(1)The cutting patterns of EcoRI, Sau3AI, HinfI, and MseI:
EcoRI 0
Sau3AI 3
Sau3AI 'GATC_ - 3 Cut(s)
39 162 215
HinfI 1
HinfI G'AnT_C - 1 Cut(s)
152
MseI 1
MseI T'TA_A - 1 Cut(s)
168
Restriction Map of Sequence
Sau3AI
\
1 aaaaccatcaaatacgttatgctggaatgcaacgaactgatcccgctgttctacgaaacc 60
ttttggtagtttatgcaatacgaccttacgttgcttgactagggcgacaagatgctttgg
^ * ^ * ^ * ^ * ^ * ^ *
K T I K Y V M L E C N E L I P L F Y E T
61 tgcccggctggtgaaaacatctgctacgaaatgttcatggttgctaccccgaaagttccg 120
acgggccgaccacttttgtagacgatgctttacaagtaccaacgatggggctttcaaggc
^ * ^ * ^ * ^ * ^ * ^ *
C P A G E N I C Y E M F M V A T P K V P
MseI
Sau3AI
HinfI
\ \ \
121 tgcgaacgtggttgcatcgacgtttgcccggaatcttctctgatcgttaaatacgtttgc 180
acgcttgcaccaacgtagctgcaaacgggccttagaagagactagcaatttatgcaaacg
^ * ^ * ^ * ^ * ^ * ^ *
C E R G C I D V C P E S S L I V K Y V C
Sau3AI
\
181 tgcaacaccgaccgttgccagtaatccagcgcctgatctctcgaaataaaagccgcatt 240
acgttgtggctggcaacggtcattaggtcgcggactagagagctttattttcggcgtaa
^ * ^ * ^ * ^ * ^ * ^ *
C N T D R C Q Z S S A Z S L E I K A A
Ladder Map of Restriction Enzyme Cut Sites
20 40 60 80 100 120 140 160 180 200 220 240
: : : : : : : : : : : :
HinfI ------------------------------------------------------------------------------------------\-----------------------------------------------------
MseI ----------------------------------------------------------------------------------------------------\-------------------------------------------
Sau3AI ----------------------\-------------------------------------------------------------------------\-------------------------------\---------------
(2)The corresponding polypeptide sequence:
MLECNELIPLFYETCPAGENICYEMFMVATPKVPCERGCIDVCPESSLIV KYVCCNTDRCQ*
(3)It is a new toxin.
Since we can not find a protein which is of 100% identities with the toxin in the protein database
(the highest is of 75% identities), David Liu must have found a new toxin.
Database: Non-redundant GenBank+EMBL+DDBJ+PDB sequences
278,785 sequences; 413,172,879 total letters.
Smallest
Sum
High Probability
Sequences producing High-scoring Segment Pairs: Score P(N) N
gb|L04640|NAJCRDTXN Malayan spitting cobra cardiotoxin m... 510 2.9e-35 1
gb|U58486|NAU58486 Naja atra cardiotoxin 3' mRNA, compl... 382 9.5e-23 1
gb|U42585|NAU42585 Naja atra cardiotoxin III mRNA, comp... 364 4.0e-21 1
gb|L04640|NAJCRDTXN Malayan spitting cobra cardiotoxin mRNA, complete cds.
