Construction of pYPK0_TEF1_PsXYL1_N272D_TDH3 (pMEC1127)

This vector is identical to pMEC1126 (pYPK0_TEF1_PsXYL1_TDH3tp) but for a N272D mutation in the XYL1 reading frame.



In [1]:

    
from pydna.all import *



In [2]:

    
pYPK0_TEF1_PsXYL1_TDH3 =read("pYPK0_TEF1_PsXYL1_TDH3.gb")



In [3]:

    
len(pYPK0_TEF1_PsXYL1_TDH3)









    Out[3]:





8015



In [4]:

    
# NBVAL_IGNORE_OUTPUT
from IPython.display import IFrame
IFrame('http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988607', width='100%', height=250)









    Out[4]:



In [5]:

    
pYPK0_TEF1_PsXYL1_TDH3.list_features()









    Out[5]:





+-----+------------------+-----+------+------+-----+-------------+------+
| Ft# | Label or Note    | Dir | Sta  | End  | Len | type        | orf? |
+-----+------------------+-----+------+------+-----+-------------+------+
|   0 | L:167            | --> | 432  | 456  |  24 | primer_bind |  no  |
|   1 | nd               | --> | 537  | 1116 | 579 | source      |  no  |
|   2 | L:417_ScTEF1tpf  | --> | 537  | 560  |  23 | primer_bind |  no  |
|   3 | L:626_ScTEF1tpr_ | <-- | 1088 | 1116 |  28 | primer_bind |  no  |
|   4 | nd               | --> | 1163 | 2120 | 957 | gene        | yes  |
|   5 | nd               | --> | 1163 | 2120 | 957 | CDS         | yes  |
|   6 | L:XR_YPK_rec_fwd | --> | 1163 | 1189 |  26 | primer_bind |  no  |
|   7 | L:XR_YPK_rec_rev | <-- | 2094 | 2120 |  26 | primer_bind |  no  |
|   8 | L:568_pCAPsAjiIR | --> | 2123 | 2143 |  20 | primer_bind |  no  |
|   9 | nd               | --> | 2159 | 2857 | 698 | source      |  no  |
|  10 | L:415_ScTDH3tpf  | --> | 2159 | 2181 |  22 | primer_bind |  no  |
|  11 | L:623_ScTDH3tpr_ | <-- | 2831 | 2857 |  26 | primer_bind |  no  |
|  12 | L:166            | <-- | 2901 | 2925 |  24 | primer_bind |  no  |
|  13 | nd               | --> | 3370 | 3371 |   1 | rep_origin  |  no  |
|  14 | L:URA3           | <-- | 4229 | 5033 | 804 | misc        |  no  |
|  15 | L:AmpR           | --> | 6961 | 7620 | 659 | CDS         |  no  |
+-----+------------------+-----+------+------+-----+-------------+------+



In [6]:

    
xyl1 = pYPK0_TEF1_PsXYL1_TDH3.extract_feature(5)



In [7]:

    
wt_protein_seq = str(xyl1.seq.translate())



In [8]:

    
print(wt_protein_seq)









    



MPSIKLNSGYDMPAVGFGCWKVDVDTCSEQIYRAIKTGYRLFDGAEDYANEKLVGAGVKKAIDEGIVKREDLFLTSKLWNNYHHPDNVEKALNRTLSDLQVDYVDLFLIHFPVTFKFVPLEEKYPPGFYCGKGDNFDYEDVPILETWKALEKLVKAGKIRSIGVSNFPGALLLDLLRGATIKPSVLQVEHHPYLQQPRLIEFAQSRGIAVTAYSSFGPQSFVELNQGRALNTSPLFENETIKAIAAKHGKSPAQVLLRWSSQRGIAIIPKSNTVPRLLENKDVNSFDLDEQDFADIAKLDINLRFNDPWDWDKIPIFV*



In [9]:

    
print(wt_protein_seq[271])



In [10]:

    
pYPK0_TEF1_PsXYL1_TDH3.features[6].location.start









    Out[10]:





ExactPosition(1163)



In [11]:

    
codon = pYPK0_TEF1_PsXYL1_TDH3[1163+271*3:1163+271*3+3]



In [12]:

    
print(codon.seq)
print(codon.seq.translate())









    



AAC
N



In [13]:

    
candidate = (pYPK0_TEF1_PsXYL1_TDH3[:1163+271*3]+
             Dseqrecord("GAC")+
             pYPK0_TEF1_PsXYL1_TDH3[1163+271*3+3:]).looped()



In [14]:

    
new_feature = pYPK0_TEF1_PsXYL1_TDH3.features[8]
new_feature.qualifiers = {"label":"PsXYL1_N272D"}
candidate.features.append(new_feature)



In [15]:

    
candidate









    Out[15]:





Dseqrecord(o8015)



In [16]:

    
candidate.cseguid()









    Out[16]:





Y_e9Pjnu1AMSxxIPez6jXh8kvUU



In [17]:

    
candidate.id = "pMEC1127"
#candidate.description = "pYPK0_TEF1_PsXYL1_N272D_TDH3tp"
candidate.stamp()









    Out[17]:





cSEGUID_Y_e9Pjnu1AMSxxIPez6jXh8kvUU



In [18]:

    
candidate.write("pYPK0_TEF1_PsXYL1_N272D_TDH3.gb")









    




pYPK0_TEF1_PsXYL1_N272D_TDH3.gb

Download sequence

pYPK0_TEF1_PsXYL1_N272D_TDH3



In [19]:

    
reloaded = read("pYPK0_TEF1_PsXYL1_N272D_TDH3.gb")



In [20]:

    
reloaded.cseguid()









    Out[20]:





Y_e9Pjnu1AMSxxIPez6jXh8kvUU