Amino acid dipepetide frequency for Phytophthora ramorum (Sudden oak death agent)

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	11.13AlaAla: 11.13 ± 0.064	1.275AlaCys: 1.275 ± 0.015	4.836AlaAsp: 4.836 ± 0.027	5.68AlaGlu: 5.68 ± 0.036	3.403AlaPhe: 3.403 ± 0.021	5.631AlaGly: 5.631 ± 0.034	1.856AlaHis: 1.856 ± 0.016	3.714AlaIle: 3.714 ± 0.025	4.754AlaLys: 4.754 ± 0.033	8.935AlaLeu: 8.935 ± 0.05	2.428AlaMet: 2.428 ± 0.022	3.049AlaAsn: 3.049 ± 0.021	4.599AlaPro: 4.599 ± 0.042	3.773AlaGln: 3.773 ± 0.03	5.218AlaArg: 5.218 ± 0.034	8.054AlaSer: 8.054 ± 0.048	6.183AlaThr: 6.183 ± 0.042	6.743AlaVal: 6.743 ± 0.033	0.961AlaTrp: 0.961 ± 0.011	2.016AlaTyr: 2.016 ± 0.02	0.0AlaXaa: 0.0 ± 0.0
Cys	1.318CysAla: 1.318 ± 0.016	0.357CysCys: 0.357 ± 0.008	0.826CysAsp: 0.826 ± 0.014	0.939CysGlu: 0.939 ± 0.011	0.662CysPhe: 0.662 ± 0.01	1.201CysGly: 1.201 ± 0.015	0.358CysHis: 0.358 ± 0.007	0.749CysIle: 0.749 ± 0.01	0.685CysLys: 0.685 ± 0.011	1.327CysLeu: 1.327 ± 0.015	0.405CysMet: 0.405 ± 0.008	0.504CysAsn: 0.504 ± 0.01	0.765CysPro: 0.765 ± 0.017	0.554CysGln: 0.554 ± 0.01	0.865CysArg: 0.865 ± 0.012	1.273CysSer: 1.273 ± 0.015	0.902CysThr: 0.902 ± 0.013	1.253CysVal: 1.253 ± 0.013	0.23CysTrp: 0.23 ± 0.005	0.429CysTyr: 0.429 ± 0.008	0.0CysXaa: 0.0 ± 0.0
Asp	5.896AspAla: 5.896 ± 0.03	0.84AspCys: 0.84 ± 0.012	4.703AspAsp: 4.703 ± 0.041	5.098AspGlu: 5.098 ± 0.038	2.223AspPhe: 2.223 ± 0.018	4.207AspGly: 4.207 ± 0.028	1.108AspHis: 1.108 ± 0.012	2.433AspIle: 2.433 ± 0.024	2.505AspLys: 2.505 ± 0.022	4.762AspLeu: 4.762 ± 0.03	1.38AspMet: 1.38 ± 0.015	1.855AspAsn: 1.855 ± 0.017	2.59AspPro: 2.59 ± 0.018	1.901AspGln: 1.901 ± 0.019	2.813AspArg: 2.813 ± 0.024	4.223AspSer: 4.223 ± 0.033	2.87AspThr: 2.87 ± 0.021	4.648AspVal: 4.648 ± 0.029	0.667AspTrp: 0.667 ± 0.011	1.555AspTyr: 1.555 ± 0.018	0.0AspXaa: 0.0 ± 0.0
