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OPENSEQ.org
mred-pbp2
Genes: A B A+B
Length: 162 240 392
Sequences: 577 3564 388
Seq/Len: 3.56 14.85 0.99
MirrorTree (Pazo et al. 2001) 0.74
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 0.05 0.50
2 0.00 0.05 0.50
5 0.00 0.05 0.50
10 0.00 0.05 0.51
20 0.00 0.06 0.53
100 0.00 0.08 0.55
∞ 0.00 0.16 0.97
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
60_F 175_V 1.64 0.84 0.10
38_W 53_R 1.42 0.70 0.05
116_I 176_I 1.37 0.67 0.05
44_L 50_Y 1.35 0.65 0.04
38_W 39_L 1.30 0.60 0.04
39_V 147_A 1.26 0.57 0.03
80_A 21_A 1.26 0.57 0.03
139_V 72_Y 1.25 0.56 0.03
125_V 176_I 1.23 0.55 0.03
47_I 224_Y 1.20 0.52 0.03
82_S 210_I 1.20 0.51 0.03
139_V 101_T 1.19 0.51 0.03
85_A 26_L 1.19 0.51 0.03
104_A 105_L 1.19 0.50 0.03
100_L 231_N 1.19 0.50 0.03
73_T 176_I 1.14 0.46 0.02
15_S 21_A 1.13 0.46 0.02
48_L 132_I 1.12 0.44 0.02
26_P 13_E 1.11 0.43 0.02
152_M 143_V 1.11 0.43 0.02
18_I 121_K 1.10 0.42 0.02
26_P 214_Y 1.10 0.42 0.02
157_Q 230_N 1.09 0.42 0.02
148_I 230_N 1.09 0.42 0.02
79_L 86_Y 1.09 0.42 0.02
45_Y 91_M 1.09 0.41 0.02
56_V 99_Q 1.08 0.41 0.02
48_L 92_P 1.06 0.39 0.02
140_V 64_I 1.06 0.39 0.02
151_L 34_V 1.06 0.39 0.02
140_V 170_S 1.05 0.38 0.02
110_L 151_Y 1.04 0.37 0.02
138_S 85_I 1.04 0.37 0.02
18_I 170_S 1.04 0.37 0.02
21_L 24_A 1.02 0.36 0.02
18_I 97_N 1.02 0.36 0.01
120_W 29_L 1.02 0.35 0.01
78_V 156_V 1.02 0.35 0.01
58_T 173_T 1.01 0.35 0.01
48_L 23_V 1.01 0.34 0.01
107_V 145_R 1.00 0.34 0.01
89_A 175_V 1.00 0.34 0.01
24_I 39_L 1.00 0.33 0.01
78_V 109_V 1.00 0.33 0.01
119_F 55_N 0.99 0.33 0.01
73_T 31_L 0.99 0.33 0.01
140_V 102_L 0.98 0.32 0.01
38_W 230_N 0.98 0.32 0.01
86_Y 44_I 0.97 0.32 0.01
139_V 110_D 0.96 0.31 0.01
71_G 186_D 0.96 0.31 0.01
149_F 108_V 0.96 0.31 0.01
19_A 113_D 0.96 0.31 0.01
17_L 158_V 0.96 0.31 0.01
140_V 78_P 0.96 0.30 0.01
158_Q 109_V 0.95 0.30 0.01
121_A 78_P 0.95 0.30 0.01
98_L 108_V 0.95 0.30 0.01
34_F 27_G 0.95 0.30 0.01
59_G 36_I 0.95 0.30 0.01
71_G 154_P 0.94 0.29 0.01
18_I 235_V 0.94 0.29 0.01
86_Y 186_D 0.94 0.29 0.01
15_S 23_V 0.94 0.29 0.01
85_A 217_V 0.94 0.29 0.01
137_S 23_V 0.93 0.28 0.01
158_Q 98_V 0.93 0.28 0.01
73_T 184_D 0.93 0.28 0.01
109_L 140_E 0.93 0.28 0.01
83_I 226_E 0.93 0.28 0.01
119_F 91_M 0.93 0.28 0.01
130_F 116_I 0.93 0.28 0.01
20_L 23_V 0.92 0.28 0.01
89_A 149_N 0.92 0.28 0.01
105_L 51_Q 0.92 0.27 0.01
23_Q 153_F 0.92 0.27 0.01
53_R 175_V 0.92 0.27 0.01
38_W 141_V 0.91 0.26 0.01
86_Y 56_E 0.90 0.26 0.01
140_V 226_E 0.90 0.26 0.01
102_Q 13_E 0.90 0.26 0.01
146_P 105_L 0.90 0.26 0.01
