Sequence Alignment of the Rhodopsin Protein (with Clustalw)a
Species Sequence Alignment
of Rhodopsin
Human MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY 60
Rabbit MNGTEGPDFYIPMSNQTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY 60
Dog MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY 60
Cat MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY 60
Mouse MNGTEGPNFYVPFSNVTGVVRSPFEQPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY 60
Rat MNGTEGPNFYVPFSNITGVVRSPFEQPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLY 60
Pig MNGTEGPNFYVPFSNKTGVVRSPFEYPQYYLAEPWQFSMLAAYMFMLIVLGFPINFLTLY 60
Cow MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLY 60
Zebrafish MNGTEGPAFYVPMSNATGVVRSPYEYPQYYLVAPWAYGFVAAYMFFLIITGFPVNFLTLY 60
Frog MNGTEGPNFYIPMSNKTGVVRSPFDYPQYYLAEPWQYSALAAYMFLLILLGLPINFMTLF 60
Chicken MNGTEGINFYVPMSNKTGVVRSPFEYPQYYLAEPWKYRLVCCYIFFLISTGLPINLLTLL 60
****** **:*:** *******:: *****. ** : :..*:*:** *:*:*::**
Human VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLG 120
Rabbit VTVQHKKLRTPLNYILLNLAVADLFMVLGGFTTTLYTSLHGYFVFGPTGCNVEGFFATLG 120
Dog VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNVEGFFATLG 120
Cat VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG 120
Mouse VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG 120
Rat VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG 120
Pig VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG 120
Cow VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG 120
Zebrafish VTIEHKKLRTPLNYILLNLAIADLFMVFGGFTTTMYTSLHGYFVFGRLGCNLEGFFATLG 120
Frog VTIQHKKLRTPLNYILLNLVFANHFMVLCGFTVTMYTSMHGYFIFGQTGCYIEGFFATLG 120
Chicken VTFKHKKLRQPLNYILVNLAVADLFMACFGFTVTFYTAWNGYFVFGPVGCAVEGFFATLG 120
**.:***** ******:**..*: **. *** *:**: :***:** ** :********
Human GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWS---- 176
Rabbit GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWIMALACAAPPLVGWS---- 176
Dog GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSSLLS 180
Cat GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWS---- 176
Mouse GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVVFTWIMALACAAPPLVGWS---- 176
Rat GEIGLWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWS---- 176
Pig GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGLALTWVMALACAAPPLVGWS---- 176
Cow GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWS---- 176
Zebrafish GEMGLKSLVVLAIERWMVVCKPVSNFRFGENHAIMGVAFTWVMACSCAVPPLVGWS---- 176
Frog GEVALWSLVVLAVERYMVVCKPMANFRFGENHAIMGVAFTWIMALSCAAPPLFGWS---- 176
Chicken GQVALWSLVVLAIERYIVVCKPMGNFRFSATHAMMGIAFTWVMAFSCAAPPLFGWS---- 176
*::.* ******:**::*****:.****. .**:**:.:**:** :**.*** ***
Human ------RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTV 230
Rabbit ------RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPLIIIFFCYGQLVFTV 230
Dog HSPLVLRYIPEGMQCSCGIDYYTLKPEINNESFVIYMFVVHFAIPMIVIFFCYGQLVFTV 240
Cat ------RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTV 230
Mouse ------RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTV 230
Rat ------RYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIVIFFCYGQLVFTV 230
Pig ------RYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFSIPLVIIFFCYGQLVFTV 230
Cow ------RYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTV 230
Zebrafish ------RYIPEGMQCSCGVDYYTRTPGVNNESFVIYMFIVHFFIPLIVIFFCYGRLVCTV 230
