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Table 3 Genes, detected both as xenologs and as core genes

From: Blueprint for a minimal photoautotrophic cell: conserved and variable genes in Synechococcus elongatus PCC 7942

Gene name Protein product Core genes* Xenologs¥ Comment
   1) 2) 3) 4) A) B) C)  
Synpcc7942_0056 perosamine synthetase    yes 29 -2   yes Next to a genomic island, also detected by SIGI-HMM method, true prediction of xenology.
Synpcc7942_0587 valyl-tRNA synthetase yes yes yes 35 -1   yes No further phylogenetic evidence of xenology, false positive prediction of xenology.
Synpcc7942_1007 fumarate hydratase   yes yes 35 -1 N-J yes The phylogenetic evidence suggests a true prediction of xenology.
Synpcc7942_1008 formyltetrahydrofolate deformylase    yes 33 -1    No phylogenetic evidence of xenology, false positive.
Synpcc7942_1064 type I restriction-modification   yes    1 Blast yes The phylogenetic evidence suggests a true prediction of xenology.
Synpcc7942_1080 K+ transporter Trk yes yes yes 35 -2   yes No further phylogenetic evidence of xenology, false positive prediction.
Synpcc7942_1081 hypothetical protein yes yes yes 35 -1    No further phylogenetic evidence of xenology, false positive prediction.
Synpcc7942_1132 hypothetical protein    yes 4 -2   yes No phylogenetic evidence of xenology, false positive prediction.
Synpcc7942_1660 potassium channel protein   yes   23 -1 Blast   No phylogenetic evidence of xenology, false positive prediction.
Synpcc7942_1851 ferredoxin--nitrite reductase     27 -2    Maby transferred among Cyanobacteria.
Synpcc7942_1852 precorrin-8X methylmutase   yes yes 35 -1    Likely transferred among Cyanobacteria.
Synpcc7942_1853 cobalt-factor II C20-methyltransferase   yes yes 35 -1    Likely related to alpha-proteobacteria.
Synpcc7942_1854 precorrin-3 methyltransferase   yes   26 -2 N-J   Closely related to alpha proteobacteria.
Synpcc7942_1855 cobyrinic acid a,c-diamide synthase   yes yes 34 -2    Likely transferred among cyanobacteria.
Synpcc7942_1873 two component transcriptional regulator     35 -2    Likely transferred among cyanobacteria.
Synpcc7942_1887 mannosyltransferase   yes   8 -1 N-J   Likely transferred among cyanobacteria.
Synpcc7942_2188 isochorismate synthase yes yes yes 33 1 N-J   Further phylogenetic analyses does not support evidence of xenology, false positive.
Synpcc7942_2436 peptide methionine sulfoxide reductase   yes   22 -1 N-J   Further phylogenetic evidence suggests a true prediction of xenology.
  1. * Criteria to detect coregenes. For each gene, it is shown if it is conserved in 1) chromatophore of P. chromathophora; 2) P. marinus SS 120; 3) CyOGs database; and 4) number of cyanobacterial genomes with homologous genes. ¥Criteria to detect xenologs. A) G+C content in number of SD from the mean; B) unusual phylogenetic relationship by BLAST or Neighbor-joining; and C) Putative Alien (PA) genes.