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OPENSEQ.org
1AHW_b4
Genes: A B A+B
Length: 202 214 379
Sequences: 5997 2523 63
Seq/Len: 29.69 11.79 0.17
MirrorTree (Pazo et al. 2001) 0.39
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.09 0.09 0.03
2 0.10 0.09 0.04
5 0.11 0.11 0.07
10 0.12 0.13 0.15
20 0.12 0.14 0.21
100 0.14 0.16 0.35
∞ 0.17 0.18 0.51
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
86_E 67_K 1.63 0.35 0.00
27_N 83_L 1.57 0.32 0.00
144_Y 158_W 1.55 0.31 0.00
55_L 136_T 1.48 0.28 0.00
17_T 129_A 1.47 0.27 0.00
118_V 148_G 1.46 0.27 0.00
83_P 129_A 1.38 0.23 0.00
73_S 111_T 1.36 0.23 0.00
148_Y 187_V 1.35 0.22 0.00
86_E 144_C 1.33 0.22 0.00
21_W 36_W 1.32 0.21 0.00
21_W 123_P 1.30 0.20 0.00
57_D 70_I 1.29 0.20 0.00
30_Y 19_K 1.29 0.20 0.00
30_Y 131_G 1.24 0.18 0.00
21_W 199_C 1.23 0.18 0.00
67_Y 83_L 1.23 0.18 0.00
67_Y 158_W 1.22 0.17 0.00
71_V 68_A 1.21 0.17 0.00
67_Y 36_W 1.19 0.17 0.00
110_V 83_L 1.19 0.16 0.00
172_K 166_G 1.19 0.16 0.00
118_V 154_V 1.17 0.16 0.00
118_V 153_P 1.14 0.15 0.00
118_V 66_G 1.14 0.15 0.00
17_T 150_F 1.14 0.15 0.00
48_T 82_Q 1.14 0.15 0.00
116_V 128_L 1.14 0.15 0.00
34_I 143_G 1.12 0.14 0.00
168_I 209_K 1.12 0.14 0.00
17_T 81_L 1.11 0.14 0.00
30_Y 92_A 1.11 0.14 0.00
41_W 112_T 1.10 0.14 0.00
30_Y 187_V 1.09 0.14 0.00
71_V 142_L 1.08 0.13 0.00
95_L 195_E 1.07 0.13 0.00
78_N 206_S 1.06 0.13 0.00
119_E 18_V 1.06 0.13 0.00
21_W 20_L 1.06 0.13 0.00
178_F 67_K 1.06 0.13 0.00
67_Y 22_C 1.06 0.13 0.00
71_V 156_V 1.05 0.13 0.00
67_Y 144_C 1.05 0.12 0.00
118_V 175_Q 1.05 0.12 0.00
78_N 131_G 1.04 0.12 0.00
4_A 84_S 1.04 0.12 0.00
181_Q 20_L 1.03 0.12 0.00
118_V 162_S 1.03 0.12 0.00
71_V 191_T 1.02 0.12 0.00
59_I 80_Y 1.02 0.12 0.00
21_W 158_W 1.01 0.12 0.00
30_Y 36_W 1.01 0.12 0.00
20_E 137_N 1.01 0.11 0.00
116_V 70_I 0.99 0.11 0.00
175_N 48_I 0.98 0.11 0.00
110_V 121_T 0.97 0.11 0.00
97_T 153_P 0.96 0.10 0.00
70_R 81_L 0.95 0.10 0.00
9_T 153_P 0.95 0.10 0.00
56_T 107_W 0.95 0.10 0.00
73_S 113_L 0.94 0.10 0.00
70_R 156_V 0.94 0.10 0.00
145_T 194_S 0.94 0.10 0.00
195_D 22_C 0.94 0.10 0.00
104_I 119_K 0.93 0.10 0.00
98_N 36_W 0.93 0.10 0.00
176_Y 158_W 0.93 0.10 0.00
153_S 103_Y 0.93 0.10 0.00
95_L 150_F 0.92 0.10 0.00
176_Y 36_W 0.92 0.10 0.00
104_I 125_V 0.92 0.10 0.00
