Amino acid dipepetide frequency for Oryza sativa subsp. japonica (Rice)

Apart from single amino acid frequencies one can also calculate so called amino acid dipeptide frequency.

There is 400 possibilites (441 if we consider Xaa as additional 21st amino acid representing all non-standard or unknown amino acids). Thus, if the dipeptides would be present randomly in proteins each amino acid dipeptide should be present with 0.25% frequency. As it is not the case in the nature, for better visablity all more than expected dipepetides are marked by red, and those which are underrepresented are marked by blue in the table.

All values are presented as per milles (‰), therefore need to be multiplied by 10^-3.

For more information see sequence space article on Wikipedia.

	Ala	Cys	Asp	Glu	Phe	Gly	His	Ile	Lys	Leu	Met	Asn	Pro	Gln	Arg	Ser	Thr	Val	Trp	Tyr	Xaa
Ala	16.224AlaAla: 16.224 ± 0.068	1.622AlaCys: 1.622 ± 0.011	4.406AlaAsp: 4.406 ± 0.019	5.03AlaGlu: 5.03 ± 0.022	2.894AlaPhe: 2.894 ± 0.016	7.357AlaGly: 7.357 ± 0.031	1.851AlaHis: 1.851 ± 0.012	3.594AlaIle: 3.594 ± 0.018	3.567AlaLys: 3.567 ± 0.019	7.762AlaLeu: 7.762 ± 0.03	2.371AlaMet: 2.371 ± 0.013	2.486AlaAsn: 2.486 ± 0.013	5.167AlaPro: 5.167 ± 0.027	2.41AlaGln: 2.41 ± 0.013	6.036AlaArg: 6.036 ± 0.026	7.595AlaSer: 7.595 ± 0.028	4.998AlaThr: 4.998 ± 0.023	7.209AlaVal: 7.209 ± 0.032	1.04AlaTrp: 1.04 ± 0.009	1.87AlaTyr: 1.87 ± 0.013	0.0AlaXaa: 0.0 ± 0.0
Cys	1.403CysAla: 1.403 ± 0.011	0.657CysCys: 0.657 ± 0.008	0.869CysAsp: 0.869 ± 0.008	0.767CysGlu: 0.767 ± 0.008	0.821CysPhe: 0.821 ± 0.008	1.564CysGly: 1.564 ± 0.012	0.551CysHis: 0.551 ± 0.006	0.878CysIle: 0.878 ± 0.008	0.91CysLys: 0.91 ± 0.008	1.821CysLeu: 1.821 ± 0.011	0.448CysMet: 0.448 ± 0.005	0.697CysAsn: 0.697 ± 0.007	1.052CysPro: 1.052 ± 0.009	0.555CysGln: 0.555 ± 0.006	1.447CysArg: 1.447 ± 0.011	1.939CysSer: 1.939 ± 0.014	0.949CysThr: 0.949 ± 0.008	1.145CysVal: 1.145 ± 0.009	0.282CysTrp: 0.282 ± 0.005	0.511CysTyr: 0.511 ± 0.006	0.0CysXaa: 0.0 ± 0.0
