ResearchPage+-+Chijioke

__Protein Enzyme Assay__
Absorbance taken @ 410 nm Molecular Weight: 33512.8 kDa

__1st Run (#39-46)__: Initial Conc.- .4 mg/mL

A: .000 B: .570 C: 1.103 D: 1.003 E: .950 F: .581 G: .616 H: 1.405

__2nd Run (#31-38)__: Initial Conc.- .5 mg/mL

A: .000 B: .417 C: .238 D: .325 E: .252 F: .893 G: .617 H: .982

__HF9 Library__


- #1 best ligand (RH00719SC)

- #2 best ligand (BTB05187SC)

- #3 best ligand (DFP00065SC)

- #4 best ligand (HTS09290SC)

- #5 best ligand (BTB08339SC)

- #6 best ligand (JFD03976SC)

- #7 best ligand (RJF00101SC)

- #8 best ligand (BR00114SC)

- #9 best ligand (HTS11989SC)

- #10 best ligand (CD03598SC)

[[image:vdsstream/coo237_ChijiokeOkorie_YopHvsCB306Top5Ligands.PNG width="800" height="135"]]
- Top 5 Ligands found in library

- #1 best ligand (7575772)



- #2 best ligand (5467784)



- #3 best ligand (7842136)



- #4 best ligand (7726180)



- #5 best ligand (6629394)

__Protein Characterization__


Well #1: Marker Well #2: Sample #0 (A) Well #3: Sample #1 (A) Well #4: Sample #2 (Flow Through) Well #5: Sample #3 (Wash) Well #6: Sample #4 (Elution #1) Well #7: Sample #5 (Elution #2)

[[image:vdsstream/coo237_ChijiokeOkorie_YopHFPLCGraph_111611.PNG width="800" height="231"]]
- After running the process, it was found that fractions #31-38 and #39-46 were the best ones for in assay and inhibition. I later would concentrate each set of fractions for use.

__Protein Purification__
- Sample #3 (Flow Through) - Sample #4 (Wash) - Sample #5 (Elution #1) - Sample #6 (Elution #2)

__Protein Expression__


- Sample #0 (A & B) - Sample #1 (A & B) - Sample #2 [made from combination of A & B samples of #0 and #1]

[[image:vdsstream/coo237_ChijiokeOkorie_YopHExpressionMasterPlate.PNG]]
- YopH Master Plate

- pNIC-Bsa4 PCR Cloning Gel

- pNIC-Bsa4 Nanodrop Graph

- Sample 1

- Sample 2 (Take 1)

- Sample 2 (Take 2)

- Sample 3

- Sample 4 (Take 1)

- Sample 4 (Take 2)

- Sample 5 (Take 1)

- Sample 5 (Take 2)

- Sample 6 (Take 1)

- Sample 6 (Take 2)

- Sample 7 (Take 1)

- Sample 7 (Take 2)

- Sample 8 (Take 1)

- Sample 8 (Take 2)

Week 6 -
Chijioke - good job. Don't need to show so much of primer design. Maybe just show your final primers (oligos). --Dr. B

__PCR Primer Design for Yersinia pestis (YopH)__
The oligonucleotide assembly is: 1 10 20 30 40 50 60 | | | | | | |

1 ---> 1 ATGCGCGAACGCCCACACACCTCTGGTCACCACGGTGCCGGCGAAGCTCGCGCAACCGC CGAGCGCGTTGGCGC

M R E R P H T S G H H G A G E A R A T A

| | | | | | |

3 ---> 61 aggctcgtgccgaactgtcttctcgtctgacc GGAAGATGGCAAAGGGGTATGCCAGGCCTCCGAGCACGGCTTGAC <--- 2 P S T V S P Y G P E A R A E L S S R L T

| | | | | | |

5 ---> 121 accctgcgtaataccctggcaccagcaa GCATGTGGT atgggaccgtggtcgttggttgctgggcgcaatggacgttcgtacacca

