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細胞色素c序列查找和分析

更新時間:2023-12-08 02:42:47 閱讀：評論：0

2023年12月8日發(作者：宋楊萬里)

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細胞色素c序列查找和分析

細胞色素c序列查找和分析1 登陸NCBI網站，查找關于細胞色素C相關的蛋白的序列，選取了human,rat,yeast,drosophila等14個物種的細胞色素C蛋白序列，制訂成表格，如下：NO.

ACC NO Organism

AAA28437 fruit fly

Protein quences

2 AAA21711 Rattus

norvegicus

3 Homo sapiens Homo sapiens

4 P00006 Bos taurus

5 CAA25046 Gallus gallus

6 S11172 yeast

7 AAC80552 Tigriopus

californicus

8 CCSF s tarfish

9 CCCA common carp

1 mgvpagdvek gkklfvqrca qchtveaggk

hkvgpnlhgl igrktgqaag faytdankak

gitwnedtlf eylenpkkyi pgtkmifagl

kkpnergdli aylksatk

1 mgdvekgkki fvqkcaqcht vekggkhktg

pnlhglfgrk tgqaagfsyt danknkgitw

gedtlmeyle npkkyipgtk mifagikkkg

eradliaylk katne

1 mgdvekgkki fimkcsqcht vekggkhktg

pnlhglfgrk tgqapgysyt aanknkgiiw

gedtlmeyle npkkyipgtk mifvgikkke

eradliaylk katne

1 gdvekgkkif vqkcaqchtv ekggkhktgp

nlhglfgrkt gqapgfsytd anknkgitwg

eetlmeylen pkkyipgtkm ifagikkkge

redliaylkk atne

1 mgdiekgkki fvqkcsqcht vekggkhktg

pnlhglfgrk tgqaegfsyt danknkgitw

gedtlmeyle npkkyipgtk mifagikkks

ervdliaylk datsk

1 mpyapgdekk gaslfktrca qchtvekgga

nkvgpnlhgv fgrktgqaeg fsyteanrdk

gitwdeetlf aylenpkkyi pgtkmafagf

kkpadrnnvi tylkkat

1 mgdidkgkki fvqkctqcht ieaggkhkvg

pnlhgmygrq tgkaagysyt dankskgvtw

neetldiylt npkkyipgtk mvfaglkkkg

dredliaylk sasss

1 gqvekgkkif vqrcaqchtv ekagkhktgp

nlngilgrkt gqaagfsytd anrnkgitwk

netlfeylen pkkyipgtkm vfaglkkqke

rqdliaylea atk

1 gdvekgkkvf vqkcaqchtv zbggkhkvgp

nlwglfgrkt gqapgfsytb abkskgivwb

zztlmeylzb pkkyipgtkm ifagikkkge 10 CCHOZ common zebra

11 AAL67777 Actinobacillus

lignieresii

12 CCHOD donkey

13 AAB86817 Pichia stipitis

14 CAA25899 Mus musculus

radliaylks ats

1 gdvekgkkif vqkcaqchtv ekggkhktgp

nlhglfgrkt gqapgfsytd anknkgitwk

eetlmeylen pkkyipgtkm ifagikkkte

redliaylkk atne

1 mtkllqkiaf ilplvfslva xaemvdtfqf

qnetdrvrav alakslrcpq cqnqnlvesn

attayklrle vyemvnqgkt deeiikimte

rfghfvnykp pfna

1 gdvekgkkif vqkcaqchtv ekggkhktgp

nlhglfgrkt gqapgfsytd anknkgitwk

eetlmeylen pkkyipgtkm ifagikkkte

redliaylkk atne

1 mpapfekg kkgatlfktr clqchtveeg

gphkvgpnlh gimgrksgqa vgysytdank

kkgvewqtmsdylenpkkyipgtkmafg

glkkpkdrnd lvtylasatk

1 mgdvekgkki fvqkcaqcht vekggkhktg

pnlhglfgrk tgqaagfsyt danknkgitw

gedtlmeyle npkkyipgtk mifagikkkg

eradliaylk katne

2 將所查找的序列作成fasta格式的文本文檔。

3 選取第二條序列（AAA21711）為代表，進行蛋白質一級，二級，三級結構的預測

a.一級結構用的是/tools/，結果如下：Ur-provided quence:

