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OPENSEQ.org
1KMI
Genes: A B A+B
Length: 129 214 324
Sequences: 88711 404 314
Seq/Len: 687.68 1.89 0.97
MirrorTree (Pazo et al. 2001) 0.38
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 0.11 0.01 0.87
2 0.13 0.01 0.89
5 0.16 0.01 0.91
10 0.19 0.01 0.91
20 0.23 0.01 0.92
100 0.32 0.01 0.94
∞ 0.34 0.03 0.96
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
15_S 29_R 1.60 0.82 0.05
63_M 32_L 1.44 0.71 0.04
96_I 150_K 1.40 0.69 0.03
68_L 18_I 1.40 0.68 0.03
104_S 169_E 1.37 0.67 0.03
27_E 71_N 1.34 0.64 0.03
115_T 49_P 1.34 0.64 0.03
107_V 48_I 1.31 0.61 0.03
21_V 100_D 1.25 0.56 0.02
80_A 30_D 1.21 0.52 0.02
86_V 100_D 1.20 0.51 0.02
120_L 192_D 1.14 0.45 0.01
58_W 142_Q 1.13 0.45 0.01
108_V 199_V 1.12 0.44 0.01
113_A 142_Q 1.09 0.41 0.01
7_K 61_M 1.09 0.41 0.01
107_V 190_Q 1.09 0.41 0.01
28_L 58_V 1.07 0.40 0.01
70_K 21_I 1.07 0.39 0.01
80_A 108_R 1.06 0.39 0.01
114_A 36_G 1.05 0.38 0.01
80_A 195_K 1.05 0.38 0.01
86_V 75_A 1.04 0.37 0.01
115_T 70_L 1.04 0.36 0.01
77_A 61_M 1.03 0.36 0.01
91_K 94_W 1.02 0.35 0.01
41_D 58_V 1.02 0.35 0.01
115_T 52_R 1.01 0.34 0.01
125_E 38_D 1.01 0.34 0.01
92_K 31_S 1.00 0.34 0.01
27_E 59_V 1.00 0.33 0.01
90_A 151_R 1.00 0.33 0.01
21_V 201_S 0.99 0.32 0.01
64_D 49_P 0.99 0.32 0.01
71_T 20_R 0.98 0.32 0.01
6_L 155_V 0.98 0.31 0.01
91_K 79_H 0.98 0.31 0.01
96_I 77_Q 0.97 0.31 0.01
68_L 193_T 0.96 0.30 0.01
7_K 158_E 0.96 0.30 0.01
79_S 125_T 0.96 0.30 0.01
56_S 101_P 0.95 0.30 0.01
103_A 36_G 0.95 0.29 0.01
114_A 141_F 0.95 0.29 0.01
21_V 21_I 0.94 0.29 0.01
92_K 192_D 0.94 0.29 0.01
54_V 167_L 0.94 0.28 0.01
97_A 27_M 0.93 0.28 0.01
117_E 152_M 0.93 0.28 0.01
27_E 58_V 0.92 0.27 0.01
62_N 70_L 0.92 0.27 0.01
86_V 190_Q 0.91 0.27 0.01
23_N 74_E 0.91 0.27 0.01
72_I 111_V 0.91 0.26 0.01
71_T 95_D 0.91 0.26 0.01
126_K 20_R 0.91 0.26 0.01
40_V 125_T 0.90 0.26 0.01
115_T 173_E 0.90 0.26 0.01
27_E 150_K 0.90 0.26 0.01
30_F 34_E 0.90 0.26 0.01
92_K 9_A 0.89 0.25 0.01
6_L 106_D 0.89 0.25 0.01
67_E 5_S 0.89 0.25 0.01
113_A 78_P 0.89 0.25 0.01
79_S 211_S 0.89 0.25 0.01
68_L 31_S 0.89 0.25 0.01
33_V 9_A 0.88 0.24 0.01
62_N 36_G 0.88 0.24 0.01
70_K 164_L 0.88 0.24 0.01
68_L 43_E 0.88 0.24 0.01
71_T 177_R 0.87 0.24 0.01
45_K 204_Q 0.87 0.24 0.01
22_R 76_S 0.87 0.23 0.01
97_A 82_Q 0.87 0.23 0.01
117_E 67_E 0.86 0.23 0.01
64_D 80_Q 0.86 0.23 0.01
103_A 35_L 0.86 0.23 0.01
67_E 60_Q 0.86 0.23 0.01
40_V 201_S 0.86 0.23 0.01
7_K 211_S 0.85 0.23 0.01
55_I 91_T 0.85 0.23 0.01
118_E 132_L 0.85 0.23 0.01
67_E 130_A 0.85 0.23 0.01
64_D 114_T 0.85 0.22 0.01
126_K 80_Q 0.84 0.22 0.01
126_K 203_D 0.84 0.22 0.01
50_G 79_H 0.84 0.22 0.01
86_V 166_V 0.84 0.22 0.01
101_A 142_Q 0.84 0.22 0.01
62_N 71_N 0.84 0.21 0.01
21_V 186_L 0.84 0.21 0.01
30_F 12_H 0.83 0.21 0.01
120_L 167_L 0.83 0.21 0.01
54_V 133_L 0.83 0.21 0.01
27_E 33_R 0.83 0.21 0.01
104_S 110_L 0.83 0.21 0.01
86_V 74_E 0.83 0.21 0.01
54_V 49_P 0.83 0.21 0.01
115_T 7_K 0.83 0.21 0.01
50_G 46_E 0.82 0.21 0.01
96_I 56_Y 0.82 0.21 0.01
66_L 142_Q 0.82 0.20 0.01
126_K 204_Q 0.82 0.20 0.01
6_L 197_G 0.82 0.20 0.01
21_V 162_Q 0.81 0.20 0.01
43_L 21_I 0.81 0.20 0.01
63_M 155_V 0.81 0.20 0.01
8_F 210_D 0.81 0.20 0.01
30_F 152_M 0.80 0.20 0.01
66_L 80_Q 0.80 0.19 0.01
80_A 170_N 0.80 0.19 0.01
118_E 52_R 0.80 0.19 0.01
54_V 101_P 0.80 0.19 0.01
72_I 167_L 0.80 0.19 0.01
92_K 44_A 0.79 0.19 0.00
64_D 166_V 0.79 0.19 0.00
73_R 38_D 0.79 0.19 0.00
42_A 29_R 0.79 0.19 0.00
97_A 129_N 0.79 0.19 0.00
90_A 135_I 0.79 0.19 0.00
125_E 67_E 0.79 0.19 0.00
70_K 184_S 0.79 0.18 0.00
66_L 20_R 0.78 0.18 0.00
27_E 186_L 0.78 0.18 0.00
5_E 157_Q 0.78 0.18 0.00
79_S 174_Q 0.78 0.18 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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