Amino acid dipepetide frequency for Mycobacterium phage Graduation

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
12.69AlaAla: 12.69 ± 1.372
0.599AlaCys: 0.599 ± 0.168
6.345AlaAsp: 6.345 ± 0.651
6.644AlaGlu: 6.644 ± 0.743
3.113AlaPhe: 3.113 ± 0.543
8.081AlaGly: 8.081 ± 0.785
1.257AlaHis: 1.257 ± 0.272
4.37AlaIle: 4.37 ± 0.581
3.711AlaLys: 3.711 ± 0.489
8.62AlaLeu: 8.62 ± 0.81
2.215AlaMet: 2.215 ± 0.401
2.394AlaAsn: 2.394 ± 0.384
5.088AlaPro: 5.088 ± 0.554
3.532AlaGln: 3.532 ± 0.462
6.644AlaArg: 6.644 ± 0.498
4.849AlaSer: 4.849 ± 0.533
5.687AlaThr: 5.687 ± 0.615
8.68AlaVal: 8.68 ± 0.708
1.856AlaTrp: 1.856 ± 0.354
2.694AlaTyr: 2.694 ± 0.339
0.0AlaXaa: 0.0 ± 0.0
Cys
0.778CysAla: 0.778 ± 0.203
0.06CysCys: 0.06 ± 0.069
0.599CysAsp: 0.599 ± 0.208
0.778CysGlu: 0.778 ± 0.247
0.18CysPhe: 0.18 ± 0.115
0.539CysGly: 0.539 ± 0.174
0.06CysHis: 0.06 ± 0.058
0.419CysIle: 0.419 ± 0.152
0.359CysLys: 0.359 ± 0.172
0.359CysLeu: 0.359 ± 0.155
0.12CysMet: 0.12 ± 0.092
0.239CysAsn: 0.239 ± 0.11
0.359CysPro: 0.359 ± 0.144
0.299CysGln: 0.299 ± 0.141
0.419CysArg: 0.419 ± 0.163
0.419CysSer: 0.419 ± 0.137
0.419CysThr: 0.419 ± 0.154
0.359CysVal: 0.359 ± 0.129
0.12CysTrp: 0.12 ± 0.076
0.18CysTyr: 0.18 ± 0.107
0.0CysXaa: 0.0 ± 0.0
Asp
6.465AspAla: 6.465 ± 0.652
0.658AspCys: 0.658 ± 0.216
4.489AspAsp: 4.489 ± 0.437
3.592AspGlu: 3.592 ± 0.554
2.334AspPhe: 2.334 ± 0.315
5.986AspGly: 5.986 ± 0.55
1.197AspHis: 1.197 ± 0.251
2.754AspIle: 2.754 ± 0.402
2.454AspLys: 2.454 ± 0.422
6.704AspLeu: 6.704 ± 0.688
0.958AspMet: 0.958 ± 0.176
1.736AspAsn: 1.736 ± 0.332
4.37AspPro: 4.37 ± 0.534
1.975AspGln: 1.975 ± 0.447
3.831AspArg: 3.831 ± 0.418
3.232AspSer: 3.232 ± 0.443
4.011AspThr: 4.011 ± 0.445
4.43AspVal: 4.43 ± 0.557
2.095AspTrp: 2.095 ± 0.343
1.736AspTyr: 1.736 ± 0.322
0.0AspXaa: 0.0 ± 0.0
Glu
6.046GluAla: 6.046 ± 0.734
0.12GluCys: 0.12 ± 0.077
4.011GluAsp: 4.011 ± 0.484
5.088GluGlu: 5.088 ± 0.634
2.334GluPhe: 2.334 ± 0.398
3.891GluGly: 3.891 ± 0.498
1.556GluHis: 1.556 ± 0.365
3.412GluIle: 3.412 ± 0.442
3.113GluLys: 3.113 ± 0.437
6.704GluLeu: 6.704 ± 0.536
1.556GluMet: 1.556 ± 0.303
1.975GluAsn: 1.975 ± 0.384
2.694GluPro: 2.694 ± 0.451
2.754GluGln: 2.754 ± 0.382
4.13GluArg: 4.13 ± 0.587
3.771GluSer: 3.771 ± 0.401
3.831GluThr: 3.831 ± 0.454
5.028GluVal: 5.028 ± 0.631
