细胞色素c序列查找和分析

2023年12月8日发(作者：宋杨万里)

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细胞色素c序列查找和分析1 登陆NCBI网站，查找关于细胞色素C相关的蛋白的序列，选取了human,rat,yeast,drosophila等14个物种的细胞色素C蛋白序列，制订成表格，如下：NO.

1

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 将所查找的序列作成fasta格式的文本文档。

3 选取第二条序列（AAA21711）为代表，进行蛋白质一级，二级，三级结构的预测

a.一级结构用的是/tools/，结果如下：Ur-provided quence:

1 11 21 31 41 51

| | | | | |

1 MGDVEKGKKI FIMKCSQCHT VEKGGKHKTG PNLHGLFGRK TGQAPGYSYT AANKNKGIIW

60

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.二级结构用的是：

/cgi-bin/npsa_?page=npsa_

结果如下：

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

70

| | | | | |

|

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．三级结构用的是/urbm/bioinfo/esypred/

结果如下：e-mail:*******************4.

用PHYLIP软件推导进化树。

a. 打开文件 →在下拉菜单file中点击load Sequence

→在弹出窗口中选择 打开 → 在下拉菜单Alignment中单击Do Complete Alignment → 单击ALIGN →在下拉菜单file中点击Save Sequence as →在弹出窗口的Format选项中选择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 NKGITWKEET LMEYLENPKK YIPGTKMIFA GIKKKTERED

PGFSYTDANK NKGITWGEET LMEYLENPKK YIPGTKMIFA GIKKKGERED

AGFSYTDANK NKGITWGEDT LMEYLENPKK YIPGTKMIFA GIKKKGERAD

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 进入EXE文件夹，点击SEQBOOT软件输入文件名，回车后，输入R更改参数，更改重复数字为200。输Y确认参数。输入奇数种子3。程序开始运行，并在EXE文件夹中产生outfile文件。

c 把文件outfile改为infile。点击protdist程序。输入M更改参数，输入D选择data ts。输入200。输Y确认参数。程序开始运行，并在EXE文件夹中产生outfile d 将outfile文件名改为infile，为避免与原先infile文件重复，将

原先文件名改为infile1。在EXE文件夹中选择通过距离矩阵推测进化树的算法，点击NEIGHBOR程序。输入M更改参数，输入D选择data ts。输入200。输入奇数种子3。输Y确认参数。程序开始运行，并在EXE文件夹中产生outfile和outtree两个结果输出。outtree文件是一个树文件，可以用treeview等软件打开。outfile是一个分析结果的输出报告，包括了树和其他一些分析报告，可以用记事本直接打开。部分结果如下：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

24.00

23.00

23.00

23.00

22.00

20.00

19.00

16.00

16.00

15.00

14.00

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

10.00

10.00 10.009.00

9.00

8.00

8.00

8.00

8.00 7.00 7.007.00

7.00

7.00

6.00

6.00

6.00

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

5.00

5.00

5.00 4.00

4.00

4.00

4.00

4.00

4.00

3.00

3.00

3.00 3.00

3.00

3.00

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

2.00

2.00

2.00

2.00

2.00

2.00

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

2.00

2.00

2.00

2.00

2.00

2.00

2.00

2.00

2.00

2.00

2.00

2.00

2.00

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

1.00

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

1.00

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

1.00

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

1.00

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 将outtree文件名改为intree，点击DRAWTREE程序，输入font1文件名，作为参数。输Y确认参数。程序开始运行，并出现Tree

Preview图。

f 点击DRAWGRAM程序，输入font1文件名，作为参数。输Y确认参数。程序开始运行，并出现Tree Preview图。 g 将EXE文件夹中的outfile文件名改为outfile1，以避免被新生成的outfile 文件覆盖。点击CONSENSE程序。输入Y确认设置。EXE文件夹中新生成outfile和outtree。Outfile文件用记事本打开，将EXE文件夹中的intree文件名改为intree1，将outtree改intree。点击DRAWTREE程序，输入font1文件名，作为参数。输Y确认参数。程序开始运行，并出现Tree Preview图。 8、点击DRAWGRAM程序，输入font1文件名，作为参数。输Y确认参数。程序开始运行，并出现Tree Preview图。

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