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OPENSEQ.org
cI_BctermL_cIII_cyt1
Genes: A B A+B
Length: 170 263 414
Sequences: 2039 574 178
Seq/Len: 11.99 2.18 0.43
MirrorTree (Pazo et al. 2001) 0.64
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 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.00
20 0.00 0.01 0.00
100 0.01 0.01 0.04
∞ 0.01 0.02 0.41
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
145_N 33_F 1.76 0.70 0.01
109_P 220_A 1.54 0.54 0.00
18_L 180_A 1.50 0.52 0.00
119_R 47_L 1.48 0.50 0.00
108_K 155_H 1.47 0.49 0.00
149_R 139_T 1.45 0.48 0.00
145_N 156_A 1.41 0.45 0.00
63_L 74_D 1.39 0.43 0.00
59_V 151_P 1.38 0.43 0.00
115_W 224_M 1.35 0.41 0.00
159_A 71_T 1.33 0.39 0.00
2_A 143_Q 1.29 0.37 0.00
21_S 85_V 1.29 0.36 0.00
59_V 41_K 1.24 0.33 0.00
24_V 204_T 1.23 0.33 0.00
106_F 151_P 1.23 0.32 0.00
63_L 100_E 1.19 0.30 0.00
71_G 210_T 1.19 0.30 0.00
126_M 178_A 1.18 0.30 0.00
161_V 17_Q 1.18 0.29 0.00
91_W 46_Q 1.16 0.28 0.00
12_L 16_A 1.16 0.28 0.00
96_W 34_S 1.16 0.28 0.00
81_N 113_T 1.15 0.28 0.00
2_A 74_D 1.15 0.28 0.00
101_L 41_K 1.15 0.28 0.00
11_S 230_V 1.14 0.27 0.00
62_I 159_T 1.14 0.27 0.00
28_I 223_K 1.14 0.27 0.00
97_G 197_Y 1.14 0.27 0.00
53_T 213_A 1.13 0.27 0.00
57_V 247_L 1.12 0.26 0.00
137_G 147_G 1.12 0.26 0.00
12_L 81_P 1.11 0.25 0.00
137_G 46_Q 1.11 0.25 0.00
66_A 161_Y 1.10 0.25 0.00
108_K 156_A 1.09 0.24 0.00
63_L 174_Y 1.09 0.24 0.00
2_A 78_P 1.07 0.23 0.00
105_V 178_A 1.07 0.23 0.00
162_V 236_I 1.06 0.22 0.00
53_T 69_L 1.06 0.22 0.00
19_I 17_Q 1.05 0.22 0.00
108_K 202_P 1.04 0.22 0.00
86_R 60_A 1.04 0.21 0.00
145_N 74_D 1.04 0.21 0.00
159_A 250_K 1.03 0.21 0.00
67_W 18_E 1.02 0.21 0.00
124_S 253_W 1.02 0.21 0.00
70_L 215_F 1.02 0.20 0.00
113_I 240_V 1.01 0.20 0.00
124_S 181_G 1.01 0.20 0.00
165_L 143_Q 1.01 0.20 0.00
117_L 156_A 1.00 0.20 0.00
160_V 203_A 1.00 0.20 0.00
133_S 191_S 0.99 0.19 0.00
77_T 258_H 0.99 0.19 0.00
58_A 106_V 0.98 0.18 0.00
104_K 197_Y 0.97 0.18 0.00
11_S 256_I 0.96 0.18 0.00
2_A 75_E 0.96 0.18 0.00
141_L 191_S 0.95 0.17 0.00
148_L 194_Q 0.95 0.17 0.00
157_I 27_H 0.95 0.17 0.00
167_M 42_F 0.94 0.17 0.00
59_V 31_I 0.94 0.17 0.00
121_P 131_A 0.94 0.17 0.00
117_L 185_Q 0.94 0.17 0.00
151_Y 222_P 0.94 0.17 0.00
164_A 73_A 0.94 0.17 0.00
105_V 93_D 0.94 0.17 0.00
12_L 94_I 0.94 0.17 0.00
65_A 214_A 0.94 0.17 0.00
28_I 147_G 0.94 0.17 0.00
58_A 213_A 0.93 0.17 0.00
130_A 33_F 0.93 0.17 0.00
65_A 44_Q 0.93 0.16 0.00
31_P 156_A 0.93 0.16 0.00
55_G 105_R 0.93 0.16 0.00
40_T 253_W 0.92 0.16 0.00
76_V 179_F 0.92 0.16 0.00
71_G 209_A 0.92 0.16 0.00
88_L 60_A 0.92 0.16 0.00
164_A 136_P 0.92 0.16 0.00
70_L 246_Y 0.92 0.16 0.00
78_S 240_V 0.92 0.16 0.00
64_L 187_A 0.91 0.16 0.00
154_S 38_P 0.91 0.16 0.00
142_L 113_T 0.91 0.16 0.00