Asp	4.92AspAla: 4.92 ± 0.02	0.877AspCys: 0.877 ± 0.009	4.46AspAsp: 4.46 ± 0.028	3.931AspGlu: 3.931 ± 0.022	1.872AspPhe: 1.872 ± 0.012	4.988AspGly: 4.988 ± 0.021	1.315AspHis: 1.315 ± 0.009	2.486AspIle: 2.486 ± 0.014	2.232AspLys: 2.232 ± 0.016	4.739AspLeu: 4.739 ± 0.02	1.336AspMet: 1.336 ± 0.009	1.706AspAsn: 1.706 ± 0.014	2.643AspPro: 2.643 ± 0.014	1.546AspGln: 1.546 ± 0.011	2.693AspArg: 2.693 ± 0.016	3.442AspSer: 3.442 ± 0.019	2.116AspThr: 2.116 ± 0.013	3.82AspVal: 3.82 ± 0.018	0.664AspTrp: 0.664 ± 0.007	1.32AspTyr: 1.32 ± 0.01	0.0AspXaa: 0.0 ± 0.0
Glu	5.457GluAla: 5.457 ± 0.02	0.821GluCys: 0.821 ± 0.008	3.516GluAsp: 3.516 ± 0.02	5.789GluGlu: 5.789 ± 0.035	1.902GluPhe: 1.902 ± 0.012	3.747GluGly: 3.747 ± 0.017	1.464GluHis: 1.464 ± 0.01	2.744GluIle: 2.744 ± 0.016	3.411GluLys: 3.411 ± 0.025	5.744GluLeu: 5.744 ± 0.024	1.611GluMet: 1.611 ± 0.012	2.033GluAsn: 2.033 ± 0.014	2.347GluPro: 2.347 ± 0.015	2.168GluGln: 2.168 ± 0.015	3.813GluArg: 3.813 ± 0.022	3.489GluSer: 3.489 ± 0.016	2.366GluThr: 2.366 ± 0.015	4.103GluVal: 4.103 ± 0.02	0.726GluTrp: 0.726 ± 0.007	1.39GluTyr: 1.39 ± 0.01	0.0GluXaa: 0.0 ± 0.0
Phe	2.753PheAla: 2.753 ± 0.014	0.782PheCys: 0.782 ± 0.008	2.045PheAsp: 2.045 ± 0.011	1.709PheGlu: 1.709 ± 0.011	1.712PhePhe: 1.712 ± 0.013	2.71PheGly: 2.71 ± 0.016	0.982PheHis: 0.982 ± 0.009	1.528PheIle: 1.528 ± 0.011	1.387PheLys: 1.387 ± 0.01	3.75PheLeu: 3.75 ± 0.02	0.829PheMet: 0.829 ± 0.008	1.23PheAsn: 1.23 ± 0.01	1.858PhePro: 1.858 ± 0.012	1.173PheGln: 1.173 ± 0.009	2.007PheArg: 2.007 ± 0.013	3.173PheSer: 3.173 ± 0.017	1.705PheThr: 1.705 ± 0.011	2.524PheVal: 2.524 ± 0.013	0.5PheTrp: 0.5 ± 0.006	1.01PheTyr: 1.01 ± 0.008	0.0PheXaa: 0.0 ± 0.0
Gly	6.686GlyAla: 6.686 ± 0.03	1.533GlyCys: 1.533 ± 0.012	4.451GlyAsp: 4.451 ± 0.018	4.531GlyGlu: 4.531 ± 0.021	2.743GlyPhe: 2.743 ± 0.014	10.258GlyGly: 10.258 ± 0.062	1.898GlyHis: 1.898 ± 0.013	3.002GlyIle: 3.002 ± 0.016	3.401GlyLys: 3.401 ± 0.018	5.845GlyLeu: 5.845 ± 0.02	1.675GlyMet: 1.675 ± 0.012	2.622GlyAsn: 2.622 ± 0.015	2.74GlyPro: 2.74 ± 0.016	2.14GlyGln: 2.14 ± 0.012	5.383GlyArg: 5.383 ± 0.023	5.992GlySer: 5.992 ± 0.025	3.308GlyThr: 3.308 ± 0.016	5.134GlyVal: 5.134 ± 0.024	1.081GlyTrp: 1.081 ± 0.009	1.98GlyTyr: 1.98 ± 0.012	0.0GlyXaa: 0.0 ± 0.0
