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Table 3 Data describing nucleotide substitution patterns within the conserved regions of the homing endonuclease domains of pairs of VMA inteins. Sd is the number of observed synonymous substitutions; Nd is the number of observed non-synonymous substitutions; S is the number of potential synonymous substitutions; N is the number of potential non-synonymous substitutions; pS is the proportion of observed synonymous substitutions; pN is the proportion of observed non-synonymous substitutions; dS is the Jukes-Cantor correction for multiple hits of pS; dN is the Jukes-Cantor correction for multiple hits of pN. EN describes the experimentally determined activity of the homing endonuclease [9], A= active, I= inactive. The activities of the endonucleases from C. glabrata and D. hansenii have not been determined, but are likely to be inactive. The species in which VMA inteins occur are labelled: Scerev, Saccharomyces cerevisiae; SspDH1A, a wild isolate of S. cerevisiae; Scarioc, S. cariocanus; Tglobosa, Torulaspora globosa; Zbailli, Zygosaccharomyces bailli; Tpret, T. pretoriensis; Zbisporus, Zygosaccharomyces bisporus; Zrouxii, Z. rouxii; Kpolysp, Kluyveromyces polysporus; Sunisp, S. (Kazachstania) unisporus; Sexiguus, S. (Kazachstania) exiguus; Ctropicalis, Candida tropicalis; Sdair, S. (Naumovia) dairenensis; Scastelli, S. (Naumovia) castellii; Cglabrata, C. glabrata; Klactis, K. lactis; Dhansenii, Debaryomyces hansenii. Inteins with active homing endonucleases are marked by asterisks*.

From: The distribution and evolutionary history of the PRP8 intein

   Sd Nd S N pS pN dS dN dS/dN EN
*Scerev *SspDH1A 9.00 0.00 52.00 158.00 0.17 0.00 0.20 0.00 NA AA
*Scerev *Scarioc 13.00 4.00 52.33 157.67 0.25 0.03 0.30 0.03 11.69 AA
*Scerev Tglobosa 31.88 36.12 52.50 157.50 0.61 0.23 1.24 0.27 4.54 AI
*Scerev *Zbailli 31.50 34.50 51.50 158.50 0.61 0.22 1.27 0.26 4.93 AA
*Scerev Tpret 34.62 41.38 52.83 157.17 0.66 0.26 1.55 0.32 4.79 AI
*Scerev Zbisporus 27.00 38.00 49.33 151.67 0.55 0.25 0.98 0.30 3.22 AI
*Scerev Zrouxii 22.38 41.62 48.50 152.50 0.46 0.27 0.72 0.34 2.11 AI
*Scerev Kpolysp 30.88 57.12 48.00 162.00 0.64 0.35 1.46 0.48 3.07 AI
*Scerev Sdair 34.75 61.25 51.50 158.50 0.67 0.39 1.72 0.54 3.18 AI
*Scerev Sunisp 27.62 70.38 52.17 157.83 0.53 0.45 0.92 0.68 1.36 AI
*Scerev Sexiguus 24.00 71.00 50.67 159.33 0.47 0.45 0.75 0.68 1.11 AI
*Scerev Ctropicalis 28.75 70.25 52.17 157.83 0.55 0.45 1.00 0.68 1.47 AI
*Scerev Scastelli 35.88 56.12 51.00 159.00 0.70 0.35 2.08 0.48 4.37 AI
*Scerev Cglabrata 25.38 67.62 45.83 143.17 0.55 0.47 1.01 0.75 1.35 AI
*Scerev Klactis 33.12 70.88 49.50 151.50 0.67 0.47 1.67 0.73 2.28 AI
*Scerev Dhansenii 32.62 50.38 52.83 154.17 0.62 0.33 1.30 0.43 3.03 AI