Length = 373
Plus Strand HSPs:
Score = 510 (140.9 bits), Expect = 2.9e-35, P = 2.9e-35
Identities = 138/183 (75%),Positives = 138/183 (75%), Strand = Plus / Plus
Query: 22 CTGGAATGCAACGAACTGATCCCGCTGTTCTACGAAACCTGCCCGGCTGGTGAAAACATC 81
||| | |||||| | ||| | || || |||||| |||| || ||||| || ||||| |
Sbjct: 98 CTGAAGTGCAACAAGCTGGTGCCCCTTTTCTACAAAACTTGTCCGGCCGGCAAAAACCTT 157
Query: 82 TGCTACGAAATGTTCATGGTTGCTACCCCGAAAGTTCCGTGCGAACGTGGTTGCATCGAC 141
|||||| |||||||||||||||| |||||||| ||||| | |||| || ||||| |||
Sbjct: 158 TGCTACAAAATGTTCATGGTTGCCACCCCGAAGGTTCCTGTCAAACGCGGGTGCATTGAC 217
Query: 142 GTTTGCCCGGAATCTTCTCTGATCGTTAAATACGTTTGCTGCAACACCGACCGTTGCCAG 201
|| ||||| | || || | || ||||| || ||||||||||||||| | ||| |
Sbjct: 218 GTATGCCCCAAGAGCTCGCTCCTGGTGAAATATGTGTGCTGCAACACCGACAGGTGCAAC 277
Query: 202 TAA 204
| |
Sbjct: 278 TGA 280
gb|U58486|NAU58486 Naja atra cardiotoxin 3' mRNA, complete cds
Length = 472
Plus Strand HSPs:
Score = 382 (105.6 bits), Expect = 9.5e-23, P = 9.5e-23
Identities = 122/179 (68%),Positives = 122/179 (68%), Strand = Plus / Plus
Query: 26 AATGCAACGAACTGATCCCGCTGTTCTACGAAACCTGCCCGGCTGGTGAAAACATCTGCT 85
|||||||| |||| | || | ||||| | || || || || || | ||| | ||||
Sbjct: 68 AATGCAACAAACTCGTTCCTTTATTCTATAAGACTTGTCCAGCAGGGAAGAACTTATGCT 127
Query: 86 ACGAAATGTTCATGGTTGCTACCCCGAAAGTTCCGTGCGAACGTGGTTGCATCGACGTTT 145
| ||||||||||||| || || || || ||||| | || | || || ||||| ||||
Sbjct: 128 ATAAAATGTTCATGGTGGCGACGCCAAAGGTTCCTGTCAAAAGGGGATGTATCGATGTTT 187
Query: 146 GCCCGGAATCTTCTCTGATCGTTAAATACGTTTGCTGCAACACCGACCGTTGCCAGTAA 204
|||| || ||| | || || || || || ||||| || ||| | ||| | | |
Sbjct: 188 GCCCTAAAAGCAGTCTCCTAGTGAAGTATGTGTGTTGCAATACAGACAGATGCAACTGA 246
gb|U42585|NAU42585 Naja atra cardiotoxin III mRNA, complete cds.
Length = 474
Plus Strand HSPs:
Score = 364 (100.6 bits), Expect = 4.0e-21, P = 4.0e-21
Identities = 120/179 (67%), Positives = 120/179 (67%), Strand = Plus / Plus
Query: 26 AATGCAACGAACTGATCCCGCTGTTCTACGAAACCTGCCCGGCTGGTGAAAACATCTGCT 85
|||| ||| |||| | || | ||||| | || || || || || | ||| | ||||
Sbjct: 68 AATGTAACAAACTCGTTCCTTTATTCTATAAGACTTGTCCAGCAGGGAAGAACTTATGCT 127
Query: 86 ACGAAATGTTCATGGTTGCTACCCCGAAAGTTCCGTGCGAACGTGGTTGCATCGACGTTT 145
| ||||||||||||| || || || || ||||| | || | || || || || ||||
Sbjct: 128 ATAAAATGTTCATGGTGGCGACGCCAAAGGTTCCTGTCAAAAGGGGATGTATTGATGTTT 187
Query: 146 GCCCGGAATCTTCTCTGATCGTTAAATACGTTTGCTGCAACACCGACCGTTGCCAGTAA 204
|||| || ||| | || || || || || ||||| || ||| | ||| | | |
Sbjct: 188 GCCCTAAAAGCAGTCTCCTAGTGAAGTATGTGTGTTGCAATACAGACAGATGCAACTGA 246
(4)Structure:
Number of H-Bonds --- 21 Number of Helices --- 0 Number of Strands --- 5 Number of Turns ----- 7 | |
 | Script:
select all
wireframe off
cartoons on
color group
|
| beta sheets : yellow [255,255,0]
turns : pale blue [96,128,255]
all other residues : white
hbonds forming sheets : yellow
turns : magenta
Script:
select all
wireframe off
ribbon on
color structure
set specpower 20
set specular on
hbond on
color hbond type
|
| ASP, GL bright red [230,10,10]
LYS, ARG blue [20,90,255]
CYS, MET yellow [230,230,0]
SER, THR orange [250,150,0]
PHE, TYR mid blue [50,50,170]
ASN, GLN cyan [230,230,0]
GLY light grey [235,235,235]
LEU, VAL, ILE green [15,130,15]
ALA dark grey [200,200,200]
TRP pink [180,90,180]
HIS pale blue [130,130,210]
PRO flesh [220,150,130]
Script:
(Display Sticks)
color amino
(Turn the molecule)
|