1.676GluTrp: 1.676 ± 0.341
2.514GluTyr: 2.514 ± 0.497
0.0GluXaa: 0.0 ± 0.0
Phe
2.275PheAla: 2.275 ± 0.339
0.359PheCys: 0.359 ± 0.184
2.813PheAsp: 2.813 ± 0.405
2.035PheGlu: 2.035 ± 0.316
0.539PhePhe: 0.539 ± 0.175
3.113PheGly: 3.113 ± 0.441
0.898PheHis: 0.898 ± 0.301
1.377PheIle: 1.377 ± 0.298
1.377PheLys: 1.377 ± 0.295
2.275PheLeu: 2.275 ± 0.445
0.658PheMet: 0.658 ± 0.242
1.317PheAsn: 1.317 ± 0.261
1.377PhePro: 1.377 ± 0.3
0.898PheGln: 0.898 ± 0.194
1.915PheArg: 1.915 ± 0.359
2.275PheSer: 2.275 ± 0.478
1.856PheThr: 1.856 ± 0.26
1.915PheVal: 1.915 ± 0.33
0.599PheTrp: 0.599 ± 0.186
0.898PheTyr: 0.898 ± 0.203
0.0PheXaa: 0.0 ± 0.0
Gly
7.363GlyAla: 7.363 ± 1.038
0.778GlyCys: 0.778 ± 0.23
5.447GlyAsp: 5.447 ± 0.508
4.669GlyGlu: 4.669 ± 0.51
2.933GlyPhe: 2.933 ± 0.459
9.099GlyGly: 9.099 ± 2.085
2.095GlyHis: 2.095 ± 0.452
4.19GlyIle: 4.19 ± 0.687
3.711GlyLys: 3.711 ± 0.507
7.782GlyLeu: 7.782 ± 0.922
1.676GlyMet: 1.676 ± 0.325
3.532GlyAsn: 3.532 ± 0.521
3.831GlyPro: 3.831 ± 0.631
2.454GlyGln: 2.454 ± 0.351
4.37GlyArg: 4.37 ± 0.545
5.866GlySer: 5.866 ± 0.871
4.849GlyThr: 4.849 ± 0.604
5.627GlyVal: 5.627 ± 0.579
2.215GlyTrp: 2.215 ± 0.347
3.113GlyTyr: 3.113 ± 0.459
0.0GlyXaa: 0.0 ± 0.0
His
1.676HisAla: 1.676 ± 0.334
0.239HisCys: 0.239 ± 0.142
1.018HisAsp: 1.018 ± 0.222
1.616HisGlu: 1.616 ± 0.296
0.838HisPhe: 0.838 ± 0.226
1.676HisGly: 1.676 ± 0.349
0.718HisHis: 0.718 ± 0.22
0.898HisIle: 0.898 ± 0.209
1.257HisLys: 1.257 ± 0.343
1.317HisLeu: 1.317 ± 0.319
0.18HisMet: 0.18 ± 0.135
0.299HisAsn: 0.299 ± 0.134
1.317HisPro: 1.317 ± 0.223
1.257HisGln: 1.257 ± 0.298
1.197HisArg: 1.197 ± 0.26
0.599HisSer: 0.599 ± 0.201
1.018HisThr: 1.018 ± 0.251
1.556HisVal: 1.556 ± 0.293
0.539HisTrp: 0.539 ± 0.165
0.599HisTyr: 0.599 ± 0.247
0.0HisXaa: 0.0 ± 0.0
Ile
6.405IleAla: 6.405 ± 0.8
0.18IleCys: 0.18 ± 0.108
3.412IleAsp: 3.412 ± 0.372
3.651IleGlu: 3.651 ± 0.455
0.718IlePhe: 0.718 ± 0.162
4.07IleGly: 4.07 ± 0.458
0.838IleHis: 0.838 ± 0.243
2.035IleIle: 2.035 ± 0.333
1.796IleLys: 1.796 ± 0.353
3.592IleLeu: 3.592 ± 0.419
0.599IleMet: 0.599 ± 0.188
1.856IleAsn: 1.856 ± 0.343
3.292IlePro: 3.292 ± 0.435
1.437IleGln: 1.437 ± 0.365
3.831IleArg: 3.831 ± 0.484
3.173IleSer: 3.173 ± 0.509
3.472IleThr: 3.472 ± 0.451
3.113IleVal: 3.113 ± 0.533
0.599IleTrp: 0.599 ± 0.152
1.437IleTyr: 1.437 ± 0.272
