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OPENSEQ.org
4he8_JK
Genes: A B A+B
Length: 160 95 252
Sequences: 1948 1164 1549
Seq/Len: 12.18 12.25 6.15
MirrorTree (Pazo et al. 2001) 0.81
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 5.57
2 0.00 0.00 5.74
5 0.00 0.00 5.83
10 0.00 0.00 5.91
20 0.00 0.00 6.07
100 0.01 0.01 6.18
∞ 0.02 0.01 6.19
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
13_L 9_L 4.54 1.00 1.00
17_V 13_L 2.95 1.00 1.00
16_G 10_L 2.64 1.00 1.00
130_L 51_L 2.41 1.00 1.00
142_V 62_A 2.32 1.00 1.00
42_V 6_T 2.23 1.00 0.99
6_G 2_S 2.19 1.00 0.99
39_L 40_L 2.05 1.00 0.99
9_L 6_T 1.84 1.00 0.98
19_V 29_L 1.71 1.00 0.97
157_V 76_V 1.69 1.00 0.96
29_A 29_L 1.67 1.00 0.96
20_V 17_G 1.54 0.99 0.94
55_Q 36_N 1.52 0.99 0.93
127_L 55_V 1.50 0.99 0.93
145_L 70_V 1.44 0.99 0.91
16_G 13_L 1.43 0.99 0.91
9_L 60_V 1.30 0.97 0.85
40_A 7_S 1.23 0.95 0.81
73_L 28_F 1.21 0.95 0.80
35_N 33_L 1.19 0.94 0.78
18_L 29_L 1.18 0.94 0.77
46_L 44_G 1.11 0.91 0.71
102_G 5_L 1.10 0.90 0.70
101_A 12_A 1.09 0.90 0.70
105_A 5_L 1.08 0.90 0.69
19_V 30_S 1.08 0.90 0.69
152_V 25_I 1.07 0.89 0.67
43_Y 40_L 1.06 0.88 0.66
128_G 68_V 1.06 0.88 0.66
39_L 36_N 1.04 0.87 0.64
4_L 93_L 1.02 0.86 0.63
158_E 36_N 1.02 0.86 0.62
71_I 10_L 1.01 0.85 0.61
20_V 13_L 1.01 0.85 0.61
42_V 3_Y 1.00 0.84 0.60
106_A 94_R 0.99 0.84 0.59
43_Y 36_N 0.99 0.83 0.59
12_L 6_T 0.99 0.83 0.58
71_I 41_S 0.98 0.83 0.58
81_I 42_L 0.97 0.81 0.56
155_A 77_A 0.97 0.81 0.56
58_V 19_L 0.95 0.80 0.54
28_A 27_V 0.95 0.79 0.54
67_F 73_G 0.94 0.79 0.53
16_G 33_L 0.94 0.79 0.53
108_L 60_V 0.93 0.77 0.51
51_L 57_A 0.93 0.77 0.51
139_L 39_N 0.93 0.77 0.51
77_A 24_A 0.92 0.77 0.50
151_V 76_V 0.92 0.76 0.49
43_Y 57_A 0.91 0.76 0.49
105_A 73_G 0.91 0.75 0.49
137_F 77_A 0.91 0.75 0.48
138_V 58_L 0.89 0.73 0.46
143_G 80_R 0.89 0.73 0.46
67_F 31_I 0.88 0.72 0.45
155_A 76_V 0.88 0.72 0.45
47_D 47_R 0.88 0.71 0.44
94_A 80_R 0.87 0.71 0.44
148_A 62_A 0.87 0.70 0.43
151_V 20_T 0.86 0.70 0.43
157_V 77_A 0.86 0.69 0.42
43_Y 14_G 0.85 0.68 0.41
149_A 66_A 0.85 0.68 0.41
128_G 64_A 0.85 0.68 0.41
62_A 71_G 0.85 0.67 0.40
141_A 90_L 0.84 0.67 0.40
