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OPENSEQ.org
1ACM
Genes: A B A+B
Length: 310 153 432
Sequences: 4521 690 542
Seq/Len: 14.58 4.51 1.25
MirrorTree (Pazo et al. 2001) 0.48
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 0.02 0.07 1.09
2 0.02 0.07 1.13
5 0.04 0.07 1.16
10 0.05 0.07 1.15
20 0.05 0.07 1.17
100 0.07 0.07 1.18
∞ 0.13 0.08 1.27
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
88_L 115_I 1.55 0.85 0.13
132_N 43_T 1.48 0.81 0.11
69_S 104_D 1.28 0.66 0.06
61_T 9_V 1.26 0.65 0.06
49_F 62_E 1.25 0.64 0.06
289_A 83_V 1.24 0.62 0.05
87_T 120_P 1.23 0.62 0.05
75_D 9_V 1.21 0.60 0.05
19_D 142_E 1.19 0.58 0.04
264_L 86_I 1.14 0.53 0.04
259_A 53_M 1.13 0.52 0.04
74_S 65_F 1.11 0.50 0.04
299_L 62_E 1.10 0.49 0.03
236_D 45_G 1.10 0.49 0.03
95_I 142_E 1.07 0.46 0.03
247_F 116_S 1.04 0.43 0.03
114_L 121_V 1.03 0.43 0.03
293_I 7_L 1.03 0.42 0.03
175_A 106_V 1.01 0.40 0.03
178_K 116_S 0.99 0.38 0.02
68_A 144_E 0.99 0.38 0.02
250_R 12_I 0.98 0.38 0.02
305_N 107_L 0.98 0.37 0.02
43_V 120_P 0.98 0.37 0.02
293_I 27_F 0.98 0.37 0.02
71_V 14_R 0.97 0.37 0.02
154_N 85_R 0.97 0.37 0.02
165_Y 86_I 0.96 0.35 0.02
274_A 85_R 0.96 0.35 0.02
242_N 61_I 0.94 0.34 0.02
237_P 117_H 0.93 0.33 0.02
49_F 91_V 0.93 0.33 0.02
227_M 11_A 0.92 0.32 0.02
297_Q 48_L 0.92 0.32 0.02
263_V 55_R 0.92 0.32 0.02
116_T 88_N 0.91 0.31 0.02
302_L 18_I 0.91 0.31 0.02
49_F 118_A 0.90 0.30 0.02
47_C 45_G 0.90 0.30 0.02
20_L 32_L 0.90 0.30 0.02
275_T 18_I 0.89 0.30 0.02
65_R 7_L 0.89 0.30 0.02
219_M 44_I 0.89 0.30 0.02
49_F 143_K 0.89 0.29 0.02
294_F 29_L 0.89 0.29 0.02
263_V 124_S 0.88 0.29 0.01
303_V 5_N 0.88 0.29 0.01
144_T 24_Q 0.88 0.29 0.01
87_T 16_T 0.87 0.28 0.01
186_F 48_L 0.87 0.28 0.01
39_L 91_V 0.87 0.28 0.01
289_A 9_V 0.87 0.28 0.01
37_E 61_I 0.87 0.28 0.01
97_T 78_A 0.86 0.28 0.01
75_D 26_G 0.86 0.28 0.01
65_R 120_P 0.86 0.28 0.01
263_V 42_I 0.86 0.27 0.01
232_K 134_I 0.86 0.27 0.01
136_T 82_T 0.86 0.27 0.01
20_L 130_R 0.86 0.27 0.01
70_V 142_E 0.86 0.27 0.01
24_L 11_A 0.86 0.27 0.01
125_L 93_G 0.86 0.27 0.01
116_T 90_E 0.85 0.27 0.01
254_L 48_L 0.85 0.26 0.01
117_E 124_S 0.85 0.26 0.01
125_L 90_E 0.84 0.26 0.01
230_V 116_S 0.84 0.26 0.01
213_S 53_M 0.84 0.26 0.01
108_Q 118_A 0.84 0.26 0.01
154_N 88_N 0.84 0.26 0.01
291_N 91_V 0.82 0.24 0.01
297_Q 43_T 0.82 0.24 0.01
76_S 104_D 0.82 0.24 0.01
133_Q 86_I 0.82 0.24 0.01
127_A 54_G 0.82 0.24 0.01
23_V 83_V 0.82 0.24 0.01
23_V 66_L 0.82 0.24 0.01
108_Q 117_H 0.82 0.24 0.01
177_A 103_I 0.82 0.24 0.01
89_A 26_G 0.81 0.24 0.01
111_A 125_F 0.81 0.24 0.01
186_F 45_G 0.81 0.24 0.01
293_I 76_L 0.81 0.23 0.01
277_V 61_I 0.81 0.23 0.01
179_F 71_V 0.80 0.23 0.01
124_V 31_S 0.80 0.23 0.01
264_L 22_P 0.80 0.23 0.01
49_F 32_L 0.80 0.23 0.01
238_S 143_K 0.79 0.22 0.01
111_A 121_V 0.79 0.22 0.01
92_I 80_Q 0.79 0.22 0.01
232_K 102_R 0.79 0.22 0.01
116_T 108_V 0.78 0.22 0.01
169_V 10_E 0.78 0.21 0.01
47_C 112_S 0.78 0.21 0.01
214_S 103_I 0.78 0.21 0.01
24_L 62_E 0.78 0.21 0.01
185_Y 135_A 0.78 0.21 0.01
74_S 88_N 0.77 0.21 0.01
191_A 116_S 0.77 0.21 0.01
293_I 10_E 0.77 0.21 0.01
304_L 42_I 0.77 0.21 0.01
133_Q 45_G 0.77 0.21 0.01
303_V 116_S 0.77 0.20 0.01
160_V 112_S 0.77 0.20 0.01
139_L 63_N 0.76 0.20 0.01
247_F 48_L 0.76 0.20 0.01
155_L 18_I 0.76 0.20 0.01
124_V 7_L 0.76 0.20 0.01
295_A 130_R 0.76 0.20 0.01
131_S 43_T 0.76 0.20 0.01
251_A 93_G 0.76 0.20 0.01
241_A 117_H 0.76 0.20 0.01
49_F 7_L 0.76 0.20 0.01
282_H 89_Y 0.75 0.20 0.01
10_I 116_S 0.75 0.20 0.01
145_I 55_R 0.75 0.20 0.01
16_S 146_S 0.75 0.19 0.01
96_S 134_I 0.75 0.19 0.01
166_G 38_T 0.75 0.19 0.01
127_A 7_L 0.75 0.19 0.01
187_I 99_L 0.75 0.19 0.01
254_L 86_I 0.75 0.19 0.01
179_F 22_P 0.74 0.19 0.01
17_R 105_N 0.74 0.19 0.01
302_L 142_E 0.74 0.19 0.01
147_Q 103_I 0.74 0.19 0.01
92_I 59_I 0.74 0.19 0.01
190_D 90_E 0.74 0.19 0.01
125_L 82_T 0.74 0.19 0.01
236_D 48_L 0.74 0.19 0.01
187_I 58_L 0.74 0.19 0.01
235_L 29_L 0.74 0.19 0.01
56_R 28_K 0.74 0.19 0.01
221_E 52_E 0.74 0.19 0.01
16_S 32_L 0.74 0.19 0.01
263_V 61_I 0.73 0.19 0.01
217_E 13_K 0.73 0.19 0.01
187_I 107_L 0.73 0.18 0.01
61_T 106_V 0.73 0.18 0.01
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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