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OPENSEQ.org
Fo_ac
Genes: A B A+B
Length: 271 79 301
Sequences: 1124 1098 545
Seq/Len: 4.15 13.9 1.81
MirrorTree (Pazo et al. 2001) 0.83
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 0.04 0.08 1.52
2 0.04 0.08 1.56
5 0.04 0.08 1.56
10 0.04 0.08 1.55
20 0.04 0.08 1.57
100 0.04 0.08 1.58
∞ 0.04 0.09 1.64
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
263_Y 54_F 1.77 0.97 0.83
213_G 65_M 1.67 0.95 0.78
182_P 40_A 1.40 0.85 0.56
179_T 25_A 1.35 0.81 0.51
263_Y 62_A 1.32 0.80 0.48
213_G 62_A 1.24 0.74 0.41
231_W 72_L 1.22 0.72 0.39
146_D 71_G 1.20 0.70 0.37
54_L 33_G 1.20 0.70 0.37
167_K 44_D 1.20 0.70 0.37
71_V 63_I 1.19 0.69 0.36
99_K 22_I 1.18 0.68 0.35
244_F 56_V 1.17 0.68 0.34
158_F 76_F 1.17 0.67 0.34
194_I 26_I 1.17 0.67 0.34
55_L 46_I 1.13 0.63 0.30
208_G 38_G 1.11 0.61 0.28
158_F 55_I 1.08 0.58 0.26
66_K 26_I 1.08 0.58 0.26
93_M 55_I 1.08 0.58 0.26
85_F 38_G 1.08 0.58 0.26
141_V 70_L 1.06 0.56 0.24
214_N 62_A 1.05 0.55 0.23
67_A 45_L 1.04 0.54 0.23
269_E 72_L 1.04 0.54 0.23
263_Y 21_A 1.02 0.52 0.21
201_L 29_G 1.02 0.51 0.21
255_I 54_F 1.01 0.51 0.21
241_W 38_G 0.98 0.47 0.18
188_F 68_V 0.98 0.47 0.18
58_V 75_M 0.97 0.47 0.18
264_L 13_A 0.97 0.47 0.18
155_L 26_I 0.96 0.46 0.17
209_L 15_V 0.95 0.44 0.17
100_L 22_I 0.95 0.44 0.17
139_L 17_M 0.95 0.44 0.16
86_V 40_A 0.94 0.43 0.16
269_E 26_I 0.94 0.43 0.16
189_I 14_A 0.94 0.43 0.16
265_S 42_Q 0.94 0.43 0.16
260_T 33_G 0.94 0.43 0.15
143_P 31_L 0.94 0.42 0.15
260_T 20_A 0.93 0.42 0.15
181_Q 70_L 0.93 0.42 0.15
254_F 34_K 0.93 0.41 0.15
95_H 58_G 0.93 0.41 0.15
97_K 14_A 0.92 0.41 0.14
258_V 15_V 0.92 0.41 0.14
178_L 42_Q 0.92 0.41 0.14
248_I 46_I 0.92 0.41 0.14
83_I 53_F 0.91 0.40 0.14
203_K 56_V 0.90 0.39 0.14
114_L 72_L 0.90 0.39 0.13
101_I 26_I 0.90 0.39 0.13
190_P 13_A 0.90 0.39 0.13
153_M 29_G 0.89 0.38 0.13
121_L 11_M 0.89 0.38 0.13
51_V 11_M 0.89 0.38 0.13
247_L 55_I 0.89 0.38 0.13
118_M 59_L 0.89 0.37 0.13
217_A 67_A 0.89 0.37 0.12
89_S 42_Q 0.88 0.37 0.12
162_L 14_A 0.88 0.37 0.12
66_K 18_G 0.88 0.36 0.12
52_L 15_V 0.88 0.36 0.12
83_I 32_G 0.88 0.36 0.12
206_S 77_A 0.88 0.36 0.12
262_V 37_E 0.87 0.36 0.12
76_Q 21_A 0.87 0.35 0.12
260_T 34_K 0.87 0.35 0.12
74_K 47_P 0.86 0.35 0.12
152_S 11_M 0.86 0.35 0.11
55_L 31_L 0.85 0.34 0.11
74_K 76_F 0.85 0.34 0.11
247_L 36_L 0.85 0.34 0.11
95_H 61_D 0.83 0.32 0.10
156_G 37_E 0.83 0.32 0.10
108_I 26_I 0.83 0.31 0.10
239_V 75_M 0.83 0.31 0.10
112_V 68_V 0.82 0.31 0.10
100_L 58_G 0.82 0.31 0.09
224_L 56_V 0.82 0.31 0.09
108_I 68_V 0.82 0.31 0.09
251_L 50_R 0.82 0.31 0.09
264_L 42_Q 0.82 0.30 0.09
221_I 38_G 0.81 0.30 0.09
143_P 65_M 0.81 0.30 0.09
225_I 38_G 0.81 0.30 0.09
239_V 20_A 0.81 0.30 0.09
262_V 54_F 0.81 0.30 0.09
230_P 28_I 0.81 0.29 0.09
194_I 33_G 0.81 0.29 0.09
118_M 33_G 0.80 0.29 0.09
62_S 45_L 0.80 0.29 0.09
202_S 44_D 0.80 0.29 0.09
245_H 28_I 0.80 0.29 0.09
235_W 75_M 0.80 0.29 0.09
46_M 45_L 0.80 0.29 0.09
205_V 69_G 0.80 0.29 0.09
124_D 71_G 0.80 0.29 0.08
58_V 19_L 0.79 0.28 0.08
144_S 37_E 0.79 0.28 0.08
114_L 14_A 0.79 0.28 0.08
191_V 25_A 0.79 0.28 0.08
104_L 55_I 0.79 0.28 0.08
218_G 28_I 0.79 0.28 0.08
202_S 13_A 0.79 0.28 0.08
217_A 33_G 0.78 0.28 0.08
43_I 42_Q 0.78 0.28 0.08
159_I 51_T 0.78 0.27 0.08
151_L 33_G 0.78 0.27 0.08
247_L 52_Q 0.77 0.27 0.08
101_I 47_P 0.77 0.27 0.08
236_I 67_A 0.77 0.27 0.08
150_T 17_M 0.77 0.27 0.08
244_F 45_L 0.77 0.26 0.07
117_L 59_L 0.77 0.26 0.07
102_A 42_Q 0.77 0.26 0.07
127_P 56_V 0.77 0.26 0.07
104_L 67_A 0.77 0.26 0.07
70_G 33_G 0.77 0.26 0.07
205_V 46_I 0.76 0.26 0.07
117_L 69_G 0.76 0.26 0.07
202_S 22_I 0.76 0.26 0.07
247_L 23_G 0.76 0.26 0.07
205_V 49_L 0.76 0.26 0.07
46_M 33_G 0.76 0.26 0.07
218_G 27_G 0.76 0.26 0.07
261_I 67_A 0.76 0.26 0.07
254_F 71_G 0.76 0.25 0.07
182_P 49_L 0.76 0.25 0.07
255_I 49_L 0.76 0.25 0.07
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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