*SspDH1A *Scarioc 15.00 4.00 52.33 157.67 0.29 0.03 0.36 0.03 13.99 AA
*SspDH1A Tglobosa 28.12 35.88 52.50 157.50 0.54 0.23 0.94 0.27 3.46 AI
*SspDH1A *Zbailli 29.25 34.75 51.50 158.50 0.57 0.22 1.06 0.26 4.09 AA
*SspDH1A Tpret 35.38 41.62 52.83 157.17 0.67 0.26 1.67 0.33 5.13 AI
*SspDH1A Zbisporus 23.75 38.25 49.33 151.67 0.48 0.25 0.77 0.31 2.51 AI
*SspDH1A Zrouxii 23.62 41.38 48.50 152.50 0.49 0.27 0.79 0.34 2.33 AI
*SspDH1A Kpolysp 30.38 56.62 48.00 162.00 0.63 0.35 1.39 0.47 2.96 AI
*SspDH1A Sdair 33.50 61.50 51.50 158.50 0.65 0.39 1.51 0.55 2.77 AI
*SspDH1A Sunisp 26.88 71.12 52.17 157.83 0.52 0.45 0.87 0.69 1.26 AI
*SspDH1A Sexiguus 23.75 71.25 50.67 159.33 0.47 0.45 0.74 0.68 1.08 AI
*SspDH1A Ctropicalis 27.00 70.00 52.17 157.83 0.52 0.44 0.88 0.67 1.31 AI
*SspDH1A Scastelli 34.62 56.38 51.00 159.00 0.68 0.35 1.77 0.48 3.68 AI
*SspDH1A Cglabrata 27.12 67.88 45.83 143.17 0.59 0.47 1.17 0.75 1.56 AI
*SspDH1A Klactis 33.88 71.12 49.50 151.50 0.68 0.47 1.83 0.74 2.48 AI
*SspDH1A Dhansenii 32.62 50.38 52.83 154.17 0.62 0.33 1.30 0.43 3.03 AI
*Scarioc Tglobosa 31.50 35.50 52.83 157.17 0.60 0.23 1.19 0.27 4.42 AI
*Scarioc *Zbailli 32.88 33.12 51.83 158.17 0.63 0.21 1.40 0.25 5.71 AA
*Scarioc Tpret 38.12 41.88 53.17 156.83 0.72 0.27 2.34 0.33 7.10 AI
*Scarioc Zbisporus 27.50 37.50 49.33 151.67 0.56 0.25 1.02 0.30 3.40 AI
*Scarioc Zrouxii 28.12 38.88 48.50 152.50 0.58 0.25 1.11 0.31 3.57 AI
*Scarioc Kpolysp 27.88 59.12 48.33 161.67 0.58 0.37 1.10 0.50 2.19 AI
*Scarioc Sdair 34.62 63.38 51.83 158.17 0.67 0.40 1.66 0.57 2.90 AI
*Scarioc Sunisp 31.12 69.88 52.50 157.50 0.59 0.44 1.17 0.67 1.75 AI
*Scarioc Sexiguus 25.75 72.25 51.00 159.00 0.50 0.45 0.84 0.70 1.20 AI
*Scarioc Ctropicalis 27.38 68.62 52.50 157.50 0.52 0.44 0.89 0.65 1.37 AI
*Scarioc Scastelli 38.88 57.12 51.33 158.67 0.76 0.36 NA 0.49 NA AI
*Scarioc Cglabrata 23.50 69.50 45.83 143.17 0.51 0.49 0.86 0.78 1.10 AI
*Scarioc Klactis 35.12 72.88 49.50 151.50 0.71 0.48 2.19 0.77 2.85 AI
*Scarioc Dhansenii 29.75 49.25 52.83 154.17 0.56 0.32 1.04 0.42 2.50 AI
Tglobosa *Zbailli 24.50 13.50 52.00 158.00 0.47 0.09 0.74 0.09 8.18 IA
Tglobosa Tpret 28.50 19.50 53.33 156.67 0.53 0.12 0.93 0.14 6.87 II
Tglobosa Zbisporus 26.12 35.88 49.33 151.67 0.53 0.24 0.92 0.28 3.23 II
Tglobosa Zrouxii 22.50 31.50 48.50 152.50 0.46 0.21 0.72 0.24 2.99 II
Tglobosa Kpolysp 24.50 65.50 48.50 161.50 0.51 0.41 0.84 0.58 1.44 II
Tglobosa Sdair 32.00 64.00 52.00 158.00 0.62 0.41 1.29 0.58 2.21 II
Tglobosa Sunisp 29.50 65.50 52.67 157.33 0.56 0.42 1.03 0.61 1.70 II
Tglobosa Sexiguus 28.12 73.88 51.17 158.83 0.55 0.47 0.99 0.73 1.36 II
Tglobosa Ctropicalis 32.25 72.75 52.67 157.33 0.61 0.46 1.27 0.72 1.77 II
Tglobosa Scastelli 35.50 52.50 51.50 158.50 0.69 0.33 1.89 0.44 4.31 II
Tglobosa Cglabrata 26.00 82.00 45.50 143.50 0.57 0.57 1.08 1.08 1.00 II
