Amino acid dipepetide frequency for Oryza punctata (Red 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	13.842AlaAla: 13.842 ± 0.063	1.534AlaCys: 1.534 ± 0.012	4.2AlaAsp: 4.2 ± 0.018	4.855AlaGlu: 4.855 ± 0.023	2.906AlaPhe: 2.906 ± 0.015	6.496AlaGly: 6.496 ± 0.029	1.701AlaHis: 1.701 ± 0.01	3.701AlaIle: 3.701 ± 0.017	3.777AlaLys: 3.777 ± 0.016	7.697AlaLeu: 7.697 ± 0.023	2.319AlaMet: 2.319 ± 0.014	2.603AlaAsn: 2.603 ± 0.013	4.523AlaPro: 4.523 ± 0.022	2.394AlaGln: 2.394 ± 0.015	5.227AlaArg: 5.227 ± 0.023	7.354AlaSer: 7.354 ± 0.025	4.837AlaThr: 4.837 ± 0.02	6.723AlaVal: 6.723 ± 0.026	0.96AlaTrp: 0.96 ± 0.008	1.899AlaTyr: 1.899 ± 0.013	0.001AlaXaa: 0.001 ± 0.0
Cys	1.309CysAla: 1.309 ± 0.01	0.602CysCys: 0.602 ± 0.007	0.92CysAsp: 0.92 ± 0.008	0.83CysGlu: 0.83 ± 0.008	0.815CysPhe: 0.815 ± 0.008	1.503CysGly: 1.503 ± 0.012	0.528CysHis: 0.528 ± 0.006	0.955CysIle: 0.955 ± 0.008	0.957CysLys: 0.957 ± 0.01	1.807CysLeu: 1.807 ± 0.013	0.449CysMet: 0.449 ± 0.005	0.74CysAsn: 0.74 ± 0.007	0.999CysPro: 0.999 ± 0.008	0.583CysGln: 0.583 ± 0.006	1.269CysArg: 1.269 ± 0.01	1.883CysSer: 1.883 ± 0.012	0.965CysThr: 0.965 ± 0.008	1.132CysVal: 1.132 ± 0.009	0.257CysTrp: 0.257 ± 0.004	0.538CysTyr: 0.538 ± 0.006	0.0CysXaa: 0.0 ± 0.0
Asp	4.707AspAla: 4.707 ± 0.019	0.921AspCys: 0.921 ± 0.008	4.362AspAsp: 4.362 ± 0.027	3.987AspGlu: 3.987 ± 0.022	1.993AspPhe: 1.993 ± 0.012	4.7AspGly: 4.7 ± 0.02	1.322AspHis: 1.322 ± 0.01	2.761AspIle: 2.761 ± 0.016	2.449AspLys: 2.449 ± 0.014	4.893AspLeu: 4.893 ± 0.022	1.434AspMet: 1.434 ± 0.011	1.881AspAsn: 1.881 ± 0.011	2.655AspPro: 2.655 ± 0.013	1.638AspGln: 1.638 ± 0.011	2.694AspArg: 2.694 ± 0.015	3.718AspSer: 3.718 ± 0.02	2.273AspThr: 2.273 ± 0.012	3.851AspVal: 3.851 ± 0.014	0.69AspTrp: 0.69 ± 0.006	1.435AspTyr: 1.435 ± 0.01	0.0AspXaa: 0.0 ± 0.0
Glu	5.302GluAla: 5.302 ± 0.022	0.887GluCys: 0.887 ± 0.007	3.668GluAsp: 3.668 ± 0.019	5.896GluGlu: 5.896 ± 0.035	2.016GluPhe: 2.016 ± 0.013	3.691GluGly: 3.691 ± 0.018	1.429GluHis: 1.429 ± 0.012	3.013GluIle: 3.013 ± 0.014	3.797GluLys: 3.797 ± 0.021	5.896GluLeu: 5.896 ± 0.023	1.698GluMet: 1.698 ± 0.011	2.314GluAsn: 2.314 ± 0.014	2.301GluPro: 2.301 ± 0.015	2.238GluGln: 2.238 ± 0.014	3.587GluArg: 3.587 ± 0.019	3.802GluSer: 3.802 ± 0.02	2.588GluThr: 2.588 ± 0.015	4.115GluVal: 4.115 ± 0.017	0.754GluTrp: 0.754 ± 0.007	1.512GluTyr: 1.512 ± 0.011	0.0GluXaa: 0.0 ± 0.0
