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Table 1 Comparative enzyme function annotation of the human proteome(1)

From: EFICAz2: enzyme function inference by a combined approach enhanced by machine learning

Level of detail of the enzyme function assignment: Three-field EC numbers

  

EFICAz2 predictions(2)

Annotation source

EC numbers with less than three fields(4): 20,889

Three-field EC numbers: 3,508/3,416(5)

 

EC numbers with less than three fields(4): 21,398

20,608

EFICAz2 novels: 798/790

    

Level of EC annotation agreement(6)

KEGG annotations(3)

  

Annotation source

None

Partial

Full

 

Three-field EC numbers: 2,954/2,907

KEGG novels: 309/281

EFICAz2

18/18

138/67

2,554/2,541

   

KEGG

18/18

73/67

 

Level of detail of the enzyme function assignment: Four-field EC numbers

  

EFICAz2 predictions(2)

Annotation source

EC numbers with less than four fields(4): 21,660

Four-field EC numbers: 2,850/2,645

 

EC numbers with less than four fields(4): 21,833

21,350

EFICAz2 novels: 522/483

    

Level of EC annotation agreement(6)

KEGG annotations(3)

  

Annotation source

None

Partial

Full

 

Four-field EC numbers: 2,523/2,472

KEGG novels: 338/310

EFICAz2

49/46

260/117

2,019/1,999

   

KEGG

46/46

120/117

 
  1. (1) The source of the 24,305 human protein sequences is the KEGG Genes database Release 47.0+/06-26, of June 26, 2008.
  2. (2) Predictions made by EFICAz2 version 13.
  3. (3) Annotations obtained from the KEGG Brite database Release 47.0+/06-26, of June 26, 2008.
  4. (4) Includes non-enzymes, considered as having zero-field EC numbers.
  5. (5) Non-bolded font indicates number of annotations while bolded font refers to the number of annotated protein sequences (a single protein can display more than one enzymatic activity, thus, multiple EC numbers can be assigned to the same protein sequence).
  6. (6) Here, we compare the agreement between annotations from KEGG and EFICAz2 that have the same level of detail, whether three-field or four-field EC numbers. Three different levels of agreement are considered: 1) Full: all EC numbers assigned to the protein by KEGG and EFICAz2 are identical, 2) Partial: at least one but not all the EC numbers assigned to the protein by KEGG and EFICAz2 agree, and 3) None: none of the EC numbers assigned to the protein by KEGG and EFICAz2 coincides.