1 11 21 31 41 51

| | | | | |

1 MGDVEKGKKI FIMKCSQCHT VEKGGKHKTG PNLHGLFGRK TGQAPGYSYT AANKNKGIIW

61 GEDTLMEYLE NPKKYIPGTK MIFVGIKKKE ERADLIAYLK KATNE

References and documentation are available. Number of amino acids: 105

Molecular weight: 11748.7

Theoretical pI: 9.59

Amino acid composition:

Ala (A) 6 5.7%

Arg (R) 2 1.9%

Asn (N) 5 4.8%

Asp (D) 3 2.9%

Cys (C) 2 1.9%

Gln (Q) 2 1.9%

Glu (E) 8 7.6%

Gly (G) 13 12.4%

His (H) 3 2.9%

Ile (I) 8 7.6%

Leu (L) 6 5.7%

Lys (K) 18 17.1%

Met (M) 4 3.8%

Phe (F) 3 2.9%

Pro (P) 4 3.8%

Ser (S) 2 1.9%

Thr (T) 7 6.7%

Trp (W) 1 1.0%

Tyr (Y) 5 4.8%

Val (V) 3 2.9%

Asx (B) 0 0.0%

Glx (Z) 0 0.0%

Xaa (X) 0 0.0%

Total number of negatively charged residues (Asp + Glu

):Total number of positively charged residues (Arg + Lys

Atomic composition:

Carbon C 526

Hydrogen H 845

Nitrogen N 143

11 20Oxygen O 149

Sulfur S 6

Formula: C526H845N143O149S6

Total number of atoms: 1669

Extinction coefficients:

Conditions: 6.0 M guanidium hydrochloride 0.02 M phosphate buffer

pH 6.5

-1-1Extinction coefficients are in units of M cm .

The first table lists values computed assuming ALL Cys

residues appear as half cystines, whereas the cond table

assumes that NONE do.

276 278 279 280 282

nm nm nm nm nm

Ext. coefficient 12795 12727 12505 12210 11720

Abs 0.1% (=1 g/l) 1.089 1.083 1.064 1.039 0.998

276 278 279 280 282

nm nm nm nm nm

Ext. coefficient 12650 12600 12385 12090 11600

Abs 0.1% (=1 g/l) 1.077 1.072 1.054 1.029 0.987

Estimated half-life:

The N-terminal of the quence considered is M (Met).

The estimated half-life is: 30 hours (mammalian reticulocytes, in vitro).

>20 hours (yeast, in vivo).

>10 hours (Escherichia coli, in vivo).

Instability index:

The instability index (II) is computed to be 11.38This classifies the protein as stable.

Aliphatic index: 66.00

Grand average of hydropathicity (GRAVY): -0.706

b.二級結構用的是：

/cgi-bin/npsa_?page=npsa_

結果如下：

GOR4 result for : UNK_162940

Abstract

GOR condary structure prediction method version IV, J. Garnier, J.-F. Gibrat, B. Robson,

Methods in Enzymology,R.F. Doolittle Ed., vol 266, 540-553, (1996)

View GOR4 in: [MPSA

(Mac, UNIX) , ] [AnTheProt

(PC) , ]

[HELP]

10 20 30 40 50 60

| | | | | |

MGDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAAGFSYTDANKNKGITWGEDTLMEYLE

cccccccceeeeeecccceeeecccccccccceeeecccccccccceeeccccccccceecccchhhhhc

NPKKYIPGTKMIFAGIKKKGERADLIAYLKKATNE

ccccccccchhhhhhhhhhcchhhhhhhhhhceec

Sequence length : 105

GOR4 :

Alpha helix (Hh) : 25 is 23.81% 310

helix (Gg) : 0 is 0.00% Pi helix (Ii) : 0 is 0.00% Beta bridge (Bb) : 0 is 0.00% Extended strand (Ee) : 21 is 20.00% Beta turn (Tt) : 0 is 0.00% Bend region (Ss) : 0 is 0.00% Random coil (Cc) : 59 is 56.19% Ambigous states (?) : 0 is 0.00% Other states : 0 is 0.00%

Prediction result file (text): [GOR4]

C．三級結構用的是/urbm/bioinfo/esypred/

結果如下：e-mail:*******************4.