141_A 34_M 0.84 0.67 0.40
4_L 78_I 0.83 0.66 0.39
48_A 44_G 0.83 0.66 0.39
28_A 92_E 0.83 0.65 0.39
153_A 55_V 0.83 0.65 0.38
154_V 17_G 0.83 0.65 0.38
156_L 43_V 0.82 0.64 0.38
94_A 40_L 0.82 0.64 0.37
143_G 61_I 0.82 0.64 0.37
131_L 59_M 0.82 0.64 0.37
24_N 13_L 0.82 0.64 0.37
132_Y 46_A 0.81 0.63 0.36
20_V 30_S 0.81 0.62 0.36
17_V 69_A 0.81 0.62 0.35
124_P 63_V 0.81 0.62 0.35
32_L 29_L 0.81 0.62 0.35
101_A 9_L 0.80 0.62 0.35
156_L 77_A 0.80 0.61 0.35
40_A 40_L 0.80 0.60 0.34
122_G 22_R 0.80 0.60 0.34
51_L 12_A 0.79 0.60 0.34
40_A 47_R 0.79 0.59 0.33
43_Y 58_L 0.79 0.59 0.33
63_I 20_T 0.79 0.59 0.33
64_V 29_L 0.79 0.59 0.33
48_A 43_V 0.79 0.59 0.33
64_V 21_R 0.78 0.59 0.33
141_A 30_S 0.78 0.59 0.33
19_V 42_L 0.78 0.58 0.32
63_I 94_R 0.77 0.57 0.31
73_L 61_I 0.77 0.57 0.31
67_F 29_L 0.77 0.57 0.31
6_G 5_L 0.77 0.57 0.31
63_I 44_G 0.77 0.56 0.31
46_L 47_R 0.77 0.56 0.31
125_Q 68_V 0.77 0.56 0.31
39_L 61_I 0.77 0.56 0.31
131_L 83_E 0.77 0.56 0.30
75_F 46_A 0.77 0.56 0.30
138_V 12_A 0.76 0.56 0.30
55_Q 61_I 0.76 0.56 0.30
92_L 2_S 0.76 0.55 0.30
21_T 16_Y 0.76 0.55 0.30
36_F 18_V 0.76 0.55 0.29
25_A 26_L 0.75 0.54 0.29
135_W 28_F 0.75 0.54 0.29
53_F 36_N 0.75 0.54 0.29
55_Q 57_A 0.75 0.53 0.28
88_R 22_R 0.74 0.53 0.28
135_W 52_D 0.74 0.53 0.28
32_L 15_V 0.74 0.53 0.28
50_F 79_F 0.74 0.53 0.28
39_L 6_T 0.74 0.53 0.28
144_F 34_M 0.74 0.52 0.28
143_G 52_D 0.74 0.52 0.28
16_G 26_L 0.74 0.52 0.27
46_L 34_M 0.74 0.52 0.27
126_A 51_L 0.74 0.52 0.27
22_L 93_L 0.73 0.51 0.27
138_V 59_M 0.73 0.51 0.27
26_I 55_V 0.73 0.51 0.27
66_L 85_T 0.73 0.51 0.27
40_A 76_V 0.73 0.51 0.27
28_A 77_A 0.73 0.51 0.27
72_M 54_Q 0.73 0.51 0.26
93_A 76_V 0.73 0.51 0.26
13_L 83_E 0.73 0.51 0.26
149_A 83_E 0.73 0.50 0.26
102_G 84_S 0.73 0.50 0.26
12_L 34_M 0.72 0.50 0.26
94_A 88_D 0.72 0.49 0.26
128_G 69_A 0.72 0.49 0.25
127_L 51_L 0.72 0.49 0.25
31_A 73_G 0.72 0.49 0.25
15_S 33_L 0.72 0.49 0.25
40_A 16_Y 0.72 0.49 0.25
15_S 23_T 0.72 0.49 0.25
152_V 35_L 0.71 0.48 0.25
133_G 61_I 0.71 0.48 0.25
20_V 16_Y 0.71 0.48 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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