165_L 237_F 0.91 0.16 0.00
3_H 143_Q 0.91 0.15 0.00
80_A 84_Q 0.90 0.15 0.00
127_N 194_Q 0.90 0.15 0.00
145_N 104_P 0.90 0.15 0.00
166_L 97_P 0.90 0.15 0.00
107_V 160_G 0.90 0.15 0.00
123_N 221_E 0.90 0.15 0.00
147_Y 60_A 0.90 0.15 0.00
108_K 146_N 0.90 0.15 0.00
100_W 128_K 0.89 0.15 0.00
44_H 46_Q 0.89 0.15 0.00
58_A 46_Q 0.89 0.15 0.00
52_I 184_I 0.89 0.15 0.00
100_W 70_R 0.88 0.15 0.00
19_I 65_R 0.88 0.15 0.00
83_A 113_T 0.88 0.15 0.00
16_V 184_I 0.88 0.14 0.00
100_W 153_Y 0.88 0.14 0.00
36_L 257_K 0.88 0.14 0.00
119_R 217_M 0.87 0.14 0.00
75_L 236_I 0.87 0.14 0.00
57_V 159_T 0.87 0.14 0.00
36_L 102_D 0.87 0.14 0.00
149_R 52_Q 0.87 0.14 0.00
74_T 256_I 0.87 0.14 0.00
161_V 220_A 0.87 0.14 0.00
73_R 236_I 0.86 0.14 0.00
132_L 220_A 0.86 0.14 0.00
90_T 206_D 0.86 0.14 0.00
114_A 47_L 0.86 0.14 0.00
132_L 223_K 0.86 0.14 0.00
11_S 195_V 0.86 0.14 0.00
125_M 257_K 0.86 0.14 0.00
64_L 104_P 0.86 0.14 0.00
127_N 154_I 0.85 0.14 0.00
9_T 47_L 0.85 0.14 0.00
3_H 233_V 0.85 0.14 0.00
12_L 141_L 0.85 0.14 0.00
124_S 182_N 0.85 0.13 0.00
44_H 214_A 0.85 0.13 0.00
18_L 90_A 0.85 0.13 0.00
137_G 239_I 0.84 0.13 0.00
42_L 196_T 0.84 0.13 0.00
97_G 76_G 0.84 0.13 0.00
165_L 179_F 0.84 0.13 0.00
46_S 93_D 0.84 0.13 0.00
141_L 99_T 0.84 0.13 0.00
126_M 133_F 0.83 0.13 0.00
108_K 100_E 0.83 0.13 0.00
53_T 143_Q 0.83 0.13 0.00
26_A 249_N 0.83 0.13 0.00
141_L 97_P 0.83 0.13 0.00
97_G 218_W 0.82 0.13 0.00
145_N 144_L 0.82 0.13 0.00
159_A 181_G 0.82 0.13 0.00
34_G 205_V 0.82 0.13 0.00
3_H 169_A 0.82 0.13 0.00
162_V 83_D 0.82 0.12 0.00
28_I 69_L 0.82 0.12 0.00
28_I 86_R 0.82 0.12 0.00
10_H 89_A 0.82 0.12 0.00
110_F 47_L 0.81 0.12 0.00
18_L 219_T 0.81 0.12 0.00
72_K 105_R 0.81 0.12 0.00
80_A 112_P 0.81 0.12 0.00
117_L 152_E 0.81 0.12 0.00
3_H 249_N 0.81 0.12 0.00
91_W 40_G 0.81 0.12 0.00
53_T 85_V 0.81 0.12 0.00
66_A 18_E 0.81 0.12 0.00
122_L 47_L 0.81 0.12 0.00
81_N 174_Y 0.81 0.12 0.00
10_H 57_V 0.81 0.12 0.00
67_W 251_K 0.81 0.12 0.00
126_M 225_M 0.81 0.12 0.00
126_M 80_L 0.81 0.12 0.00
100_W 131_A 0.81 0.12 0.00
132_L 36_E 0.81 0.12 0.00
87_L 229_Q 0.81 0.12 0.00
117_L 179_F 0.81 0.12 0.00
67_W 100_E 0.81 0.12 0.00
113_I 241_L 0.80 0.12 0.00
70_L 203_A 0.80 0.12 0.00
81_N 209_A 0.80 0.12 0.00
137_G 208_M 0.80 0.12 0.00
117_L 101_E 0.80 0.12 0.00
126_M 128_K 0.80 0.12 0.00
117_L 9_T 0.80 0.12 0.00
86_R 27_H 0.80 0.12 0.00
138_K 107_P 0.80 0.12 0.00
130_A 185_Q 0.80 0.12 0.00
108_K 246_Y 0.80 0.12 0.00
106_F 244_L 0.80 0.12 0.00
92_W 234_S 0.80 0.12 0.00
143_S 82_E 0.80 0.12 0.00
98_F 111_F 0.80 0.12 0.00
157_I 31_I 0.80 0.12 0.00
46_S 225_M 0.80 0.12 0.00
163_L 153_Y 0.80 0.12 0.00
140_L 249_N 0.79 0.12 0.00
86_R 248_T 0.79 0.12 0.00
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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