Phe	2.764PheAla: 2.764 ± 0.014	0.779PheCys: 0.779 ± 0.008	2.154PheAsp: 2.154 ± 0.012	1.848PheGlu: 1.848 ± 0.012	1.673PhePhe: 1.673 ± 0.012	2.836PheGly: 2.836 ± 0.014	1.019PheHis: 1.019 ± 0.008	1.657PheIle: 1.657 ± 0.012	1.512PheLys: 1.512 ± 0.011	3.809PheLeu: 3.809 ± 0.019	0.862PheMet: 0.862 ± 0.008	1.307PheAsn: 1.307 ± 0.009	1.905PhePro: 1.905 ± 0.012	1.245PheGln: 1.245 ± 0.011	2.03PheArg: 2.03 ± 0.014	3.317PheSer: 3.317 ± 0.019	1.763PheThr: 1.763 ± 0.012	2.613PheVal: 2.613 ± 0.014	0.508PheTrp: 0.508 ± 0.006	1.059PheTyr: 1.059 ± 0.009	0.0PheXaa: 0.0 ± 0.0
Gly	5.906GlyAla: 5.906 ± 0.029	1.468GlyCys: 1.468 ± 0.012	4.174GlyAsp: 4.174 ± 0.015	4.17GlyGlu: 4.17 ± 0.017	2.835GlyPhe: 2.835 ± 0.015	8.583GlyGly: 8.583 ± 0.055	1.783GlyHis: 1.783 ± 0.011	3.187GlyIle: 3.187 ± 0.016	3.635GlyLys: 3.635 ± 0.016	5.81GlyLeu: 5.81 ± 0.019	1.655GlyMet: 1.655 ± 0.012	2.808GlyAsn: 2.808 ± 0.017	2.637GlyPro: 2.637 ± 0.015	2.135GlyGln: 2.135 ± 0.011	4.693GlyArg: 4.693 ± 0.023	6.079GlySer: 6.079 ± 0.024	3.375GlyThr: 3.375 ± 0.015	4.734GlyVal: 4.734 ± 0.021	1.011GlyTrp: 1.011 ± 0.009	2.039GlyTyr: 2.039 ± 0.015	0.0GlyXaa: 0.0 ± 0.0
His	1.917HisAla: 1.917 ± 0.01	0.544HisCys: 0.544 ± 0.006	1.305HisAsp: 1.305 ± 0.009	1.252HisGlu: 1.252 ± 0.01	0.94HisPhe: 0.94 ± 0.007	2.15HisGly: 2.15 ± 0.014	1.154HisHis: 1.154 ± 0.012	1.097HisIle: 1.097 ± 0.01	1.002HisLys: 1.002 ± 0.008	2.596HisLeu: 2.596 ± 0.014	0.572HisMet: 0.572 ± 0.006	0.855HisAsn: 0.855 ± 0.007	1.57HisPro: 1.57 ± 0.011	0.978HisGln: 0.978 ± 0.008	1.795HisArg: 1.795 ± 0.012	1.757HisSer: 1.757 ± 0.011	0.981HisThr: 0.981 ± 0.008	1.654HisVal: 1.654 ± 0.011	0.31HisTrp: 0.31 ± 0.005	0.672HisTyr: 0.672 ± 0.007	0.0HisXaa: 0.0 ± 0.0
Ile	3.602IleAla: 3.602 ± 0.018	0.991IleCys: 0.991 ± 0.008	2.577IleAsp: 2.577 ± 0.014	2.534IleGlu: 2.534 ± 0.014	1.758IlePhe: 1.758 ± 0.012	3.099IleGly: 3.099 ± 0.02	1.165IleHis: 1.165 ± 0.009	2.308IleIle: 2.308 ± 0.017	2.298IleLys: 2.298 ± 0.013	4.373IleLeu: 4.373 ± 0.021	1.008IleMet: 1.008 ± 0.008	1.746IleAsn: 1.746 ± 0.012	2.563IlePro: 2.563 ± 0.02	1.609IleGln: 1.609 ± 0.012	2.443IleArg: 2.443 ± 0.015	3.992IleSer: 3.992 ± 0.017	2.37IleThr: 2.37 ± 0.013	3.092IleVal: 3.092 ± 0.018	0.615IleTrp: 0.615 ± 0.007	1.261IleTyr: 1.261 ± 0.009	0.0IleXaa: 0.0 ± 0.0