T L R N T L A P A T N D P R Y L Q A C G

| | | | | | |

181 GGTGAAAAACTCAACCGCTTCCGTGACATCCAATGCCGTCGTCAGACCGCA ccactttttga GGCAGCAGTCTGGCGTCAAGCACGC <--- 4 G E K L N R F R D I Q C R R Q T A V R A

| | | | | | |

7 ---> 241 actacatccaggttggtaacactcgcaccatcgcctgccagtacccg CTAGACTTGCGCTTGATGTAGGTCCAACCATTGTG gggc <--- 6 D L N A N Y I Q V G N T R T I A C Q Y P

| | | | | | |

9 ---> 301 ctgcagtctcaac TGAAAACCGTACCCCGGTTCTG gacgtcagagttgaccttagagtgaaggcgtacgaccgacttttggcatggggcca <--- 8 L Q S Q L E S H F R M L A E N R T P V L

| | | | | | |

1 361 GCTGTGCTGGCGTCTTCTTCTGAGATCGCGAATCAGCG c  GACTCTAGCGCTTAGTCGCAAAGCCATACGGCCTGATGAAG

A V L A S S S E I A N Q R F G M P D Y F

| | | | | | |

1 ---> 421 cgtcaatctggtacctacggttctatcaccgttgaatccaaaatgacccagcaggtcgg GCAGTTAGACCATGGATGC tactgggtcgtccagcca <--- 10 R Q S G T Y G S I T V E S K M T Q Q V G

| | | | | | |

13 ---> 481 GACATGTACACCCTGACCATCCGTGAAGCGGGTCAGAAA gacccactgccatagtaccgcctgtacatgtgggactggtag <--- 12 L G D G I M A D M Y T L T I R E A G Q K

| | | | | | |

15 ---> 541 ACCATCTCTGTTCCGGTTGTT aaaccgccgtttctagc GGTAGAGACAAGGCCAACAAGTGCAGCCATTGACCGGCCTAGTTTGGCGGCAAAGATCG <--- 1 T I S V P V V H V G N W P D Q T A V S S

| | | | | | |

601 gaggtcactaaagcgctcgcttctctggttgatcagactgcgg C gaccaactagtctgacgcctctggtttgcattgtac 4 E V T K A L A S L V D Q T A E T K R N M

| | | | | | |

17 ---> 661 TGAATCTAAAGGTTCCTCTGCCGTTGCGGACGACTCCAAACTGCGTCCAGTTATCCAC atacttagatttccaaggagacgg GACGCAGGTCAATAGGTG <--- 16 Y E S K G S S A V A D D S K L R P V I H

| | | | | | |

19 ---> 721 TG gcagctgatcggtgcgatgtgcatgaacgactct ACAGCGCGTCCACAACCAGCATGCCGCGTCGACTAGCCACGC <--- 18 C R A G V G R T A Q L I G A M C M N D S

| | | | | | |

21 ---> 781 cgtaactctcagctctctgtcgagga CCAGCGCAATGGT gagtcgagagacagctcctgtaccaaagagtttacgcacaggtcgcgttacca

R N S Q L S V E D M V S Q M R V Q R N G

| | | | | | |

841 ATTATGGTTCAGAAAGACGAACAGCTGGACGTTCTCATTAAACTGGC taatacc CCTGCAAGAGTAATTTGACCGCCTTCCGGTCCCG <--- 20 I M V Q K D E Q L D V L I K L A E G Q G

| | | | | | |

901 GCAGGCGACGACTTGAGAATT <--- 22 R P L L N S X

Frequency Range Number of Codons - 0% - 4% 0  5% - 9% 4  10% - 14% 7  15% - 19% 18  20% - 24% 12  25% - 29% 13  30% - 34% 44  35% - 39% 19  40% - 44% 3  45% - 49% 3  >= 50% 184  -  Total Codons Used = 307

Tm Range # of Overlaps - <59 0  59 0  60 0  61 10  62 11  63 0  64 0  65 0  66 0  >=67 0  -  Tm Range = 1.9

Ovrlap Len Range # of Oligos - <15 1  15 0  16 2  17 4  18 2  19 3  20 5  21 2  22 2  23 0  24 0  >=25 0  -  Lowest Overlap = 14

