HOMEWORK#7
Sequence comparison / Homology search
* due on 5/28
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* David Liu, a student in department of Life Sciences, was bitten by a
snake in the backyard of life science building. He was so angry! Thus,
he killed the snake and purified several toxins from its venoms. He
sequenced one of the toxin, got this sequence:
1 L K C N K L V P L F Y K T C P A G K N L C Y K M F M V A T P
31 K V P V K R G C I D V C P K S S L L V K Y V C C N T D R C N
(1) Is this a new toxin? Please help him to identify this toxin.
This is not a new toxin; here is the result from SCOP:
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Protein: Cardiotoxin III from taiwan cobra (Naja naja atra)
Lineage:
1. Root: scop
2. Class: Small proteins
Usually dominated by metal ligand, heme, and/or disulfide bridges
3. Fold: Snake toxin-like
disulphide-rich fold: nearly all-beta
4. Superfamily: Snake toxin-like
5. Family: Snake venom toxins
6. Protein: Cardiotoxin III
7. Species: taiwan cobra (Naja naja atra)
PDB Entries:
1. 2crs [seq]
2. 2crt [seq]
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(2) Can you find proteins that share sequence homology with this toxin?
Show them in multiple alignment form.
Here are some proteins I found from homologysearch:
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Best Sum Statistic for Each Similar Database Sequence
Db|Acc|Name Description P(n) n
sw|Q02454|CX1_NAJSP CARDIOTOXIN PRECURSOR. 3.07e-41 1
sw|P01444|CX3_NAJAT CYTOTOXIN 3 PRECURSOR (CARDIOTOXIN ANA... 3.07e-41 1
sw|P01440|CX2_NAJNA CYTOTOXIN 2 (CYTOTOXIN II). 5.99e-40 1
sw|P24779|CX5_NAJKA CYTOTOXIN 5 (CYTOTOXIN II). 3.14e-38 1
sw|P07525|CX5_NAJAT CYTOTOXIN 5 (CARDIOTOXIN T) (CTX5) (CY... 4.36e-38 1
sw|P80245|CX6_NAJAT CYTOTOXIN 6 (CARDIOTOXIN 6) (CTX6). 1.17e-37 1
sw|P49124|CXN_NAJAT CYTOTOXIN N PRECURSOR (CARDIOTOXIN N) ... 1.17e-37 1
sw|P01441|CX2_NAJOX CYTOTOXIN 2. 4.39e-37 1
sw|P01442|CX2_NAJAT CYTOTOXIN 2 (CARDIOTOXIN ANALOGUE II) ... 1.18e-36 1
sw|P01445|CX2_NAJKA CYTOTOXIN 2 (CYTOTOXIN CM-7A). 2.28e-36 1
sw|P49123|CX8_NAJAT CYTOTOXIN 8 PRECURSOR (CARDIOTOXIN 8) ... 3.18e-36 1
sw|P01443|CX4_NAJAT CYTOTOXIN 4 (CARDIOTOXIN ANALOGUE IV) ... 4.42e-36 1
sw|P01446|CX3_NAJKA CYTOTOXIN 3 (CYTOTOXIN CM-7). 8.55e-36 1
sw|P24780|CX3_NAJNA CYTOTOXIN 3 (CYTOTOXIN IIA). 1.65e-35 1
sw|P01451|CX1_NAJOX CYTOTOXIN 1. 1.66e-34 1
sw|P01447|CX1_NAJNA CYTOTOXIN 1 (CYTOTOXIN XI). 3.22e-34 1
