Amino acid dipepetide frequency for Streptomyces phage ShakeNBake

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.

AlaCysAspGluPheGlyHisIleLysLeuMetAsnProGlnArgSerThrValTrpTyrXaa
Ala
15.154AlaAla: 15.154 ± 2.358
1.169AlaCys: 1.169 ± 0.291
6.822AlaAsp: 6.822 ± 0.532
9.063AlaGlu: 9.063 ± 0.959
2.583AlaPhe: 2.583 ± 0.395
8.04AlaGly: 8.04 ± 0.769
1.559AlaHis: 1.559 ± 0.246
4.093AlaIle: 4.093 ± 0.372
5.409AlaLys: 5.409 ± 0.75
7.699AlaLeu: 7.699 ± 0.728
2.972AlaMet: 2.972 ± 0.457
3.801AlaAsn: 3.801 ± 0.512
3.85AlaPro: 3.85 ± 0.421
4.142AlaGln: 4.142 ± 0.708
5.506AlaArg: 5.506 ± 0.486
4.142AlaSer: 4.142 ± 0.377
6.968AlaThr: 6.968 ± 1.166
6.188AlaVal: 6.188 ± 0.606
1.657AlaTrp: 1.657 ± 0.315
2.144AlaTyr: 2.144 ± 0.396
0.0AlaXaa: 0.0 ± 0.0
Cys
0.975CysAla: 0.975 ± 0.242
0.292CysCys: 0.292 ± 0.127
0.877CysAsp: 0.877 ± 0.201
1.121CysGlu: 1.121 ± 0.252
0.292CysPhe: 0.292 ± 0.128
0.975CysGly: 0.975 ± 0.265
0.244CysHis: 0.244 ± 0.1
0.39CysIle: 0.39 ± 0.151
0.78CysLys: 0.78 ± 0.226
0.731CysLeu: 0.731 ± 0.244
0.439CysMet: 0.439 ± 0.147
0.439CysAsn: 0.439 ± 0.167
0.633CysPro: 0.633 ± 0.18
0.633CysGln: 0.633 ± 0.17
0.828CysArg: 0.828 ± 0.208
0.585CysSer: 0.585 ± 0.164
0.731CysThr: 0.731 ± 0.195
0.633CysVal: 0.633 ± 0.202
0.244CysTrp: 0.244 ± 0.107
0.39CysTyr: 0.39 ± 0.135
0.0CysXaa: 0.0 ± 0.0
Asp
7.114AspAla: 7.114 ± 0.762
0.731AspCys: 0.731 ± 0.2
6.237AspAsp: 6.237 ± 0.762
7.845AspGlu: 7.845 ± 1.187
2.29AspPhe: 2.29 ± 0.383
5.409AspGly: 5.409 ± 0.585
1.072AspHis: 1.072 ± 0.223
2.826AspIle: 2.826 ± 0.31
2.534AspLys: 2.534 ± 0.438
6.237AspLeu: 6.237 ± 0.558
1.705AspMet: 1.705 ± 0.299
2.29AspAsn: 2.29 ± 0.392
4.775AspPro: 4.775 ± 0.805
2.583AspGln: 2.583 ± 0.393
3.752AspArg: 3.752 ± 0.472
3.85AspSer: 3.85 ± 0.431
3.752AspThr: 3.752 ± 0.634
4.093AspVal: 4.093 ± 0.479
1.169AspTrp: 1.169 ± 0.273
2.047AspTyr: 2.047 ± 0.274
0.0AspXaa: 0.0 ± 0.0
Glu
7.943GluAla: 7.943 ± 0.763
0.975GluCys: 0.975 ± 0.242
6.188GluAsp: 6.188 ± 1.038
5.604GluGlu: 5.604 ± 0.968
2.29GluPhe: 2.29 ± 0.296
4.483GluGly: 4.483 ± 0.505
1.9GluHis: 1.9 ± 0.283
2.631GluIle: 2.631 ± 0.389
2.534GluLys: 2.534 ± 0.432
6.919GluLeu: 6.919 ± 0.648
2.388GluMet: 2.388 ± 0.43
2.095GluAsn: 2.095 ± 0.413
3.265GluPro: 3.265 ± 0.593
3.314GluGln: 3.314 ± 0.534
4.288GluArg: 4.288 ± 0.625
2.972GluSer: 2.972 ± 0.479
3.411GluThr: 3.411 ± 0.503
4.727GluVal: 4.727 ± 0.515
