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OPENSEQ.org
GJ
Genes: A B A+B
Length: 140 198 325
Sequences: 1248 618 499
Seq/Len: 8.91 3.12 1.54
MirrorTree (Pazo et al. 2001) 0.56
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 0.08 0.00 0.00
2 0.09 0.00 0.10
5 0.09 0.00 1.44
10 0.09 0.00 1.47
20 0.09 0.00 1.48
100 0.09 0.00 1.49
∞ 0.13 0.03 1.52
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
4_Q 5_A 1.62 0.92 0.45
87_P 115_Y 1.33 0.77 0.23
30_L 52_Q 1.30 0.74 0.21
120_L 189_L 1.25 0.70 0.18
105_Q 114_S 1.24 0.68 0.17
14_V 16_A 1.13 0.58 0.12
81_P 188_R 1.12 0.57 0.12
39_R 149_A 1.10 0.55 0.11
93_R 23_L 1.07 0.53 0.10
119_S 144_Q 1.07 0.52 0.10
26_V 47_R 1.07 0.52 0.10
119_S 11_V 1.07 0.52 0.10
70_L 91_I 1.06 0.51 0.10
1_M 19_I 1.05 0.51 0.10
51_G 29_T 1.03 0.48 0.09
133_G 95_R 1.01 0.46 0.08
19_L 47_R 1.00 0.45 0.08
93_R 20_L 1.00 0.45 0.08
32_G 188_R 0.99 0.44 0.07
129_N 45_G 0.99 0.44 0.07
23_A 20_L 0.98 0.43 0.07
57_K 185_E 0.98 0.42 0.07
120_L 147_V 0.97 0.41 0.07
46_L 39_T 0.96 0.41 0.07
132_I 33_N 0.96 0.40 0.07
90_G 115_Y 0.95 0.39 0.06
63_Y 164_W 0.95 0.39 0.06
120_L 5_A 0.94 0.39 0.06
74_V 181_E 0.94 0.39 0.06
131_D 160_W 0.93 0.38 0.06
76_A 29_T 0.92 0.36 0.06
117_I 49_Q 0.91 0.36 0.06
93_R 30_V 0.91 0.36 0.05
12_I 114_S 0.91 0.35 0.05
31_M 46_G 0.90 0.35 0.05
81_P 147_V 0.90 0.35 0.05
107_L 29_T 0.90 0.35 0.05
112_H 23_L 0.90 0.35 0.05
46_L 18_A 0.89 0.34 0.05
57_K 26_A 0.89 0.34 0.05
106_L 127_Y 0.89 0.34 0.05
66_T 193_T 0.89 0.34 0.05
60_N 188_R 0.88 0.33 0.05
7_F 51_L 0.88 0.33 0.05
19_L 179_T 0.88 0.33 0.05
67_E 39_T 0.88 0.33 0.05
16_I 28_V 0.87 0.32 0.05
30_L 157_S 0.86 0.31 0.04
124_G 94_S 0.86 0.31 0.04
52_A 106_P 0.86 0.31 0.04
120_L 171_P 0.85 0.30 0.04
28_P 188_R 0.85 0.30 0.04
25_L 192_L 0.85 0.30 0.04
28_P 55_F 0.85 0.30 0.04
46_L 172_Q 0.85 0.30 0.04
21_V 184_G 0.85 0.30 0.04
30_L 17_L 0.85 0.30 0.04
51_G 163_E 0.85 0.30 0.04
35_E 93_F 0.84 0.30 0.04
43_V 145_R 0.84 0.30 0.04
117_I 3_Q 0.84 0.30 0.04
46_L 58_M 0.84 0.30 0.04
90_G 31_L 0.84 0.30 0.04
10_L 15_L 0.84 0.29 0.04
45_D 27_A 0.84 0.29 0.04
30_L 22_A 0.84 0.29 0.04
42_V 170_L 0.84 0.29 0.04
100_W 16_A 0.84 0.29 0.04
12_I 155_Y 0.83 0.29 0.04
4_Q 21_A 0.83 0.28 0.04
71_Q 37_A 0.81 0.27 0.04
78_S 176_V 0.81 0.27 0.04
53_L 148_Q 0.80 0.26 0.03
12_I 180_L 0.80 0.26 0.03
112_H 87_D 0.79 0.26 0.03
65_T 73_S 0.79 0.25 0.03
46_L 31_L 0.79 0.25 0.03
97_Q 25_V 0.79 0.25 0.03
95_L 11_V 0.79 0.25 0.03
45_D 187_R 0.79 0.25 0.03
103_D 91_I 0.78 0.25 0.03
45_D 95_R 0.78 0.25 0.03
34_K 27_A 0.78 0.24 0.03
134_N 11_V 0.77 0.24 0.03
87_P 28_V 0.77 0.24 0.03
49_L 144_Q 0.77 0.24 0.03
19_L 14_L 0.77 0.24 0.03
65_T 3_Q 0.77 0.24 0.03
89_G 97_G 0.77 0.23 0.03
56_Y 61_D 0.77 0.23 0.03
134_N 35_M 0.76 0.23 0.03
43_V 157_S 0.76 0.23 0.03
8_T 96_N 0.76 0.23 0.03
129_N 91_I 0.76 0.23 0.03
110_G 178_L 0.76 0.23 0.03
71_Q 186_I 0.76 0.23 0.03
92_I 44_K 0.76 0.23 0.03
43_V 192_L 0.76 0.23 0.03
1_M 58_M 0.75 0.22 0.03
108_S 26_A 0.75 0.22 0.03
115_V 25_V 0.75 0.22 0.03
136_T 34_V 0.75 0.22 0.03
70_L 110_I 0.75 0.22 0.03
120_L 76_L 0.74 0.22 0.03
67_E 130_Q 0.74 0.22 0.03
57_K 75_S 0.74 0.22 0.03
55_M 46_G 0.74 0.22 0.03
10_L 22_A 0.74 0.22 0.03
36_K 24_S 0.74 0.22 0.03
71_Q 11_V 0.74 0.21 0.03
20_G 173_G 0.73 0.21 0.03
27_V 110_I 0.73 0.21 0.03
16_I 20_L 0.73 0.21 0.03
74_V 92_A 0.73 0.21 0.03
89_G 55_F 0.73 0.21 0.03
16_I 152_L 0.73 0.21 0.03
23_A 13_M 0.73 0.21 0.03
93_R 57_Q 0.73 0.21 0.02
25_L 23_L 0.73 0.21 0.02
118_F 51_L 0.73 0.21 0.02
31_M 13_M 0.72 0.20 0.02
102_S 35_M 0.72 0.20 0.02
83_A 39_T 0.72 0.20 0.02
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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