sw|P01462|CX2_NAJHA CYTOTOXIN 2 (TOXINS V-II-2 AND V-II-2A... 3.22e-34 1
sw|P01448|CX1_NAJME CYTOTOXIN 1 (CYTOTOXIN V-II-1). 4.48e-34 1
sw|P01454|CX9_NAJHA CYTOTOXIN 9 (TOXIN CM-2E). 4.48e-34 1
sw|P01463|CX2_NAJNI CYTOTOXIN 2 (TOXIN V-II-2). 6.23e-34 1
sw|P01464|CX5_NAJHA CYTOTOXIN 5 (TOXIN CM-6). 6.23e-34 1
sw|P01449|CX1_NAJAT CYTOTOXIN 1 PRECURSOR (CARDIOTOXIN F8)... 8.66e-34 1
sw|P01453|CX10_NAJHA CYTOTOXIN 10 (TOXIN CM-4A). 1.68e-33 1
sw|P01465|CX6_NAJHA CYTOTOXIN 6 (TOXIN CM-2H). 1.68e-33 1
sw|P01468|CX1_NAJPA CYTOTOXIN 1 (CARDIOTOXIN GAMMA). 2.33e-33 1
sw|P01458|CX3_NAJNI CYTOTOXIN 3 (TOXIN V-II-3). 2.33e-33 1
sw|P01461|CX4_NAJHA CYTOTOXIN 4 (TOXIN CM-11). 3.24e-33 1
sw|P01459|CX3_NAJHA CYTOTOXIN 3 (TOXINS CM-8 AND CM-8A). 6.27e-33 1
sw|P01470|CX3_NAJMO CYTOTOXIN 3 (CYTOTOXIN V-II-3). 6.27e-33 1
sw|P01466|CX7_NAJHA CYTOTOXIN 7 (TOXIN CM-4B). 8.72e-33 1
sw|P01467|CX1_NAJMO CYTOTOXIN 1 (CARDIOTOXIN XIIB) (CYTOTO... 1.21e-32 1
sw|P01460|CX8_NAJHA CYTOTOXIN 8 (TOXIN CM-7). 1.21e-32 1
sw|P01469|CX2_NAJMO CYTOTOXIN 2 (CARDIOTOXIN XIIA) (CYTOTO... 1.69e-32 1
sw|P01457|CX5_NAJHH CYTOTOXIN 5 (CYTOTOXIN CM-8). 1.69e-32 1
sw|P01455|CX1_NAJHA CYTOTOXIN 1 (TOXIN V-II-1). 2.35e-32 1
sw|P01456|CX1_NAJNI CYTOTOXIN 1 (TOXIN V-II-1). 3.26e-32 1
sw|P25517|CX5_NAJMO CYTOTOXIN 5 (CTX V). 4.54e-32 1
sw|P01452|CX4_NAJMO CYTOTOXIN 4 (CARDIOTOXIN V-II-4). 3.28e-31 1
sw|P01471|CX1_HEMHA CYTOTOXIN 1 (HEMOLYTIC PROTEIN 12B). 4.66e-28 1
sw|P24777|CX3_HEMHA CYTOTOXIN 3 (TOXINS 11 AND 11A). 1.25e-27 1
sw|P24776|CX2_HEMHA CYTOTOXIN 2 (TOXIN 12A). 9.13e-26 1
sw|P19003|CXH2_ASPSC CYTOTOXIN HOMOLOG S3C2. 4.27e-22 2
sw|P01473|CX3_NAJME CYTOTOXIN 3 (COMPONENT 3.20). 1.30e-21 1
sw|P01474|CX2_NAJME CYTOTOXIN 2 (CYTOTOXINS V-II-2 AND V-I... 6.78e-21 1
sw|P14541|CXH_NAJKA CYTOTOXIN HOMOLOG (CLBP). 7.58e-20 2
sw|P49122|CX7_NAJAT CYTOTOXIN 7 PRECURSOR (CARDIOTOXIN 7) ... 9.49e-20 1
sw|P14554|CXH_NAJNA CYTOTOXIN HOMOLOG PRECURSOR (CLBP) (LE... 2.66e-19 2
sw|P01472|CX11_NAJHA CYTOTOXIN 11 (TOXIN CM-13A) (TOXIN CM-... 1.40e-18 2
sw|P24778|CXH_HEMHA CYTOTOXIN HOMOLOG (TOXINS 9B AND 9BB). 6.42e-15 2
sw|P19004|CXH4_ASPSC CYTOTOXIN HOMOLOG S4C8. 8.62e-08 2
sw|P01397|NXL2_DENPO LONG NEUROTOXIN 2 (NEUROTOXIN DELTA) (... 1.32e-07 2
sw|P01383|NXL1_NAJME LONG NEUROTOXIN 1 (NEUROTOXIN 3.9.4). 2.48e-07 2
sw|P25667|NXL3_DENPO LONG NEUROTOXIN 3 (TOXIN VN2). 2.51e-07 2
sw|P01378|NXL1_BUNMU LONG NEUROTOXIN 1 (ALPHA-BUNGAROTOXIN)... 3.54e-07 2
sw|P18328|TXM2_DENAN MUSCARINIC TOXIN 2 PRECURSOR. 4.07e-07 2
