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OPENSEQ.org
L5-vs-S7
Genes: A B A+B
Length: 179 179 335
Sequences: 2042 1685 1186
Seq/Len: 11.41 9.41 3.54
MirrorTree (Pazo et al. 2001) 0.82
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 0.09 0.11 0.01
2 0.09 0.11 0.01
5 0.09 0.11 0.05
10 0.09 0.11 0.07
20 0.09 0.11 2.38
100 0.09 0.11 2.78
∞ 0.09 0.11 3.31
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
68_T 76_K 1.06 0.76 0.03
56_D 53_R 1.02 0.72 0.03
24_S 83_S 1.01 0.71 0.03
146_V 143_R 1.00 0.70 0.03
163_D 138_R 0.97 0.66 0.02
27_Q 4_R 0.91 0.59 0.02
69_K 2_P 0.90 0.58 0.02
35_T 18_F 0.88 0.55 0.02
156_I 66_L 0.86 0.53 0.02
66_L 128_A 0.85 0.51 0.02
157_T 68_N 0.84 0.50 0.01
70_A 85_Y 0.82 0.47 0.01
135_Q 149_K 0.81 0.47 0.01
157_T 129_E 0.81 0.46 0.01
31_V 106_E 0.80 0.45 0.01
173_F 5_R 0.78 0.42 0.01
111_I 138_R 0.78 0.42 0.01
129_S 24_A 0.77 0.41 0.01
117_L 105_V 0.76 0.40 0.01
15_K 64_V 0.76 0.39 0.01
47_K 101_M 0.76 0.39 0.01
79_I 106_E 0.76 0.39 0.01
146_V 37_S 0.76 0.39 0.01
143_Y 154_Y 0.76 0.39 0.01
74_V 23_L 0.75 0.39 0.01
104_I 50_L 0.75 0.38 0.01
46_D 113_D 0.75 0.38 0.01
57_L 141_V 0.75 0.38 0.01
26_M 28_N 0.75 0.38 0.01
24_S 100_A 0.74 0.37 0.01
97_W 17_K 0.74 0.37 0.01
57_L 58_E 0.74 0.37 0.01
153_D 26_F 0.73 0.36 0.01
81_Q 128_A 0.73 0.36 0.01
172_A 156_W 0.73 0.36 0.01
115_R 102_R 0.72 0.34 0.01
46_D 77_S 0.71 0.34 0.01
24_S 101_M 0.71 0.34 0.01
76_G 63_E 0.71 0.34 0.01
153_D 43_V 0.71 0.34 0.01
59_A 134_A 0.71 0.33 0.01
48_K 134_A 0.71 0.33 0.01
113_D 79_R 0.70 0.33 0.01
20_F 68_N 0.70 0.33 0.01
16_L 87_V 0.70 0.32 0.01
61_S 121_A 0.69 0.32 0.01
102_R 108_A 0.69 0.32 0.01
31_V 107_A 0.69 0.32 0.01
47_K 76_K 0.69 0.31 0.01
137_I 107_A 0.69 0.31 0.01
133_R 40_E 0.69 0.31 0.01
73_S 108_A 0.69 0.31 0.01
10_D 138_R 0.68 0.31 0.01
12_V 87_V 0.68 0.30 0.01
93_G 2_P 0.68 0.30 0.01
121_S 43_V 0.68 0.30 0.01
178_R 114_K 0.68 0.30 0.01
175_F 70_R 0.68 0.30 0.01
178_R 32_V 0.68 0.30 0.01
41_G 155_R 0.67 0.29 0.01
68_T 134_A 0.67 0.29 0.01
38_M 156_W 0.67 0.29 0.01
162_S 19_G 0.67 0.29 0.01
45_A 26_F 0.66 0.28 0.01
143_Y 131_K 0.66 0.28 0.01
59_A 50_L 0.66 0.28 0.01
143_Y 4_R 0.66 0.28 0.01
148_R 56_K 0.66 0.28 0.01
79_I 73_V 0.65 0.27 0.01
66_L 76_K 0.65 0.27 0.01
172_A 67_E 0.65 0.27 0.01
70_A 53_R 0.65 0.27 0.01
149_V 41_S 0.65 0.27 0.01
174_D 152_A 0.65 0.27 0.01
141_I 114_K 0.64 0.26 0.01
152_L 154_Y 0.64 0.26 0.01
19_E 72_T 0.64 0.26 0.01
79_I 16_P 0.64 0.26 0.01
38_M 25_K 0.64 0.26 0.01
70_A 62_F 0.64 0.26 0.01
65_P 40_E 0.64 0.26 0.01
36_L 94_V 0.64 0.26 0.01
11_E 52_Q 0.64 0.26 0.01
36_L 118_L 0.63 0.25 0.01
154_I 24_A 0.63 0.25 0.01
102_R 156_W 0.63 0.25 0.01
38_M 113_D 0.63 0.25 0.01
132_V 113_D 0.62 0.24 0.01
76_G 40_E 0.62 0.24 0.01
110_R 111_R 0.62 0.24 0.01
81_Q 76_K 0.62 0.24 0.01
32_E 11_K 0.62 0.24 0.01
54_A 32_V 0.62 0.24 0.01
84_P 110_K 0.62 0.24 0.01
71_R 64_V 0.62 0.24 0.01
75_A 126_D 0.62 0.24 0.01
27_Q 55_G 0.61 0.23 0.01
175_F 43_V 0.61 0.23 0.01
28_V 12_I 0.61 0.23 0.01
66_L 98_A 0.61 0.23 0.01
88_K 24_A 0.61 0.23 0.01
45_A 18_F 0.61 0.23 0.01
65_P 135_V 0.61 0.23 0.01
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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