Tglobosa Klactis 33.75 73.25 49.50 151.50 0.68 0.48 1.80 0.78 2.32 II
Tglobosa Dhansenii 31.25 55.75 53.00 154.00 0.59 0.36 1.16 0.49 2.34 II
*Zbailli Tpret 32.75 21.25 52.33 157.67 0.63 0.13 1.35 0.15 9.08 AI
*Zbailli Zbisporus 30.62 33.38 48.50 152.50 0.63 0.22 1.38 0.26 5.35 AI
*Zbailli Zrouxii 31.75 31.25 47.67 153.33 0.67 0.20 1.64 0.24 6.91 AI
*Zbailli Kpolysp 30.75 65.25 47.50 162.50 0.65 0.40 1.49 0.57 2.59 AI
*Zbailli Sdair 31.62 63.38 51.00 159.00 0.62 0.40 1.31 0.57 2.31 AI
*Zbailli Sunisp 30.38 68.62 51.67 158.33 0.59 0.43 1.15 0.65 1.78 AI
*Zbailli Sexiguus 29.00 73.00 50.17 159.83 0.58 0.46 1.10 0.70 1.57 AI
*Zbailli Ctropicalis 35.75 74.25 51.67 158.33 0.69 0.47 1.92 0.74 2.61 AI
*Zbailli Scastelli 31.25 53.75 50.50 159.50 0.62 0.34 1.31 0.45 2.92 AI
*Zbailli Cglabrata 21.62 76.38 44.67 144.33 0.48 0.53 0.78 0.92 0.85 AI
*Zbailli Klactis 28.88 71.12 48.67 152.33 0.59 0.47 1.17 0.73 1.61 AI
*Zbailli Dhansenii 34.75 59.25 52.00 155.00 0.67 0.38 1.66 0.53 3.11 AI
Tpret Zbisporus 28.38 36.62 50.00 151.00 0.57 0.24 1.06 0.29 3.62 II
Tpret Zrouxii 26.00 37.00 49.17 151.83 0.53 0.24 0.92 0.29 3.11 II
Tpret Kpolysp 27.38 59.62 48.83 161.17 0.56 0.37 1.03 0.51 2.02 II
Tpret Sdair 27.62 62.38 52.33 157.67 0.53 0.40 0.91 0.56 1.62 II
Tpret Sunisp 27.62 71.38 53.00 157.00 0.52 0.45 0.89 0.70 1.27 II
Tpret Sexiguus 32.00 71.00 51.50 158.50 0.62 0.45 1.32 0.68 1.94 II
Tpret Ctropicalis 30.62 65.38 53.00 157.00 0.58 0.42 1.10 0.61 1.82 II
Tpret Scastelli 29.00 55.00 51.83 158.17 0.56 0.35 1.03 0.47 2.20 II
Tpret Cglabrata 29.88 80.12 46.50 142.50 0.64 0.56 1.46 1.04 1.40 II
Tpret Klactis 38.38 77.62 50.17 150.83 0.76 0.51 NA 0.87 NA II
Tpret Dhansenii 34.25 57.75 53.33 153.67 0.64 0.38 1.45 0.52 2.79 II
Zbisporus Zrouxii 18.12 25.88 47.83 153.17 0.38 0.17 0.53 0.19 2.76 II
Zbisporus Kpolysp 27.38 55.62 45.67 155.33 0.60 0.36 1.20 0.49 2.47 II
Zbisporus Sdair 29.25 59.75 48.67 152.33 0.60 0.39 1.21 0.56 2.18 II
Zbisporus Sunisp 27.38 61.62 49.00 152.00 0.56 0.41 1.02 0.58 1.76 II
Zbisporus Sexiguus 19.25 62.75 48.50 152.50 0.40 0.41 0.57 0.60 0.95 II
Zbisporus Ctropicalis 26.75 66.25 49.33 151.67 0.54 0.44 0.96 0.65 1.47 II
Zbisporus Scastelli 30.50 55.50 48.33 152.67 0.63 0.36 1.38 0.50 2.78 II
Zbisporus Cglabrata 24.88 71.12 44.50 144.50 0.56 0.49 1.03 0.80 1.28 II
Zbisporus Klactis 33.38 76.62 48.83 152.17 0.68 0.50 1.82 0.83 2.18 II
Zbisporus Dhansenii 29.88 58.12 50.33 150.67 0.59 0.39 1.18 0.54 2.17 II
Zrouxii Kpolysp 24.00 58.00 44.83 156.17 0.54 0.37 0.94 0.51 1.83 II
Zrouxii Sdair 28.50 63.50 47.83 153.17 0.60 0.41 1.19 0.60 1.97 II
Zrouxii Sunisp 27.88 68.12 48.17 152.83 0.58 0.45 1.11 0.68 1.64 II
Zrouxii Sexiguus 24.50 64.50 47.67 153.33 0.51 0.42 0.87 0.62 1.40 II
Zrouxii Ctropicalis 25.88 66.12 48.50 152.50 0.53 0.43 0.93 0.65 1.44 II