sw|P25679|TXW9_NAJKA WEAK TOXIN CM-9A. 7.43e-07 1
sw|P01396|NXL1_DENPO LONG NEUROTOXIN 1 (NEUROTOXIN GAMMA) (... 8.98e-07 2
sw|P01395|NXL2_DENVI LONG NEUROTOXIN 2 (TOXINS I AND V). 9.09e-07 2
sw|P80495|TXMB_DENPO MUSCARINIC TOXIN BETA (MT-BETA). 1.12e-06 2
sw|P01393|NXL1_DENJA LONG NEUROTOXIN 1 (TOXIN V-III-N1). 1.70e-06 2
sw|P17696|TSYL_DENAN SYNERGISTIC-LIKE VENOM PROTEIN PRECURS... 2.75e-06 2
sw|P25670|NXL1_ASPSC LONG NEUROTOXIN 1 (TOXIN S4C6). 3.04e-06 2
sw|P25518|TSYL_DENPO SYNERGISTIC-LIKE VENOM PROTEIN CM-3. 4.01e-06 2
sw|P01384|NXL1_NOTSC LONG NEUROTOXIN 1 (NOTECHIS III-4). 4.46e-06 2
sw|P01394|NXL1_DENVI LONG NEUROTOXIN 1 (NEUROTOXINS 4.7.3 A... 1.14e-05 2
sw|P01387|NXL1_OPHHA LONG NEUROTOXIN 1 (NEUROTOXIN A). 1.59e-05 2
sw|P01400|TXW4_NAJME WEAK TOXIN S4C11. 2.69e-05 2
sw|P01380|NXL1_ASTST LONG NEUROTOXIN 1 (TOXIN B). 2.88e-05 2
sw|P01381|NXL2_ASTST LONG NEUROTOXIN 2 (TOXIN C). 2.96e-05 2
sw|P01386|NXL2_OPHHA LONG NEUROTOXIN 2 (NEUROTOXIN B). 3.00e-05 2
sw|P01382|NXL1_NAJOX LONG NEUROTOXIN 1 (NEUROTOXIN I). 4.11e-05 2
sw|P01401|TXW1_NAJHH WEAK TOXIN CM-11. 5.07e-05 2
sw|P29181|TXW7_NAJNA WEAK NEUROTOXIN 7. 5.07e-05 2
sw|P01407|TS24_DENJA SYNERGISTIC-TYPE VENOM PROTEIN S2C4. 9.15e-05 2
sw|P01399|TXWB_NAJHA WEAK TOXIN CM-13B. 9.55e-05 2
sw|P01385|NXL1_ACAAN LONG NEUROTOXIN 1. 1.06e-04 2
sw|P01434|NXS1_ACAAN SHORT NEUROTOXIN 1 (TOXIN AA C). 1.26e-04 2
sw|P15818|NXLH_BUNMU LONG NEUROTOXIN HOMOLOG PRECURSOR. 1.46e-04 1
sw|P34073|NXLD_ACAAN ACANTHOPHIN D (POSTSYNAPTIC NEUROTOXIN... 1.48e-04 2
sw|P01406|TX54_DENJA TOXIN S5C4. 1.67e-04 2
sw|P01379|NXL1_LATSE LONG NEUROTOXIN 1 (COMPONENT LSIII). 1.82e-04 2
sw|P01389|NXL1_NAJHC LONG NEUROTOXIN 1 (TOXIN III). 1.97e-04 2
sw|P01408|TS91_DENAN SYNERGISTIC-TYPE VENOM PROTEIN C9S3, C... 2.40e-04 2
sw|P07526|NXL3_OPHHA LONG NEUROTOXIN 3 (NEUROTOXIN CM-9). 2.74e-04 2
sw|P25680|TXW0_NAJNI WEAK TOXIN CM-10. 3.38e-04 2
sw|P80156|NXL4_OPHHA LONG NEUROTOXIN 4 (ALPHA-NEUROTOXIN). 3.71e-04 2
sw|P29182|TXW8_NAJNA WEAK NEUROTOXIN 8. 4.63e-04 2
sw|P25684|TX02_DENAN TOXIN C10S2C2. 8.09e-04 2
sw|P25496|NXSB_LATCR SHORT NEUROTOXIN B. 8.34e-04 2
sw|P10459|NXSB_LATLA SHORT NEUROTOXIN B. 8.34e-04 2
sw|P25495|NXSA_LATCR SHORT NEUROTOXIN A. 2.14e-03 2
sw|P01410|TS81_DENAN SYNERGISTIC-TYPE VENOM PROTEIN C8S2, C... 2.14e-03 2
sw|P10460|NXSC_LATLA SHORT NEUROTOXIN C. 2.93e-03 2
sw|P10458|NXSC_LATCR SHORT NEUROTOXIN C. 4.01e-03 2
sw|P10455|NXSC_LATCO SHORT NEUROTOXIN C. 5.48e-03 2
sw|P10456|NXSD_LATCO SHORT NEUROTOXIN D. 5.48e-03 2