Glu	6.234GluAla: 6.234 ± 0.04	0.882GluCys: 0.882 ± 0.011	4.517GluAsp: 4.517 ± 0.035	6.261GluGlu: 6.261 ± 0.06	2.214GluPhe: 2.214 ± 0.02	3.482GluGly: 3.482 ± 0.026	1.556GluHis: 1.556 ± 0.015	2.714GluIle: 2.714 ± 0.019	3.732GluLys: 3.732 ± 0.034	6.756GluLeu: 6.756 ± 0.038	1.765GluMet: 1.765 ± 0.015	2.254GluAsn: 2.254 ± 0.019	2.371GluPro: 2.371 ± 0.03	3.115GluGln: 3.115 ± 0.028	4.247GluArg: 4.247 ± 0.033	4.319GluSer: 4.319 ± 0.03	3.625GluThr: 3.625 ± 0.031	4.401GluVal: 4.401 ± 0.029	0.809GluTrp: 0.809 ± 0.013	1.689GluTyr: 1.689 ± 0.016	0.001GluXaa: 0.001 ± 0.0
Phe	3.28PheAla: 3.28 ± 0.025	0.742PheCys: 0.742 ± 0.011	2.351PheAsp: 2.351 ± 0.019	2.277PheGlu: 2.277 ± 0.02	1.612PhePhe: 1.612 ± 0.018	2.824PheGly: 2.824 ± 0.026	0.931PheHis: 0.931 ± 0.012	1.409PheIle: 1.409 ± 0.014	1.481PheLys: 1.481 ± 0.015	3.514PheLeu: 3.514 ± 0.028	0.977PheMet: 0.977 ± 0.013	1.276PheAsn: 1.276 ± 0.014	1.611PhePro: 1.611 ± 0.015	1.482PheGln: 1.482 ± 0.013	2.045PheArg: 2.045 ± 0.018	2.852PheSer: 2.852 ± 0.021	2.05PheThr: 2.05 ± 0.019	2.978PheVal: 2.978 ± 0.025	0.475PheTrp: 0.475 ± 0.008	1.171PheTyr: 1.171 ± 0.014	0.0PheXaa: 0.0 ± 0.0
Gly	5.553GlyAla: 5.553 ± 0.037	1.129GlyCys: 1.129 ± 0.015	4.024GlyAsp: 4.024 ± 0.026	3.775GlyGlu: 3.775 ± 0.025	2.49GlyPhe: 2.49 ± 0.02	5.467GlyGly: 5.467 ± 0.065	1.498GlyHis: 1.498 ± 0.017	2.674GlyIle: 2.674 ± 0.026	3.264GlyLys: 3.264 ± 0.023	5.205GlyLeu: 5.205 ± 0.03	1.523GlyMet: 1.523 ± 0.015	2.342GlyAsn: 2.342 ± 0.023	2.236GlyPro: 2.236 ± 0.024	2.059GlyGln: 2.059 ± 0.018	3.55GlyArg: 3.55 ± 0.025	5.791GlySer: 5.791 ± 0.051	3.475GlyThr: 3.475 ± 0.033	4.867GlyVal: 4.867 ± 0.038	0.797GlyTrp: 0.797 ± 0.012	1.975GlyTyr: 1.975 ± 0.022	0.001GlyXaa: 0.001 ± 0.0
His	2.025HisAla: 2.025 ± 0.018	0.412HisCys: 0.412 ± 0.007	1.277HisAsp: 1.277 ± 0.016	1.508HisGlu: 1.508 ± 0.015	1.004HisPhe: 1.004 ± 0.013	1.57HisGly: 1.57 ± 0.015	0.714HisHis: 0.714 ± 0.011	0.872HisIle: 0.872 ± 0.011	1.001HisLys: 1.001 ± 0.013	2.159HisLeu: 2.159 ± 0.02	0.537HisMet: 0.537 ± 0.009	0.678HisAsn: 0.678 ± 0.01	1.198HisPro: 1.198 ± 0.014	0.973HisGln: 0.973 ± 0.011	1.494HisArg: 1.494 ± 0.017	1.65HisSer: 1.65 ± 0.015	1.107HisThr: 1.107 ± 0.013	1.778HisVal: 1.778 ± 0.015	0.338HisTrp: 0.338 ± 0.007	0.627HisTyr: 0.627 ± 0.01	0.0HisXaa: 0.0 ± 0.0
