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OPENSEQ.org
cI_BctermL_E
Genes: A B A+B
Length: 170 147 288
Sequences: 2039 3696 1641
Seq/Len: 11.99 25.14 5.7
MirrorTree (Pazo et al. 2001) 0.78
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 0.02
2 0.00 0.00 0.05
5 0.00 0.00 0.21
10 0.00 0.00 1.91
20 0.00 0.00 4.21
100 0.01 0.01 4.85
∞ 0.01 0.01 5.18
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
24_V 34_G 1.58 0.99 0.90
59_V 24_I 1.35 0.97 0.79
160_V 16_F 1.29 0.96 0.76
60_V 32_V 1.18 0.93 0.66
147_Y 76_V 1.06 0.87 0.53
149_R 38_G 1.04 0.85 0.51
107_V 76_V 1.04 0.85 0.51
52_I 32_V 1.04 0.85 0.51
153_A 86_F 1.01 0.83 0.48
115_W 21_I 1.01 0.83 0.48
149_R 73_M 1.00 0.82 0.47
32_L 40_R 0.99 0.81 0.45
156_S 50_F 0.97 0.80 0.43
160_V 77_I 0.97 0.79 0.43
107_V 67_K 0.96 0.78 0.42
132_L 31_L 0.95 0.78 0.41
105_V 107_I 0.93 0.76 0.39
149_R 80_V 0.93 0.76 0.39
114_A 45_S 0.93 0.75 0.38
61_G 85_L 0.92 0.74 0.37
102_Y 120_I 0.91 0.73 0.36
149_R 76_V 0.91 0.73 0.36
114_A 44_R 0.89 0.71 0.34
62_I 41_A 0.89 0.70 0.34
96_W 113_G 0.88 0.70 0.33
45_G 36_F 0.88 0.69 0.33
4_A 87_A 0.87 0.69 0.32
122_L 55_D 0.87 0.69 0.32
32_L 93_R 0.86 0.67 0.30
14_L 58_G 0.85 0.66 0.30
149_R 63_R 0.85 0.66 0.30
137_G 39_G 0.85 0.65 0.29
20_L 67_K 0.85 0.65 0.29
21_S 67_K 0.85 0.65 0.29
24_V 69_Y 0.85 0.65 0.29
164_A 36_F 0.84 0.65 0.29
16_V 41_A 0.84 0.64 0.28
144_E 74_F 0.83 0.63 0.28
46_S 52_S 0.83 0.63 0.28
101_L 10_I 0.83 0.63 0.28
98_F 122_A 0.83 0.62 0.27
92_W 103_A 0.82 0.62 0.27
128_I 107_I 0.82 0.62 0.27
24_V 29_L 0.82 0.62 0.27
88_L 115_V 0.82 0.61 0.27
12_L 105_I 0.81 0.61 0.26
161_V 108_F 0.81 0.60 0.26
123_N 108_F 0.81 0.60 0.26
15_I 39_G 0.81 0.60 0.26
89_S 17_A 0.81 0.60 0.26
161_V 97_W 0.81 0.60 0.26
143_S 101_V 0.81 0.60 0.25
54_S 57_V 0.80 0.59 0.25
78_S 25_G 0.80 0.58 0.24
133_S 82_A 0.79 0.57 0.24
81_N 32_V 0.79 0.57 0.24
48_L 34_G 0.79 0.57 0.24
61_G 25_G 0.79 0.57 0.23
20_L 57_V 0.79 0.57 0.23
58_A 30_M 0.78 0.56 0.23
12_L 28_C 0.78 0.56 0.23
68_L 20_L 0.78 0.56 0.23
70_L 18_I 0.78 0.56 0.23
9_T 34_G 0.77 0.55 0.22
147_Y 80_V 0.77 0.55 0.22
113_I 89_S 0.77 0.54 0.22
149_R 65_S 0.77 0.54 0.21
155_M 65_S 0.76 0.53 0.21
130_A 10_I 0.76 0.53 0.21
60_V 82_A 0.76 0.52 0.21
140_L 26_L 0.76 0.52 0.21
148_L 14_W 0.75 0.52 0.20
109_P 99_G 0.75 0.52 0.20
20_L 65_S 0.75 0.52 0.20
2_A 28_C 0.75 0.51 0.20
136_A 64_L 0.75 0.51 0.20
63_L 28_C 0.75 0.51 0.20
56_V 83_L 0.75 0.51 0.20
86_R 112_A 0.75 0.51 0.20
98_F 110_L 0.74 0.50 0.19
140_L 108_F 0.73 0.48 0.18
126_M 56_S 0.73 0.48 0.18
77_T 77_I 0.73 0.48 0.18
138_K 37_L 0.73 0.48 0.18
156_S 71_V 0.72 0.48 0.18
101_L 11_A 0.72 0.47 0.18
153_A 59_S 0.72 0.47 0.18
114_A 25_G 0.72 0.47 0.18
144_E 103_A 0.72 0.47 0.18
60_V 21_I 0.72 0.47 0.17
72_K 16_F 0.72 0.47 0.17
18_L 72_A 0.71 0.46 0.17
110_F 52_S 0.71 0.46 0.17
148_L 47_N 0.71 0.46 0.17
98_F 82_A 0.71 0.46 0.17
65_A 88_W 0.71 0.45 0.17
5_V 120_I 0.70 0.45 0.16
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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