Length Range # of Oligos - <51 0  51-52 0  53-54 0  55-56 1  57-58 0  59-60 21  61-62 0  63-64 0  65-66 0  67-68 0  69-70 0  >=71 0  -  Longest = 60

22 oligonucleotides need to be synthesized 1 ATGCGCGAACGCCCACACACCTCTGGTCACCACGGTGCCGGCGAAGCTCGCGCAACCGC 59 2 CAGTTCGGCACGAGCCTCCGGACCGTATGGGGAAACGGTAGAAGGCGCGGTTGCGCGAGC 60 3 AGGCTCGTGCCGAACTGTCTTCTCGTCTGACCACCCTGCGTAATACCCTGGCACCAGCAA 60 4 AGTTTTTCACCACCACATGCTTGCAGGTAACGCGGGTCGTTGGTTGCTGGTGCCAGGGTA 60 5 GCATGTGGTGGTGAAAAACTCAACCGCTTCCGTGACATCCAATGCCGTCGTCAGACCGCA 60 6 GTGTTACCAACCTGGATGTAGTTCGCGTTCAGATCCGCACGAACTGCGGTCTGACGACGG 60 7 ACTACATCCAGGTTGGTAACACTCGCACCATCGCCTGCCAGTACCCGCTGCAGTCTCAAC 60 8 ACCGGGGTACGGTTTTCAGCCAGCATGCGGAAGTGAGATTCCAGTTGAGACTGCAGCGGG 60 9 TGAAAACCGTACCCCGGTTCTGGCTGTGCTGGCGTCTTCTTCTGAGATCGCGAATCAGCG 60 10 CGTAGGTACCAGATTGACGGAAGTAGTCCGGCATACCGAAACGCTGATTCGCGATCTCAG 60 11 CCGTCAATCTGGTACCTACGGTTCTATCACCGTTGAATCCAAAATGACCCAGCAGGTCGG 60 12 GATGGTCAGGGTGTACATGTCCGCCATGATACCGTCACCCAGACCGACCTGCTGGGTCAT 60 13 GACATGTACACCCTGACCATCCGTGAAGCGGGTCAGAAAACCATCTCTGTTCCGGTTGTT 60 14 CGCTAGAAACGGCGGTTTGATCCGGCCAGTTACCGACGTGAACAACCGGAACAGAGATGG 60 15 AAACCGCCGTTTCTAGCGAGGTCACTAAAGCGCTCGCTTCTCTGGTTGATCAGACTGCGG 60 16 GGCAGAGGAACCTTTAGATTCATACATGTTACGTTTGGTCTCCGCAGTCTGATCAACCAG 60 17 TGAATCTAAAGGTTCCTCTGCCGTTGCGGACGACTCCAAACTGCGTCCAGTTATCCACTG 60 18 CGCACCGATCAGCTGCGCCGTACGACCAACACCTGCGCGACAGTGGATAACTGGACGCAG 60 19 GCAGCTGATCGGTGCGATGTGCATGAACGACTCTCGTAACTCTCAGCTCTCTGTCGAGGA 60 20 CCATAATACCATTGCGCTGGACACGCATTTGAGAAACCATGTCCTCGACAGAGAGCTGAG 60 21 CCAGCGCAATGGTATTATGGTTCAGAAAGACGAACAGCTGGACGTTCTCATTAAACTGGC 60 22 TTAAGAGTTCAGCAGCGGACGGCCCTGGCCTTCCGCCAGTTTAATGAGAACGTCC 55

FINAL SUMMARY FOR 1 SOLUTION
 * 1) Tm Len | Score TmRange Short Long #Olig #Repeat #Misprime

1 62 60 | 0.000 1.9 14 60 22 0 0

__PCR Overlap__


Lane 1: skipped Lane 2: 100 bp Ladder Lane 3: Primary (1**°**) PCR Primer - YopH Lane 4: Secondary (2**°**) PCR Primer - YopH

- Nanodrop Graph of PCR² Primer with Yersinia pestis (YopH)