Zrouxii Scastelli 24.50 56.50 47.50 153.50 0.52 0.37 0.87 0.51 1.72 II
Zrouxii Cglabrata 29.38 79.62 44.33 144.67 0.66 0.55 1.61 0.99 1.62 II
Zrouxii Klactis 31.38 76.62 48.00 153.00 0.65 0.50 1.54 0.83 1.86 II
Zrouxii Dhansenii 29.75 55.25 49.50 151.50 0.60 0.36 1.21 0.50 2.43 II
Kpolysp Sdair 19.25 69.75 48.33 164.67 0.40 0.42 0.57 0.62 0.91 II
Kpolysp Sunisp 19.88 77.12 49.17 163.83 0.40 0.47 0.58 0.74 0.78 II
Kpolysp Sexiguus 21.12 74.88 47.67 165.33 0.44 0.45 0.67 0.69 0.97 II
Kpolysp Ctropicalis 20.25 78.75 49.00 164.00 0.41 0.48 0.60 0.77 0.78 II
Kpolysp Scastelli 28.50 71.50 47.67 165.33 0.60 0.43 1.20 0.64 1.86 II
Kpolysp Cglabrata 20.12 70.88 42.50 146.50 0.47 0.48 0.75 0.78 0.96 II
Kpolysp Klactis 28.38 80.62 45.83 155.17 0.62 0.52 1.31 0.89 1.48 II
Kpolysp Dhansenii 30.12 70.88 48.67 158.33 0.62 0.45 1.31 0.68 1.92 II
Sdair Sunisp 19.25 48.75 53.50 165.50 0.36 0.29 0.49 0.37 1.31 II
Sdair Sexiguus 21.62 59.38 52.00 167.00 0.42 0.36 0.61 0.48 1.26 II
Sdair Ctropicalis 26.12 48.88 52.67 163.33 0.50 0.30 0.81 0.38 2.13 II
Sdair Scastelli 30.38 25.62 51.00 162.00 0.60 0.16 1.19 0.18 6.67 II
Sdair Cglabrata 23.75 76.25 44.67 144.33 0.53 0.53 0.93 0.91 1.01 II
Sdair Klactis 29.25 75.75 48.83 152.17 0.60 0.50 1.20 0.82 1.47 II
Sdair Dhansenii 30.38 55.62 52.00 155.00 0.58 0.36 1.13 0.49 2.32 II
Sunisp Sexiguus 17.12 61.88 53.17 165.83 0.32 0.37 0.42 0.52 0.82 II
Sunisp Ctropicalis 21.50 59.50 53.50 162.50 0.40 0.37 0.58 0.50 1.15 II
Sunisp Scastelli 29.88 57.12 51.83 161.17 0.58 0.35 1.10 0.48 2.29 II
Sunisp Cglabrata 23.00 65.00 45.00 144.00 0.51 0.45 0.86 0.69 1.24 II
Sunisp Klactis 27.88 67.12 49.17 151.83 0.57 0.44 1.06 0.67 1.58 II
Sunisp Dhansenii 28.50 69.50 52.67 154.33 0.54 0.45 0.96 0.69 1.39 II
Sexiguus Ctropicalis 21.25 65.75 52.33 163.67 0.41 0.40 0.58 0.58 1.02 II
Sexiguus Scastelli 35.00 55.00 50.33 162.67 0.70 0.34 1.96 0.45 4.37 II
Sexiguus Cglabrata 17.88 73.12 44.83 144.17 0.40 0.51 0.57 0.85 0.67 II
Sexiguus Klactis 29.12 81.88 48.67 152.33 0.60 0.54 1.20 0.95 1.27 II
Sexiguus Dhansenii 25.50 65.50 51.50 155.50 0.50 0.42 0.81 0.62 1.31 II
Ctropicalis Scastelli 36.25 55.75 51.67 161.33 0.70 0.35 2.06 0.46 4.44 II
Ctropicalis Cglabrata 29.38 74.62 45.50 143.50 0.65 0.52 1.48 0.89 1.67 II
Ctropicalis Klactis 32.25 78.75 49.50 151.50 0.65 0.52 1.52 0.89 1.72 II
Ctropicalis Dhansenii 32.00 66.00 52.67 154.33 0.61 0.43 1.25 0.63 1.97 II
Scastelli Cglabrata 27.88 83.12 44.83 144.17 0.62 0.58 1.32 1.10 1.21 II
Scastelli Klactis 31.50 78.50 48.50 152.50 0.65 0.51 1.51 0.87 1.73 II
Scastelli Dhansenii 33.38 53.62 51.83 155.17 0.64 0.35 1.47 0.46 3.17 II
Cglabrata Klactis 26.38 61.62 44.83 144.17 0.59 0.43 1.15 0.63 1.82 II
Cglabrata Dhansenii 22.75 81.25 46.50 142.50 0.49 0.57 0.79 1.07 0.74 II
Klactis Dhansenii 34.12 71.88 50.50 150.50 0.68 0.48 1.73 0.76 2.28 II