His	2.075HisAla: 2.075 ± 0.012	0.569HisCys: 0.569 ± 0.006	1.327HisAsp: 1.327 ± 0.012	1.237HisGlu: 1.237 ± 0.009	0.88HisPhe: 0.88 ± 0.008	2.389HisGly: 2.389 ± 0.015	1.353HisHis: 1.353 ± 0.015	1.044HisIle: 1.044 ± 0.009	0.921HisLys: 0.921 ± 0.008	2.671HisLeu: 2.671 ± 0.015	0.539HisMet: 0.539 ± 0.006	0.781HisAsn: 0.781 ± 0.007	1.695HisPro: 1.695 ± 0.011	1.001HisGln: 1.001 ± 0.01	2.158HisArg: 2.158 ± 0.014	1.664HisSer: 1.664 ± 0.011	0.973HisThr: 0.973 ± 0.008	1.738HisVal: 1.738 ± 0.011	0.314HisTrp: 0.314 ± 0.005	0.621HisTyr: 0.621 ± 0.006	0.0HisXaa: 0.0 ± 0.0
Ile	3.43IleAla: 3.43 ± 0.018	0.951IleCys: 0.951 ± 0.009	2.379IleAsp: 2.379 ± 0.013	2.293IleGlu: 2.293 ± 0.012	1.659IlePhe: 1.659 ± 0.011	2.925IleGly: 2.925 ± 0.017	1.105IleHis: 1.105 ± 0.009	2.085IleIle: 2.085 ± 0.013	2.068IleLys: 2.068 ± 0.013	4.084IleLeu: 4.084 ± 0.023	0.94IleMet: 0.94 ± 0.008	1.583IleAsn: 1.583 ± 0.013	2.454IlePro: 2.454 ± 0.017	1.457IleGln: 1.457 ± 0.011	2.345IleArg: 2.345 ± 0.013	3.687IleSer: 3.687 ± 0.017	2.202IleThr: 2.202 ± 0.012	2.904IleVal: 2.904 ± 0.018	0.586IleTrp: 0.586 ± 0.007	1.18IleTyr: 1.18 ± 0.01	0.0IleXaa: 0.0 ± 0.0
Lys	3.549LysAla: 3.549 ± 0.017	0.755LysCys: 0.755 ± 0.008	2.451LysAsp: 2.451 ± 0.015	3.352LysGlu: 3.352 ± 0.022	1.495LysPhe: 1.495 ± 0.012	2.842LysGly: 2.842 ± 0.015	1.089LysHis: 1.089 ± 0.009	2.302LysIle: 2.302 ± 0.015	3.427LysLys: 3.427 ± 0.024	4.535LysLeu: 4.535 ± 0.022	1.189LysMet: 1.189 ± 0.01	1.854LysAsn: 1.854 ± 0.012	2.238LysPro: 2.238 ± 0.016	1.735LysGln: 1.735 ± 0.013	2.989LysArg: 2.989 ± 0.017	3.149LysSer: 3.149 ± 0.019	2.082LysThr: 2.082 ± 0.015	3.008LysVal: 3.008 ± 0.017	0.572LysTrp: 0.572 ± 0.007	1.236LysTyr: 1.236 ± 0.009	0.0LysXaa: 0.0 ± 0.0
Leu	8.328LeuAla: 8.328 ± 0.03	1.815LeuCys: 1.815 ± 0.012	4.933LeuAsp: 4.933 ± 0.019	5.323LeuGlu: 5.323 ± 0.026	3.29LeuPhe: 3.29 ± 0.018	5.893LeuGly: 5.893 ± 0.022	2.872LeuHis: 2.872 ± 0.017	3.535LeuIle: 3.535 ± 0.018	4.327LeuLys: 4.327 ± 0.02	10.617LeuLeu: 10.617 ± 0.036	1.977LeuMet: 1.977 ± 0.014	2.862LeuAsn: 2.862 ± 0.016	6.219LeuPro: 6.219 ± 0.024	3.88LeuGln: 3.88 ± 0.02	6.604LeuArg: 6.604 ± 0.026	7.538LeuSer: 7.538 ± 0.032	4.11LeuThr: 4.11 ± 0.018	6.539LeuVal: 6.539 ± 0.025	1.104LeuTrp: 1.104 ± 0.008	2.185LeuTyr: 2.185 ± 0.014	0.0LeuXaa: 0.0 ± 0.0