__Virtual Screening Refresher__
- Table of Top 11 Ligands

__Top 10 Ligands Images__
- BindingDB_50228029, #1 best ligand

- 5193911, #2 best ligand

- 5157370, #3 best ligand

- 5185261, #4 best ligand

- 5224221, #5 best ligand

- 5143470, #6 best ligand

- 5109057, #7 best ligand

- 5186972, #8 best ligand

- 5230391, #9 best ligand

- 5159193, #10 best ligand

__Top 3 Ligands__


ID: BindingDB_50228029 Mol. Weight: 610.719343 Molecular Formula: C30H31FN4O5S2 Mol. Name: 3-fluoro-N-[1-[5-(4-phenylbutyl)-1H-imidazol-2-yl]-2-[4-(1,1,3-trioxo-1, 2-thiazolidin-5-yl)phenyl]ethyl]benzenesulfonamide hDon: 3 hAcc: 7



__PCR pNIC-Bsa4 Gel Run__


Lane 1: Skipped Lane 2: 100 bp Ladder Lane 3: PCR pNIC-Bsa4 (Highest Conc. of pLIC) Lane 4: PCR pNIC-Bsa4 (Medium Conc. of pLIC) Lane 5: PCR pNIC-Bsa4 (Lowest Conc. of pLIC) Lane 6: PCR pNIC-Bsa4 (No pLIC; Control)

__PyMol Refresher__
- View of the chains, active sites,and polar contacts in 2H2Q

- View of the chains, active sites,and polar contacts in 3CL9

- View of the chains, active sites,and polar contacts in 1U72

- Combination of the active sites for 1U72 & 3CL9, showing each of their polar contacts

- Four different chains involved in the protein 3HBB

- Comparison of both NAP (MTX) for the 1st chain in 3HBB

__Submitting DNA Sequence__
__Forward Reaction__

NNNNNNNNNNNNNNNNNNNNNNNNANTGGGCNNGNCGTCNCATGCTCCCGGCCGCCNTGGCCGCGGNNTTTTAGTGANGNTNNNGGNGNNGACCNNNAATGATTCTNATTGNTTGANGGATAANTNNNNNGNNTGNGATCGTTAANCNNNNGNCCNANANGGNTTNTNNGGGAGGCACNNNNAATGCACACTACTTTNANGGCCAAGGCNATGGAAAACGAANNCCTTANGAGGGGGANNANAGGGCAAAGCTNACTGNCACCNANGGTGGACCTCTGCCNTTTGCTTGGGATATTTNATCACCACTGNCTCNANACNGAANCATACNATTNACCNGNNNNCCNGAATACATCCCTGANNATGTAAANCANTCATTCCCTGAGGGATANACATGGGAGAGGATCATGAACTTNNNANATNGNNNGGNGTGTACTGTCNNCNATGATNNCAGNATCNGANGAAACTGNTTNNTCTACNNNNNNCANTNTCNNAAAGTGAANTTTCCNCCCCNTGNACNTGNTATGCNGAAAAANANATNNGCCTGNNAACAANANNNNNANANNCTCNNTNCGNTGGATGNCANGNTCAGCTGAAACNACTTNNNGNNTCTNAAGTTGNNNNNANGTGGTTACAATNTNNGTGAATNNNCTTCTACTGNTGAGCATGNANGNCNGNGNGGACGCNNGGNANANNNNNTNNCCCTCACACTGNNNGTANCCANGCNCGNCNAGGATTNAANATTCGTNGANNNATNNNTAAATATCCNNTGNACGCCGCTCNTNCNNNNTCANCTNCATNNNCATCTNTAAAANNTCNNNANGNNTGNNNNGTCNGGNANCATGNNNNNCNGGNCCAANTCNNGCTCNNNNNGANNNNNANNNNNNNNTTCCTTGGGCCACCGGTTTTCNANNNNNNNNNTNNNNNAAAACTTCGANTTTCCNNNNNATTGNCNANNNNNNTCGTCCCCCNTTCCCNNCNTNGNNNNNNAAN

