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OPENSEQ.org
1Z5Y
Genes: A B A+B
Length: 143 149 256
Sequences: 458 9788 161
Seq/Len: 3.2 65.69 0.63
MirrorTree (Pazo et al. 2001) 0.62
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 0.00 0.02 0.46
2 0.00 0.02 0.47
5 0.00 0.03 0.50
10 0.00 0.04 0.53
20 0.00 0.05 0.55
100 0.00 0.09 0.65
∞ 0.04 0.20 1.04
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
77_Y 114_R 1.69 0.77 0.02
85_V 70_A 1.54 0.66 0.01
22_F 92_L 1.30 0.47 0.01
29_L 131_K 1.30 0.47 0.01
72_G 34_W 1.22 0.41 0.01
14_A 121_L 1.14 0.34 0.00
92_A 130_I 1.13 0.34 0.00
37_D 118_A 1.12 0.34 0.00
45_Q 78_G 1.10 0.32 0.00
125_N 31_L 1.09 0.31 0.00
46_I 2_P 1.09 0.31 0.00
21_D 58_V 1.08 0.30 0.00
60_L 61_M 1.08 0.30 0.00
100_Y 93_G 1.07 0.30 0.00
44_K 36_T 1.07 0.30 0.00
101_Q 119_G 1.07 0.30 0.00
16_Q 51_L 1.07 0.29 0.00
5_A 30_L 1.06 0.29 0.00
30_N 116_R 1.06 0.29 0.00
14_A 4_P 1.06 0.29 0.00
29_L 21_D 1.06 0.29 0.00
46_I 126_W 1.05 0.28 0.00
64_V 104_T 1.04 0.28 0.00
16_Q 127_E 1.04 0.28 0.00
96_L 31_L 1.01 0.26 0.00
17_A 60_G 1.01 0.26 0.00
30_N 29_V 1.01 0.26 0.00
26_Q 59_V 1.01 0.25 0.00
105_D 26_G 1.00 0.25 0.00
122_V 61_M 0.99 0.25 0.00
33_W 4_P 0.99 0.24 0.00
19_A 18_Y 0.99 0.24 0.00
37_D 75_K 0.98 0.24 0.00
53_A 27_K 0.97 0.24 0.00
76_I 12_D 0.97 0.24 0.00
60_L 12_D 0.96 0.23 0.00
67_E 121_L 0.95 0.22 0.00
104_A 4_P 0.95 0.22 0.00
71_Y 46_Q 0.94 0.22 0.00
31_L 18_Y 0.94 0.22 0.00
119_L 121_L 0.93 0.21 0.00
19_A 52_S 0.93 0.21 0.00
40_Y 44_E 0.93 0.21 0.00
44_K 73_W 0.92 0.21 0.00
45_Q 79_N 0.92 0.21 0.00
29_L 60_G 0.92 0.21 0.00
87_I 27_K 0.92 0.20 0.00
87_I 28_P 0.92 0.20 0.00
113_E 130_I 0.92 0.20 0.00
16_Q 123_P 0.91 0.20 0.00
15_D 59_V 0.91 0.20 0.00
60_L 48_L 0.91 0.20 0.00
103_S 41_S 0.90 0.20 0.00
113_E 109_G 0.90 0.20 0.00
85_V 126_W 0.90 0.19 0.00
107_G 104_T 0.90 0.19 0.00
72_G 35_A 0.90 0.19 0.00
46_I 120_D 0.90 0.19 0.00
102_G 38_C 0.89 0.19 0.00
102_G 102_P 0.89 0.19 0.00
109_C 38_C 0.89 0.19 0.00
109_C 102_P 0.89 0.19 0.00
79_D 117_H 0.89 0.19 0.00
36_K 61_M 0.88 0.18 0.00
85_V 31_L 0.88 0.18 0.00
63_G 32_N 0.88 0.18 0.00
29_L 31_L 0.88 0.18 0.00
54_K 22_V 0.87 0.18 0.00
16_Q 76_E 0.87 0.18 0.00
111_P 4_P 0.87 0.18 0.00
37_D 22_V 0.87 0.18 0.00
50_P 70_A 0.87 0.18 0.00
92_A 36_T 0.86 0.18 0.00
116_T 5_K 0.86 0.18 0.00
14_A 21_D 0.86 0.17 0.00
54_K 87_D 0.86 0.17 0.00
115_K 48_L 0.86 0.17 0.00
108_F 134_W 0.85 0.17 0.00
111_P 34_W 0.85 0.17 0.00
60_L 20_A 0.85 0.17 0.00
96_L 14_P 0.85 0.17 0.00
93_G 83_L 0.85 0.17 0.00
28_D 3_V 0.85 0.17 0.00
16_Q 7_R 0.85 0.17 0.00
46_I 76_E 0.84 0.17 0.00
100_Y 124_R 0.84 0.17 0.00
21_D 10_S 0.84 0.17 0.00
38_G 65_D 0.84 0.17 0.00
114_T 114_R 0.84 0.17 0.00
47_R 59_V 0.84 0.17 0.00
46_I 26_G 0.83 0.16 0.00
7_G 95_D 0.83 0.16 0.00
34_Q 123_P 0.83 0.16 0.00
112_P 41_S 0.83 0.16 0.00
28_D 95_D 0.83 0.16 0.00
11_F 105_F 0.82 0.16 0.00
20_F 88_G 0.82 0.16 0.00
41_L 60_G 0.82 0.15 0.00
101_Q 38_C 0.81 0.15 0.00
101_Q 102_P 0.81 0.15 0.00
16_Q 75_K 0.81 0.15 0.00
57_D 43_A 0.81 0.15 0.00
106_A 48_L 0.81 0.15 0.00
12_V 83_L 0.81 0.15 0.00
10_Q 88_G 0.81 0.15 0.00
100_Y 64_K 0.80 0.15 0.00
37_D 25_Q 0.80 0.15 0.00
69_E 51_L 0.80 0.15 0.00
100_Y 131_K 0.80 0.15 0.00
61_P 108_D 0.80 0.15 0.00
76_I 30_L 0.80 0.15 0.00
9_S 33_V 0.79 0.14 0.00
39_Y 20_A 0.79 0.14 0.00
103_S 38_C 0.79 0.14 0.00
103_S 102_P 0.79 0.14 0.00
18_F 51_L 0.79 0.14 0.00
63_G 127_E 0.79 0.14 0.00
82_T 2_P 0.79 0.14 0.00
92_A 88_G 0.79 0.14 0.00
25_N 10_S 0.78 0.14 0.00
14_A 78_G 0.78 0.14 0.00
74_S 36_T 0.78 0.14 0.00
45_Q 58_V 0.78 0.14 0.00
67_E 106_L 0.78 0.14 0.00
70_F 73_W 0.78 0.14 0.00
119_L 124_R 0.78 0.14 0.00
122_V 95_D 0.78 0.14 0.00
75_E 3_V 0.77 0.14 0.00
66_H 100_G 0.77 0.14 0.00
37_D 48_L 0.77 0.14 0.00
70_F 6_F 0.77 0.14 0.00
32_T 13_N 0.77 0.14 0.00
114_T 103_E 0.77 0.14 0.00
44_K 33_V 0.77 0.14 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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