0.0IleXaa: 0.0 ± 0.0
Lys
3.412LysAla: 3.412 ± 0.543
0.419LysCys: 0.419 ± 0.154
2.694LysAsp: 2.694 ± 0.397
2.095LysGlu: 2.095 ± 0.403
1.496LysPhe: 1.496 ± 0.313
2.514LysGly: 2.514 ± 0.417
0.958LysHis: 0.958 ± 0.28
2.634LysIle: 2.634 ± 0.443
1.856LysLys: 1.856 ± 0.449
3.592LysLeu: 3.592 ± 0.492
1.137LysMet: 1.137 ± 0.217
1.377LysAsn: 1.377 ± 0.234
2.694LysPro: 2.694 ± 0.378
1.377LysGln: 1.377 ± 0.335
2.873LysArg: 2.873 ± 0.401
2.275LysSer: 2.275 ± 0.413
2.454LysThr: 2.454 ± 0.362
3.472LysVal: 3.472 ± 0.543
0.838LysTrp: 0.838 ± 0.212
1.137LysTyr: 1.137 ± 0.243
0.0LysXaa: 0.0 ± 0.0
Leu
8.979LeuAla: 8.979 ± 0.86
0.419LeuCys: 0.419 ± 0.155
5.687LeuAsp: 5.687 ± 0.592
5.447LeuGlu: 5.447 ± 0.65
2.095LeuPhe: 2.095 ± 0.392
7.303LeuGly: 7.303 ± 0.854
1.616LeuHis: 1.616 ± 0.284
5.148LeuIle: 5.148 ± 0.539
3.951LeuLys: 3.951 ± 0.594
5.447LeuLeu: 5.447 ± 0.592
1.975LeuMet: 1.975 ± 0.334
2.694LeuAsn: 2.694 ± 0.383
5.148LeuPro: 5.148 ± 0.525
2.574LeuGln: 2.574 ± 0.372
5.806LeuArg: 5.806 ± 0.597
5.507LeuSer: 5.507 ± 0.584
6.225LeuThr: 6.225 ± 0.498
4.549LeuVal: 4.549 ± 0.606
1.437LeuTrp: 1.437 ± 0.349
2.754LeuTyr: 2.754 ± 0.439
0.0LeuXaa: 0.0 ± 0.0
Met
2.394MetAla: 2.394 ± 0.338
0.0MetCys: 0.0 ± 0.0
1.257MetAsp: 1.257 ± 0.269
1.377MetGlu: 1.377 ± 0.294
0.599MetPhe: 0.599 ± 0.175
1.496MetGly: 1.496 ± 0.255
0.299MetHis: 0.299 ± 0.117
0.599MetIle: 0.599 ± 0.188
1.137MetLys: 1.137 ± 0.273
1.257MetLeu: 1.257 ± 0.261
0.18MetMet: 0.18 ± 0.095
0.898MetAsn: 0.898 ± 0.192
1.077MetPro: 1.077 ± 0.239
0.599MetGln: 0.599 ± 0.164
1.137MetArg: 1.137 ± 0.275
2.155MetSer: 2.155 ± 0.351
2.215MetThr: 2.215 ± 0.29
1.257MetVal: 1.257 ± 0.285
0.239MetTrp: 0.239 ± 0.11
0.419MetTyr: 0.419 ± 0.159
0.0MetXaa: 0.0 ± 0.0
Asn
3.352AsnAla: 3.352 ± 0.483
0.299AsnCys: 0.299 ± 0.136
2.095AsnAsp: 2.095 ± 0.352
1.676AsnGlu: 1.676 ± 0.283
1.137AsnPhe: 1.137 ± 0.252
3.711AsnGly: 3.711 ± 0.517
0.718AsnHis: 0.718 ± 0.162
1.377AsnIle: 1.377 ± 0.259
0.599AsnLys: 0.599 ± 0.181
2.574AsnLeu: 2.574 ± 0.372
0.599AsnMet: 0.599 ± 0.176
0.718AsnAsn: 0.718 ± 0.167
2.454AsnPro: 2.454 ± 0.409
0.958AsnGln: 0.958 ± 0.221
1.616AsnArg: 1.616 ± 0.348
1.915AsnSer: 1.915 ± 0.428
1.676AsnThr: 1.676 ± 0.278
2.574AsnVal: 2.574 ± 0.403
0.778AsnTrp: 0.778 ± 0.178
1.317AsnTyr: 1.317 ± 0.257
0.0AsnXaa: 0.0 ± 0.0
Pro
5.088ProAla: 5.088 ± 0.511