Lys	3.811LysAla: 3.811 ± 0.02	0.809LysCys: 0.809 ± 0.008	2.714LysAsp: 2.714 ± 0.016	3.701LysGlu: 3.701 ± 0.022	1.64LysPhe: 1.64 ± 0.012	3.071LysGly: 3.071 ± 0.016	1.187LysHis: 1.187 ± 0.01	2.593LysIle: 2.593 ± 0.016	3.659LysLys: 3.659 ± 0.021	4.96LysLeu: 4.96 ± 0.024	1.288LysMet: 1.288 ± 0.009	2.044LysAsn: 2.044 ± 0.014	2.364LysPro: 2.364 ± 0.014	1.927LysGln: 1.927 ± 0.012	3.156LysArg: 3.156 ± 0.018	3.49LysSer: 3.49 ± 0.018	2.269LysThr: 2.269 ± 0.013	3.244LysVal: 3.244 ± 0.015	0.606LysTrp: 0.606 ± 0.007	1.345LysTyr: 1.345 ± 0.01	0.0LysXaa: 0.0 ± 0.0
Leu	8.055LeuAla: 8.055 ± 0.027	1.823LeuCys: 1.823 ± 0.013	5.109LeuAsp: 5.109 ± 0.023	5.664LeuGlu: 5.664 ± 0.025	3.388LeuPhe: 3.388 ± 0.018	5.832LeuGly: 5.832 ± 0.022	2.79LeuHis: 2.79 ± 0.015	3.749LeuIle: 3.749 ± 0.019	4.762LeuLys: 4.762 ± 0.023	10.53LeuLeu: 10.53 ± 0.033	2.006LeuMet: 2.006 ± 0.012	3.162LeuAsn: 3.162 ± 0.017	5.859LeuPro: 5.859 ± 0.024	4.025LeuGln: 4.025 ± 0.02	6.273LeuArg: 6.273 ± 0.026	7.857LeuSer: 7.857 ± 0.032	4.304LeuThr: 4.304 ± 0.022	6.475LeuVal: 6.475 ± 0.025	1.119LeuTrp: 1.119 ± 0.009	2.303LeuTyr: 2.303 ± 0.013	0.0LeuXaa: 0.0 ± 0.0
Met	2.732MetAla: 2.732 ± 0.014	0.36MetCys: 0.36 ± 0.005	1.477MetAsp: 1.477 ± 0.009	1.888MetGlu: 1.888 ± 0.011	0.774MetPhe: 0.774 ± 0.007	1.501MetGly: 1.501 ± 0.01	0.573MetHis: 0.573 ± 0.005	1.028MetIle: 1.028 ± 0.009	1.308MetLys: 1.308 ± 0.01	2.259MetLeu: 2.259 ± 0.013	0.675MetMet: 0.675 ± 0.008	0.867MetAsn: 0.867 ± 0.008	1.265MetPro: 1.265 ± 0.01	0.91MetGln: 0.91 ± 0.008	1.369MetArg: 1.369 ± 0.008	1.796MetSer: 1.796 ± 0.011	1.084MetThr: 1.084 ± 0.009	1.735MetVal: 1.735 ± 0.013	0.294MetTrp: 0.294 ± 0.005	0.597MetTyr: 0.597 ± 0.006	0.0MetXaa: 0.0 ± 0.0
Asn	2.628AsnAla: 2.628 ± 0.014	0.727AsnCys: 0.727 ± 0.007	1.777AsnAsp: 1.777 ± 0.012	1.881AsnGlu: 1.881 ± 0.013	1.465AsnPhe: 1.465 ± 0.011	2.877AsnGly: 2.877 ± 0.014	0.923AsnHis: 0.923 ± 0.008	2.058AsnIle: 2.058 ± 0.013	1.882AsnLys: 1.882 ± 0.013	3.796AsnLeu: 3.796 ± 0.026	1.009AsnMet: 1.009 ± 0.008	1.784AsnAsn: 1.784 ± 0.016	1.939AsnPro: 1.939 ± 0.011	1.327AsnGln: 1.327 ± 0.01	1.815AsnArg: 1.815 ± 0.011	2.994AsnSer: 2.994 ± 0.017	1.754AsnThr: 1.754 ± 0.012	2.321AsnVal: 2.321 ± 0.013	0.455AsnTrp: 0.455 ± 0.006	1.032AsnTyr: 1.032 ± 0.01	0.0AsnXaa: 0.0 ± 0.0
