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OPENSEQ.org
cI_E_G
Genes: A B A+B
Length: 147 100 220
Sequences: 3696 1241 1197
Seq/Len: 25.14 12.41 5.44
MirrorTree (Pazo et al. 2001) 0.79
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.13
2 0.00 0.00 0.18
5 0.00 0.00 0.45
10 0.00 0.00 3.63
20 0.00 0.00 4.24
100 0.01 0.01 4.54
∞ 0.01 0.02 4.85
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
84_Y 67_S 1.97 1.00 0.98
69_Y 73_A 1.83 1.00 0.97
54_I 40_N 1.61 0.99 0.94
80_V 66_I 1.51 0.99 0.92
24_I 13_I 1.50 0.99 0.92
13_H 76_G 1.40 0.98 0.88
14_W 42_S 1.28 0.96 0.82
80_V 67_S 1.22 0.94 0.77
122_A 21_G 1.20 0.93 0.76
58_G 66_I 1.16 0.92 0.72
19_F 23_V 1.14 0.91 0.70
108_F 19_L 1.12 0.90 0.69
33_G 11_A 1.12 0.90 0.69
80_V 40_N 1.06 0.86 0.63
86_F 46_F 1.06 0.86 0.63
68_F 86_R 1.04 0.85 0.61
114_L 55_Q 1.03 0.84 0.60
26_L 31_M 1.03 0.84 0.59
114_L 81_L 1.02 0.83 0.59
19_F 46_F 1.02 0.83 0.58
61_R 50_G 1.01 0.82 0.57
10_I 31_M 1.01 0.82 0.57
80_V 76_G 0.98 0.80 0.54
58_G 18_G 0.98 0.79 0.53
70_L 81_L 0.97 0.79 0.53
87_A 37_I 0.97 0.79 0.53
68_F 83_L 0.97 0.78 0.52
70_L 93_D 0.97 0.78 0.52
113_G 74_S 0.96 0.78 0.52
92_I 29_L 0.95 0.77 0.50
76_V 47_V 0.94 0.75 0.48
76_V 3_P 0.94 0.75 0.48
26_L 34_G 0.93 0.74 0.48
54_I 24_I 0.93 0.74 0.48
69_Y 95_V 0.93 0.74 0.47
27_C 82_Q 0.93 0.74 0.47
72_A 93_D 0.93 0.74 0.47
83_L 84_H 0.92 0.73 0.47
28_C 38_M 0.92 0.73 0.46
110_L 67_S 0.91 0.71 0.45
24_I 60_V 0.91 0.71 0.45
66_A 50_G 0.90 0.71 0.44
95_S 2_I 0.90 0.70 0.43
69_Y 45_A 0.89 0.69 0.42
37_L 32_L 0.89 0.69 0.42
11_A 41_A 0.88 0.68 0.41
122_A 42_S 0.86 0.66 0.39
74_F 34_G 0.86 0.66 0.39
89_S 71_A 0.86 0.66 0.39
19_F 32_L 0.86 0.65 0.39
26_L 13_I 0.86 0.65 0.38
66_A 89_N 0.86 0.65 0.38
52_S 58_G 0.85 0.65 0.38
59_S 95_V 0.84 0.63 0.36
44_R 66_I 0.84 0.63 0.36
19_F 79_L 0.84 0.62 0.36
23_A 18_G 0.84 0.62 0.36
82_A 75_I 0.83 0.62 0.36
103_A 43_A 0.83 0.62 0.36
17_A 85_R 0.83 0.62 0.35
65_S 40_N 0.83 0.62 0.35
55_D 11_A 0.83 0.62 0.35
25_G 60_V 0.83 0.62 0.35
24_I 48_V 0.82 0.60 0.34
35_W 98_M 0.82 0.60 0.34
58_G 63_I 0.82 0.60 0.34
85_L 91_N 0.82 0.60 0.34
63_R 45_A 0.81 0.59 0.33
120_I 62_Y 0.81 0.59 0.33
97_W 65_A 0.81 0.59 0.33
46_K 92_I 0.81 0.58 0.32
122_A 33_I 0.81 0.58 0.32
72_A 29_L 0.80 0.57 0.31
76_V 45_A 0.79 0.56 0.31
112_A 88_Q 0.79 0.56 0.30
76_V 81_L 0.78 0.55 0.30
104_A 34_G 0.78 0.55 0.29
69_Y 8_L 0.78 0.55 0.29
41_A 12_A 0.78 0.54 0.29
69_Y 63_I 0.78 0.54 0.29
56_S 97_E 0.77 0.53 0.28
19_F 4_L 0.77 0.53 0.28
82_A 63_I 0.77 0.53 0.28
30_M 34_G 0.77 0.53 0.28
107_I 23_V 0.77 0.52 0.28
91_S 68_L 0.76 0.52 0.27
56_S 82_Q 0.76 0.52 0.27
76_V 50_G 0.76 0.52 0.27
83_L 75_I 0.76 0.51 0.27
107_I 9_I 0.76 0.51 0.26
60_A 66_I 0.75 0.51 0.26
112_A 12_A 0.75 0.51 0.26
88_W 61_M 0.75 0.50 0.26
117_L 64_L 0.75 0.50 0.26
67_K 78_A 0.75 0.50 0.26
116_Y 70_A 0.75 0.49 0.25
14_W 37_I 0.75 0.49 0.25
120_I 74_S 0.74 0.49 0.25
31_L 58_G 0.74 0.49 0.25
15_A 99_R 0.74 0.48 0.25
70_L 25_R 0.74 0.48 0.25
74_F 39_I 0.74 0.48 0.25
12_H 57_D 0.74 0.48 0.24
80_V 29_L 0.74 0.48 0.24
94_E 93_D 0.74 0.48 0.24
25_G 84_H 0.73 0.48 0.24
77_I 98_M 0.73 0.48 0.24
111_L 91_N 0.73 0.48 0.24
56_S 75_I 0.73 0.47 0.24
40_R 28_L 0.73 0.47 0.24
74_F 11_A 0.73 0.47 0.24
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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