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OPENSEQ.org
ExbDHasB_Sm
Genes: A B A+B
Length: 263 140 375
Sequences: 116 4105 95
Seq/Len: 0.44 29.32 0.25
MirrorTree (Pazo et al. 2001) 0.65
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.10 0.24
2 0.00 0.10 0.24
5 0.00 0.10 0.24
10 0.00 0.10 0.24
20 0.00 0.10 0.24
100 0.00 0.14 0.24
∞ 0.04 0.24 0.27
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
178_R 67_S 1.77 0.54 0.00
178_R 101_T 1.68 0.48 0.00
101_I 61_E 1.51 0.38 0.00
147_A 125_A 1.49 0.37 0.00
84_P 61_E 1.42 0.32 0.00
212_L 121_T 1.41 0.32 0.00
223_R 130_V 1.31 0.27 0.00
117_N 23_F 1.31 0.27 0.00
201_L 88_S 1.30 0.26 0.00
27_L 100_T 1.28 0.25 0.00
54_V 108_K 1.28 0.25 0.00
249_E 89_V 1.27 0.25 0.00
27_L 66_L 1.27 0.24 0.00
94_P 130_V 1.25 0.24 0.00
253_P 110_V 1.25 0.24 0.00
30_L 124_K 1.24 0.23 0.00
50_P 102_I 1.21 0.22 0.00
226_Q 41_A 1.20 0.21 0.00
30_L 53_S 1.19 0.21 0.00
123_P 65_F 1.19 0.21 0.00
52_V 131_G 1.19 0.21 0.00
181_R 45_I 1.19 0.21 0.00
184_K 93_R 1.18 0.21 0.00
55_L 84_D 1.17 0.20 0.00
185_D 121_T 1.15 0.19 0.00
224_E 67_S 1.14 0.19 0.00
14_A 41_A 1.13 0.19 0.00
14_A 134_G 1.11 0.18 0.00
227_A 102_I 1.10 0.17 0.00
27_L 46_R 1.09 0.17 0.00
237_T 53_S 1.09 0.17 0.00
232_A 26_V 1.08 0.17 0.00
68_Q 102_I 1.07 0.16 0.00
254_I 66_L 1.06 0.16 0.00
162_Q 66_L 1.05 0.16 0.00
214_S 53_S 1.05 0.15 0.00
20_C 36_V 1.04 0.15 0.00
33_A 92_Q 1.03 0.15 0.00
27_L 51_A 1.03 0.15 0.00
45_P 87_T 1.03 0.15 0.00
197_V 108_K 1.03 0.15 0.00
231_R 86_L 1.03 0.15 0.00
104_P 130_V 1.02 0.15 0.00
247_T 119_M 1.02 0.15 0.00
218_L 104_F 1.02 0.15 0.00
217_G 106_A 1.02 0.14 0.00
70_P 130_V 1.01 0.14 0.00
49_P 115_L 1.01 0.14 0.00
103_V 83_A 1.01 0.14 0.00
178_R 128_L 1.01 0.14 0.00
55_L 119_M 1.00 0.14 0.00
226_Q 121_T 1.00 0.14 0.00
21_L 72_K 1.00 0.14 0.00
94_P 59_R 1.00 0.14 0.00
166_D 85_Q 0.99 0.14 0.00
21_L 55_K 0.99 0.14 0.00
103_V 72_K 0.98 0.14 0.00
47_V 67_S 0.98 0.13 0.00
129_I 92_Q 0.98 0.13 0.00
207_V 29_V 0.97 0.13 0.00
207_V 33_I 0.97 0.13 0.00
35_L 99_E 0.97 0.13 0.00
117_N 134_G 0.96 0.13 0.00
178_R 131_G 0.96 0.13 0.00
221_L 65_F 0.95 0.13 0.00
51_A 128_L 0.95 0.13 0.00
86_E 52_S 0.95 0.12 0.00
54_V 102_I 0.95 0.12 0.00
207_V 28_L 0.94 0.12 0.00
73_R 130_V 0.94 0.12 0.00
205_G 31_L 0.94 0.12 0.00
205_G 34_F 0.94 0.12 0.00
205_G 50_P 0.94 0.12 0.00
205_G 107_D 0.94 0.12 0.00
205_G 126_G 0.94 0.12 0.00
134_V 41_A 0.94 0.12 0.00
245_N 108_K 0.94 0.12 0.00
133_K 61_E 0.93 0.12 0.00