Pro	5.125ProAla: 5.125 ± 0.024	0.95ProCys: 0.95 ± 0.008	2.738ProAsp: 2.738 ± 0.015	3.25ProGlu: 3.25 ± 0.018	1.862ProPhe: 1.862 ± 0.011	3.22ProGly: 3.22 ± 0.017	1.273ProHis: 1.273 ± 0.011	1.977ProIle: 1.977 ± 0.013	2.309ProLys: 2.309 ± 0.017	4.604ProLeu: 4.604 ± 0.017	1.087ProMet: 1.087 ± 0.009	1.896ProAsn: 1.896 ± 0.012	5.817ProPro: 5.817 ± 0.043	1.767ProGln: 1.767 ± 0.013	3.318ProArg: 3.318 ± 0.017	5.403ProSer: 5.403 ± 0.026	2.834ProThr: 2.834 ± 0.015	3.468ProVal: 3.468 ± 0.017	0.701ProTrp: 0.701 ± 0.008	1.291ProTyr: 1.291 ± 0.011	0.0ProXaa: 0.0 ± 0.0
Gln	2.579GlnAla: 2.579 ± 0.017	0.604GlnCys: 0.604 ± 0.006	1.628GlnAsp: 1.628 ± 0.01	2.269GlnGlu: 2.269 ± 0.014	1.174GlnPhe: 1.174 ± 0.009	2.128GlnGly: 2.128 ± 0.014	1.002GlnHis: 1.002 ± 0.009	1.641GlnIle: 1.641 ± 0.011	1.855GlnLys: 1.855 ± 0.013	3.532GlnLeu: 3.532 ± 0.016	0.945GlnMet: 0.945 ± 0.009	1.367GlnAsn: 1.367 ± 0.012	1.928GlnPro: 1.928 ± 0.014	2.221GlnGln: 2.221 ± 0.026	2.232GlnArg: 2.232 ± 0.013	2.461GlnSer: 2.461 ± 0.015	1.467GlnThr: 1.467 ± 0.011	2.153GlnVal: 2.153 ± 0.011	0.458GlnTrp: 0.458 ± 0.006	0.902GlnTyr: 0.902 ± 0.009	0.0GlnXaa: 0.0 ± 0.0
Arg	4.833ArgAla: 4.833 ± 0.022	1.316ArgCys: 1.316 ± 0.01	2.969ArgAsp: 2.969 ± 0.017	3.524ArgGlu: 3.524 ± 0.015	2.215ArgPhe: 2.215 ± 0.012	4.209ArgGly: 4.209 ± 0.02	1.673ArgHis: 1.673 ± 0.01	2.664ArgIle: 2.664 ± 0.012	3.365ArgLys: 3.365 ± 0.018	5.927ArgLeu: 5.927 ± 0.019	1.526ArgMet: 1.526 ± 0.01	2.137ArgAsn: 2.137 ± 0.014	3.183ArgPro: 3.183 ± 0.016	2.046ArgGln: 2.046 ± 0.013	6.538ArgArg: 6.538 ± 0.035	4.933ArgSer: 4.933 ± 0.022	2.667ArgThr: 2.667 ± 0.012	3.772ArgVal: 3.772 ± 0.015	1.033ArgTrp: 1.033 ± 0.009	1.597ArgTyr: 1.597 ± 0.011	0.001ArgXaa: 0.001 ± 0.0
Ser	6.417SerAla: 6.417 ± 0.024	1.753SerCys: 1.753 ± 0.011	4.111SerAsp: 4.111 ± 0.02	4.086SerGlu: 4.086 ± 0.019	3.301SerPhe: 3.301 ± 0.015	6.025SerGly: 6.025 ± 0.024	1.857SerHis: 1.857 ± 0.011	3.762SerIle: 3.762 ± 0.02	3.874SerLys: 3.874 ± 0.02	7.85SerLeu: 7.85 ± 0.029	2.022SerMet: 2.022 ± 0.011	3.215SerAsn: 3.215 ± 0.018	5.093SerPro: 5.093 ± 0.02	2.529SerGln: 2.529 ± 0.015	4.747SerArg: 4.747 ± 0.02	10.438SerSer: 10.438 ± 0.048	4.544SerThr: 4.544 ± 0.021	4.898SerVal: 4.898 ± 0.019	1.157SerTrp: 1.157 ± 0.01	2.153SerTyr: 2.153 ± 0.013	0.001SerXaa: 0.001 ± 0.0
Thr	4.446ThrAla: 4.446 ± 0.021	0.93ThrCys: 0.93 ± 0.008	2.35ThrAsp: 2.35 ± 0.014	2.616ThrGlu: 2.616 ± 0.013	1.778ThrPhe: 1.778 ± 0.011	3.523ThrGly: 3.523 ± 0.018	0.988ThrHis: 0.988 ± 0.008	2.389ThrIle: 2.389 ± 0.013	2.285ThrLys: 2.285 ± 0.013	4.249ThrLeu: 4.249 ± 0.018	1.256ThrMet: 1.256 ± 0.009	1.837ThrAsn: 1.837 ± 0.012	2.856ThrPro: 2.856 ± 0.017	1.378ThrGln: 1.378 ± 0.01	2.598ThrArg: 2.598 ± 0.013	4.4ThrSer: 4.4 ± 0.021	3.235ThrThr: 3.235 ± 0.02	3.562ThrVal: 3.562 ± 0.017	0.605ThrTrp: 0.605 ± 0.007	1.295ThrTyr: 1.295 ± 0.01	0.0ThrXaa: 0.0 ± 0.0