1.364GluTrp: 1.364 ± 0.254
1.608GluTyr: 1.608 ± 0.271
0.0GluXaa: 0.0 ± 0.0
Phe
2.29PheAla: 2.29 ± 0.447
0.341PheCys: 0.341 ± 0.111
2.29PheAsp: 2.29 ± 0.475
2.047PheGlu: 2.047 ± 0.405
0.682PhePhe: 0.682 ± 0.219
2.972PheGly: 2.972 ± 0.316
0.39PheHis: 0.39 ± 0.164
1.169PheIle: 1.169 ± 0.219
1.511PheLys: 1.511 ± 0.269
1.852PheLeu: 1.852 ± 0.3
1.072PheMet: 1.072 ± 0.231
1.267PheAsn: 1.267 ± 0.319
1.413PhePro: 1.413 ± 0.397
0.975PheGln: 0.975 ± 0.238
1.608PheArg: 1.608 ± 0.264
1.559PheSer: 1.559 ± 0.492
1.413PheThr: 1.413 ± 0.279
1.852PheVal: 1.852 ± 0.313
0.633PheTrp: 0.633 ± 0.163
0.78PheTyr: 0.78 ± 0.181
0.0PheXaa: 0.0 ± 0.0
Gly
6.676GlyAla: 6.676 ± 0.741
0.975GlyCys: 0.975 ± 0.287
6.286GlyAsp: 6.286 ± 1.11
5.458GlyGlu: 5.458 ± 0.543
2.485GlyPhe: 2.485 ± 0.311
6.091GlyGly: 6.091 ± 0.672
1.413GlyHis: 1.413 ± 0.329
3.606GlyIle: 3.606 ± 0.478
4.093GlyLys: 4.093 ± 0.574
5.701GlyLeu: 5.701 ± 0.583
2.144GlyMet: 2.144 ± 0.447
2.778GlyAsn: 2.778 ± 0.396
3.898GlyPro: 3.898 ± 0.507
2.436GlyGln: 2.436 ± 0.327
4.434GlyArg: 4.434 ± 0.598
5.263GlySer: 5.263 ± 0.71
4.629GlyThr: 4.629 ± 0.645
5.799GlyVal: 5.799 ± 0.607
2.241GlyTrp: 2.241 ± 0.376
2.29GlyTyr: 2.29 ± 0.323
0.0GlyXaa: 0.0 ± 0.0
His
1.559HisAla: 1.559 ± 0.231
0.244HisCys: 0.244 ± 0.121
1.169HisAsp: 1.169 ± 0.265
1.559HisGlu: 1.559 ± 0.299
0.487HisPhe: 0.487 ± 0.147
1.121HisGly: 1.121 ± 0.275
0.536HisHis: 0.536 ± 0.208
1.023HisIle: 1.023 ± 0.183
1.608HisLys: 1.608 ± 0.33
1.754HisLeu: 1.754 ± 0.309
0.731HisMet: 0.731 ± 0.235
0.439HisAsn: 0.439 ± 0.118
1.023HisPro: 1.023 ± 0.25
0.731HisGln: 0.731 ± 0.178
1.608HisArg: 1.608 ± 0.363
1.023HisSer: 1.023 ± 0.193
1.218HisThr: 1.218 ± 0.303
1.218HisVal: 1.218 ± 0.198
0.487HisTrp: 0.487 ± 0.15
0.536HisTyr: 0.536 ± 0.153
0.0HisXaa: 0.0 ± 0.0
Ile
4.532IleAla: 4.532 ± 0.403
0.487IleCys: 0.487 ± 0.148
3.655IleAsp: 3.655 ± 0.433
2.631IleGlu: 2.631 ± 0.403
0.877IlePhe: 0.877 ± 0.184
3.119IleGly: 3.119 ± 0.457
0.926IleHis: 0.926 ± 0.241
1.657IleIle: 1.657 ± 0.396
2.826IleLys: 2.826 ± 0.357
3.362IleLeu: 3.362 ± 0.478
0.78IleMet: 0.78 ± 0.186
1.608IleAsn: 1.608 ± 0.277
2.631IlePro: 2.631 ± 0.384
2.144IleGln: 2.144 ± 0.354
2.778IleArg: 2.778 ± 0.428
2.436IleSer: 2.436 ± 0.46
3.216IleThr: 3.216 ± 0.496
2.436IleVal: 2.436 ± 0.333
0.731IleTrp: 0.731 ± 0.242
0.926IleTyr: 0.926 ± 0.183
0.0IleXaa: 0.0 ± 0.0
Lys
5.506LysAla: 5.506 ± 0.835
