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OPENSEQ.org
cI_BctermL_F
Genes: A B A+B
Length: 170 184 349
Sequences: 2039 2037 1802
Seq/Len: 11.99 11.07 5.16
MirrorTree (Pazo et al. 2001) 0.84
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 0.06
2 0.00 0.00 3.95
5 0.00 0.00 4.21
10 0.00 0.00 4.75
20 0.00 0.00 4.87
100 0.01 0.01 4.94
∞ 0.01 0.02 5.09
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
65_A 149_L 1.34 0.96 0.59
10_H 154_V 1.32 0.96 0.58
54_S 160_R 1.18 0.92 0.45
148_L 8_C 1.15 0.91 0.42
54_S 159_G 1.13 0.89 0.40
148_L 133_L 1.12 0.89 0.39
20_L 63_I 1.09 0.87 0.36
57_V 40_S 1.07 0.86 0.34
149_R 57_I 1.04 0.84 0.32
164_A 102_I 1.03 0.82 0.30
57_V 63_I 1.01 0.81 0.29
144_E 5_F 1.01 0.81 0.29
100_W 141_V 1.01 0.81 0.29
12_L 172_K 1.01 0.81 0.29
20_L 57_I 1.01 0.81 0.29
21_S 77_G 1.00 0.80 0.28
109_P 57_I 0.99 0.79 0.27
149_R 84_E 0.98 0.78 0.26
22_T 3_F 0.97 0.78 0.26
22_T 58_V 0.95 0.75 0.24
66_A 153_V 0.94 0.74 0.23
12_L 94_I 0.93 0.73 0.23
114_A 63_I 0.93 0.72 0.22
101_L 123_P 0.92 0.71 0.21
50_L 58_V 0.91 0.71 0.21
163_L 120_D 0.91 0.70 0.21
28_I 45_S 0.91 0.70 0.21
150_W 19_V 0.91 0.70 0.21
141_L 140_A 0.91 0.70 0.21
91_W 99_L 0.91 0.70 0.20
149_R 36_L 0.90 0.69 0.20
120_D 148_L 0.89 0.68 0.20
25_G 62_A 0.89 0.68 0.19
73_R 135_G 0.88 0.67 0.19
98_F 28_A 0.88 0.67 0.19
153_A 77_G 0.88 0.66 0.18
52_I 143_L 0.87 0.65 0.18
95_A 58_V 0.87 0.65 0.18
163_L 24_N 0.86 0.64 0.18
161_V 129_V 0.85 0.63 0.17
157_I 11_I 0.85 0.63 0.17
98_F 65_V 0.85 0.62 0.17
91_W 43_F 0.84 0.62 0.16
149_R 75_N 0.84 0.62 0.16
14_L 46_L 0.83 0.60 0.15
137_G 133_L 0.83 0.59 0.15
125_M 19_V 0.82 0.59 0.15
88_L 132_T 0.82 0.59 0.15
46_S 132_T 0.82 0.58 0.15
27_L 21_T 0.82 0.58 0.15
79_I 133_L 0.82 0.58 0.15
148_L 58_V 0.82 0.58 0.15
166_L 12_A 0.81 0.58 0.14
14_L 73_M 0.81 0.57 0.14
61_G 150_A 0.81 0.57 0.14
111_L 15_A 0.81 0.57 0.14
24_V 60_A 0.80 0.56 0.14
14_L 20_I 0.80 0.56 0.14
21_S 43_F 0.80 0.55 0.14
162_V 152_L 0.80 0.55 0.14
137_G 140_A 0.80 0.55 0.13
159_A 107_I 0.79 0.55 0.13
13_P 67_F 0.79 0.54 0.13
118_K 75_N 0.79 0.54 0.13
76_V 52_G 0.78 0.53 0.13
100_W 26_V 0.78 0.53 0.13
155_M 30_L 0.78 0.53 0.13
157_I 128_A 0.78 0.53 0.13
133_S 95_G 0.78 0.53 0.12
61_G 62_A 0.78 0.52 0.12
163_L 28_A 0.78 0.52 0.12
70_L 28_A 0.77 0.52 0.12
26_A 89_K 0.77 0.52 0.12
20_L 60_A 0.77 0.51 0.12
126_M 151_G 0.77 0.51 0.12
10_H 53_A 0.76 0.50 0.12
155_M 153_V 0.76 0.50 0.12
6_K 155_A 0.76 0.49 0.11
68_L 107_I 0.76 0.49 0.11
152_V 19_V 0.76 0.49 0.11
110_F 54_L 0.76 0.49 0.11
167_M 139_L 0.75 0.49 0.11
23_F 13_I 0.75 0.49 0.11
96_W 64_M 0.75 0.49 0.11
76_V 89_K 0.75 0.49 0.11
61_G 69_F 0.75 0.48 0.11
100_W 42_V 0.75 0.48 0.11
102_Y 152_L 0.75 0.48 0.11
96_W 49_Y 0.74 0.47 0.11
65_A 47_G 0.74 0.47 0.11
152_V 70_V 0.74 0.47 0.11
69_W 160_R 0.74 0.47 0.11
63_L 111_I 0.74 0.47 0.11
76_V 103_M 0.74 0.47 0.11
132_L 119_I 0.74 0.47 0.11
103_D 75_N 0.74 0.47 0.11
161_V 101_A 0.74 0.47 0.10
4_A 161_E 0.73 0.46 0.10
94_N 97_A 0.73 0.46 0.10
128_I 33_I 0.73 0.46 0.10
85_G 58_V 0.73 0.46 0.10
145_N 149_L 0.73 0.46 0.10
149_R 55_E 0.73 0.45 0.10
12_L 114_V 0.73 0.45 0.10
163_L 94_I 0.73 0.45 0.10
99_D 36_L 0.73 0.45 0.10
96_W 90_P 0.72 0.45 0.10
91_W 134_F 0.72 0.45 0.10
12_L 166_E 0.72 0.44 0.10
36_L 112_L 0.72 0.44 0.10
161_V 108_V 0.72 0.44 0.10
145_N 135_G 0.72 0.44 0.10
112_G 106_V 0.71 0.43 0.09
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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