Frog ------RYIPEGMQCSCGVDYYTLKPEVNNESFVIYMFVVHFTIPLIVIFFCYGRLLCTV 230
Chicken ------RYMPEGMQCSCGPDYYTHNPDYHNESYVLYMFVIHFIIPVVVIFFSYGRLICKV 230
**:***:***** **** :***:*:***::** **:::***.**:*: .*
Human KEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTI 290
Rabbit KEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTI 290
Dog KEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSDFGPIFMTL 300
Cat KEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTL 290
Mouse KEAAAQQQESATTQKAEKEVTRMVIIMVIFFLICWLPYASVAFYIFTHQGSNFGPIFMTL 290
Rat KEAAAQQQESATTQKAEKEVTRMVIIMVIFFLICWLPYASVAMYIFTHQGSNFGPIFMTL 290
Pig KEAAAQQQESATTQKAEKEVTRMVIIMVVAFLICWLPYASVAFYIFTHQGSDFGPIFMTI 290
Cow KEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTI 290
Zebrafish KEAARQQQESETTQRAEREVTRMVIIMVIAFLICWLPYAGVAWYIFTHQGSEFGPVFMTL 290
Frog KEAAAQQQESATTQKAEKEVTRMVVIMVVFFLICWVPYAYVAFYIFTHQGSDFGPVFMTV 290
Chicken REAAAQQQESATTQKAEKEVTRMVILMVLGFMLAWTPYAVVAFWIFTNKGADFTATLMAV 290
:*** ***** ***:**:******::**: *::.* *** ** :***::*::* . :*::
Human PAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE--ASATVSKTETSQVAPA 348
Rabbit PAFFAKSSSIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDE--ASATASKTETSQVAPA 348
Dog PAFFAKSSSIYNPVIYIMMNKQFRNCMITTLCCGKNPLGDDE--ASASASKTETSQVAPA 358
Cat PAFFAKSSSIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDE--ASTTGSKTETSQVAPA 348
Mouse PAFFAKSSSIYNPVIYIMLNKQFRNCMLTTLCCGKNPLGDDD--ASATASKTETSQVAPA 348
Rat PAFFAKTASIYNPIIYIMMNKQFRNCMLTTLCCGKNPLGDDE--ASATASKTETSQVAPA 348
Pig PAFFAKSASIYNPVIYIMMNKQFRNCMLTTLCCGKNPLGDDE--ASTTTSKTETSQVAPA 348
Cow PAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDE--ASTTVSKTETSQVAPA 348
Zebrafish PAFFAKTSAVYNPCIYICMNKQFRHCMITTLCCGKNPFEEEEG-ASTTASKTEASSVSSS 349
Frog PAFFAKSSAIYNPVIYIVLNKQFRNCLITTLCCGKNPFGDEDG-SSAATSKTEASSVSSS 349
Chicken PAFFSKSSSLYNPIIYVLMNKQFRNCMITTICCGKNPFGDEDVSSTVSQSKTEVSSVSSS 350
****:*::::*** **: :*****:*::**:******: ::: ::.: ****.*.*:.:
Human -----
Rabbit -----
Dog -----
Cat -----
Mouse -----
Rat -----
Pig -----
Cow -----
Zebrafish SVSPA 354
Frog QVSPA 354
Chicken QVSPA 355
Accession numbers of the rhodopsin protein sequences used in the protein sequence alignment: human - NP_000530; cow - NP_001014890; mouse - NP_663358; rat - NP_254276; dog - NP_001008277; cat - NP_001009242; pig - NP_999386; rabbit - NP_001075818; zebrafish - NP_571159; frog - NP_001080517
Predicted General Properties of the Rhodopsin Protein (Homo sapiens) - Primary Sequence Analysis (with ProtParam)b
Number of amino acids: 348
Molecular weight: 38892.6
Theoretical pI: 6.21
Total number of negatively charged residues (Asp + Glu): 20
Total number of positively charged residues (Arg + Lys): 18
Atomic composition: Carbon C 1814 Hydrogen H 2725 Nitrogen N 423 Oxygen O 477 Sulfur S 25
Formula: C1814H2725N423O477S25
Total number of atoms: 5464
Extinction coefficients: Extinction coefficients are in units of M-1 cm-1, at 280 nm measured in water. Ext. coefficient 56435 Abs 0.1% (=1 g/l) 1.451, assuming ALL Cys residues appear as half cystines Ext. coefficient 55810 Abs 0.1% (=1 g/l) 1.435, 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 34.05 This classifies the protein as stable.
Aliphatic index: 93.59
Grand average of hydropathicity (GRAVY): 0.519
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.