0.439LysCys: 0.439 ± 0.165
2.826LysAsp: 2.826 ± 0.478
2.436LysGlu: 2.436 ± 0.407
1.121LysPhe: 1.121 ± 0.212
3.703LysGly: 3.703 ± 0.525
1.023LysHis: 1.023 ± 0.25
1.754LysIle: 1.754 ± 0.289
2.388LysLys: 2.388 ± 0.441
4.337LysLeu: 4.337 ± 0.458
1.852LysMet: 1.852 ± 0.38
1.364LysAsn: 1.364 ± 0.266
3.216LysPro: 3.216 ± 0.496
2.144LysGln: 2.144 ± 0.449
3.411LysArg: 3.411 ± 0.449
2.875LysSer: 2.875 ± 0.369
3.508LysThr: 3.508 ± 0.442
3.265LysVal: 3.265 ± 0.552
1.316LysTrp: 1.316 ± 0.304
1.413LysTyr: 1.413 ± 0.256
0.0LysXaa: 0.0 ± 0.0
Leu
7.455LeuAla: 7.455 ± 0.547
1.316LeuCys: 1.316 ± 0.261
5.75LeuAsp: 5.75 ± 0.53
4.727LeuGlu: 4.727 ± 0.517
2.241LeuPhe: 2.241 ± 0.294
5.604LeuGly: 5.604 ± 0.538
1.803LeuHis: 1.803 ± 0.307
3.411LeuIle: 3.411 ± 0.334
4.386LeuLys: 4.386 ± 0.63
5.506LeuLeu: 5.506 ± 0.495
2.047LeuMet: 2.047 ± 0.335
2.534LeuAsn: 2.534 ± 0.374
3.947LeuPro: 3.947 ± 0.494
2.534LeuGln: 2.534 ± 0.294
5.555LeuArg: 5.555 ± 0.687
5.799LeuSer: 5.799 ± 0.546
4.58LeuThr: 4.58 ± 0.727
5.945LeuVal: 5.945 ± 0.592
1.364LeuTrp: 1.364 ± 0.243
2.388LeuTyr: 2.388 ± 0.317
0.0LeuXaa: 0.0 ± 0.0
Met
2.826MetAla: 2.826 ± 0.431
0.244MetCys: 0.244 ± 0.097
2.144MetAsp: 2.144 ± 0.325
1.559MetGlu: 1.559 ± 0.353
0.536MetPhe: 0.536 ± 0.146
1.9MetGly: 1.9 ± 0.438
0.292MetHis: 0.292 ± 0.116
1.023MetIle: 1.023 ± 0.235
1.316MetLys: 1.316 ± 0.301
2.339MetLeu: 2.339 ± 0.337
0.585MetMet: 0.585 ± 0.158
0.78MetAsn: 0.78 ± 0.224
1.316MetPro: 1.316 ± 0.308
1.462MetGln: 1.462 ± 0.233
2.339MetArg: 2.339 ± 0.388
2.875MetSer: 2.875 ± 0.318
1.949MetThr: 1.949 ± 0.512
1.316MetVal: 1.316 ± 0.273
0.633MetTrp: 0.633 ± 0.137
0.633MetTyr: 0.633 ± 0.214
0.0MetXaa: 0.0 ± 0.0
Asn
3.801AsnAla: 3.801 ± 0.489
0.487AsnCys: 0.487 ± 0.123
2.485AsnAsp: 2.485 ± 0.345
2.583AsnGlu: 2.583 ± 0.406
0.633AsnPhe: 0.633 ± 0.207
2.826AsnGly: 2.826 ± 0.422
0.926AsnHis: 0.926 ± 0.231
1.316AsnIle: 1.316 ± 0.288
1.462AsnLys: 1.462 ± 0.235
1.705AsnLeu: 1.705 ± 0.314
0.975AsnMet: 0.975 ± 0.234
1.023AsnAsn: 1.023 ± 0.244
1.852AsnPro: 1.852 ± 0.379
1.754AsnGln: 1.754 ± 0.382
1.949AsnArg: 1.949 ± 0.304
1.608AsnSer: 1.608 ± 0.3
1.998AsnThr: 1.998 ± 0.35
2.29AsnVal: 2.29 ± 0.352
0.633AsnTrp: 0.633 ± 0.177
0.585AsnTyr: 0.585 ± 0.164
0.0AsnXaa: 0.0 ± 0.0
Pro
4.532ProAla: 4.532 ± 0.529
0.39ProCys: 0.39 ± 0.142
3.557ProAsp: 3.557 ± 0.494
3.947ProGlu: 3.947 ± 0.489
1.218ProPhe: 1.218 ± 0.235
