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The Cyclooxgenase (COX) Protein

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Sequence Alignment of the Cyclooxgyenase (COX) Protein (Homo sapiens) (with Clustalw)a

Isoform Sequence Alignment of Cyclooxygenase

COX-1.1   -MSRSLLLWFLLFLLLLPPLPVLLADPGAPTPVNPCCYYPCQHQGICVRFGLDRYQCDCT 59
COX-1.2   -MSRSLLLWFLLFLLLLPPLPVLLADPGAPTPVNPCCYYPCQHQGICVRFGLDRYQCDCT 59
COX-2     MLARALLLCAVLALS---------------HTANPCCSHPCQNRGVCMSVGFDQYKCDCT 45
           ::*:***  :* *                 ..**** :***::*:*: .*:*:*:****

COX-1.1   RTGYSGPNCTIPGLWTWLRNSLRPSPSFTHFLLTHGRWFWEFVN-ATFIREMLMRLVLTV 118
COX-1.2   RTGYSGPNCTIPGLWTWLRNSLRPSPSFTHFLLTHGRWFWEFVN-ATFIREMLMRLVLTV 118
COX-2     RTGFYGENCSTPEFLTRIKLFLKPTPNTVHYILTHFKGFWNVVNNIPFLRNAIMSYVLTS 105
          ***: * **: * : * ::  *:*:*. .*::*** : **:.**  .*:*: :*  *** 

COX-1.1   RSNLIPSPPTYNSAHDYISWESFSNVSYYTRILPSVPKDCPTPMGTKGKKQLPDAQLLAR 178
COX-1.2   RSNLIPSPPTYNSAHDYISWESFSNVSYYTRILPSVPKDCPTPMGTKGKKQLPDAQLLAR 178
COX-2     RSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVE 165
          **:** ******: :.* ***:***:***** **.**.*****:*.********:: :..

COX-1.1   RFLLRRKFIPDPQGTNLMFAFFAQHFTHQFFKTSGKMGPGFTKALGHGVDLGHIYGDNLE 238
COX-1.2   RFLLRRKFIPDPQGTNLMFAFFAQHFTHQFFKTSGKMGPGFTKALGHGVDLGHIYGDNLE 238
COX-2     KLLLRRKFIPDPQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLA 225
          ::************:*:****************. * **.**:.*******.****:.* 

COX-1.1   RQYQLRLFKDGKLKYQVLDGEMYPPSVEEAPVLMHYPRGIPPQSQMAVGQEVFGLLPGLM 298
COX-1.2   RQYQLRLFKDGKLKYQVLDGEMYPPSVEEAPVLMHYPRGIPPQSQMAVGQEVFGLLPGLM 298
COX-2     RQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVGQEVFGLVPGLM 285
          ** :********:***::*******:*::: . * **  :* : ::*********:****

COX-1.1   LYATLWLREHNRVCDLLKAEHPTWGDEQLFQTTRLILIGETIKIVIEEYVQQLSGYFLQL 358
COX-1.2   LYATLWLREHNRVCDLLKAEHPTWGDEQLFQTTRLILIGETIKIVIEEYVQQLSGYFLQL 358
COX-2     MYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKL 345
          :***:**********:** *** *********:**************:***:****.::*

COX-1.1   KFDPELLFGVQFQYRNRIAMEFNHLYHWHPLMPDSFKVGSQEYSYEQFLFNTSMLVDYGV 418
COX-1.2   KFDPELLFGVQFQYRNRIAMEFNHLYHWHPLMPDSFKIG--------------------- 397
COX-2     KFDPELLFNKQFQYQNRIAAEFNTLYHWHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGI 405
          ********. ****:**** *** *******:**:*::                      

COX-1.1   EALVDAFSRQIAGRIGGGRNMDHHILHVAVDVIRESREMRLQPFNEYRKRFGMKPYTSFQ 478
COX-1.2   ----------------GGRNMDHHILHVAVDVIRESREMRLQPFNEYRKRFGMKPYTSFQ 441
COX-2     TQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFE 465
                          ****:   : :*:   * :**:*: *.******** :*** **:

COX-1.1   ELVGEKEMAAELEELYGDIDALEFYPGLLLEKCHPNSIFGESMIEIGAPFSLKGLLGNPI 538
COX-1.2   ELVGEKEMAAELEELYGDIDALEFYPGLLLEKCHPNSIFGESMIEIGAPFSLKGLLGNPI 501
COX-2     ELTGEKEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVI 525
          **.*****:**** *******:*:**.**:** :*::****:*:*:*********:** *

COX-1.1   CSPEYWKPSTFGGEVGFNIVKTATLKKLVCLNTKTCPYVSFRVPD----------AS--- 585
COX-1.2   CSPEYWKPSTFGGEVGFNIVKTATLKKLVCLNTKTCPYVSFRVPD----------AS--- 548
COX-2     CSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSVPDPELIKTVTINASSSR 585
          *** *************:*::**:::.*:* *.* **:.** ***          **   

COX-1.1   ---QDDGPAVERP--STEL 599
COX-1.2   ---QDDGPAVERP--STEL 562
COX-2     SGLDDINPTVLLKERSTEL 604
             :* .*:*     ****

Accession numbers of the cyclooxygenase sequences used in the protein sequence alignment: NP_000953 prostaglandin-endoperoxide synthase 1 isoform 1 (COX-1.1) ; NP_542158 prostaglandin-endoperoxide synthase 1 isoform 2 (COX-1.2); NP_000954 prostaglandin-endoperoxide synthase 2 (COX-2)

Predicted General Properties of the Cyclooxygenase (COX) 1.1  Protein  (Homo sapiens) - Primary Sequence Analysis (with ProtParam)b

Number of amino acids: 599

Molecular weight: 68686.3

Theoretical pI: 6.81

Total number of negatively charged residues (Asp + Glu): 60

Total number of positively charged residues (Arg + Lys): 58

Atomic composition: Carbon C 3144 Hydrogen H 4781 Nitrogen N 815 Oxygen O 856 Sulfur S 31

Formula: C3144H4781N815O856S31

Total number of atoms: 9627

Extinction coefficients: Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water. Ext. coefficient 95980 Abs 0.1% (=1 g/l) 1.397, assuming ALL Cys residues appear as half cystines Ext. coefficient 95230 Abs 0.1% (=1 g/l) 1.386, 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 44.50 This classifies the protein as unstable.

Aliphatic index: 84.12

Grand average of hydropathicity (GRAVY): -0.181

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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