94_L 28_I 0.90 0.26 0.01
16_F 25_F 0.90 0.26 0.01
158_Q 61_L 0.90 0.26 0.01
83_I 24_A 0.89 0.26 0.01
59_G 134_V 0.89 0.26 0.01
61_V 169_G 0.89 0.25 0.01
143_V 141_V 0.89 0.25 0.01
8_G 216_D 0.88 0.25 0.01
81_M 32_T 0.88 0.25 0.01
86_Y 165_Y 0.88 0.24 0.01
159_F 111_L 0.87 0.24 0.01
86_Y 76_G 0.87 0.24 0.01
55_N 111_L 0.87 0.24 0.01
64_A 231_N 0.87 0.24 0.01
56_V 194_G 0.87 0.24 0.01
102_Q 108_V 0.87 0.24 0.01
110_L 47_F 0.87 0.24 0.01
60_F 85_I 0.86 0.23 0.01
102_Q 52_T 0.86 0.23 0.01
18_I 29_L 0.86 0.23 0.01
66_L 135_K 0.86 0.23 0.01
11_V 117_A 0.86 0.23 0.01
102_Q 230_N 0.86 0.23 0.01
12_I 219_H 0.86 0.23 0.01
35_R 52_T 0.85 0.23 0.01
142_G 146_F 0.85 0.23 0.01
143_V 106_R 0.85 0.23 0.01
58_T 35_L 0.85 0.23 0.01
141_N 81_L 0.85 0.23 0.01
41_L 229_V 0.85 0.23 0.01
43_L 187_V 0.85 0.23 0.01
116_I 31_L 0.85 0.23 0.01
51_P 71_I 0.85 0.22 0.01
150_L 148_V 0.85 0.22 0.01
121_A 26_L 0.85 0.22 0.01
17_L 170_S 0.84 0.22 0.01
68_L 135_K 0.84 0.22 0.01
54_V 227_V 0.84 0.22 0.01
143_V 158_V 0.84 0.22 0.01
112_L 169_G 0.84 0.22 0.01
99_A 67_S 0.84 0.22 0.01
132_P 42_L 0.84 0.22 0.01
69_I 230_N 0.84 0.22 0.01
15_S 145_R 0.84 0.22 0.01
41_L 113_D 0.84 0.22 0.01
112_L 48_T 0.84 0.22 0.01
110_L 62_V 0.84 0.22 0.01
129_S 148_V 0.83 0.22 0.01
136_W 28_I 0.83 0.21 0.01
120_W 100_Q 0.83 0.21 0.01
132_P 33_G 0.83 0.21 0.01
68_L 186_D 0.83 0.21 0.01
85_A 9_D 0.83 0.21 0.01
105_L 225_E 0.83 0.21 0.01
17_L 217_V 0.83 0.21 0.01
56_V 190_L 0.82 0.21 0.01
57_G 185_K 0.82 0.21 0.01
18_I 33_G 0.82 0.21 0.01
64_A 30_L 0.82 0.21 0.01
99_A 224_Y 0.82 0.21 0.01
25_M 64_I 0.82 0.21 0.01
65_I 214_Y 0.82 0.21 0.01
82_S 54_S 0.82 0.21 0.01
37_N 90_M 0.82 0.21 0.01
132_P 29_L 0.82 0.21 0.01
65_I 238_Q 0.82 0.21 0.01
142_G 47_F 0.81 0.20 0.01
45_Y 116_I 0.81 0.20 0.01
147_W 54_S 0.81 0.20 0.01
112_L 191_N 0.81 0.20 0.01
37_N 161_Y 0.81 0.20 0.01
72_S 60_K 0.81 0.20 0.01
107_V 88_I 0.81 0.20 0.01
94_L 55_N 0.81 0.20 0.01
16_F 152_R 0.81 0.20 0.01
139_V 108_V 0.81 0.20 0.01
77_R 159_K 0.81 0.20 0.01
145_W 80_A 0.81 0.20 0.01
14_L 75_N 0.81 0.20 0.01
5_R 34_V 0.80 0.20 0.01
111_S 172_L 0.80 0.20 0.01
68_L 236_I 0.80 0.20 0.01
15_S 104_A 0.80 0.20 0.01
89_A 147_A 0.80 0.20 0.01
84_I 202_T 0.80 0.20 0.01
73_T 35_L 0.80 0.19 0.01
42_I 189_R 0.80 0.19 0.01
3_S 134_V 0.79 0.19 0.01
116_I 23_V 0.79 0.19 0.01
115_D 229_V 0.79 0.19 0.01
11_V 45_V 0.79 0.19 0.01
54_V 112_T 0.79 0.19 0.01
117_I 197_A 0.79 0.19 0.01
70_S 47_F 0.79 0.19 0.01
74_L 202_T 0.79 0.19 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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