Met	2.808MetAla: 2.808 ± 0.015	0.34MetCys: 0.34 ± 0.005	1.402MetAsp: 1.402 ± 0.01	1.788MetGlu: 1.788 ± 0.012	0.76MetPhe: 0.76 ± 0.007	1.513MetGly: 1.513 ± 0.011	0.559MetHis: 0.559 ± 0.005	0.962MetIle: 0.962 ± 0.008	1.185MetLys: 1.185 ± 0.01	2.176MetLeu: 2.176 ± 0.013	0.692MetMet: 0.692 ± 0.008	0.801MetAsn: 0.801 ± 0.007	1.307MetPro: 1.307 ± 0.01	0.875MetGln: 0.875 ± 0.008	1.381MetArg: 1.381 ± 0.01	1.743MetSer: 1.743 ± 0.011	1.03MetThr: 1.03 ± 0.009	1.7MetVal: 1.7 ± 0.011	0.278MetTrp: 0.278 ± 0.004	0.579MetTyr: 0.579 ± 0.006	0.0MetXaa: 0.0 ± 0.0
Asn	2.509AsnAla: 2.509 ± 0.014	0.684AsnCys: 0.684 ± 0.007	1.61AsnAsp: 1.61 ± 0.01	1.682AsnGlu: 1.682 ± 0.012	1.333AsnPhe: 1.333 ± 0.012	2.707AsnGly: 2.707 ± 0.015	0.856AsnHis: 0.856 ± 0.008	1.832AsnIle: 1.832 ± 0.014	1.7AsnLys: 1.7 ± 0.011	3.503AsnLeu: 3.503 ± 0.023	0.92AsnMet: 0.92 ± 0.008	1.609AsnAsn: 1.609 ± 0.015	1.831AsnPro: 1.831 ± 0.012	1.184AsnGln: 1.184 ± 0.011	1.69AsnArg: 1.69 ± 0.011	2.712AsnSer: 2.712 ± 0.016	1.611AsnThr: 1.611 ± 0.01	2.118AsnVal: 2.118 ± 0.014	0.425AsnTrp: 0.425 ± 0.005	0.944AsnTyr: 0.944 ± 0.009	0.0AsnXaa: 0.0 ± 0.0
Pro	5.813ProAla: 5.813 ± 0.025	1.028ProCys: 1.028 ± 0.009	2.736ProAsp: 2.736 ± 0.014	3.214ProGlu: 3.214 ± 0.017	1.842ProPhe: 1.842 ± 0.012	3.456ProGly: 3.456 ± 0.019	1.428ProHis: 1.428 ± 0.01	1.883ProIle: 1.883 ± 0.011	2.138ProLys: 2.138 ± 0.016	4.877ProLeu: 4.877 ± 0.022	1.127ProMet: 1.127 ± 0.01	1.779ProAsn: 1.779 ± 0.011	7.057ProPro: 7.057 ± 0.054	1.828ProGln: 1.828 ± 0.013	4.03ProArg: 4.03 ± 0.022	5.707ProSer: 5.707 ± 0.027	2.928ProThr: 2.928 ± 0.018	3.603ProVal: 3.603 ± 0.017	0.735ProTrp: 0.735 ± 0.007	1.242ProTyr: 1.242 ± 0.01	0.0ProXaa: 0.0 ± 0.0
Gln	2.571GlnAla: 2.571 ± 0.014	0.586GlnCys: 0.586 ± 0.006	1.51GlnAsp: 1.51 ± 0.01	2.158GlnGlu: 2.158 ± 0.013	1.081GlnPhe: 1.081 ± 0.009	2.096GlnGly: 2.096 ± 0.013	1.025GlnHis: 1.025 ± 0.009	1.545GlnIle: 1.545 ± 0.011	1.67GlnLys: 1.67 ± 0.012	3.438GlnLeu: 3.438 ± 0.019	0.874GlnMet: 0.874 ± 0.009	1.22GlnAsn: 1.22 ± 0.01	2.029GlnPro: 2.029 ± 0.014	2.208GlnGln: 2.208 ± 0.027	2.425GlnArg: 2.425 ± 0.015	2.259GlnSer: 2.259 ± 0.014	1.36GlnThr: 1.36 ± 0.011	2.158GlnVal: 2.158 ± 0.013	0.456GlnTrp: 0.456 ± 0.006	0.834GlnTyr: 0.834 ± 0.007	0.0GlnXaa: 0.0 ± 0.0
