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Table 8 Examples of differential genome display of Pyrococcus abyssi and Pyrococcus horikoshii using the COG approach

From: Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs)

Gene/COG Number Phylogenetic pattern* Function Comment
Present in P.abyssi but not P. horikoshii
   PAB2044/0547 amt-szyqvdcebrhuj- - - - - -n- Anthranilate phosphoribosyltransferase The entire branched pathway for aromatic amino acid biosynthesis appears to be present in P. abyssi but not in P. horikoshii
   PAB2045/0147 amt-szyqvdcebrhuj- - - - - -n- Anthranilate synthase component I  
   PAB2046/0512 amt-szyqvdcebrhuj- - - - - -n- Anthranilate synthase component II  
   PAB0307/0082 - - - -szyqvdceb-huj- - - - -inx DAHP synthase  
   PAB2049/0159 amt-szyqvdcebrhuj- - - - -in- Tryptophan synthase a subunit  
   PAB2048/0133 amt-szyqvdcebrhuj- - - - -in- Tryptophan synthase ß subunit  
   PAB0250/0031 - - - -szyqvdcebrhuj- - - - - -n- Cysteine synthase P. abyssi appears to be the only euryarchaeon that encodes the typical cysteine biosynthesis pathway which it shares with A. pernix
   PAB1595/2046 a- - -szyq-dc-b- - -j- - - - - - - - ATP sulfurylase  
   PAB0781/0529 a- - -szyq-dcebr- -j- - - - - -n- Adenylylsulfate kinase  
   PAB1839/0035 - -t-szyqvdcebrh-jwgp-l-n- Uracil phosphoribosyltransferase  
   PAB2246/0827 -m- -s- - - - - - -brhu-w-p- - - - - Adenine-specific DNA methyltransferases  
   PAB2154/0610 amt-s- - - - - -e- -hujw-p- - -n- Restriction enzymes type I helicase subunit  
Present in P. horikoshii but not P. abyssi
   PH0369/0153 - - -k- -y-v- -ebrh- - - - - -I--- Galactokinase  
   PH1048, PH1046/2309 - - -k-z-q-d- -b- - - - - - -o- - - - Leucyl aminopeptidase (aminopeptidase T)  
   PH0365/1085 a- -k- -y-v- -e-rh- - - - - - - - - - Galactose-1-phosphate uridylyltransferase  
   PH0896/1230 - - -k- -yqvd-eb- - -j- - - - - -n- Co/Zn/Cd efflux system component  
   PH0162/1353 amtk- - -qv- - - -r- - - - - - - - - - - Predicted hydrolase of the HD superfamily  
   PH1032/0338 -m-k- - - - - -ce- -hu- - - - -I- - - Site-specific DNA methylase dam  
   PH0873/1401 - -tk- - -q-dceb-uj- - - - - - - - GTPase subunit (McrB) of a restriction endonuclease  
  1. *The designations are as in Table 6.