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Macromolecule Insights - Protein Bioinformatics Analysis

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The Cytochrome c Protein

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Sequence Alignment of the Cytochrome c Protein (with Clustalw)a

Species Sequence Alignment of Cytochrome c

human           ---------------------------MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNL 33
mouse           ---------------------------MGDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNL 33
rat             ---------------------------MGDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNL 33
chicken         ---------------------------MGDIEKGKKIFVQKCSQCHTVEKGGKHKTGPNL 33
fugu            --------------------------MSGDIAKGKKAFVQKCAQCHTVEQGGKHKTGPNL 34
fly-proximal    -----------------------MGVPAGDVEKGKKLFVQRCAQCHTVEAGGKHKVGPNL 37
fly-distal      -------------------------MGSGDAENGKKIFVQKCAQCHTYEVGGKHKVGPNL 35
yeast           ---------------------MPAPFEKGSEKKGATLFKTRCLQCHTVEEGGPHKVGPNL 39
yersinia        ------------------------MRKIPIIAGVFSLLITSCTFAASLQDDMNILIAN-- 34
hyphomicrobium  MGGRAFRLRRAEVSIKHAMSAMLPKTRTKALLTALTLAAAAAAAPALADVEFRHALDDSA 60
                                                   .     .      :           

human           HGLFGRK------TGQAPGYSYTAANKNK--------GIIWGEDTLMEYLENPKKYIPGT 79
mouse           HGLFGRK------TGQAAGFSYTDANKNK--------GITWGEDTLMEYLENPKKYIPGT 79
rat             HGLFGRK------TGQAAGFSYTDANKNK--------GITWGEDTLMEYLENPKKYIPGT 79
chicken         HGLFGRK------TGQAEGFSYTDANKNK--------GITWGEDTLMEYLENPKKYIPGT 79
fugu            WGLFGRK------TGQAEGFSYTDANKSK--------GIIWSEETLMVYLENPKKYIPGT 80
fly-proximal    HGLIGRK------TGQAAGFAYTDANKAK--------GITWNEDTLFEYLENPKKYIPGT 83
fly-distal      GGVVGRK------CGTAAGYKYTDANIKK--------GVTWTEGNLDEYLKDPKKYIPGT 81
yeast           HGIMGRK------SGQAVGYSYTDANKKK--------GVEWSEQTMSDYLENPKKYIPGT 85
yersinia        LGIVSSSTDTKVITSSLEKMRNAALDAQK--------AIPPKLEGKAEDSPEIKDYRHGF 86
hyphomicrobium  LDLSPIKGEE--ITDAVKSFRKDGVNPYNGNAEALAAGKTIYEDNCQACHLDDGRGGMGP 118
                 .:   .       .          :  :        .             :      * 

human           KMIFVGIKKKEERAD--LIAYLKKATNE--------------------------- 105
mouse           KMIFAGIKKKGERAD--LIAYLKKATNE--------------------------- 105
rat             KMIFAGIKKKGERAD--LIAYLKKATNE--------------------------- 105
chicken         KMIFAGIKKKSERVD--LIAYLKDATSK--------------------------- 105
fugu            KMIFAGIKKKTERAD--LIAYLKSSTS---------------------------- 105
fly-proximal    KMIFAGLKKPNERGD--LIAYLKSATK---------------------------- 108
fly-distal      KMVFAGLKKAEERAD--LIAFLKSNK----------------------------- 105
yeast           KMAFGGLKKPKDRND--LVTYLASATK---------------------------- 110
yersinia        DLLIEQIDKTKQWAEEGNIQEVKKSVGEVINIRNTYHSRYR-------------- 127
hyphomicrobium  SLIDNVFVNARANTDVGMFEIIHSGASGAMRSFSQRGVTQDQILKVIAYIHSLKK 173
                .:    : :     :   .  : .               

Accession numbers of the cytochrome c sequences used in the protein sequence alignment:  human - NP_061820; mouse - CAA25899; rat - AAA21711; chicken - CAA25046; fufu - ABF22472; fly-proximal - NP_477176; fly-distal - NP_47716; yeast - O13393; yersinia -AAD37314; hyphomicrobium - CAC85638

Predicted General Properties of the Cytochrome c Protein  (Homo sapiens) - Primary Sequence Analysis (with ProtParam)b

Number of amino acids: 105

Molecular weight: 11748.7

Theoretical pI: 9.59

Total number of negatively charged residues (Asp + Glu): 11

Total number of positively charged residues (Arg + Lys): 20

Atomic composition: Carbon C 526 Hydrogen H 845 Nitrogen N 143 Oxygen O 149 Sulfur S 6

Formula: C526H845N143O149S6

Total number of atoms: 1669

Extinction coefficients: Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water. Ext. coefficient 13075 Abs 0.1% (=1 g/l) 1.113, assuming ALL Cys residues appear as half cystines Ext. coefficient 12950 Abs 0.1% (=1 g/l) 1.102, assuming NO Cys residues appear as half cystines

Estimated half-life: The N-terminal of the sequence 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 11.38 This classifies the protein as stable.

Aliphatic index: 66.00

Grand average of hydropathicity (GRAVY): -0.706

Bioinformatics References

a Higgins D., Thompson J., Gibson T. Thompson J. D., Higgins D. G., Gibson T. J.(1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting,position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.

b Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., Bairoch A.; Protein Identification and Analysis Tools on the ExPASy Server;
(In) John M. Walker (ed): The Proteomics Protocols Handbook, Humana Press (2005). pp. 571-607  Full text - Copyright Humana Press.

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