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OPENSEQ.org
PlsXY
Genes: A B A+B
Length: 333 193 483
Sequences: 1972 2500 1093
Seq/Len: 5.92 12.95 2.26
MirrorTree (Pazo et al. 2001) 0.57
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.10 0.08 0.00
2 0.10 0.08 0.00
5 0.10 0.08 0.03
10 0.10 0.08 0.06
20 0.10 0.08 0.11
100 0.10 0.08 0.41
∞ 0.10 0.10 2.08
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
100_N 41_A 1.02 0.59 0.00
161_Y 31_I 0.91 0.45 0.00
34_T 182_I 0.86 0.41 0.00
118_I 166_L 0.85 0.39 0.00
88_A 84_G 0.84 0.38 0.00
100_N 84_G 0.83 0.37 0.00
78_S 127_F 0.83 0.36 0.00
20_G 171_V 0.82 0.36 0.00
18_I 167_L 0.82 0.35 0.00
257_K 100_K 0.81 0.35 0.00
192_T 146_I 0.81 0.35 0.00
156_I 150_I 0.79 0.33 0.00
107_A 49_G 0.79 0.33 0.00
101_T 134_T 0.78 0.32 0.00
259_A 19_G 0.78 0.32 0.00
293_K 17_P 0.78 0.31 0.00
64_P 87_A 0.77 0.31 0.00
155_A 190_V 0.77 0.31 0.00
130_V 183_I 0.76 0.30 0.00
177_N 94_P 0.76 0.30 0.00
20_G 97_A 0.76 0.29 0.00
80_M 56_V 0.75 0.29 0.00
118_I 151_Y 0.75 0.29 0.00
27_A 8_I 0.75 0.29 0.00
153_Q 32_R 0.75 0.28 0.00
196_L 7_I 0.75 0.28 0.00
263_L 56_V 0.74 0.28 0.00
177_N 45_F 0.74 0.28 0.00
274_M 94_P 0.74 0.28 0.00
251_T 37_G 0.74 0.28 0.00
44_S 121_I 0.74 0.28 0.00
204_F 23_G 0.74 0.28 0.00
267_L 179_I 0.74 0.28 0.00
135_F 109_G 0.74 0.28 0.00
41_T 4_A 0.73 0.27 0.00
80_M 68_T 0.73 0.27 0.00
173_V 28_G 0.73 0.27 0.00
262_V 169_I 0.73 0.26 0.00
111_I 108_S 0.72 0.26 0.00
123_L 119_L 0.72 0.26 0.00
271_K 50_V 0.72 0.26 0.00
170_S 9_L 0.72 0.26 0.00
280_G 127_F 0.72 0.26 0.00
234_T 152_S 0.72 0.26 0.00
33_I 97_A 0.72 0.26 0.00
211_R 137_V 0.71 0.25 0.00
173_V 153_F 0.71 0.25 0.00
41_T 69_A 0.71 0.25 0.00
173_V 168_T 0.71 0.25 0.00
127_L 100_K 0.71 0.25 0.00
80_M 154_F 0.71 0.25 0.00
81_V 48_L 0.71 0.25 0.00
234_T 16_I 0.70 0.25 0.00
125_P 94_P 0.70 0.24 0.00
118_I 26_A 0.70 0.24 0.00
105_M 41_A 0.70 0.24 0.00
282_A 96_F 0.70 0.24 0.00
75_K 34_H 0.70 0.24 0.00
254_L 133_L 0.69 0.24 0.00
221_V 16_I 0.69 0.24 0.00
95_C 19_G 0.69 0.23 0.00
172_R 100_K 0.69 0.23 0.00
108_G 108_S 0.69 0.23 0.00
64_P 185_K 0.69 0.23 0.00
26_E 95_I 0.68 0.23 0.00
276_Y 120_F 0.68 0.23 0.00
148_P 169_I 0.68 0.23 0.00
169_T 130_F 0.68 0.22 0.00
15_K 54_S 0.68 0.22 0.00
204_F 62_L 0.68 0.22 0.00
216_D 112_L 0.67 0.22 0.00
267_L 19_G 0.67 0.22 0.00
106_T 135_K 0.67 0.22 0.00
225_G 15_S 0.67 0.22 0.00
289_A 97_A 0.67 0.22 0.00
260_A 24_K 0.67 0.22 0.00
54_T 130_F 0.67 0.22 0.00
293_K 94_P 0.67 0.21 0.00
253_T 164_V 0.67 0.21 0.00
261_A 58_A 0.66 0.21 0.00
175_L 145_G 0.66 0.21 0.00
55_V 165_T 0.66 0.21 0.00
262_V 5_L 0.66 0.21 0.00
274_M 10_A 0.65 0.20 0.00
21_V 98_K 0.65 0.20 0.00
213_L 92_V 0.65 0.20 0.00
283_S 39_L 0.65 0.20 0.00
42_I 143_L 0.65 0.20 0.00
58_A 98_K 0.65 0.20 0.00
123_L 144_T 0.65 0.20 0.00
186_N 41_A 0.65 0.20 0.00
91_R 68_T 0.65 0.20 0.00
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
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