Ile	3.623IleAla: 3.623 ± 0.023	0.732IleCys: 0.732 ± 0.011	2.409IleAsp: 2.409 ± 0.02	2.401IleGlu: 2.401 ± 0.019	1.547IlePhe: 1.547 ± 0.019	2.419IleGly: 2.419 ± 0.026	0.871IleHis: 0.871 ± 0.013	1.536IleIle: 1.536 ± 0.019	1.841IleLys: 1.841 ± 0.019	3.293IleLeu: 3.293 ± 0.027	0.917IleMet: 0.917 ± 0.014	1.329IleAsn: 1.329 ± 0.015	1.941IlePro: 1.941 ± 0.017	1.499IleGln: 1.499 ± 0.015	2.259IleArg: 2.259 ± 0.02	2.845IleSer: 2.845 ± 0.022	2.167IleThr: 2.167 ± 0.023	3.119IleVal: 3.119 ± 0.024	0.458IleTrp: 0.458 ± 0.008	1.093IleTyr: 1.093 ± 0.015	0.001IleXaa: 0.001 ± 0.0
Lys	4.283LysAla: 4.283 ± 0.031	0.729LysCys: 0.729 ± 0.01	2.516LysAsp: 2.516 ± 0.019	3.395LysGlu: 3.395 ± 0.032	1.685LysPhe: 1.685 ± 0.018	2.386LysGly: 2.386 ± 0.021	1.25LysHis: 1.25 ± 0.014	1.877LysIle: 1.877 ± 0.017	3.919LysLys: 3.919 ± 0.039	4.942LysLeu: 4.942 ± 0.032	1.326LysMet: 1.326 ± 0.015	1.779LysAsn: 1.779 ± 0.016	2.181LysPro: 2.181 ± 0.022	2.35LysGln: 2.35 ± 0.022	3.821LysArg: 3.821 ± 0.03	3.449LysSer: 3.449 ± 0.026	3.176LysThr: 3.176 ± 0.025	3.068LysVal: 3.068 ± 0.021	0.686LysTrp: 0.686 ± 0.01	1.471LysTyr: 1.471 ± 0.017	0.001LysXaa: 0.001 ± 0.0
Leu	8.468LeuAla: 8.468 ± 0.045	1.506LeuCys: 1.506 ± 0.018	5.159LeuAsp: 5.159 ± 0.03	6.339LeuGlu: 6.339 ± 0.039	3.374LeuPhe: 3.374 ± 0.03	5.335LeuGly: 5.335 ± 0.027	2.504LeuHis: 2.504 ± 0.019	2.949LeuIle: 2.949 ± 0.026	4.63LeuLys: 4.63 ± 0.034	9.681LeuLeu: 9.681 ± 0.056	2.181LeuMet: 2.181 ± 0.019	2.971LeuAsn: 2.971 ± 0.023	4.523LeuPro: 4.523 ± 0.026	4.697LeuGln: 4.697 ± 0.033	6.344LeuArg: 6.344 ± 0.035	7.151LeuSer: 7.151 ± 0.035	4.907LeuThr: 4.907 ± 0.028	6.619LeuVal: 6.619 ± 0.038	1.049LeuTrp: 1.049 ± 0.011	2.313LeuTyr: 2.313 ± 0.02	0.002LeuXaa: 0.002 ± 0.0