用PHYLIP軟件推導進化樹。

a. 打開文件 →在下拉菜單file中點擊load Sequence

→在彈出窗口中選擇打開 → 在下拉菜單Alignment中單擊Do Complete Alignment → 單擊ALIGN →在下拉菜單file中點擊Save Sequence as →在彈出窗口的Format選項中選擇PHYLIP→OK→得到文件。如下：14 111

fruit --MGVPAGDV EKGKKLFVQR CAQCHTVEAG GKHKVGPNLH GLIGRKTGQA

starfish -------GQV EKGKKIFVQR CAQCHTVEKA GKHKTGPNLN GILGRKTGQA

common -------GDV EKGKKIFVQK CAQCHTVEKG GKHKTGPNLH GLFGRKTGQA

donkey -------GDV EKGKKIFVQK CAQCHTVEKG GKHKTGPNLH GLFGRKTGQA

Bos -------GDV EKGKKIFVQK CAQCHTVEKG GKHKTGPNLH GLFGRKTGQA

Rattus ------MGDV EKGKKIFVQK CAQCHTVEKG GKHKTGPNLH GLFGRKTGQA

Mus ------MGDV EKGKKIFVQK CAQCHTVEKG GKHKTGPNLH GLFGRKTGQA

Homo ------MGDV EKGKKIFIMK CSQCHTVEKG GKHKTGPNLH GLFGRKTGQA

Gallus ------MGDI EKGKKIFVQK CSQCHTVEKG GKHKTGPNLH GLFGRKTGQA

carp -------GDV EKGKKVFVQK CAQCHTVZBG GKHKVGPNLW GLFGRKTGQA

Tigriopus ------MGDI DKGKKIFVQK CTQCHTIEAG GKHKVGPNLH GMYGRQTGKA

yeast --MPYAPGDE KKGASLFKTR CAQCHTVEKG GANKVGPNLH GVFGRKTGQA

Pichia MPAPFEKGSE KKGATLFKTR CLQCHTVEEG GPHKVGPNLH GIMGRKSGQA

Actinobaci -----MTKLL QKIAFILPLV FSLVAXAEMV DTFQFQNETD RVR--AVALA

AGFAYTDANK AKGITWNEDT LFEYLENPKK YIPGTKMIFA GLKKPNERGD

AGFSYTDANR NKGITWKNET LFEYLENPKK YIPGTKMVFA GLKKQKERQD

PGFSYTDANK NKGITWKEET LMEYLENPKK YIPGTKMIFA GIKKKTERED

PGFSYTDANK NKGITWGEET LMEYLENPKK YIPGTKMIFA GIKKKGERED

AGFSYTDANK NKGITWGEDT LMEYLENPKK YIPGTKMIFA GIKKKGERAD

PGYSYTAANK NKGIIWGEDT LMEYLENPKK YIPGTKMIFV GIKKKEERAD

EGFSYTDANK NKGITWGEDT LMEYLENPKK YIPGTKMIFA GIKKKSERVD

PGFSYTBABK SKGIVWBZZT LMEYLZBPKK YIPGTKMIFA GIKKKGE---

AGYSYTDANK SKGVTWNEET LDIYLTNPKK YIPGTKMVFA GLKKKGDRED

EGFSYTEANR DKGITWDEET LFAYLENPKK YIPGTKMAFA GFKKPADRNN

VGYSYTDANK KKGVEWSEQT MSDYLENPKK YIPGTKMAFG GLKKPKDRND

KSLRCPQCQN QNLVESNATT AYKLRLEVYE MVNQGKTDEE IIKIMTERFG

LIAYLKSATK -

LIAYLEAATK - LIAYLKKATN E LIAYLKKATN E LIAYLKKATN E LIAYLKKATN E LIAYLKKATN E LIAYLKKATN E LIAYLKDATS K ---------- - LIAYLKSASS S

