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Table 5 Domains absent in lineages under positive selection

From: Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates

Under-Represented CATH Domain Topologies in TAED
CATH domain topology Mapped Lineages Under Positive Selection Lineages Under Positive Selection Mapped Uncorrected P-value FDR P-value Bonferroni P-value
Smad3 Chain A 0.08% <  0.01% <  0.0001 <  0.0001 <  0.0001
A middle domain of Talin 1 0.24% <  0.01% <  0.0001 <  0.0001 <  0.0001
Endonuclease - Pi-scei_ Chain A domain 1 0.27% <  0.01% <  0.0001 <  0.0001 <  0.0001
Undecaprenyl pyrophosphate synthetase 0.33% <  0.01% <  0.0001 <  0.0001 <  0.0001
Neurophysin II Chain A 0.38% <  0.01% <  0.0001 <  0.0001 0.0002
Major Prion Protein 0.43% <  0.01% <  0.0001 <  0.0001 0.0010
Archaeosine Trna-guanine Transglycosylase Chain: A domain 4 0.45% <  0.01% <  0.0001 <  0.0001 0.0023
Translation Eukaryotic Peptide Chain Release Factor Subunit 1 Chain A 0.52% <  0.01% <  0.0001 0.0002 0.0140
PWI domain 0.53% <  0.01% <  0.0001 0.0003 0.0206
copper amine oxidase-like fold 0.57% <  0.01% 0.0001 0.0005 0.0472
ERH-like fold 0.58% <  0.01% 0.0001 0.0007 0.0608
Smad Anchor For Receptor Activation Chain B 0.61% <  0.01% 0.0002 0.0010 0.1011
protein kinase ck2 holoenzyme chain C domain 1 0.61% <  0.01% 0.0002 0.0010 0.1011
Elongin C Chain C domain 1 0.65% <  0.01% 0.0003 0.0017 0.1785
Conserved hypothetical protein from pyrococcus furiosus pfu- 392,566-001 ParB domain 0.90% <  0.01% 0.0042 0.0195 1.0000
titin filament fold 0.92% <  0.01% 0.0048 0.0214 1.0000
Transcription Regulator spoIIAA 0.98% <  0.01% 0.0073 0.0311 1.0000
cAMP-dependent Protein Kinase Chain A 0.36% <  0.01% <  0.0001 <  0.0001 <  0.0001
Inorganic Pyrophosphatase 0.45% <  0.01% <  0.0001 <  0.0001 <  0.0001
subunit c (vma5p) of the yeast v-atpase domain 2 0.51% <  0.01% <  0.0001 <  0.0001 <  0.0001
Deoxyuridine 5′-Triphosphate Nucleotidohydrolase_ Chain A 0.88% <  0.01% <  0.0001 0.0002 0.0135
50s Ribosomal Protein L19e Chain O domain 1 0.96% <  0.01% 0.0001 0.0005 0.0451
Glutathione Synthetase Chain A domain 3 1.15% <  0.01% 0.0006 0.0031 0.3377
Deoxyhypusine Synthase 1.18% <  0.01% 0.0007 0.0037 0.4263
DNA Excision Repair Uvrb Chain A 1.29% <  0.01% 0.0017 0.0084 1.0000
  1. Enrichment analysis of CATH domain topologies in TAED showing CATH domains topologies present in lowest % of lineages under positive selection. All pathways were significant at the 0.05 level after correction with the false discovery rate (FDR). Bold numbers indicate not significant at the 0.05 level. Lineages with dN/dS > 1 considered under positive selection