8_L 18_V 0.92 0.10 0.00
104_I 72_A 0.92 0.10 0.00
55_L 154_V 0.91 0.09 0.00
34_I 186_T 0.91 0.09 0.00
86_E 199_C 0.90 0.09 0.00
55_L 158_W 0.90 0.09 0.00
30_Y 158_W 0.89 0.09 0.00
86_E 90_D 0.89 0.09 0.00
34_I 83_L 0.89 0.09 0.00
102_P 90_D 0.89 0.09 0.00
146_L 11_L 0.89 0.09 0.00
122_R 207_S 0.89 0.09 0.00
148_Y 144_C 0.89 0.09 0.00
174_E 144_C 0.89 0.09 0.00
86_E 111_T 0.88 0.09 0.00
114_V 97_A 0.88 0.09 0.00
166_F 144_C 0.88 0.09 0.00
112_T 155_T 0.88 0.09 0.00
78_N 18_V 0.88 0.09 0.00
98_N 16_A 0.88 0.09 0.00
59_I 34_M 0.87 0.09 0.00
31_T 119_K 0.86 0.09 0.00
162_N 156_V 0.86 0.09 0.00
141_D 113_L 0.86 0.08 0.00
105_Q 212_K 0.86 0.08 0.00
21_W 94_Y 0.86 0.08 0.00
30_Y 130_P 0.85 0.08 0.00
71_V 36_W 0.85 0.08 0.00
121_E 83_L 0.85 0.08 0.00
14_N 156_V 0.85 0.08 0.00
86_E 149_Y 0.85 0.08 0.00
173_G 83_L 0.85 0.08 0.00
140_K 206_S 0.85 0.08 0.00
144_Y 36_W 0.85 0.08 0.00
178_F 94_Y 0.84 0.08 0.00
107_F 60_Y 0.84 0.08 0.00
55_L 116_S 0.83 0.08 0.00
32_V 21_S 0.83 0.08 0.00
69_A 120_T 0.83 0.08 0.00
168_I 146_V 0.83 0.08 0.00
98_N 185_V 0.83 0.08 0.00
166_F 64_F 0.83 0.08 0.00
8_L 172_A 0.82 0.08 0.00
8_L 180_T 0.82 0.08 0.00
183_V 198_T 0.82 0.08 0.00
76_A 142_L 0.82 0.08 0.00
110_V 107_W 0.82 0.08 0.00
21_W 15_G 0.82 0.08 0.00
20_E 210_V 0.82 0.08 0.00
86_E 142_L 0.82 0.08 0.00
64_K 12_V 0.82 0.08 0.00
8_L 123_P 0.82 0.08 0.00
30_Y 11_L 0.81 0.08 0.00
27_N 153_P 0.81 0.08 0.00
24_K 142_L 0.81 0.08 0.00
119_E 130_P 0.81 0.08 0.00
146_L 158_W 0.81 0.07 0.00
116_V 112_T 0.81 0.07 0.00
95_L 197_V 0.80 0.07 0.00
125_V 32_Y 0.80 0.07 0.00
67_Y 90_D 0.80 0.07 0.00
50_D 86_L 0.80 0.07 0.00
71_V 90_D 0.80 0.07 0.00
40_D 176_S 0.80 0.07 0.00
185_P 170_F 0.80 0.07 0.00
21_W 187_V 0.79 0.07 0.00
54_D 129_A 0.79 0.07 0.00
190_N 34_M 0.79 0.07 0.00
189_V 142_L 0.79 0.07 0.00
40_D 174_L 0.79 0.07 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)
ID Seq/Len Name Options I_Prob Status
7995 0 pred_1AHW_l_u_ApdbAfas_1AHW_r_u_HpdbHfastable_PRtxt Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
4721 0.17 1AHW_b4 Δgene:(1, 10) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done
4720 0.23 1AHW_b4 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done
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