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Table 1 Annotation errors identified, by gene

From: Purine biosynthesis in archaea: variations on a theme

  pur genes
  F D N T La Sa Qa M K E C B H1c P P2d H2 O
Protein name errors                  
Partial misannotation/over-attribution    3    2    1 b        
Inappropriately vague name       23     1 1    27   1 4
Not justified due to missing features 14 2      1         4   
E. C. number errors                  
One or more missing    6    13    23 35 1       
One or more incorrect/unjustified 14 2 2 2       2    1 1 31 2  
Gene structure errors                  
Start codon mis-called 3         1         
Pseudogene label unjustified            1       
Gene symbol errors                  
Incorrect gene symbol        2     1      1 1
Number of genes examined 72 60 31 23 58 51 58 58 28 59 63e 60 13c 46e 31 2f 25
  1. a The three gene products share an EC number.
  2. b Naming of PurE is problematic. Some PurEs are not clearly class I or class II, and some organisms lack a PurK, making a class II type name more appropriate even when PurE appears class I. We counted either a class I or class II-type name as correct in this analysis.
  3. c Halobacteria fusions of PurN and PurH1 are counted under PurN.
  4. d Separate counts were maintained for PurP-like proteins in cluster II. We preferred generic names and no EC number, given a lack of demonstrated function for proteins in this cluster.
  5. e A split or frame-shifted gene was counted as one gene.
  6. f Excludes full-length PurH, counted under PurH1.