Arg	5.611ArgAla: 5.611 ± 0.024	1.491ArgCys: 1.491 ± 0.011	3.039ArgAsp: 3.039 ± 0.017	3.6ArgGlu: 3.6 ± 0.018	2.195ArgPhe: 2.195 ± 0.015	4.922ArgGly: 4.922 ± 0.027	2.078ArgHis: 2.078 ± 0.014	2.552ArgIle: 2.552 ± 0.014	3.137ArgLys: 3.137 ± 0.018	6.358ArgLeu: 6.358 ± 0.027	1.549ArgMet: 1.549 ± 0.011	2.018ArgAsn: 2.018 ± 0.011	3.871ArgPro: 3.871 ± 0.021	2.265ArgGln: 2.265 ± 0.015	9.182ArgArg: 9.182 ± 0.054	5.157ArgSer: 5.157 ± 0.024	2.714ArgThr: 2.714 ± 0.013	4.126ArgVal: 4.126 ± 0.018	1.216ArgTrp: 1.216 ± 0.011	1.543ArgTyr: 1.543 ± 0.011	0.001ArgXaa: 0.001 ± 0.0
Ser	6.633SerAla: 6.633 ± 0.027	1.777SerCys: 1.777 ± 0.012	3.797SerAsp: 3.797 ± 0.02	3.702SerGlu: 3.702 ± 0.018	3.197SerPhe: 3.197 ± 0.015	6.017SerGly: 6.017 ± 0.025	1.812SerHis: 1.812 ± 0.011	3.49SerIle: 3.49 ± 0.017	3.49SerLys: 3.49 ± 0.019	7.596SerLeu: 7.596 ± 0.032	1.981SerMet: 1.981 ± 0.011	2.902SerAsn: 2.902 ± 0.016	5.443SerPro: 5.443 ± 0.027	2.325SerGln: 2.325 ± 0.014	4.951SerArg: 4.951 ± 0.018	10.592SerSer: 10.592 ± 0.044	4.489SerThr: 4.489 ± 0.019	4.67SerVal: 4.67 ± 0.018	1.165SerTrp: 1.165 ± 0.009	1.979SerTyr: 1.979 ± 0.011	0.0SerXaa: 0.0 ± 0.0
Thr	4.651ThrAla: 4.651 ± 0.021	0.925ThrCys: 0.925 ± 0.007	2.188ThrAsp: 2.188 ± 0.013	2.375ThrGlu: 2.375 ± 0.012	1.701ThrPhe: 1.701 ± 0.011	3.462ThrGly: 3.462 ± 0.015	0.945ThrHis: 0.945 ± 0.009	2.237ThrIle: 2.237 ± 0.016	2.108ThrLys: 2.108 ± 0.013	4.044ThrLeu: 4.044 ± 0.018	1.243ThrMet: 1.243 ± 0.01	1.682ThrAsn: 1.682 ± 0.012	2.931ThrPro: 2.931 ± 0.017	1.255ThrGln: 1.255 ± 0.009	2.682ThrArg: 2.682 ± 0.014	4.306ThrSer: 4.306 ± 0.02	3.353ThrThr: 3.353 ± 0.021	3.435ThrVal: 3.435 ± 0.017	0.63ThrTrp: 0.63 ± 0.007	1.222ThrTyr: 1.222 ± 0.011	0.0ThrXaa: 0.0 ± 0.0
Val	7.253ValAla: 7.253 ± 0.029	1.169ValCys: 1.169 ± 0.01	3.949ValAsp: 3.949 ± 0.017	4.207ValGlu: 4.207 ± 0.021	2.46ValPhe: 2.46 ± 0.015	4.855ValGly: 4.855 ± 0.022	1.764ValHis: 1.764 ± 0.012	2.802ValIle: 2.802 ± 0.015	2.926ValLys: 2.926 ± 0.015	6.626ValLeu: 6.626 ± 0.024	1.539ValMet: 1.539 ± 0.011	1.984ValAsn: 1.984 ± 0.012	3.753ValPro: 3.753 ± 0.017	2.238ValGln: 2.238 ± 0.012	4.09ValArg: 4.09 ± 0.019	4.931ValSer: 4.931 ± 0.021	3.228ValThr: 3.228 ± 0.014	6.086ValVal: 6.086 ± 0.025	0.814ValTrp: 0.814 ± 0.008	1.738ValTyr: 1.738 ± 0.011	0.0ValXaa: 0.0 ± 0.0