sw|P18329|TX31_DENAN TOXIN C13S1C1 PRECURSOR. 6.89e-03 2
sw|P25683|TX48_DENJA TOXIN S4C8. 7.27e-03 2
sw|P29180|TXW6_NAJNA WEAK NEUROTOXIN 6. 7.60e-03 1
sw|P22947|TXCA_DENPO CALCISEPTINE (L-TYPE CALCIUM CHANNEL B... 9.93e-03 2
sw|P25676|TXWC_HEMHA WEAK TOXIN CM-1C. 1.01e-02 2
sw|P01415|TXW2_NAJHH WEAK TOXIN CM-2. 1.06e-02 1
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And, I also get the first ten sequences below:
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CX1_NAJSP LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN
CX3_NAJAT LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN
CX2_NAJNA LKCNKLVPLFYKTCPAGKNLCYKMYMVATPKVPVKRGCIDVCPKSSLVLKYVCCNTDRCN
CX5_NAJKA LKCNKLIPLAYKTCPAGKNLCYKMFMVAAPKVPVKRGCIDACPKNSLLVKYVCCNTDRCN
CX5_NAJAT LKCNKLVPLFYKTCPAGKNLCYKMFMVSNKMVPVKRGCIDVCPKSSLLVKYVCCNTDRCN
CX6_NAJAT LKCNQLIPPFYKTCAAGKNLCYKMFMVAAPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN
CXN_NAJAT LKCNQLIPPFYKTCAAGKNLCYKMFMVAAPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN
CX2_NAJOX LKCKKLVPLFSKTCPAGKNLCYKMFMVAAPHVPVKRGCIDVCPKSSLLVKYVCCNTDKCN
CX2_NAJAT LKCNKLVPLFYKTCPAGKNLCYKMFMVSNLTVPVKRGCIDVCPKNSALVKYVCCNTDRCN
CX2_NAJKA LKCNKLIPLAYKTCPAGKNLCYKMFMVSNKTVPVKRGCIDVCPKNSLLVKYVCCNTDRCN
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(3) Please predict its secondary structure.
I tried two different sites and get the results:
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Results of nnpredict query
Tertiary structure class: none
Sequence 2CRST:
LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN
____________________HHHHHH_____________E________EEEE________
Secondary structure prediction (H = helix, E = strand, - = no prediction):
========================================================================
BCM PSSP result
Name: 2CRST
First three lines of sequence:
LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN
ssp Fri Jun 13 06:21:24 CDT 1997
2CRST
pred A:
AA
pred B: bbbbbbbb bbbbbbbb bbbbbb
BB N 3.5 C N 2.3 C N 3.
Predic bbbbbbbb bbbbbbbb bbbbbb
a/acid LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVK
10 20 30 40 50
pred A:
AA
pred B: bbbb
BB 3 C
Predic bbbb
a/acid YVCCNTDRCN
60
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(4) Please show its charge distribution.
I am not sure what to show, and I colour the Ras-Mol graph of 2crt in 'charge':
(green : 0, blue : +, red : -, darker for larger value)
And here are graphs of isolate the backbone and the rest part!