3.996ProGly: 3.996 ± 0.567
1.023ProHis: 1.023 ± 0.218
1.998ProIle: 1.998 ± 0.373
2.485ProLys: 2.485 ± 0.438
3.314ProLeu: 3.314 ± 0.44
1.121ProMet: 1.121 ± 0.235
1.413ProAsn: 1.413 ± 0.221
1.316ProPro: 1.316 ± 0.257
1.559ProGln: 1.559 ± 0.259
2.485ProArg: 2.485 ± 0.513
2.778ProSer: 2.778 ± 0.386
4.044ProThr: 4.044 ± 0.676
3.557ProVal: 3.557 ± 0.372
0.731ProTrp: 0.731 ± 0.222
1.754ProTyr: 1.754 ± 0.322
0.0ProXaa: 0.0 ± 0.0
Gln
4.337GlnAla: 4.337 ± 0.864
0.439GlnCys: 0.439 ± 0.163
1.852GlnAsp: 1.852 ± 0.272
2.144GlnGlu: 2.144 ± 0.365
1.267GlnPhe: 1.267 ± 0.253
2.534GlnGly: 2.534 ± 0.331
0.633GlnHis: 0.633 ± 0.188
1.559GlnIle: 1.559 ± 0.305
2.339GlnLys: 2.339 ± 0.354
3.314GlnLeu: 3.314 ± 0.354
1.169GlnMet: 1.169 ± 0.21
1.218GlnAsn: 1.218 ± 0.246
1.316GlnPro: 1.316 ± 0.262
1.803GlnGln: 1.803 ± 0.312
3.46GlnArg: 3.46 ± 0.524
2.29GlnSer: 2.29 ± 0.446
1.852GlnThr: 1.852 ± 0.314
2.534GlnVal: 2.534 ± 0.291
0.682GlnTrp: 0.682 ± 0.162
1.413GlnTyr: 1.413 ± 0.406
0.0GlnXaa: 0.0 ± 0.0
Arg
5.847ArgAla: 5.847 ± 0.595
0.682ArgCys: 0.682 ± 0.189
4.142ArgAsp: 4.142 ± 0.511
4.337ArgGlu: 4.337 ± 0.699
1.9ArgPhe: 1.9 ± 0.285
4.483ArgGly: 4.483 ± 0.428
1.511ArgHis: 1.511 ± 0.379
4.142ArgIle: 4.142 ± 0.538
4.044ArgLys: 4.044 ± 0.548
5.75ArgLeu: 5.75 ± 0.748
2.144ArgMet: 2.144 ± 0.401
1.9ArgAsn: 1.9 ± 0.297
2.972ArgPro: 2.972 ± 0.323
1.559ArgGln: 1.559 ± 0.276
4.629ArgArg: 4.629 ± 0.697
3.07ArgSer: 3.07 ± 0.448
2.924ArgThr: 2.924 ± 0.429
3.655ArgVal: 3.655 ± 0.373
1.316ArgTrp: 1.316 ± 0.237
2.436ArgTyr: 2.436 ± 0.324
0.0ArgXaa: 0.0 ± 0.0
Ser
5.458SerAla: 5.458 ± 0.743
0.975SerCys: 0.975 ± 0.183
3.752SerAsp: 3.752 ± 0.431
3.314SerGlu: 3.314 ± 0.574
1.413SerPhe: 1.413 ± 0.257
6.237SerGly: 6.237 ± 1.114
1.023SerHis: 1.023 ± 0.252
2.631SerIle: 2.631 ± 0.476
2.534SerLys: 2.534 ± 0.399
4.873SerLeu: 4.873 ± 0.622
1.9SerMet: 1.9 ± 0.331
1.998SerAsn: 1.998 ± 0.274
2.193SerPro: 2.193 ± 0.45
1.852SerGln: 1.852 ± 0.34
2.485SerArg: 2.485 ± 0.397
3.85SerSer: 3.85 ± 0.498
3.314SerThr: 3.314 ± 0.382
4.532SerVal: 4.532 ± 0.818
0.828SerTrp: 0.828 ± 0.165
1.803SerTyr: 1.803 ± 0.285
0.0SerXaa: 0.0 ± 0.0
Thr
5.799ThrAla: 5.799 ± 0.741
0.487ThrCys: 0.487 ± 0.147
3.216ThrAsp: 3.216 ± 0.355
2.778ThrGlu: 2.778 ± 0.389
2.144ThrPhe: 2.144 ± 0.441
6.335ThrGly: 6.335 ± 1.04
1.218ThrHis: 1.218 ± 0.283
3.021ThrIle: 3.021 ± 0.507
2.241ThrLys: 2.241 ± 0.374