Val	6.734ValAla: 6.734 ± 0.025	1.177ValCys: 1.177 ± 0.009	3.95ValAsp: 3.95 ± 0.018	4.158ValGlu: 4.158 ± 0.019	2.534ValPhe: 2.534 ± 0.014	4.488ValGly: 4.488 ± 0.022	1.699ValHis: 1.699 ± 0.009	2.975ValIle: 2.975 ± 0.013	3.169ValLys: 3.169 ± 0.017	6.591ValLeu: 6.591 ± 0.023	1.589ValMet: 1.589 ± 0.01	2.143ValAsn: 2.143 ± 0.012	3.622ValPro: 3.622 ± 0.015	2.292ValGln: 2.292 ± 0.013	3.767ValArg: 3.767 ± 0.018	5.132ValSer: 5.132 ± 0.018	3.358ValThr: 3.358 ± 0.017	5.764ValVal: 5.764 ± 0.026	0.813ValTrp: 0.813 ± 0.007	1.804ValTyr: 1.804 ± 0.012	0.0ValXaa: 0.0 ± 0.0
Trp	0.949TrpAla: 0.949 ± 0.009	0.271TrpCys: 0.271 ± 0.004	0.673TrpAsp: 0.673 ± 0.007	0.737TrpGlu: 0.737 ± 0.008	0.479TrpPhe: 0.479 ± 0.006	0.764TrpGly: 0.764 ± 0.008	0.319TrpHis: 0.319 ± 0.005	0.613TrpIle: 0.613 ± 0.007	0.759TrpLys: 0.759 ± 0.008	1.269TrpLeu: 1.269 ± 0.01	0.379TrpMet: 0.379 ± 0.005	0.58TrpAsn: 0.58 ± 0.007	0.597TrpPro: 0.597 ± 0.007	0.455TrpGln: 0.455 ± 0.005	1.086TrpArg: 1.086 ± 0.01	1.023TrpSer: 1.023 ± 0.009	0.657TrpThr: 0.657 ± 0.006	0.782TrpVal: 0.782 ± 0.008	0.264TrpTrp: 0.264 ± 0.005	0.337TrpTyr: 0.337 ± 0.005	0.0TrpXaa: 0.0 ± 0.0
Tyr	1.887TyrAla: 1.887 ± 0.013	0.598TyrCys: 0.598 ± 0.007	1.51TyrAsp: 1.51 ± 0.011	1.357TyrGlu: 1.357 ± 0.011	1.113TyrPhe: 1.113 ± 0.01	2.023TyrGly: 2.023 ± 0.015	0.713TyrHis: 0.713 ± 0.007	1.277TyrIle: 1.277 ± 0.01	1.226TyrLys: 1.226 ± 0.011	2.639TyrLeu: 2.639 ± 0.015	0.715TyrMet: 0.715 ± 0.006	1.157TyrAsn: 1.157 ± 0.01	1.213TyrPro: 1.213 ± 0.011	0.849TyrGln: 0.849 ± 0.008	1.49TyrArg: 1.49 ± 0.011	2.003TyrSer: 2.003 ± 0.012	1.249TyrThr: 1.249 ± 0.01	1.668TyrVal: 1.668 ± 0.012	0.386TyrTrp: 0.386 ± 0.005	0.951TyrTyr: 0.951 ± 0.009	0.0TyrXaa: 0.0 ± 0.0
Xaa	0.001XaaAla: 0.001 ± 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	0.001XaaLeu: 0.001 ± 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	0.001XaaArg: 0.001 ± 0.0	0.0XaaSer: 0.0 ± 0.0	0.001XaaThr: 0.001 ± 0.0	0.0XaaVal: 0.0 ± 0.0	0.0XaaTrp: 0.0 ± 0.0	0.0XaaTyr: 0.0 ± 0.0	0.006XaaXaa: 0.006 ± 0.003

Statistics based on 38431 proteins (16585171 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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