pMEC1139

This vector expresses eight genes and was assembled from the eight single gene expression cassettes below:

Gene	Enzyme	Acronym	Cassette
SsXYL1	D-xylose reductase	XR	pYPK0_TEF1_PsXYL1_TDH3
SsXYL2	xylitol dehydrogenase	XDH	pYPK0_TDH3_PsXYL2_PGI1
ScXKS1	Xylulokinase	XK	pYPK0_PGI1_ScXKS1_FBA1
ScTAL1	Transaldolase	tal1p	pYPK0_FBA1_ScTAL1_PDC1
ScTKL1	Transketolase	TKL	pYPK0_PDC1_ScTKL1_RPS19b
ScRPE1	xylitol dehydrogenase	RPE	pYPK0_RPS19b_ScRPE1_RPS19a
ScRKI1	Xylulokinase	RKI	pYPK0_RPS19a_ScRKI1_TPI1
CiGXF1	Transaldolase	GXF	pYPK0_TPI1_CiGXF1_ENO2

TEF1_XR_TDH3
        TDH3_XDH_PGI1
                 PGI1_XK_FBA1
                         FBA1_TAL1_PDC1


                                   PDC1_ScTKL1_RPS19b
                                               RPS19b_ScRPE1_RPS19a
                                                             RPS19a_ScRKI1_TPI1
                                                                           TPI1_CiGXF1_ENO2

pMEC1136

pMEC1137



In [1]:

    
from pydna.all import *



In [2]:

    
# NBVAL_IGNORE_OUTPUT
from ipynb.fs.full.pMEC1136 import cas1, cas2, cas3, p4, p409









    




pMEC1136.gb



In [3]:

    
# NBVAL_IGNORE_OUTPUT
from ipynb.fs.full.pMEC1137 import p1 as p5, cas2 as cas6, cas3 as cas7, cas4 as cas8, p625, p647, p413









    




pMEC1137.gb



In [4]:

    
cas4 = pcr(p409, p625, p4)



In [5]:

    
cas5 = pcr(p413, p647, p5)



In [6]:

    
pYPK0 = read("pYPK0.gb")



In [7]:

    
pYPK0.description









    Out[7]:





'cSEGUID_qSJ95NM815X60yBy4l6iI69a_Dw_2018-05-15T07:40:31.009387'



In [8]:

    
pYPK0.cseguid()









    Out[8]:





qSJ95NM815X60yBy4l6iI69a_Dw



In [9]:

    
from Bio.Restriction import ZraI, AjiI, EcoRV



In [10]:

    
pYPK0_E_Z, stuffer = pYPK0.cut((EcoRV, ZraI))



In [11]:

    
pYPK0_E_Z, stuffer









    Out[11]:





(Dseqrecord(-5681), Dseqrecord(-81))



In [12]:

    
pYPK0_E_Z, cas1, cas2, cas3, cas4, cas5, cas6, cas7, cas8









    Out[12]:





(Dseqrecord(-5681),
 Amplicon(2432),
 Amplicon(2889),
 Amplicon(3532),
 Amplicon(2693),
 Amplicon(3723),
 Amplicon(2005),
 Amplicon(2022),
 Amplicon(2906))



In [13]:

    
asm = Assembly( (pYPK0_E_Z, cas1, cas2, cas3, cas4, cas5, cas6, cas7, cas8) , limit = 61)



In [14]:

    
asm









    Out[14]:





Assembly
fragments..: 5681bp 2432bp 2889bp 3532bp 2693bp 3723bp 2005bp 2022bp 2906bp
limit(bp)..: 61
G.nodes....: 20
algorithm..: common_sub_strings



In [15]:

    
candidate = asm.assemble_circular()[0]



In [16]:

    
candidate.figure()









    Out[16]:





 -|name|98
|       \/
|       /\
|       98|2432bp_PCR_prod|712
|                          \/
|                          /\
|                          712|2889bp_PCR_prod|1013
|                                              \/
|                                              /\
|                                              1013|3532bp_PCR_prod|644
|                                                                   \/
|                                                                   /\
|                                                                   644|2693bp_PCR_prod|969
|                                                                                       \/
|                                                                                       /\
|                                                                                       969|3723bp_PCR_prod|639
|                                                                                                           \/
|                                                                                                           /\
|                                                                                                           639|2005bp_PCR_prod|557
|                                                                                                                               \/
|                                                                                                                               /\
|                                                                                                                               557|2022bp_PCR_prod|596
|                                                                                                                                                   \/
|                                                                                                                                                   /\
|                                                                                                                                                   596|2906bp_PCR_prod|61
|                                                                                                                                                                       \/
|                                                                                                                                                                       /\
|                                                                                                                                                                       61-
|                                                                                                                                                                          |
 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------



In [17]:

    
pw = candidate.synced(pYPK0)



In [18]:

    
len(pw)









    Out[18]:





22594



In [19]:

    
pw.cseguid()









    Out[19]:





rjjimx-cVzquS3V5BPVMOWPSwAI



In [20]:

    
pw.name = "pMEC1138"
pw.description="pYPK0_TEF1_XR_TPI1_XDH_PDC1_XK_FBA1_TAL1_PDC1tpPDC1_ScTKL1_RPS19b_ScRPE1_RPS19a_ScRKI1_TPI1_CiGXF1_ENO2 (alternative name pYPK0_8)"
pw.stamp()









    Out[20]:





cSEGUID_rjjimx-cVzquS3V5BPVMOWPSwAI



In [21]:

    
import textwrap



In [22]:

    
pw.description = "\n".join( textwrap.wrap( pw.description, 40) )



In [23]:

    
pw.write("pMEC1139.gb")









    




pMEC1139.gb