250_L 102_I 0.93 0.12 0.00
221_L 74_L 0.93 0.12 0.00
121_R 130_V 0.93 0.12 0.00
84_P 75_Y 0.92 0.12 0.00
213_V 52_S 0.92 0.12 0.00
93_A 137_G 0.91 0.12 0.00
215_S 73_Q 0.91 0.12 0.00
234_P 86_L 0.91 0.11 0.00
18_R 81_V 0.91 0.11 0.00
22_V 67_S 0.91 0.11 0.00
248_V 102_I 0.90 0.11 0.00
19_R 93_R 0.90 0.11 0.00
234_P 25_D 0.90 0.11 0.00
125_Q 15_L 0.90 0.11 0.00
149_K 65_F 0.90 0.11 0.00
120_P 102_I 0.89 0.11 0.00
92_K 24_I 0.89 0.11 0.00
120_P 51_A 0.89 0.11 0.00
124_P 87_T 0.89 0.11 0.00
31_V 114_T 0.89 0.11 0.00
201_L 32_I 0.89 0.11 0.00
54_V 129_K 0.88 0.11 0.00
244_V 85_Q 0.88 0.11 0.00
234_P 49_L 0.88 0.11 0.00
66_A 62_K 0.88 0.11 0.00
24_V 66_L 0.88 0.11 0.00
20_C 102_I 0.88 0.11 0.00
78_Q 37_A 0.88 0.11 0.00
43_E 134_G 0.88 0.11 0.00
235_L 25_D 0.87 0.11 0.00
241_D 138_A 0.87 0.10 0.00
182_Y 129_K 0.87 0.10 0.00
98_Q 131_G 0.87 0.10 0.00
179_F 115_L 0.87 0.10 0.00
49_P 110_V 0.87 0.10 0.00
139_V 53_S 0.87 0.10 0.00
134_V 76_V 0.87 0.10 0.00
186_A 74_L 0.87 0.10 0.00
22_V 51_A 0.87 0.10 0.00
94_P 101_T 0.87 0.10 0.00
22_V 138_A 0.87 0.10 0.00
156_R 92_Q 0.86 0.10 0.00
56_M 84_D 0.86 0.10 0.00
50_P 68_V 0.86 0.10 0.00
113_P 59_R 0.86 0.10 0.00
84_P 85_Q 0.86 0.10 0.00
54_V 51_A 0.86 0.10 0.00
152_A 86_L 0.86 0.10 0.00
51_A 102_I 0.86 0.10 0.00
104_P 64_V 0.86 0.10 0.00
238_P 136_E 0.86 0.10 0.00
195_G 104_F 0.86 0.10 0.00
12_G 111_D 0.86 0.10 0.00
193_G 125_A 0.85 0.10 0.00
132_P 93_R 0.85 0.10 0.00
232_A 20_V 0.85 0.10 0.00
217_G 31_L 0.84 0.10 0.00
217_G 34_F 0.84 0.10 0.00
217_G 50_P 0.84 0.10 0.00
217_G 107_D 0.84 0.10 0.00
217_G 126_G 0.84 0.10 0.00
78_Q 76_V 0.84 0.10 0.00
180_K 110_V 0.84 0.10 0.00
71_G 75_Y 0.84 0.10 0.00
152_A 123_R 0.84 0.10 0.00
21_L 74_L 0.84 0.10 0.00
193_G 129_K 0.84 0.10 0.00
56_M 110_V 0.83 0.10 0.00
149_K 115_L 0.83 0.10 0.00
124_P 131_G 0.83 0.10 0.00
167_N 73_Q 0.83 0.10 0.00
254_I 87_T 0.83 0.10 0.00
168_W 42_T 0.83 0.10 0.00
124_P 65_F 0.83 0.10 0.00
168_W 74_L 0.83 0.10 0.00
55_L 78_D 0.83 0.10 0.00
177_N 74_L 0.83 0.10 0.00
195_G 76_V 0.82 0.09 0.00
58_A 59_R 0.82 0.09 0.00
156_R 61_E 0.82 0.09 0.00
49_P 125_A 0.82 0.09 0.00
64_A 81_V 0.82 0.09 0.00
207_V 40_L 0.82 0.09 0.00
17_W 123_R 0.82 0.09 0.00
237_T 101_T 0.82 0.09 0.00
238_P 123_R 0.82 0.09 0.00
149_K 104_F 0.82 0.09 0.00
122_T 73_Q 0.82 0.09 0.00
93_A 109_S 0.82 0.09 0.00
123_P 47_V 0.82 0.09 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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