- Blast made through Nucleotides

__Reverse Reaction__

NNNNNNNNNNNGGTGANCTATAGAATACTCAAGCTATGCATCCNACGCGTTGGGAGCTCTCCCATATGGTCGACCTGCAGGCGGCCGCACTAGTGATTTTGATTGATTGAAGGAGAAATATCATGAGTGTGATCGCTAAACAAATGACCTACAAGGTTTATATGTCAGGCACGGTCAATGGACACTACTTTGAGGTCGAAGGCGATGGAAAAGGAAAGCCTTACGAGGGGGAGCAGACGGTAAAGCTCACTGTCACCAAGGGTGGACCTCTGCCATTTGCTTGGGATATTTTATCACCACTGTCTCAATACGGAAGCATACCATTCACCAAGTACCCTGAAGACATCCCTGATTATGTAAAGCAGTCATTCCCTGAGGGATATACATGGGAGAGGATCATGAACTTTGAAGATGGTGCAGTGTGTACTGTCAGCAATGATTCCAGCATCCAAGGCAACTGTTTCATCTACAATGTCAAAATCTCTGGTGTGAACTTTCCTCCCAATGGACCTGTTATGCAGAAGAAGACACAGGGCTGGGAACCCAACACTGAGCGTCTCTTTGCACGAGATGGAATGCTGATAGGAAACAACTTTATGGCTCTGAAGTTGGAAGGAGGTGGTTACTATTTGTGTGAATTCAAATCTACTTACAAGGCAAAGAAGCCTGTGAGGATGCCAGGGTATCACTATGTTGACCGCAAACTGGATGTAACCAGTCACAACAAGGATTACACATTTGTTGAGCAGTGTGAAATATCCATTGCACGCCACTCTTTGCTCGGTCATCACCATCACCATCACTAAAATCCCGCGGCCATGGCGGCCGGGAGCATGCGACGTCGGGCCCAATTCGCCCTATAGTGAGTCGTATTACAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGNGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGANGCCCGCACCGATCGCCNTTCCCANCAGTTGCGCAGCCTGNATGGNGAATGGNCNCNNCCNGNANNGNNCATNAGCGCGNNNNNNNNNNNNCNNNCAGNNNNACGCTANNNTTNCNNCNCNANCNNCGNNCTTNNGNTTNNNNNNTTTNNNNCNNNNTNNCNNTTTCCNTCAGNNNNNNNNGGGNNNNNNTNNNNCNANTNNNNTNNNNNNNNNCNNNNNNNNNNNNGGNNNNNNGNNNNNCNNNNNNNNNNNNNNN

- Human Blast

- Nucleotide Blast

__Restriction Enzyme Digest__


Lane 1: Skipped Lane 2: 1 kb Ladder Lane 3: Uncut pGBR-22 Lane 4: EcoRI, cut with pGBR-22 (Tube A) Lane 5: PvuII, cut with pGBR-22 (Tube B) Lane 6: EcoRI + PvuII, cut with pGBR-22 (Tube C)

1st Attempt:
Lane 1: Skipped Lane 2: 100 bp Ladder Lane 3: PCR pGBR-22 (Tube A), none shown Lane 4: PCR pGBR-22 (Tube B), none shown Lane 5: PCR pGBR-22 (Tube C), none shown Lane 6: PCR pGBR-22 (Tube D), none shown

2nd Attempt:


Lane 1: Skipped Lane 2: 100 bp Ladder Lane 3: PCR pGBR-22 (Tube A), none shown Lane 4: PCR pGBR-22 (Tube B), none shown Lane 5: PCR pGBR-22 (Tube C), none shown Lane 6: PCR pGBR-22 (Tube D), none shown

3rd Attempt:



Lane 1: Skipped Lane 2: 100 bp Ladder Lane 3: PCR pGBR-22 (Tube A) Lane 4: PCR pGBR-22 (Tube B) Lane 5: PCR pGBR-22 (Tube C) Lane 6: PCR pGBR-22 (Tube D)

