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OPENSEQ.org
1LZW
Genes: A B A+B
Length: 106 146 242
Sequences: 1110 1245 95
Seq/Len: 10.47 8.53 0.39
MirrorTree (Pazo et al. 2001) 0.75
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 0.06 0.01 0.36
2 0.06 0.01 0.37
5 0.06 0.01 0.38
10 0.06 0.01 0.38
20 0.06 0.01 0.38
100 0.06 0.02 0.44
∞ 0.09 0.08 1.27
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
71_A 116_Q 1.68 0.61 0.00
79_E 100_R 1.65 0.60 0.00
79_E 83_S 1.63 0.58 0.00
76_F 45_E 1.56 0.53 0.00
78_A 117_E 1.44 0.44 0.00
71_A 109_L 1.42 0.43 0.00
41_E 33_A 1.38 0.40 0.00
63_L 120_A 1.37 0.40 0.00
64_A 50_D 1.35 0.38 0.00
101_C 112_I 1.29 0.34 0.00
39_P 136_N 1.29 0.34 0.00
78_A 134_V 1.28 0.34 0.00
27_M 10_L 1.24 0.31 0.00
105_K 123_L 1.23 0.31 0.00
30_V 58_L 1.23 0.30 0.00
80_V 35_L 1.22 0.30 0.00
41_E 7_E 1.22 0.30 0.00
75_V 56_Q 1.21 0.29 0.00
39_P 2_L 1.19 0.28 0.00
28_Y 13_A 1.19 0.28 0.00
80_V 129_V 1.18 0.28 0.00
26_S 117_E 1.18 0.27 0.00
54_D 61_F 1.18 0.27 0.00
95_N 144_K 1.17 0.27 0.00
76_F 94_H 1.17 0.27 0.00
71_A 128_E 1.16 0.26 0.00
28_Y 117_E 1.16 0.26 0.00
54_D 39_S 1.12 0.24 0.00
62_M 28_E 1.11 0.24 0.00
86_A 50_D 1.11 0.24 0.00
19_R 137_F 1.10 0.23 0.00
39_P 105_G 1.10 0.23 0.00
31_I 49_V 1.10 0.23 0.00
77_T 65_T 1.09 0.23 0.00
27_M 59_E 1.09 0.23 0.00
101_C 119_Q 1.09 0.22 0.00
15_E 92_V 1.08 0.22 0.00
66_A 28_E 1.08 0.22 0.00
76_F 58_L 1.07 0.22 0.00
39_P 38_P 1.07 0.22 0.00
75_V 139_S 1.07 0.22 0.00
39_P 30_L 1.07 0.22 0.00
56_E 51_L 1.07 0.22 0.00
97_H 105_G 1.07 0.21 0.00
77_T 129_V 1.06 0.21 0.00
79_E 27_V 1.06 0.21 0.00
22_L 119_Q 1.05 0.21 0.00
84_K 118_S 1.04 0.20 0.00
85_V 10_L 1.04 0.20 0.00
46_V 109_L 1.04 0.20 0.00
101_C 113_F 1.03 0.20 0.00
39_P 9_S 1.02 0.19 0.00
76_F 42_E 0.98 0.18 0.00
48_Q 79_Q 0.98 0.18 0.00
75_V 60_A 0.98 0.17 0.00
79_E 79_Q 0.97 0.17 0.00
105_K 65_T 0.97 0.17 0.00
96_E 117_E 0.97 0.17 0.00
56_E 137_F 0.97 0.17 0.00
19_R 9_S 0.96 0.17 0.00
101_C 80_P 0.96 0.17 0.00
23_K 42_E 0.95 0.17 0.00
37_Y 73_E 0.95 0.17 0.00
97_H 30_L 0.95 0.16 0.00
96_E 142_T 0.94 0.16 0.00
37_Y 107_N 0.94 0.16 0.00
103_L 100_R 0.94 0.16 0.00
42_F 26_T 0.94 0.16 0.00
17_K 64_Q 0.94 0.16 0.00