Met	2.379MetAla: 2.379 ± 0.019	0.388MetCys: 0.388 ± 0.007	1.482MetAsp: 1.482 ± 0.016	1.735MetGlu: 1.735 ± 0.016	0.791MetPhe: 0.791 ± 0.014	1.434MetGly: 1.434 ± 0.017	0.563MetHis: 0.563 ± 0.009	0.908MetIle: 0.908 ± 0.012	1.378MetLys: 1.378 ± 0.015	2.416MetLeu: 2.416 ± 0.019	0.7MetMet: 0.7 ± 0.01	0.866MetAsn: 0.866 ± 0.011	1.151MetPro: 1.151 ± 0.012	1.143MetGln: 1.143 ± 0.015	1.494MetArg: 1.494 ± 0.015	1.807MetSer: 1.807 ± 0.015	1.518MetThr: 1.518 ± 0.015	1.57MetVal: 1.57 ± 0.015	0.306MetTrp: 0.306 ± 0.006	0.635MetTyr: 0.635 ± 0.01	0.0MetXaa: 0.0 ± 0.0
Asn	3.414AsnAla: 3.414 ± 0.027	0.535AsnCys: 0.535 ± 0.009	1.938AsnAsp: 1.938 ± 0.02	2.143AsnGlu: 2.143 ± 0.02	1.256AsnPhe: 1.256 ± 0.015	2.787AsnGly: 2.787 ± 0.025	0.67AsnHis: 0.67 ± 0.011	1.33AsnIle: 1.33 ± 0.017	1.565AsnLys: 1.565 ± 0.015	2.776AsnLeu: 2.776 ± 0.02	0.819AsnMet: 0.819 ± 0.01	1.181AsnAsn: 1.181 ± 0.015	1.743AsnPro: 1.743 ± 0.017	1.274AsnGln: 1.274 ± 0.014	1.783AsnArg: 1.783 ± 0.018	2.453AsnSer: 2.453 ± 0.02	1.745AsnThr: 1.745 ± 0.018	2.543AsnVal: 2.543 ± 0.019	0.435AsnTrp: 0.435 ± 0.008	0.958AsnTyr: 0.958 ± 0.013	0.0AsnXaa: 0.0 ± 0.0
Pro	4.458ProAla: 4.458 ± 0.041	0.554ProCys: 0.554 ± 0.012	2.46ProAsp: 2.46 ± 0.021	3.09ProGlu: 3.09 ± 0.026	1.68ProPhe: 1.68 ± 0.016	2.717ProGly: 2.717 ± 0.025	1.001ProHis: 1.001 ± 0.012	1.618ProIle: 1.618 ± 0.017	2.14ProLys: 2.14 ± 0.021	3.947ProLeu: 3.947 ± 0.026	1.131ProMet: 1.131 ± 0.013	1.533ProAsn: 1.533 ± 0.015	3.243ProPro: 3.243 ± 0.035	1.886ProGln: 1.886 ± 0.018	2.838ProArg: 2.838 ± 0.025	4.583ProSer: 4.583 ± 0.035	3.534ProThr: 3.534 ± 0.04	3.532ProVal: 3.532 ± 0.027	0.525ProTrp: 0.525 ± 0.01	1.034ProTyr: 1.034 ± 0.013	0.001ProXaa: 0.001 ± 0.0
Gln	3.487GlnAla: 3.487 ± 0.026	0.552GlnCys: 0.552 ± 0.01	2.134GlnAsp: 2.134 ± 0.018	2.938GlnGlu: 2.938 ± 0.028	1.445GlnPhe: 1.445 ± 0.015	2.032GlnGly: 2.032 ± 0.017	1.138GlnHis: 1.138 ± 0.013	1.559GlnIle: 1.559 ± 0.016	2.031GlnLys: 2.031 ± 0.02	4.581GlnLeu: 4.581 ± 0.028	1.079GlnMet: 1.079 ± 0.014	1.234GlnAsn: 1.234 ± 0.011	1.796GlnPro: 1.796 ± 0.021	3.199GlnGln: 3.199 ± 0.04	3.173GlnArg: 3.173 ± 0.026	2.727GlnSer: 2.727 ± 0.023	2.41GlnThr: 2.41 ± 0.021	2.811GlnVal: 2.811 ± 0.02	0.616GlnTrp: 0.616 ± 0.01	1.053GlnTyr: 1.053 ± 0.011	0.001GlnXaa: 0.001 ± 0.0