0.479ProCys: 0.479 ± 0.161
3.891ProAsp: 3.891 ± 0.466
4.37ProGlu: 4.37 ± 0.548
1.975ProPhe: 1.975 ± 0.422
4.669ProGly: 4.669 ± 0.558
1.137ProHis: 1.137 ± 0.271
2.514ProIle: 2.514 ± 0.393
1.975ProLys: 1.975 ± 0.311
4.549ProLeu: 4.549 ± 0.551
0.958ProMet: 0.958 ± 0.258
1.676ProAsn: 1.676 ± 0.291
2.694ProPro: 2.694 ± 0.408
1.437ProGln: 1.437 ± 0.292
2.873ProArg: 2.873 ± 0.407
3.711ProSer: 3.711 ± 0.565
4.13ProThr: 4.13 ± 0.457
4.07ProVal: 4.07 ± 0.503
0.958ProTrp: 0.958 ± 0.286
1.676ProTyr: 1.676 ± 0.342
0.0ProXaa: 0.0 ± 0.0
Gln
2.813GlnAla: 2.813 ± 0.459
0.12GlnCys: 0.12 ± 0.072
1.496GlnAsp: 1.496 ± 0.319
1.736GlnGlu: 1.736 ± 0.276
1.197GlnPhe: 1.197 ± 0.274
2.574GlnGly: 2.574 ± 0.292
0.599GlnHis: 0.599 ± 0.18
3.113GlnIle: 3.113 ± 0.5
1.437GlnLys: 1.437 ± 0.297
3.831GlnLeu: 3.831 ± 0.485
0.778GlnMet: 0.778 ± 0.239
0.539GlnAsn: 0.539 ± 0.169
2.035GlnPro: 2.035 ± 0.348
1.915GlnGln: 1.915 ± 0.439
1.915GlnArg: 1.915 ± 0.426
1.556GlnSer: 1.556 ± 0.311
1.975GlnThr: 1.975 ± 0.318
2.754GlnVal: 2.754 ± 0.393
0.599GlnTrp: 0.599 ± 0.163
0.778GlnTyr: 0.778 ± 0.203
0.0GlnXaa: 0.0 ± 0.0
Arg
6.165ArgAla: 6.165 ± 0.609
0.599ArgCys: 0.599 ± 0.209
2.993ArgAsp: 2.993 ± 0.494
5.028ArgGlu: 5.028 ± 0.661
1.437ArgPhe: 1.437 ± 0.296
4.609ArgGly: 4.609 ± 0.591
1.137ArgHis: 1.137 ± 0.266
2.993ArgIle: 2.993 ± 0.463
2.993ArgLys: 2.993 ± 0.453
6.046ArgLeu: 6.046 ± 0.699
1.736ArgMet: 1.736 ± 0.304
2.215ArgAsn: 2.215 ± 0.416
3.053ArgPro: 3.053 ± 0.478
2.095ArgGln: 2.095 ± 0.375
4.789ArgArg: 4.789 ± 0.661
3.951ArgSer: 3.951 ± 0.544
3.232ArgThr: 3.232 ± 0.478
4.549ArgVal: 4.549 ± 0.545
1.377ArgTrp: 1.377 ± 0.306
1.796ArgTyr: 1.796 ± 0.314
0.0ArgXaa: 0.0 ± 0.0
Ser
6.405SerAla: 6.405 ± 0.73
0.419SerCys: 0.419 ± 0.169
3.592SerAsp: 3.592 ± 0.413
4.07SerGlu: 4.07 ± 0.526
2.035SerPhe: 2.035 ± 0.369
6.944SerGly: 6.944 ± 0.908
1.137SerHis: 1.137 ± 0.3
2.394SerIle: 2.394 ± 0.412
2.215SerLys: 2.215 ± 0.317
4.849SerLeu: 4.849 ± 0.65
1.736SerMet: 1.736 ± 0.367
2.514SerAsn: 2.514 ± 0.412
3.232SerPro: 3.232 ± 0.429
1.915SerGln: 1.915 ± 0.281
3.053SerArg: 3.053 ± 0.39
3.232SerSer: 3.232 ± 0.503
3.412SerThr: 3.412 ± 0.488
3.532SerVal: 3.532 ± 0.451
1.437SerTrp: 1.437 ± 0.342
1.257SerTyr: 1.257 ± 0.224
0.0SerXaa: 0.0 ± 0.0
Thr
6.644ThrAla: 6.644 ± 0.86
0.599ThrCys: 0.599 ± 0.219