69_G 110_V 0.94 0.16 0.00
85_V 112_I 0.94 0.16 0.00
97_H 86_R 0.93 0.16 0.00
93_R 117_E 0.93 0.16 0.00
36_D 85_Q 0.93 0.15 0.00
16_E 24_F 0.92 0.15 0.00
56_E 110_V 0.92 0.15 0.00
61_L 101_N 0.92 0.15 0.00
65_V 99_G 0.92 0.15 0.00
42_F 138_I 0.92 0.15 0.00
97_H 107_N 0.91 0.15 0.00
58_A 118_S 0.91 0.15 0.00
41_E 138_I 0.91 0.15 0.00
27_M 35_L 0.91 0.15 0.00
88_V 115_E 0.91 0.15 0.00
33_V 32_L 0.90 0.15 0.00
69_G 85_Q 0.90 0.15 0.00
84_K 120_A 0.90 0.14 0.00
17_K 145_D 0.90 0.14 0.00
24_P 48_S 0.89 0.14 0.00
27_M 74_E 0.89 0.14 0.00
85_V 38_P 0.89 0.14 0.00
39_P 46_A 0.89 0.14 0.00
82_E 86_R 0.89 0.14 0.00
46_V 12_M 0.89 0.14 0.00
97_H 27_V 0.89 0.14 0.00
74_G 29_H 0.88 0.14 0.00
15_E 121_A 0.88 0.14 0.00
59_T 33_A 0.87 0.14 0.00
101_C 103_V 0.87 0.14 0.00
88_V 141_G 0.87 0.13 0.00
39_P 32_L 0.87 0.13 0.00
84_K 34_L 0.87 0.13 0.00
63_L 58_L 0.87 0.13 0.00
45_D 35_L 0.86 0.13 0.00
60_Q 72_S 0.86 0.13 0.00
28_Y 95_V 0.86 0.13 0.00
105_K 117_E 0.86 0.13 0.00
63_L 127_H 0.85 0.13 0.00
31_I 137_F 0.85 0.13 0.00
32_L 112_I 0.85 0.13 0.00
78_A 129_V 0.84 0.13 0.00
77_T 88_L 0.84 0.12 0.00
41_E 12_M 0.84 0.12 0.00
56_E 24_F 0.84 0.12 0.00
100_L 62_I 0.84 0.12 0.00
106_A 4_Q 0.84 0.12 0.00
76_F 128_E 0.84 0.12 0.00
101_C 85_Q 0.83 0.12 0.00
33_V 12_M 0.83 0.12 0.00
39_P 80_P 0.83 0.12 0.00
37_Y 55_R 0.83 0.12 0.00
30_V 44_L 0.83 0.12 0.00
73_C 27_V 0.82 0.12 0.00
53_Y 38_P 0.82 0.12 0.00
88_V 34_L 0.81 0.12 0.00
32_L 55_R 0.81 0.12 0.00
37_Y 139_S 0.81 0.12 0.00
101_C 122_Y 0.81 0.12 0.00
94_E 23_E 0.81 0.12 0.00
16_E 27_V 0.81 0.12 0.00
83_T 81_T 0.81 0.12 0.00
78_A 137_F 0.81 0.12 0.00
104_E 99_G 0.81 0.12 0.00
31_I 30_L 0.81 0.11 0.00
97_H 104_T 0.81 0.11 0.00
75_V 142_T 0.81 0.11 0.00
100_L 93_F 0.81 0.11 0.00
79_E 2_L 0.80 0.11 0.00
32_L 52_V 0.80 0.11 0.00
79_E 101_N 0.80 0.11 0.00
102_T 130_S 0.80 0.11 0.00
58_A 30_L 0.80 0.11 0.00
50_F 66_T 0.80 0.11 0.00
65_V 98_S 0.80 0.11 0.00
58_A 31_L 0.80 0.11 0.00
96_E 55_R 0.80 0.11 0.00
102_T 2_L 0.79 0.11 0.00
88_V 90_R 0.79 0.11 0.00
65_V 9_S 0.79 0.11 0.00
97_H 81_T 0.79 0.11 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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