VITYLKKATS E LVTYLASATK -

HFVNYKPPFN Ab 進入EXE文件夾，點擊SEQBOOT軟件輸入文件名，回車后，輸入R更改參數，更改重復數字為200。輸Y確認參數。輸入奇數種子3。程序開始運行，并在EXE文件夾中產生outfile文件。

c 把文件outfile改為infile。點擊protdist程序。輸入M更改參數，輸入D選擇data ts。輸入200。輸Y確認參數。程序開始運行，并在EXE文件夾中產生outfile d 將outfile文件名改為infile，為避免與原先infile文件重復，將

原先文件名改為infile1。在EXE文件夾中選擇通過距離矩陣推測進化樹的算法，點擊NEIGHBOR程序。輸入M更改參數，輸入D選擇data ts。輸入200。輸入奇數種子3。輸Y確認參數。程序開始運行，并在EXE文件夾中產生outfile和outtree兩個結果輸出。outtree文件是一個樹文件，可以用treeview等軟件打開。outfile是一個分析結果的輸出報告，包括了樹和其他一些分析報告，可以用記事本直接打開。部分結果如下：Connsus tree program, version 3.6bSpecies in order:

1. Homo 2. Mus

3. Rattus 4. Bos

5. common 6. donkey 7. carp

8. Tigriopus 9. yeast

10. Actinobaci 11. Pichia 12. Gallus

13. starfish 14. fruit

Sets included in the connsus tree

Set (species in order) How many times out of 200.00

....**.... .... 166.00

.**....... .... 161.00

.......*** *.** ** *.** 93.00

...******* **** ***.... .... 83.00

........** .... 80.00

.......*** **** ** *.*. 68.00

........** *... 61.00

...****... .... 57.00

Sets NOT included in connsus tree:

Set (species in order) How many times out of

200.00

......**** *.** 63.00

...******* *.** *. *... 57.00

......**** **** .* ..*. 45.00

.........* *...

.********* *.**

...*..*... ....

........** *..*

....****** *.**

.**....*** ****

.........* ..**

.......*** *..*

........** ..**

........** ..*.

........** ...*

......**.. ....

.........* ...*

....****** ****

.........* *.*.

.......*** *.*.

.......**. *...

37.00

37.0035.00

29.00

26.00

24.00

23.00

22.00

20.00

19.00

16.00

15.00

14.00

.......*.. *... 13.00

........** **** ***... .... *.* ...* 11.00

.******... .... *****.. ....

.**...**** ****

..******** ****

.***...... ....

........*. *.*.

.......*.* ..**

.........* .*..

...*.*.... ....

.***..**** ****

.*.******* ****

....**.*** *.**

.......... *.*.

.......*** *...

.......*.* ....

......**** *..*

.***..*... ....

....**.*** ****

10.00

10.00 10.009.00

9.00

8.00

8.00 7.00 7.007.00

7.00

6.00

.......**. *.** .* .**. .* *.** ** .*** **..... .... 5.00

.......*.* *.**

......***. *.**

.**.****** ****

.......*.* .*.*

.......*.* *.*.

........** .*..

........*. *.**

.......*.. ...*

.......*.* *...

.....***.. ....

..**...... ....

.***..***. *.**

......*.** *.**

........** ***.

...*****.. *...

....****.. ....

......*... ...*

5.00

5.00 4.00

4.00

3.00

3.00 3.00

3.00

......*..* ...* 3.00.**....... .*.. 3.00

...*..**** *.** **.. *... 3.00

.*.****... .... ***. *...

.......*.* .***

...***.*** *.**

.......*** ....

.********. *.**

......*..* ....

.......... ..**

.......*.* ..*.

......**.. .*..

.......*.* .**.

.******... .*..

...******. *.**

.*******.. ....

......*.*. *...

....*....* .*..

...*.**... ....

....**...* .*..

3.00

2.00

2.002.00

2.00

.*******.. *... **.*... .... 2.00

..******.. .... *. *..* 2.00

.*****.... .... *.. *.**

....*..*** *.**

....*.*... ....

.......**. *.*.

.**.....** ****

......*... .*..

.........* .***

...***.*.. ....

.......*** ...*

......*.*. *.*.

........** **..