Arg	5.145ArgAla: 5.145 ± 0.031	0.924ArgCys: 0.924 ± 0.012	3.238ArgAsp: 3.238 ± 0.027	4.213ArgGlu: 4.213 ± 0.035	2.329ArgPhe: 2.329 ± 0.019	3.559ArgGly: 3.559 ± 0.026	1.597ArgHis: 1.597 ± 0.016	2.283ArgIle: 2.283 ± 0.017	3.45ArgLys: 3.45 ± 0.024	5.699ArgLeu: 5.699 ± 0.037	1.491ArgMet: 1.491 ± 0.014	1.997ArgAsn: 1.997 ± 0.02	2.547ArgPro: 2.547 ± 0.021	2.87ArgGln: 2.87 ± 0.024	5.333ArgArg: 5.333 ± 0.046	4.777ArgSer: 4.777 ± 0.035	2.981ArgThr: 2.981 ± 0.022	4.346ArgVal: 4.346 ± 0.025	0.843ArgTrp: 0.843 ± 0.011	1.599ArgTyr: 1.599 ± 0.014	0.001ArgXaa: 0.001 ± 0.0
Ser	7.501SerAla: 7.501 ± 0.04	1.159SerCys: 1.159 ± 0.014	4.696SerAsp: 4.696 ± 0.031	4.492SerGlu: 4.492 ± 0.033	2.907SerPhe: 2.907 ± 0.024	5.874SerGly: 5.874 ± 0.06	1.505SerHis: 1.505 ± 0.015	3.102SerIle: 3.102 ± 0.022	3.637SerLys: 3.637 ± 0.026	6.544SerLeu: 6.544 ± 0.034	1.863SerMet: 1.863 ± 0.014	2.687SerAsn: 2.687 ± 0.021	4.213SerPro: 4.213 ± 0.034	2.599SerGln: 2.599 ± 0.023	4.499SerArg: 4.499 ± 0.032	9.625SerSer: 9.625 ± 0.074	5.673SerThr: 5.673 ± 0.049	5.483SerVal: 5.483 ± 0.035	0.94SerTrp: 0.94 ± 0.012	1.889SerTyr: 1.889 ± 0.017	0.0SerXaa: 0.0 ± 0.0
Thr	5.686ThrAla: 5.686 ± 0.038	0.899ThrCys: 0.899 ± 0.013	2.944ThrAsp: 2.944 ± 0.025	3.506ThrGlu: 3.506 ± 0.035	2.191ThrPhe: 2.191 ± 0.021	3.785ThrGly: 3.785 ± 0.032	1.174ThrHis: 1.174 ± 0.013	2.401ThrIle: 2.401 ± 0.022	2.905ThrLys: 2.905 ± 0.025	5.314ThrLeu: 5.314 ± 0.033	1.336ThrMet: 1.336 ± 0.015	1.905ThrAsn: 1.905 ± 0.016	3.901ThrPro: 3.901 ± 0.043	2.244ThrGln: 2.244 ± 0.021	3.132ThrArg: 3.132 ± 0.024	5.374ThrSer: 5.374 ± 0.038	4.552ThrThr: 4.552 ± 0.058	3.851ThrVal: 3.851 ± 0.031	0.672ThrTrp: 0.672 ± 0.011	1.463ThrTyr: 1.463 ± 0.016	0.001ThrXaa: 0.001 ± 0.0
Val	7.238ValAla: 7.238 ± 0.039	1.238ValCys: 1.238 ± 0.013	4.479ValAsp: 4.479 ± 0.028	4.824ValGlu: 4.824 ± 0.029	2.899ValPhe: 2.899 ± 0.028	4.369ValGly: 4.369 ± 0.034	1.652ValHis: 1.652 ± 0.014	2.639ValIle: 2.639 ± 0.021	3.492ValLys: 3.492 ± 0.024	7.079ValLeu: 7.079 ± 0.037	1.716ValMet: 1.716 ± 0.018	2.409ValAsn: 2.409 ± 0.021	3.411ValPro: 3.411 ± 0.022	2.911ValGln: 2.911 ± 0.025	3.934ValArg: 3.934 ± 0.026	5.195ValSer: 5.195 ± 0.04	4.195ValThr: 4.195 ± 0.033	6.089ValVal: 6.089 ± 0.039	0.855ValTrp: 0.855 ± 0.011	1.878ValTyr: 1.878 ± 0.019	0.0ValXaa: 0.0 ± 0.0