__Analyzing DNA Sequence__
`NNNNNNNNNNNTATNGNATACTCAAGCTATGCATCCAACGCGTTGGGAGCTCTCCCATATGGTCGACCTGCAGGCGGCCGCACTAGTGATTTTGATTGATTGAAGGAGAAATATCATGAGTGTGATCGCTAAACAAATGACCTACAAGGTTTATATGTCAGGCACGGTCAATGGACACTACTTTGAGGTCGAAGGCGATGGAAAAGGAAAGCCTTACGAGGGGGAGCAGACGGTAAAGCTCACTGTCACCAAGGGTGGACCTCTGCCATTTGCTTGGGATATTTTATCACCACTGTCTCAATACGGAAGCATACCATTCACCAAGTACCCTGAAGACATCCCTGATTATGTAAAGCAGTCATTCCCTGAGGGATATACATGGGAGAGGATCATGAACTTTGAAGATGGTGCAGTGTGTACTGTCAGCAATGATTCCAGCATCCAAGGCAACTGTTTCATCTACAATGTCAAAATCTCTGGTGTGAACTTTCCTCCCAATGGACCTGTTATGCAGAAGAAGACACAGGGCTGGGAACCCAACACTGAGCGTCTCTTTGCACGAGATGGAATGCTGATAGGAAACAACTTTATGGCTCTGAAGTTGGAAGGAGGTGGTTACTATTTGTGTGAATTCAAATCTACTTACAAGGCAAAGAAGCCTGTGAGGATGCCAGGGTATCACTATGTTGACCGCAAACTGGATGTAACCAGTCACAACAAGGATTACACATTTGTTGAGCAGTGTGAAATATCCATTGCACGCCACTCTTTGCTCGGTCATCACCATCACCATCACTAAAATCCCGCGGCCATGGCGGCCGGGAGCATGCGACGTCGGGCCCAATTCGCCCTATAGTGAGTCGTATTACAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAANAGGCCCGCACCGATCGCCCTTCCCACAGTTGCGCAGCCTGATGGCNATGGACGCNNCCTGNANCGNCGCATTAGCNCGGCNGGNNNGNGNNCNCGCAGCGNGACNCTACANTTNCNGCNNCNANCNNNNNCNTTCNNTTNTNCNNNTNNNNNNNNNNNNNNNTTNCCGNNAGNTNNAANNGGGGNNNNNNNNNATNNGNTNNNNNNNNNNCCAAANTGNNNGNNNNGNNNNNNNNGNNNNNNNNNNNNNNNNNNNNNNNGANCNNNNNNNNNNNNANNNNNNNNNNNCNNNNNAANNNNNCCNNTNNN
 * VDS4_M13R.. Original Sequence: **

TATNGNATACTCAAGCTATGCATCCAACGCGTTGGGAGCTCTCCCATATGGTCGACCTGCAGGCGGCCGCACTAGTGATTTTGATTGATTGAAGGAGAAATATCATGAGTGTGATCGCTAAACAAATGACCTACAAGGTTTATATGTCAGGCACGGTCAATGGACACTACTTTGAGGTCGAAGGCGATGGAAAAGGAAAGCCTTACGAGGGGGAGCAGACGGTAAAGCTCACTGTCACCAAGGGTGGACCTCTGCCATTTGCTTGGGATATTTTATCACCACTGTCTCAATACGGAAGCATACCATTCACCAAGTACCCTGAAGACATCCCTGATTATGTAAAGCAGTCATTCCCTGAGGGATATACATGGGAGAGGATCATGAACTTTGAAGATGGTGCAGTGTGTACTGTCAGCAATGATTCCAGCATCCAAGGCAACTGTTTCATCTACAATGTCAAAATCTCTGGTGTGAACTTTCCTCCCAATGGACCTGTTATGCAGAAGAAGACACAGGGCTGGGAACCCAACACTGAGCGTCTCTTTGCACGAGATGGAATGCTGATAGGAAACAACTTTATGGCTCTGAAGTTGGAAGGAGGTGGTTACTATTTGTGTGAATTCAAATCTACTTACAAGGCAAAGAAGCCTGTGAGGATGCCAGGGTATCACTATGTTGACCGCAAACTGGATGTAACCAGTCACAACAAGGATTACACATTTGTTGAGCAGTGTGAAATATCCATTGCACGCCACTCTTTGCTCGGTCATCACCATCACCATCACTAAAATCCCGCGGCCATGGCGGCCGGGAGCATGCGACGTCGGGCCCAATTCGCCCTATAGTGAGTCGTATTACAATTCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAANAGGCCCGCACCGATCGCCCTTCCCACAGTTGCGCAGCCTGATGGCNATGGACGCNNCCTGNANCGNCGCATTAGCNCGGCNGGNNNGNGNNCNCGCAGCGNGACNCTACANTTNCNGCNNCNANCNNNNNCNTTCNNTTNTNCNNNT
 * VDS_M13R.. Without the N’s: **