4.922ThrLeu: 4.922 ± 0.591
1.657ThrMet: 1.657 ± 0.549
1.949ThrAsn: 1.949 ± 0.293
3.508ThrPro: 3.508 ± 0.506
1.705ThrGln: 1.705 ± 0.304
4.288ThrArg: 4.288 ± 0.457
3.021ThrSer: 3.021 ± 0.83
3.46ThrThr: 3.46 ± 0.696
5.116ThrVal: 5.116 ± 0.609
1.267ThrTrp: 1.267 ± 0.248
1.657ThrTyr: 1.657 ± 0.277
0.0ThrXaa: 0.0 ± 0.0
Val
6.188ValAla: 6.188 ± 0.748
0.731ValCys: 0.731 ± 0.208
5.896ValAsp: 5.896 ± 0.789
4.727ValGlu: 4.727 ± 0.6
2.095ValPhe: 2.095 ± 0.287
5.458ValGly: 5.458 ± 0.54
1.608ValHis: 1.608 ± 0.368
3.265ValIle: 3.265 ± 0.342
3.362ValLys: 3.362 ± 0.538
5.019ValLeu: 5.019 ± 0.645
1.218ValMet: 1.218 ± 0.304
2.388ValAsn: 2.388 ± 0.396
2.388ValPro: 2.388 ± 0.354
2.583ValGln: 2.583 ± 0.321
4.434ValArg: 4.434 ± 0.513
4.337ValSer: 4.337 ± 0.553
3.947ValThr: 3.947 ± 0.481
5.019ValVal: 5.019 ± 0.584
1.218ValTrp: 1.218 ± 0.306
2.193ValTyr: 2.193 ± 0.43
0.0ValXaa: 0.0 ± 0.0
Trp
1.852TrpAla: 1.852 ± 0.257
0.439TrpCys: 0.439 ± 0.16
1.413TrpAsp: 1.413 ± 0.294
1.462TrpGlu: 1.462 ± 0.303
0.682TrpPhe: 0.682 ± 0.206
0.828TrpGly: 0.828 ± 0.217
0.341TrpHis: 0.341 ± 0.123
1.072TrpIle: 1.072 ± 0.255
0.926TrpLys: 0.926 ± 0.197
1.9TrpLeu: 1.9 ± 0.227
0.487TrpMet: 0.487 ± 0.152
0.633TrpAsn: 0.633 ± 0.215
0.78TrpPro: 0.78 ± 0.192
0.731TrpGln: 0.731 ± 0.201
1.218TrpArg: 1.218 ± 0.3
1.072TrpSer: 1.072 ± 0.237
1.511TrpThr: 1.511 ± 0.345
1.267TrpVal: 1.267 ± 0.308
0.244TrpTrp: 0.244 ± 0.099
0.585TrpTyr: 0.585 ± 0.164
0.0TrpXaa: 0.0 ± 0.0
Tyr
3.119TyrAla: 3.119 ± 0.358
0.39TyrCys: 0.39 ± 0.17
1.803TyrAsp: 1.803 ± 0.341
1.559TyrGlu: 1.559 ± 0.302
0.877TyrPhe: 0.877 ± 0.275
2.583TyrGly: 2.583 ± 0.433
0.633TyrHis: 0.633 ± 0.209
1.169TyrIle: 1.169 ± 0.198
1.121TyrLys: 1.121 ± 0.242
1.657TyrLeu: 1.657 ± 0.267
0.633TyrMet: 0.633 ± 0.179
0.975TyrAsn: 0.975 ± 0.229
0.926TyrPro: 0.926 ± 0.231
1.511TyrGln: 1.511 ± 0.272
2.388TyrArg: 2.388 ± 0.478
1.559TyrSer: 1.559 ± 0.315
1.364TyrThr: 1.364 ± 0.274
2.631TyrVal: 2.631 ± 0.768
0.682TyrTrp: 0.682 ± 0.215
0.536TyrTyr: 0.536 ± 0.175
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
0.0XaaXaa: 0.0 ± 0.0
Statistics based on 104 proteins (20523 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
See this proteome in: uniprot_link
Proteome-pI is available under Creative Commons Attribution-NoDerivs license, for more details see here

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