4.908ThrAsp: 4.908 ± 0.596
4.19ThrGlu: 4.19 ± 0.505
2.095ThrPhe: 2.095 ± 0.378
5.986ThrGly: 5.986 ± 0.467
1.018ThrHis: 1.018 ± 0.305
2.813ThrIle: 2.813 ± 0.528
2.394ThrLys: 2.394 ± 0.372
5.926ThrLeu: 5.926 ± 0.648
1.018ThrMet: 1.018 ± 0.231
1.975ThrAsn: 1.975 ± 0.395
3.592ThrPro: 3.592 ± 0.473
1.915ThrGln: 1.915 ± 0.314
3.592ThrArg: 3.592 ± 0.573
3.113ThrSer: 3.113 ± 0.505
4.011ThrThr: 4.011 ± 0.555
5.507ThrVal: 5.507 ± 0.749
1.317ThrTrp: 1.317 ± 0.282
2.095ThrTyr: 2.095 ± 0.383
0.0ThrXaa: 0.0 ± 0.0
Val
6.465ValAla: 6.465 ± 0.683
0.299ValCys: 0.299 ± 0.139
5.268ValAsp: 5.268 ± 0.551
4.549ValGlu: 4.549 ± 0.563
2.334ValPhe: 2.334 ± 0.368
4.789ValGly: 4.789 ± 0.704
1.437ValHis: 1.437 ± 0.276
3.412ValIle: 3.412 ± 0.448
3.292ValLys: 3.292 ± 0.515
5.327ValLeu: 5.327 ± 0.58
1.377ValMet: 1.377 ± 0.323
2.394ValAsn: 2.394 ± 0.342
4.31ValPro: 4.31 ± 0.459
2.514ValGln: 2.514 ± 0.434
4.849ValArg: 4.849 ± 0.571
4.849ValSer: 4.849 ± 0.471
6.225ValThr: 6.225 ± 0.665
4.968ValVal: 4.968 ± 0.553
1.197ValTrp: 1.197 ± 0.259
2.394ValTyr: 2.394 ± 0.395
0.0ValXaa: 0.0 ± 0.0
Trp
1.437TrpAla: 1.437 ± 0.31
0.239TrpCys: 0.239 ± 0.128
1.496TrpAsp: 1.496 ± 0.301
1.257TrpGlu: 1.257 ± 0.215
0.778TrpPhe: 0.778 ± 0.229
1.736TrpGly: 1.736 ± 0.298
0.479TrpHis: 0.479 ± 0.171
1.437TrpIle: 1.437 ± 0.291
0.419TrpLys: 0.419 ± 0.214
1.736TrpLeu: 1.736 ± 0.289
0.539TrpMet: 0.539 ± 0.186
0.539TrpAsn: 0.539 ± 0.19
0.778TrpPro: 0.778 ± 0.218
0.718TrpGln: 0.718 ± 0.164
1.437TrpArg: 1.437 ± 0.34
1.377TrpSer: 1.377 ± 0.274
1.437TrpThr: 1.437 ± 0.31
2.035TrpVal: 2.035 ± 0.303
0.658TrpTrp: 0.658 ± 0.259
0.359TrpTyr: 0.359 ± 0.12
0.0TrpXaa: 0.0 ± 0.0
Tyr
2.215TyrAla: 2.215 ± 0.34
0.18TyrCys: 0.18 ± 0.141
1.496TyrAsp: 1.496 ± 0.321
2.334TyrGlu: 2.334 ± 0.379
0.599TyrPhe: 0.599 ± 0.15
2.813TyrGly: 2.813 ± 0.445
0.658TyrHis: 0.658 ± 0.208
1.616TyrIle: 1.616 ± 0.324
1.257TyrLys: 1.257 ± 0.272
2.275TyrLeu: 2.275 ± 0.36
0.539TyrMet: 0.539 ± 0.146
1.257TyrAsn: 1.257 ± 0.298
1.437TyrPro: 1.437 ± 0.295
1.137TyrGln: 1.137 ± 0.255
2.574TyrArg: 2.574 ± 0.392
1.556TyrSer: 1.556 ± 0.272
2.574TyrThr: 2.574 ± 0.387
2.275TyrVal: 2.275 ± 0.348
0.359TyrTrp: 0.359 ± 0.147
0.419TyrTyr: 0.419 ± 0.181
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 97 proteins (16707 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