 (0.0%)</td></tr></table></td><td width="20%"><table border="1" cellspacing="0" width="100%"><tr><td width="50%">M (Met)</td><td width="50%">1 (2.4%)</td></tr><tr><td width="50%">F (Phe)</td><td width="50%">0 (0.0%)</td></tr><tr><td width="50%">P (Pro)</td><td width="50%">0 (0.0%)</td></tr><tr><td width="50%">S (Ser)</td><td width="50%">8 (19.5%)</td></tr></table></td><td width="20%"><table border="1" cellspacing="0" width="100%"><tr><td width="50%">T (Thr)</td><td width="50%">1 (2.4%)</td></tr><tr><td width="50%">W (Trp)</td><td width="50%">0 (0.0%)</td></tr><tr><td width="50%">Y (Tyr)</td><td width="50%">0 (0.0%)</td></tr><tr><td width="50%">V (Val)</td><td width="50%">0 (0.0%)</td></tr></table></td></tr></table></td></tr><tr><td width="40%"><strong>Amino acid counting</strong><table border="0" cellspacing="0" width="100%"><tr><td width=" 7%"></td><td width="53%">Total number:</td><td width="40%">41</td></tr><tr><td width=" 7%"></td><td width="53%">Positively charged (Arg+Lys):</td><td width="40%">0 (0.0%)</td></tr><tr><td width=" 7%"></td><td width="53%">Negatively charged (Asp+Glu):</td><td width="40%">5 (12.2%)</td></tr></table></td><td width="60%"><strong>Biochemical parameters</strong><table border="0" cellspacing="0" width="100%"><tr><td width=" 5%"></td><td width="55%">Molecular mass [Da]:</td><td width="40%">3089.9</td></tr><tr><td width=" 5%"></td><td width="55%">Theoretical pI:</td><td width="40%">3.51</td></tr><tr><td width=" 5%"></td><td width="55%">Extinction coefficient at 280 nm [M<sup>-1</sup> cm<sup>-1</sup>]:</td><td width="40%">0 / 0 (all Cys red/ox)</td></tr></table></td></tr><tr><td colspan="2" width="100%"><strong>Codon usage</strong><table border="0" cellspacing="0" width="75%"><tr><td width=" 4%"></td><td width="21%">Organism:</td><td width="15%"><i>E. coli</i></td><td width="15%"><i>B. subtilis</i></td><td width="15%"><i>S. cerevisiae</i></td><td width="15%"><i>A. thaliana</i></td><td width="15%">Mammals</td></tr><tr><td width=" 4%"></td><td width="21%">Codon quality (CAI):</td><td width="15%">excellent (0.89)</td><td width="15%">good (0.75)</td><td width="15%">good (0.63)</td><td width="15%">good (0.61)</td><td width="15%">good (0.80)</td></tr></table></td></tr><tr><td colspan="2" width="100%"> The BioBrick-AutoAnnotator was created by <a href="http://2013.igem.org/Team:TU-Munich">TU-Munich 2013</a> iGEM team. For more information please see the <a href="http://2013.igem.org/Team:TU-Munich/Results/Software">documentation</a>.<br>If you have any questions, comments or suggestions, please email us at <a href="mailto:igem@wzw.tum.de?Subject=AutoAnnotator" target="_top">igem@wzw.tum.de</a>.</td></tr></table><br></html>