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        UniProt Knowledgebase:
          Swiss-Prot Protein Knowledgebase
          TrEMBL Protein Database
        SIB Swiss Institute of Bioinformatics; Geneva, Switzerland
        European Bioinformatics Institute (EBI); Hinxton, United Kingdom
        Protein Information Resource (PIR); Washington DC, USA
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Description: Controlled vocabulary of posttranslational modifications (PTM)
Name:        ptmlist.txt
Release:     2018_01 of 31-Jan-2018

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  This document lists the posttranslational modifications used in the
  UniProt knowledgebase (Swiss-Prot and TrEMBL).

  The definition of the posttranslational modifications usage as well as
  other information is provided in the following format:

  ---------  ---------------------------     ------------------------------
  Line code  Content                         Occurrence in an entry
  ---------  ---------------------------     ------------------------------
  ID         Identifier (FT description)     Once; starts a PTM entry
  AC         Accession (PTM-xxxx)            Once
  FT         Feature key                     Once
  TG         Target                          Once; two targets separated by
                                             a dash in case of intrachain
                                             crosslinks
  PA         Position of the modification    Optional; once
             on the amino acid
  PP         Position of the modification    Optional; once
             in the polypeptide
  CF         Correction formula              Optional; once
  MM         Monoisotopic mass difference    Optional; once
  MA         Average mass difference         Optional; once
  LC         Cellular location               Optional; once; alternatives
                                             can be proposed
  TR         Taxonomic range                 Optional; once or more
  KW         Keyword                         Optional; once or more
  DR         Cross-reference to PTM          Optional; once or more
             databases
  BM		 Backbone modification           Optional; once; alternatives can be
                                             proposed; if present, the
                                             affected fragment types are
                                             listed after the modification
  //         Terminator                      Once; ends an entry


___________________________________________________________________________
################################## METALS
ID   Sodium
TG   A or C or G or U
PP   Anywhere.
MT   Metal
CF   H-1 Na1
DR   Unimod; 30.
//
ID   Potassium
TG   A or C or G or U
PP   Anywhere.
MT   Metal
CF   H-1 K1
DR   Unimod; 530.
//
################################## Biological
ID   2'-O-Methyladenosine
TG   A
PP   Anywhere.
MT   Biological
CF   C1 H2
BL   Suppressed
DR   Unimod; 34.
//
ID   N6-methyladenosine
TG   A
PP   Anywhere.
MT   Biological
CF   C1 H2
BL   Modified
DR   Unimod; 34.
//
ID   2'-O-Methyluridine
TG   U
PP   Anywhere.
MT   Biological
CF   C1 H2
BL   Suppressed
DR   Unimod; 34.
//
ID   5-Methylcytidine
TG   C
PP   Anywhere.
MT   Biological
CF   C1 H2
BL   Modified:C1H2
DR   Unimod; 34.
//
ID   N6,2'-O-dimethyladenosine
TG   A
PP   Anywhere.
MT   Biological
CF   C2 H4
BL   Suppressed:C1H2
DR   Unimod; 36.
//
################################## Simple Biological
ID   Methylation
TG   A or C or G or U or T or Y
PP   Anywhere.
MT   Simple Biological
CF   C1 H2
//
ID   Dimethylation
TG   A or C or G or U or T or Y
PP   Anywhere.
MT   Simple Biological
CF   C2 H4
//
ID   MethoxyEthoxylation
TG   A or C or G or U
PP   Anywhere.
MT   Simple Biological
CF   C3 H6 O1
//
################################## Base Conversion
ID   Deoxylnosine
TG   T
PP   Anywhere.
MT   Base Conversion
CF   N-1H-1
//
ID   Deoxylnosine
TG   G
PP   Anywhere.
MT   Base Conversion
CF   N-1H-1O-1
//
################################## Common Artificial
ID   DeoxyFluoronation
TG   A or C or G or U
PP   Anywhere.
MT   Common Artificial
CF   O-1 H-1 F1
//
################################## Terminal Shifts
ID   Cyclic Phosphate
TG   X
PP   Oligo 3'-terminal.
MT   Digestion Termini
CF   H-2 O-1
//
ID   Terminal Phosphorylation
TG   X
PP   Oligo 5'-terminal.
MT   Digestion Termini
CF   H1 O3 P1
//
ID   Terminal Dephosphorylation
TG   X
PP   Oligo 5'-terminal.
MT   Digestion Termini
CF   P-1 O-3 H-1
//
ID   Pfizer 5'-Cap
TG   X
PP   5'-terminal.
MT   Standard
CF   C13H22N5O14P3
//
################################## Backbone Shift
ID   Phosphorothioate
TG   X
FT   Backbone
PP   Anywhere.
MT   Common Variable
CF   SO-1
BM   w,x,c,d 
//
ID   Boranophosphate
TG   X
PP   Anywhere.
FT   Backbone
MT   Therapeutic
CF   B1 H3 O-1
BM   w,x,c,d                    
//
ID   N3'-Phosphoramidate
TG   X
PP   Anywhere.
FT   Backbone
MT   Therapeutic
CF   N1 H1 O-1                      # Replace 3'-O with NH
BM   w,b,c,d 
//
ID   Methylphosphonate
TG   X
PP   Anywhere.
FT   Backbone
MT   Therapeutic
CF   C1 H2 O-1
BM   w,x,c,d 
//