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OPENSEQ.org
10vs11_tthe
Genes: A B A+B
Length: 176 95 266
Sequences: 2002 1164 1560
Seq/Len: 11.38 12.25 5.86
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 5.27
2 0.00 0.00 5.45
5 0.00 0.00 5.56
10 0.00 0.00 5.62
20 0.00 0.00 5.76
100 0.01 0.01 5.90
∞ 0.02 0.01 5.89
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 4.53 1.00 1.00
17_V 13_L 2.94 1.00 1.00
16_G 10_L 2.57 1.00 1.00
130_L 51_L 2.43 1.00 1.00
42_V 6_T 2.33 1.00 1.00
142_V 62_A 2.27 1.00 0.99
6_G 2_S 2.16 1.00 0.99
39_L 40_L 1.98 1.00 0.99
29_A 29_L 1.82 1.00 0.98
9_L 6_T 1.77 1.00 0.97
157_V 76_V 1.75 1.00 0.97
19_V 29_L 1.61 0.99 0.95
20_V 17_G 1.55 0.99 0.94
127_L 55_V 1.55 0.99 0.94
145_L 70_V 1.50 0.99 0.93
55_Q 36_N 1.44 0.98 0.91
16_G 13_L 1.40 0.98 0.90
102_G 5_L 1.35 0.97 0.88
40_A 7_S 1.24 0.95 0.82
73_L 28_F 1.16 0.93 0.76
19_V 30_S 1.16 0.92 0.75
4_L 93_L 1.15 0.92 0.75
18_L 29_L 1.15 0.92 0.75
35_N 33_L 1.15 0.92 0.74
42_V 3_Y 1.14 0.92 0.74
101_A 12_A 1.13 0.91 0.73
9_L 60_V 1.12 0.91 0.72
152_V 25_I 1.11 0.90 0.71
28_A 27_V 1.07 0.88 0.68
46_L 44_G 1.06 0.88 0.67
12_L 6_T 1.05 0.86 0.65
128_G 68_V 1.04 0.86 0.65
43_Y 40_L 1.03 0.85 0.63
71_I 10_L 1.03 0.85 0.63
108_L 60_V 1.01 0.84 0.61
155_A 77_A 1.01 0.84 0.61
101_A 9_L 1.00 0.83 0.60
84_D 23_T 1.00 0.83 0.59
67_F 31_I 1.00 0.83 0.59
105_A 5_L 0.99 0.82 0.59
94_A 88_D 0.97 0.81 0.56
94_A 80_R 0.97 0.80 0.55
20_V 13_L 0.96 0.80 0.55
139_L 39_N 0.96 0.80 0.55
137_F 77_A 0.96 0.80 0.55
39_L 36_N 0.96 0.79 0.55
160_G 94_R 0.96 0.79 0.55
67_F 73_G 0.95 0.78 0.53
47_D 47_R 0.94 0.77 0.52
155_A 76_V 0.93 0.76 0.51
71_I 41_S 0.93 0.76 0.51
138_V 58_L 0.93 0.76 0.51
43_Y 36_N 0.93 0.76 0.51
156_L 43_V 0.93 0.76 0.50
160_G 4_L 0.92 0.76 0.50
106_A 94_R 0.92 0.75 0.50
16_G 33_L 0.92 0.75 0.50
51_L 57_A 0.91 0.74 0.49
24_N 13_L 0.91 0.74 0.48
153_A 55_V 0.91 0.73 0.48
62_A 71_G 0.90 0.73 0.47
143_G 80_R 0.90 0.73 0.47
58_V 19_L 0.87 0.69 0.44
26_I 55_V 0.87 0.69 0.43
40_A 16_Y 0.86 0.69 0.43
154_V 17_G 0.86 0.68 0.42
43_Y 57_A 0.86 0.68 0.42
173_E 57_A 0.86 0.67 0.42
81_I 42_L 0.85 0.67 0.41
127_L 51_L 0.84 0.66 0.40
136_L 19_L 0.84 0.66 0.40
141_A 90_L 0.84 0.65 0.40
51_L 12_A 0.83 0.65 0.39
63_I 94_R 0.83 0.64 0.39
4_L 78_I 0.83 0.64 0.39
