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OPENSEQ.org
1AHW_b4
Genes: A B A+B
Length: 202 214 378
Sequences: 5997 2523 87
Seq/Len: 29.69 11.79 0.23
MirrorTree (Pazo et al. 2001) 0.35
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
21_W 123_P 1.59 0.40 0.00
21_W 36_W 1.50 0.35 0.00
30_Y 19_K 1.38 0.28 0.00
41_W 112_T 1.35 0.27 0.00
110_V 83_L 1.22 0.21 0.00
118_V 154_V 1.22 0.21 0.00
4_A 84_S 1.22 0.21 0.00
148_Y 144_C 1.19 0.20 0.00
144_Y 158_W 1.18 0.19 0.00
55_L 136_T 1.17 0.19 0.00
86_E 67_K 1.17 0.19 0.00
17_T 129_A 1.16 0.19 0.00
83_P 129_A 1.15 0.18 0.00
172_K 166_G 1.15 0.18 0.00
148_Y 187_V 1.14 0.18 0.00
8_L 18_V 1.14 0.18 0.00
181_Q 20_L 1.13 0.18 0.00
114_V 97_A 1.12 0.17 0.00
73_S 142_L 1.08 0.16 0.00
73_S 111_T 1.08 0.16 0.00
30_Y 131_G 1.08 0.16 0.00
21_W 199_C 1.07 0.15 0.00
27_N 83_L 1.07 0.15 0.00
98_N 158_W 1.06 0.15 0.00
21_W 20_L 1.02 0.14 0.00
34_I 83_L 1.02 0.14 0.00
179_S 80_Y 1.02 0.14 0.00
118_V 153_P 1.02 0.14 0.00
30_Y 92_A 1.02 0.14 0.00
118_V 148_G 1.01 0.14 0.00
34_I 186_T 1.00 0.14 0.00
63_V 108_G 1.00 0.13 0.00
71_V 68_A 1.00 0.13 0.00
30_Y 146_V 0.99 0.13 0.00
178_F 94_Y 0.99 0.13 0.00
67_Y 36_W 0.97 0.13 0.00
168_I 208_T 0.97 0.13 0.00
49_T 86_L 0.97 0.13 0.00
30_Y 156_V 0.97 0.13 0.00
69_A 41_P 0.96 0.12 0.00
104_I 134_A 0.96 0.12 0.00
14_N 184_S 0.96 0.12 0.00
71_V 36_W 0.95 0.12 0.00
114_V 172_A 0.95 0.12 0.00
71_V 142_L 0.95 0.12 0.00
47_Y 131_G 0.94 0.12 0.00
144_Y 90_D 0.94 0.12 0.00
67_Y 83_L 0.94 0.12 0.00
21_W 158_W 0.93 0.12 0.00
168_I 209_K 0.93 0.12 0.00
67_Y 144_C 0.93 0.11 0.00
67_Y 158_W 0.93 0.11 0.00
173_G 194_S 0.93 0.11 0.00
87_N 85_S 0.92 0.11 0.00
150_K 161_G 0.92 0.11 0.00
152_S 169_T 0.91 0.11 0.00
67_Y 15_G 0.89 0.11 0.00
8_L 197_V 0.89 0.10 0.00
100_G 140_V 0.89 0.10 0.00
56_T 142_L 0.89 0.10 0.00
176_Y 36_W 0.89 0.10 0.00
169_D 124_S 0.88 0.10 0.00
141_D 113_L 0.88 0.10 0.00
98_N 36_W 0.88 0.10 0.00
102_P 90_D 0.88 0.10 0.00
30_Y 199_C 0.87 0.10 0.00
71_V 119_K 0.87 0.10 0.00
146_L 109_Q 0.87 0.10 0.00
74_Y 111_T 0.86 0.10 0.00
56_T 100_N 0.86 0.10 0.00
118_V 152_E 0.86 0.10 0.00
30_Y 130_P 0.86 0.10 0.00
110_V 121_T 0.86 0.10 0.00
20_E 137_N 0.85 0.10 0.00
118_V 123_P 0.85 0.10 0.00
53_C 170_F 0.85 0.10 0.00
24_K 138_S 0.85 0.10 0.00
102_P 48_I 0.85 0.10 0.00
168_I 76_S 0.85 0.10 0.00
100_G 169_T 0.84 0.10 0.00
116_V 206_S 0.84 0.10 0.00
48_T 82_Q 0.84 0.09 0.00
110_V 156_V 0.84 0.09 0.00
68_L 19_K 0.84 0.09 0.00
148_Y 15_G 0.84 0.09 0.00
18_I 50_L 0.84 0.09 0.00
56_T 161_G 0.84 0.09 0.00
176_Y 158_W 0.83 0.09 0.00
64_K 12_V 0.83 0.09 0.00
146_L 194_S 0.83 0.09 0.00
98_N 21_S 0.83 0.09 0.00
31_T 119_K 0.82 0.09 0.00
106_S 122_P 0.82 0.09 0.00
17_T 178_L 0.82 0.09 0.00
39_G 10_E 0.82 0.09 0.00
69_A 155_T 0.81 0.09 0.00
116_V 83_L 0.81 0.09 0.00
14_N 161_G 0.81 0.09 0.00
178_F 67_K 0.81 0.09 0.00
151_S 125_V 0.81 0.09 0.00
41_W 94_Y 0.81 0.09 0.00
145_T 35_H 0.81 0.09 0.00
9_T 153_P 0.81 0.09 0.00
179_S 184_S 0.81 0.09 0.00
121_E 83_L 0.80 0.09 0.00
182_A 83_L 0.80 0.09 0.00
116_V 128_L 0.80 0.09 0.00
47_Y 140_V 0.80 0.09 0.00
116_V 143_G 0.80 0.09 0.00
56_T 185_V 0.80 0.09 0.00
164_N 45_L 0.80 0.09 0.00
76_A 88_S 0.79 0.08 0.00
145_T 194_S 0.79 0.08 0.00
30_Y 76_S 0.79 0.08 0.00
83_P 77_N 0.79 0.08 0.00
8_L 123_P 0.79 0.08 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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