 * Blast #1: **


 * Blast #2: **




 * Comparison to Known DNA: **



Translation with the PurpleProteinCodingSequenceforBB.txt:

>rf 1 UntitledMSVIAKQMTYKVYMSGTVNGHYFEVEGDGKGKPYEGEQTVKLTVTKGGPLPFAWDILSPLSQYGSIPFTKYPEDIPDYVKQSFPEGYTWERIMNFEDGAVCTVSNDSSIQGNCFIYNVKISGVNFPPNGPVMQKKTQGWEPNTERLFARDGMLIGNNFMALKLEGGGYYLCEFKSTYKAKKPVRMPGYHYVDRKLDVTSHNKDYTFVEQCEISIARHSLLGHHHHHH* ORF: >1c1|Sequence 1 ORF:105...788 Frame +3ATGAGTGTGATCGCTAAACAAATGACCTACAAGGTTTATATGTCAGGCACGGTCAATGGACACTACTTTGAGGTCGAAGGCGATGGAAAAGGAAAGCCTTACGAGGGGGAGCAGACGGTAAAGCTCACTGTCACCAAGGGTGGACCTCTGCCATTTGCTTGGGATATTTTATCACCACTGTCTCAATACGGAAGCATACCATTCACCAAGTACCCTGAAGACATCCCTGATTATGTAAAGCAGTCATTCCCTGAGGGATATACATGGGAGAGGATCATGAACTTTGAAGATGGTGCAGTGTGTACTGTCAGCAATGATTCCAGCATCCAAGGCAACTGTTTCATCTACAATGTCAAAATCTCTGGTGTGAACTTTCCTCCCAATGGACCTGTTATGCAGAAGAAGACACAGGGCTGGGAACCCAACACTGAGCGTCTCTTTGCACGAGATGGAATGCTGATAGGAAACAACTTTATGGCTCTGAAGTTGGAAGGAGGTGGTTACTATTTGTGTGAATTCAAATCTACTTACAAGGCAAAGAAGCCTGTGAGGATGCCAGGGTATCACTATGTTGACCGCAAACTGGATGTAACCAGTCACAACAAGGATTACACATTTGTTGAGCAGTGTGAAATATCCATTGCACGCCACTCTTTGCTCGGTCATCACCATCACCATCACTAA
 * Compare Protein Tranlsations: **


 * Lost In Translation: **

Translation 1:

>rf 1 UntitledXXXXXXYSSYASNALGALPYGRPAGGRTSDFD*LKEKYHECDR*TNDLQGLYVRHGQWTLL*GRRRWKRKALRGGADGKAHCHQGWTSAICLGYFITTVSIRKHTIHQVP*RHP*LCKAVIP*GIYMGEDHEL*RWCSVYCQQ*FQHPRQLFHLQCQNLWCELSSQWTCYAEEDTGLGTQH*ASLCTRWNADRKQLYGSEVGRRWLLFV*IQIYLQGKEACEDARVSLC*PQTGCNQSQQGLHIC*AV*NIHCTPLFARSSPSPSLKSRGHGGREHATSGPIRPIVSRITIHWPSFYNVVTGKTLALPNLIALQHIPLSPAGVIAXRPAPIALPTVAQPDGXGRXLXRRISXAGXXXRSXTLXXXXXXXXFXXXXXXXXXXPXXXXGXXXXXXXXXPXXXXXXXXXXXXXXXXXXXXXXXXXXXXXPX

Translation 2:

>rf 2 UntitledXXXXXXTQAMHPTRWELSHMVDLQAAALVILID*RRNIMSVIAKQMTYKVYMSGTVNGHYFEVEGDGKGKPYEGEQTVKLTVTKGGPLPFAWDILSPLSQYGSIPFTKYPEDIPDYVKQSFPEGYTWERIMNFEDGAVCTVSNDSSIQGNCFIYNVKISGVNFPPNGPVMQKKTQGWEPNTERLFARDGMLIGNNFMALKLEGGGYYLCEFKSTYKAKKPVRMPGYHYVDRKLDVTSHNKDYTFVEQCEISIARHSLLGHHHHHH*NPAAMAAGSMRRRAQFAL**VVLQFTGRRFTTS*LGKPWRYPT*SPCSTSPFRQLA**RXGPHRSPFPQLRSLMAMDAXXXXALARXXXXXAAXXYXXXXXXXXSXXXXXXXXXXRXXXXGXXXXXXXXXQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Translation 3:

>rf 3 UntitledXXXYXILKLCIQRVGSSPIWSTCRRPH**F*LIEGEIS*V*SLNK*PTRFICQARSMDTTLRSKAMEKESLTRGSRR*SSLSPRVDLCHLLGIFYHHCLNTEAYHSPSTLKTSLIM*SSHSLRDIHGRGS*TLKMVQCVLSAMIPASKATVSSTMSKSLV*TFLPMDLLCRRRHRAGNPTLSVSLHEMEC**ETTLWL*SWKEVVTICVNSNLLTRQRSL*GCQGITMLTANWM*PVTTRITHLLSSVKYPLHATLCSVITITITKIPRPWRPGACDVGPNSPYSESYYNSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEXARTDRPSHSCAA*WXWTXPXXXH*XGXXXXXQRDXTXXAXXXXXXXXXXXXXXXXXXXXXGXXXXXXXXXKXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Translation with the PurpleProteinCodingSequenceforBB.txt:

>rf 1 UntitledMSVIAKQMTYKVYMSGTVNGHYFEVEGDGKGKPYEGEQTVKLTVTKGGPLPFAWDILSPLSQYGSIPFTKYPEDIPDYVKQSFPEGYTWERIMNFEDGAVCTVSNDSSIQGNCFIYNVKISGVNFPPNGPVMQKKTQGWEPNTERLFARDGMLIGNNFMALKLEGGGYYLCEFKSTYKAKKPVRMPGYHYVDRKLDVTSHNKDYTFVEQCEISIARHSLLGHHHHHH* ORF: >1c1|Sequence 1 ORF:105...788 Frame +3ATGAGTGTGATCGCTAAACAAATGACCTACAAGGTTTATATGTCAGGCACGGTCAATGGACACTACTTTGAGGTCGAAGGCGATGGAAAAGGAAAGCCTTACGAGGGGGAGCAGACGGTAAAGCTCACTGTCACCAAGGGTGGACCTCTGCCATTTGCTTGGGATATTTTATCACCACTGTCTCAATACGGAAGCATACCATTCACCAAGTACCCTGAAGACATCCCTGATTATGTAAAGCAGTCATTCCCTGAGGGATATACATGGGAGAGGATCATGAACTTTGAAGATGGTGCAGTGTGTACTGTCAGCAATGATTCCAGCATCCAAGGCAACTGTTTCATCTACAATGTCAAAATCTCTGGTGTGAACTTTCCTCCCAATGGACCTGTTATGCAGAAGAAGACACAGGGCTGGGAACCCAACACTGAGCGTCTCTTTGCACGAGATGGAATGCTGATAGGAAACAACTTTATGGCTCTGAAGTTGGAAGGAGGTGGTTACTATTTGTGTGAATTCAAATCTACTTACAAGGCAAAGAAGCCTGTGAGGATGCCAGGGTATCACTATGTTGACCGCAAACTGGATGTAACCAGTCACAACAAGGATTACACATTTGTTGAGCAGTGTGAAATATCCATTGCACGCCACTCTTTGCTCGGTCATCACCATCACCATCACTAA

Slicing & Dicing
- DNA cut with only EcoRI

- DNA cut with only PvuII

- DNA cut with both EcoRI & PvuII