95_L 9_L 0.83 0.64 0.38
170_K 42_L 0.83 0.63 0.38
17_V 69_A 0.83 0.63 0.38
131_L 87_V 0.82 0.63 0.38
151_V 76_V 0.82 0.63 0.37
159_P 81_H 0.82 0.62 0.37
48_A 44_G 0.81 0.62 0.36
158_E 36_N 0.81 0.62 0.36
77_A 24_A 0.81 0.61 0.36
128_G 64_A 0.81 0.61 0.36
148_A 62_A 0.81 0.61 0.35
126_A 51_L 0.81 0.61 0.35
47_D 48_A 0.80 0.60 0.35
32_L 29_L 0.80 0.59 0.34
55_Q 57_A 0.80 0.59 0.34
25_A 26_L 0.80 0.59 0.34
107_G 12_A 0.80 0.59 0.34
159_P 44_G 0.80 0.59 0.34
20_V 30_S 0.79 0.59 0.34
64_V 21_R 0.79 0.59 0.34
75_F 46_A 0.79 0.58 0.33
149_A 66_A 0.79 0.58 0.33
104_L 92_E 0.79 0.58 0.33
149_A 83_E 0.79 0.57 0.33
32_L 15_V 0.78 0.57 0.32
157_V 77_A 0.78 0.57 0.32
46_L 47_R 0.78 0.57 0.32
144_F 7_S 0.78 0.57 0.32
132_Y 46_A 0.78 0.56 0.32
15_S 33_L 0.78 0.56 0.32
40_A 76_V 0.78 0.56 0.32
87_V 70_V 0.78 0.56 0.32
43_Y 14_G 0.77 0.55 0.31
12_L 34_M 0.77 0.55 0.31
66_L 85_T 0.77 0.55 0.31
63_I 44_G 0.77 0.55 0.30
130_L 52_D 0.76 0.54 0.30
135_W 28_F 0.76 0.54 0.30
97_A 8_A 0.76 0.54 0.30
73_L 61_I 0.76 0.54 0.30
6_G 5_L 0.76 0.54 0.30
41_G 6_T 0.76 0.53 0.29
17_V 94_R 0.76 0.53 0.29
156_L 77_A 0.76 0.53 0.29
28_A 77_A 0.76 0.53 0.29
138_V 59_M 0.76 0.53 0.29
36_F 18_V 0.75 0.53 0.29
161_K 25_I 0.75 0.53 0.29
46_L 48_A 0.75 0.53 0.29
94_A 40_L 0.75 0.53 0.29
19_V 42_L 0.75 0.52 0.28
141_A 34_M 0.75 0.52 0.28
151_V 20_T 0.75 0.52 0.28
151_V 24_A 0.75 0.52 0.28
43_Y 58_L 0.74 0.51 0.28
160_G 23_T 0.74 0.51 0.28
131_L 83_E 0.74 0.51 0.28
105_A 73_G 0.74 0.51 0.28
138_V 12_A 0.74 0.51 0.27
2_S 2_S 0.74 0.51 0.27
48_A 43_V 0.74 0.50 0.27
50_F 79_F 0.74 0.50 0.27
39_L 6_T 0.74 0.50 0.27
141_A 30_S 0.73 0.50 0.27
72_M 54_Q 0.73 0.50 0.27
160_G 56_A 0.73 0.50 0.27
125_Q 68_V 0.73 0.50 0.26
25_A 68_V 0.73 0.49 0.26
64_V 29_L 0.73 0.49 0.26
22_L 93_L 0.73 0.49 0.26
67_F 29_L 0.72 0.48 0.25
133_G 61_I 0.72 0.48 0.25
124_P 63_V 0.72 0.48 0.25
131_L 59_M 0.72 0.48 0.25
62_A 82_R 0.72 0.48 0.25
15_S 78_I 0.72 0.48 0.25
128_G 69_A 0.72 0.48 0.25
152_V 35_L 0.72 0.47 0.25
74_L 70_V 0.72 0.47 0.25
13_L 83_E 0.72 0.47 0.25
140_L 5_L 0.71 0.47 0.24
31_A 73_G 0.71 0.47 0.24
125_Q 85_T 0.71 0.47 0.24
77_A 75_I 0.71 0.47 0.24
31_A 58_L 0.71 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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