Trp	0.84TrpAla: 0.84 ± 0.013	0.198TrpCys: 0.198 ± 0.007	0.705TrpAsp: 0.705 ± 0.01	0.73TrpGlu: 0.73 ± 0.01	0.477TrpPhe: 0.477 ± 0.009	0.709TrpGly: 0.709 ± 0.01	0.318TrpHis: 0.318 ± 0.006	0.548TrpIle: 0.548 ± 0.009	0.754TrpLys: 0.754 ± 0.01	1.277TrpLeu: 1.277 ± 0.016	0.413TrpMet: 0.413 ± 0.007	0.521TrpAsn: 0.521 ± 0.009	0.424TrpPro: 0.424 ± 0.009	0.486TrpGln: 0.486 ± 0.009	0.831TrpArg: 0.831 ± 0.012	0.873TrpSer: 0.873 ± 0.014	0.771TrpThr: 0.771 ± 0.012	0.804TrpVal: 0.804 ± 0.012	0.177TrpTrp: 0.177 ± 0.005	0.368TrpTyr: 0.368 ± 0.007	0.0TrpXaa: 0.0 ± 0.0
Tyr	2.28TyrAla: 2.28 ± 0.02	0.548TyrCys: 0.548 ± 0.01	1.582TyrAsp: 1.582 ± 0.017	1.601TyrGlu: 1.601 ± 0.017	1.151TyrPhe: 1.151 ± 0.012	1.907TyrGly: 1.907 ± 0.024	0.659TyrHis: 0.659 ± 0.009	0.981TyrIle: 0.981 ± 0.013	1.121TyrLys: 1.121 ± 0.013	2.493TyrLeu: 2.493 ± 0.021	0.675TyrMet: 0.675 ± 0.011	0.981TyrAsn: 0.981 ± 0.012	1.059TyrPro: 1.059 ± 0.014	0.981TyrGln: 0.981 ± 0.012	1.55TyrArg: 1.55 ± 0.014	1.866TyrSer: 1.866 ± 0.02	1.395TyrThr: 1.395 ± 0.015	2.002TyrVal: 2.002 ± 0.017	0.384TyrTrp: 0.384 ± 0.009	0.882TyrTyr: 0.882 ± 0.013	0.0TyrXaa: 0.0 ± 0.0
Xaa	0.001XaaAla: 0.001 ± 0.0	0.0XaaCys: 0.0 ± 0.0	0.001XaaAsp: 0.001 ± 0.0	0.001XaaGlu: 0.001 ± 0.0	0.0XaaPhe: 0.0 ± 0.0	0.001XaaGly: 0.001 ± 0.0	0.0XaaHis: 0.0 ± 0.0	0.0XaaIle: 0.0 ± 0.0	0.001XaaLys: 0.001 ± 0.0	0.0XaaLeu: 0.0 ± 0.0	0.001XaaMet: 0.001 ± 0.0	0.0XaaAsn: 0.0 ± 0.0	0.0XaaPro: 0.0 ± 0.0	0.001XaaGln: 0.001 ± 0.0	0.001XaaArg: 0.001 ± 0.0	0.001XaaSer: 0.001 ± 0.0	0.0XaaThr: 0.0 ± 0.0	0.001XaaVal: 0.001 ± 0.0	0.0XaaTrp: 0.0 ± 0.0	0.0XaaTyr: 0.0 ± 0.0	0.0XaaXaa: 0.0 ± 0.0

Statistics based on 15349 proteins (7381725 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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