Trp	0.963TrpAla: 0.963 ± 0.008	0.302TrpCys: 0.302 ± 0.004	0.642TrpAsp: 0.642 ± 0.007	0.706TrpGlu: 0.706 ± 0.005	0.48TrpPhe: 0.48 ± 0.006	0.774TrpGly: 0.774 ± 0.008	0.323TrpHis: 0.323 ± 0.005	0.604TrpIle: 0.604 ± 0.007	0.715TrpLys: 0.715 ± 0.008	1.284TrpLeu: 1.284 ± 0.009	0.38TrpMet: 0.38 ± 0.005	0.551TrpAsn: 0.551 ± 0.007	0.663TrpPro: 0.663 ± 0.007	0.454TrpGln: 0.454 ± 0.006	1.266TrpArg: 1.266 ± 0.01	1.048TrpSer: 1.048 ± 0.009	0.667TrpThr: 0.667 ± 0.007	0.803TrpVal: 0.803 ± 0.008	0.319TrpTrp: 0.319 ± 0.005	0.33TrpTyr: 0.33 ± 0.005	0.0TrpXaa: 0.0 ± 0.0
Tyr	1.85TyrAla: 1.85 ± 0.013	0.584TyrCys: 0.584 ± 0.006	1.396TyrAsp: 1.396 ± 0.01	1.247TyrGlu: 1.247 ± 0.01	1.05TyrPhe: 1.05 ± 0.009	1.931TyrGly: 1.931 ± 0.014	0.677TyrHis: 0.677 ± 0.007	1.214TyrIle: 1.214 ± 0.012	1.131TyrLys: 1.131 ± 0.009	2.478TyrLeu: 2.478 ± 0.013	0.662TyrMet: 0.662 ± 0.007	1.055TyrAsn: 1.055 ± 0.01	1.153TyrPro: 1.153 ± 0.009	0.803TyrGln: 0.803 ± 0.007	1.455TyrArg: 1.455 ± 0.01	1.886TyrSer: 1.886 ± 0.011	1.188TyrThr: 1.188 ± 0.01	1.588TyrVal: 1.588 ± 0.01	0.366TyrTrp: 0.366 ± 0.005	0.898TyrTyr: 0.898 ± 0.009	0.0TyrXaa: 0.0 ± 0.0
Xaa	0.0XaaAla: 0.0 ± 0.0	0.0XaaCys: 0.0 ± 0.0	0.0XaaAsp: 0.0 ± 0.0	0.0XaaGlu: 0.0 ± 0.0	0.0XaaPhe: 0.0 ± 0.0	0.0XaaGly: 0.0 ± 0.0	0.0XaaHis: 0.0 ± 0.0	0.0XaaIle: 0.0 ± 0.0	0.0XaaLys: 0.0 ± 0.0	0.0XaaLeu: 0.0 ± 0.0	0.0XaaMet: 0.0 ± 0.0	0.0XaaAsn: 0.0 ± 0.0	0.0XaaPro: 0.0 ± 0.0	0.0XaaGln: 0.0 ± 0.0	0.0XaaArg: 0.0 ± 0.0	0.0XaaSer: 0.0 ± 0.0	0.0XaaThr: 0.0 ± 0.0	0.0XaaVal: 0.0 ± 0.0	0.0XaaTrp: 0.0 ± 0.0	0.0XaaTyr: 0.0 ± 0.0	0.048XaaXaa: 0.048 ± 0.03

Statistics based on 49223 proteins (15125169 amino acids)

Note: The error has been estimated with the bootstraping (x100) at the protein level

Above dipeptide statistics (among other stats for this proteome) you can download from this CSV file

Reference: Kozlowski LP. Proteome-pI 2.0: Proteome Isoelectric Point Database Update. Nucleic Acids Res. 2021, doi: 10.1093/nar/gkab944

Contact: Lukasz P. Kozlowski

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