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OPENSEQ.org
1LZW-2
Genes: A B A+B
Length: 87 142 228
Sequences: 1074 1232 92
Seq/Len: 12.34 8.68 0.4
MirrorTree (Pazo et al. 2001) 0.72
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 0.39
2 0.06 0.01 0.40
5 0.06 0.01 0.40
10 0.06 0.01 0.40
20 0.06 0.01 0.40
100 0.06 0.02 0.48
∞ 0.09 0.08 1.42
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
60_E 83_S 1.75 0.67 0.01
60_E 100_R 1.71 0.64 0.00
52_A 116_Q 1.53 0.52 0.00
22_E 33_A 1.49 0.49 0.00
56_V 56_Q 1.34 0.39 0.00
44_L 120_A 1.32 0.37 0.00
86_K 123_L 1.30 0.36 0.00
8_M 10_L 1.28 0.34 0.00
20_P 136_N 1.28 0.34 0.00
20_P 38_P 1.26 0.33 0.00
11_V 58_L 1.24 0.32 0.00
45_A 50_D 1.23 0.31 0.00
20_P 2_L 1.23 0.31 0.00
59_A 117_E 1.22 0.31 0.00
37_E 51_L 1.21 0.30 0.00
3_L 119_Q 1.20 0.29 0.00
43_M 28_E 1.20 0.29 0.00
52_A 109_L 1.19 0.29 0.00
22_E 7_E 1.19 0.28 0.00
9_Y 13_A 1.18 0.28 0.00
57_F 94_H 1.18 0.28 0.00
47_A 28_E 1.17 0.27 0.00
52_A 128_E 1.16 0.27 0.00
37_E 137_F 1.15 0.26 0.00
82_C 112_I 1.12 0.24 0.00
20_P 30_L 1.11 0.24 0.00
26_D 35_L 1.11 0.24 0.00
57_F 45_E 1.11 0.24 0.00
77_E 117_E 1.09 0.23 0.00
59_A 134_V 1.07 0.22 0.00
66_V 10_L 1.07 0.22 0.00
29_Q 79_Q 1.06 0.22 0.00
65_K 118_S 1.06 0.22 0.00
82_C 113_F 1.06 0.21 0.00
60_E 27_V 1.05 0.21 0.00
4_K 42_E 1.05 0.21 0.00
78_H 105_G 1.05 0.21 0.00
8_M 59_E 1.05 0.21 0.00
42_L 36_S 1.04 0.21 0.00
42_L 101_N 1.04 0.20 0.00
22_E 127_H 1.03 0.20 0.00
7_S 117_E 1.01 0.19 0.00
9_Y 117_E 1.01 0.19 0.00
67_A 50_D 1.01 0.19 0.00
61_V 129_V 1.01 0.19 0.00
41_Q 72_S 0.99 0.18 0.00
86_K 117_E 0.99 0.18 0.00
78_H 30_L 0.98 0.18 0.00
20_P 105_G 0.98 0.18 0.00
82_C 119_Q 0.97 0.18 0.00
18_Y 73_E 0.97 0.17 0.00
13_L 112_I 0.97 0.17 0.00
66_V 112_I 0.96 0.17 0.00
20_P 9_S 0.96 0.17 0.00
78_H 86_R 0.96 0.17 0.00
60_E 79_Q 0.96 0.17 0.00
3_L 20_H 0.95 0.17 0.00
23_F 26_T 0.95 0.17 0.00
22_E 12_M 0.95 0.17 0.00
18_Y 107_N 0.95 0.17 0.00
22_E 138_I 0.95 0.17 0.00
58_T 129_V 0.95 0.17 0.00
57_F 117_E 0.94 0.16 0.00
78_H 27_V 0.94 0.16 0.00
12_I 49_V 0.94 0.16 0.00
18_Y 139_S 0.93 0.16 0.00
5_P 48_S 0.93 0.16 0.00
56_V 139_S 0.93 0.16 0.00
40_T 33_A 0.92 0.15 0.00
74_R 117_E 0.92 0.15 0.00
55_G 29_H 0.92 0.15 0.00
56_V 60_A 0.91 0.15 0.00
48_Y 68_V 0.91 0.15 0.00
30_K 63_E 0.91 0.15 0.00
78_H 107_N 0.91 0.15 0.00
66_V 38_P 0.91 0.15 0.00
56_V 142_T 0.90 0.15 0.00
17_D 85_Q 0.90 0.15 0.00
77_E 142_T 0.90 0.15 0.00
60_E 19_E 0.90 0.14 0.00
86_K 65_T 0.90 0.14 0.00
57_F 58_L 0.90 0.14 0.00
82_C 80_P 0.89 0.14 0.00
20_P 32_L 0.89 0.14 0.00
65_K 120_A 0.89 0.14 0.00
12_I 137_F 0.89 0.14 0.00
58_T 77_D 0.89 0.14 0.00
14_V 32_L 0.89 0.14 0.00
60_E 101_N 0.89 0.14 0.00
18_Y 55_R 0.88 0.14 0.00
69_V 141_G 0.88 0.14 0.00
4_K 55_R 0.88 0.14 0.00
50_G 110_V 0.88 0.14 0.00
12_I 98_S 0.86 0.13 0.00
34_Y 38_P 0.86 0.13 0.00
8_M 62_I 0.86 0.13 0.00
63_E 86_R 0.85 0.13 0.00
77_E 55_R 0.85 0.13 0.00
22_E 109_L 0.85 0.13 0.00
8_M 35_L 0.85 0.13 0.00
58_T 65_T 0.85 0.13 0.00
51_K 82_L 0.85 0.13 0.00
23_F 138_I 0.85 0.13 0.00
9_Y 126_K 0.84 0.13 0.00
84_L 100_R 0.84 0.13 0.00
65_K 34_L 0.84 0.13 0.00
48_Y 78_T 0.84 0.13 0.00
37_E 24_F 0.84 0.13 0.00
37_E 110_V 0.84 0.13 0.00
31_F 104_T 0.84 0.13 0.00
14_V 12_M 0.83 0.12 0.00
20_P 80_P 0.83 0.12 0.00
53_I 52_V 0.83 0.12 0.00
9_Y 95_V 0.83 0.12 0.00
76_N 125_R 0.83 0.12 0.00
54_C 27_V 0.83 0.12 0.00
43_M 31_L 0.82 0.12 0.00
68_M 137_F 0.82 0.12 0.00
52_A 92_V 0.82 0.12 0.00
83_T 2_L 0.82 0.12 0.00
27_V 109_L 0.82 0.12 0.00
27_V 12_M 0.82 0.12 0.00
11_V 44_L 0.82 0.12 0.00
59_A 137_F 0.82 0.12 0.00
12_I 55_R 0.81 0.12 0.00
50_G 85_Q 0.81 0.12 0.00
35_D 39_S 0.81 0.12 0.00
87_A 76_R 0.81 0.12 0.00
64_T 81_T 0.81 0.12 0.00
46_V 99_G 0.80 0.12 0.00
87_A 4_Q 0.80 0.11 0.00
81_L 62_I 0.80 0.11 0.00
8_M 74_E 0.80 0.11 0.00
81_L 93_F 0.80 0.11 0.00
34_Y 2_L 0.80 0.11 0.00
76_N 63_E 0.80 0.11 0.00
55_G 31_L 0.79 0.11 0.00
46_V 9_S 0.79 0.11 0.00
34_Y 101_N 0.79 0.11 0.00
47_A 31_L 0.79 0.11 0.00
53_I 142_T 0.79 0.11 0.00
42_L 4_Q 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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