.........* .*.*

.*......** ****

.......... *.**

...*..***. *.**

.*.....*** ****

.........* ***.

2.00

.......*.* *..* 2.00

.**.****.. .... *.** .*** *.*. *.** ***.... ..*. 1.00

...****.** *.**

..*...*... ....

.**......* ....

.**...**.. ....

.*******.. ..*.

....*....* .**.

.......*.* ****

.***...*** ****

......**.* ...*

....*..*** ****

.****...** ****

.****..... ....

...****... ...*

.*.......* ....

....*****. ****

.*****.*** ****

........*. ...*

1.001.00

1.00

1.00 1.00

1.00

1.00 1.00

1.00 1.00 1.00

1.00

1.00 1.001.00

......*... *... 1.00

.*****.*** *.** **..** *.** 1.00.**.**...* .*.* 1.00

.***....** **** 1.00..*.....** ****

......*.*. *..*

....**.... ..*.

...*..**.. ....

......*.** ****

.......*.* .*..

....*...** ....

...*****.. ..*.

....**...* .**.

..*****... ....

.****..*** ****

...*.*.*** *.**

......*.** *.*.

...****.*. *.*.

....**..** ****

......**.* .*.*

....**...* .*.*

1.00

.....**... .... 1.00

....***.*. *.*. *.*. .... 1.00

....**..** .... 1.00.*.....*.. .... 1.00

....***..* .***

.******.** ****

.******... ...*

...***.*** ****

......***. ...*

.**....*.. ....

.**.*..... ....

......**.. ...*

.......**. *..*

.......*.. .*..

...****..* .***

.**...***. *.**

.*.......* .*..

.**..***.. ....

.**......* .*..

...*..**.. *.**

....**.*.* .*.*

1.00 1.00 1.00 1.00 1.00

1.00

1.00 1.001.00

1.00

.*.*...... .... 1.00

......***. **** ** **.* 1.00

.******..* .*** ****... .*.. 1.00

.......*.. *.*.

.********. ****

.*.....*.* .*.*

.**....*.* .*.*

.**....*.* .**.

..******.. ..*.

......***. *.*.

.*******.. **..

..*....*** ****

......*.*. ...*

.***..**** *.**

.*****..** ****

...*...*** *.**

.**...*... ....

......*..* .*..

...******. ****

.......*** .*..

1.00

1.00 1.00

1.00

.**.....** .*** 1.00

.*.*..*... .... 1.00

Extended majority rule connsus tree

CONSENSUS TREE:

the numbers on the branches indicate the number

of times the partition of the species into the two tswhich are parated by that branch occurred

among the trees, out of 200.00 trees

+-------------Pichia

+-61.0-|

+------yeast

+-68.0-|

+-80.0-|

+------Actinobaci

+-93.0-| | |

+--------------------starfish

+133.0-| |

+---------------------------fruit

+-70.0-| | |

+----------------------------------Tigriopus | |

+-----------------------------------------Gallus +-84.0-|

+------common

+166.0-|

| |

+------donkey

| |

+------| +----------------------57.0-|

| |

+--------------------carp

| |

+-83.0-|

| |+-------------Bos | |

+------Rattus

| +------------------------------------------161.0-|

+------Mus |

+--------------------------------------------------------------Homo

e 將outtree文件名改為intree，點擊DRAWTREE程序，輸入font1文件名，作為參數。輸Y確認參數。程序開始運行，并出現Tree

Preview圖。

f 點擊DRAWGRAM程序，輸入font1文件名，作為參數。輸Y確認參數。程序開始運行，并出現Tree Preview圖。 g 將EXE文件夾中的outfile文件名改為outfile1，以避免被新生成的outfile 文件覆蓋。點擊CONSENSE程序。輸入Y確認設置。EXE文件夾中新生成outfile和outtree。Outfile文件用記事本打開，將EXE文件夾中的intree文件名改為intree1，將outtree改intree。點擊DRAWTREE程序，輸入font1文件名，作為參數。輸Y確認參數。程序開始運行，并出現Tree Preview圖。 8、點擊DRAWGRAM程序，輸入font1文件名，作為參數。輸Y確認參數。程序開始運行，并出現Tree Preview圖。