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OPENSEQ.org
1kmi_Z_Y
Genes: A B A+B
Length: 214 129 324
Sequences: 404 88711 313
Seq/Len: 1.89 687.68 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 0.01 0.11 0.88
2 0.01 0.13 0.90
5 0.01 0.16 0.90
10 0.01 0.19 0.90
20 0.01 0.23 0.91
100 0.01 0.32 0.92
∞ 0.03 0.34 0.95
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
29_R 15_S 1.60 0.82 0.05
150_K 96_I 1.45 0.72 0.04
32_L 63_M 1.44 0.71 0.04
18_I 68_L 1.41 0.69 0.03
49_P 115_T 1.35 0.65 0.03
48_I 107_V 1.31 0.61 0.02
71_N 27_E 1.30 0.60 0.02
100_D 21_V 1.29 0.60 0.02
169_E 104_S 1.27 0.58 0.02
100_D 86_V 1.22 0.53 0.02
30_D 80_A 1.21 0.52 0.02
192_D 120_L 1.17 0.48 0.02
199_V 108_V 1.14 0.45 0.01
142_Q 58_W 1.13 0.44 0.01
190_Q 107_V 1.10 0.42 0.01
142_Q 113_A 1.09 0.41 0.01
125_T 79_S 1.09 0.41 0.01
195_K 80_A 1.06 0.39 0.01
75_A 86_V 1.06 0.38 0.01
58_V 28_L 1.06 0.38 0.01
36_G 114_A 1.03 0.36 0.01
52_R 115_T 1.02 0.35 0.01
21_I 70_K 1.02 0.35 0.01
70_L 115_T 1.02 0.35 0.01
94_W 91_K 1.02 0.35 0.01
58_V 41_D 1.01 0.34 0.01
61_M 7_K 1.01 0.34 0.01
61_M 77_A 1.01 0.34 0.01
38_D 125_E 1.01 0.34 0.01
151_R 90_A 1.00 0.34 0.01
108_R 80_A 1.00 0.33 0.01
95_D 71_T 0.99 0.32 0.01
77_Q 96_I 0.98 0.32 0.01
20_R 71_T 0.98 0.32 0.01
201_S 21_V 0.98 0.32 0.01
141_F 114_A 0.98 0.32 0.01
59_V 27_E 0.98 0.32 0.01
31_S 92_K 0.97 0.31 0.01
79_H 91_K 0.97 0.31 0.01
125_T 40_V 0.97 0.31 0.01
27_M 97_A 0.97 0.31 0.01
155_V 6_L 0.95 0.29 0.01
49_P 64_D 0.95 0.29 0.01
36_G 103_A 0.94 0.29 0.01
133_L 54_V 0.94 0.29 0.01
5_S 67_E 0.94 0.29 0.01
101_P 56_S 0.94 0.29 0.01
193_T 68_L 0.94 0.28 0.01
192_D 92_K 0.94 0.28 0.01
21_I 21_V 0.93 0.28 0.01
58_V 27_E 0.93 0.28 0.01
167_L 54_V 0.93 0.28 0.01
158_E 7_K 0.92 0.27 0.01
152_M 117_E 0.92 0.27 0.01
190_Q 86_V 0.91 0.27 0.01
20_R 126_K 0.91 0.27 0.01
80_Q 64_D 0.90 0.26 0.01
70_L 62_N 0.89 0.25 0.01
74_E 23_N 0.89 0.25 0.01
130_A 67_E 0.89 0.25 0.01
111_V 72_I 0.89 0.25 0.01
78_P 113_A 0.89 0.25 0.01
211_S 79_S 0.88 0.24 0.01
9_A 33_V 0.88 0.24 0.01
204_Q 45_K 0.88 0.24 0.01
82_Q 30_F 0.88 0.24 0.01
9_A 92_K 0.88 0.24 0.01
150_K 27_E 0.87 0.24 0.01
31_S 68_L 0.87 0.24 0.01
67_E 117_E 0.87 0.24 0.01
173_E 115_T 0.87 0.24 0.01
101_P 54_V 0.87 0.23 0.01
82_Q 97_A 0.86 0.23 0.01
7_K 115_T 0.86 0.23 0.01
76_S 22_R 0.86 0.23 0.01
43_E 68_L 0.86 0.23 0.01
132_L 118_E 0.86 0.23 0.01
201_S 40_V 0.85 0.23 0.01
35_L 103_A 0.85 0.22 0.01
80_Q 126_K 0.85 0.22 0.01
36_G 62_N 0.85 0.22 0.01
114_T 64_D 0.84 0.22 0.01
167_L 120_L 0.84 0.22 0.01
166_V 86_V 0.84 0.22 0.01
12_H 30_F 0.84 0.22 0.01
46_E 50_G 0.84 0.22 0.01
34_E 30_F 0.84 0.21 0.01
74_E 86_V 0.84 0.21 0.01
33_R 27_E 0.83 0.21 0.01
195_K 55_I 0.83 0.21 0.01
60_Q 67_E 0.83 0.21 0.01
177_R 71_T 0.82 0.21 0.01
203_D 126_K 0.82 0.21 0.01
142_Q 66_L 0.82 0.20 0.01
142_Q 101_A 0.82 0.20 0.01
106_D 6_L 0.82 0.20 0.01
182_N 121_N 0.82 0.20 0.01
110_L 104_S 0.82 0.20 0.01
186_L 21_V 0.81 0.20 0.01
197_G 80_A 0.81 0.20 0.01
91_T 55_I 0.81 0.20 0.01
174_Q 79_S 0.81 0.20 0.01
67_E 62_N 0.81 0.20 0.01
184_S 70_K 0.81 0.20 0.01
204_Q 126_K 0.81 0.20 0.01
170_N 80_A 0.81 0.20 0.01
49_P 54_V 0.81 0.20 0.01
162_Q 10_V 0.81 0.20 0.01
162_Q 21_V 0.80 0.20 0.01
182_N 96_I 0.80 0.20 0.01
211_S 7_K 0.80 0.19 0.01
79_H 50_G 0.80 0.19 0.01
52_R 118_E 0.80 0.19 0.01
21_I 43_L 0.80 0.19 0.01
175_E 52_G 0.80 0.19 0.01
166_V 64_D 0.80 0.19 0.00
56_Y 96_I 0.79 0.19 0.00
106_D 52_G 0.79 0.19 0.00
135_I 90_A 0.79 0.19 0.00
29_R 42_A 0.79 0.19 0.00
71_N 62_N 0.79 0.19 0.00
129_N 52_G 0.79 0.19 0.00
80_Q 66_L 0.79 0.19 0.00
38_D 73_R 0.79 0.18 0.00
167_L 72_I 0.78 0.18 0.00
210_D 8_F 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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