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OPENSEQ.org
1WQ1
Genes: A B A+B
Length: 334 166 483
Sequences: 848 11837 106
Seq/Len: 2.54 71.31 0.22
MirrorTree (Pazo et al. 2001) 0.22
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 0.03 0.05 0.02
2 0.03 0.06 0.03
5 0.03 0.08 0.06
10 0.03 0.10 0.11
20 0.03 0.13 0.21
100 0.04 0.23 0.63
∞ 0.07 0.28 0.98
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
247_I 48_G 1.97 0.62 0.01
121_K 147_K 1.25 0.22 0.00
220_V 118_C 1.19 0.19 0.00
154_P 119_D 1.14 0.18 0.00
183_V 123_R 1.11 0.16 0.00
220_V 131_Q 1.10 0.16 0.00
195_A 5_K 1.07 0.15 0.00
165_Q 23_L 1.06 0.15 0.00
174_T 113_L 1.02 0.14 0.00
104_S 128_R 1.02 0.14 0.00
8_E 155_A 1.01 0.13 0.00
183_V 83_A 1.01 0.13 0.00
246_F 19_L 1.00 0.13 0.00
187_V 142_I 1.00 0.13 0.00
83_T 109_V 0.99 0.13 0.00
257_F 13_G 0.99 0.13 0.00
248_K 44_V 0.96 0.12 0.00
64_E 119_D 0.95 0.12 0.00
46_I 23_L 0.95 0.12 0.00
247_I 150_Q 0.94 0.12 0.00
72_T 112_V 0.94 0.11 0.00
177_T 151_G 0.94 0.11 0.00
46_I 91_E 0.92 0.11 0.00
247_I 152_V 0.92 0.11 0.00
196_I 61_Q 0.90 0.11 0.00
133_T 148_T 0.89 0.10 0.00
47_F 126_E 0.89 0.10 0.00
205_I 20_T 0.89 0.10 0.00
257_F 105_D 0.89 0.10 0.00
154_P 15_G 0.88 0.10 0.00
154_P 16_K 0.88 0.10 0.00
117_L 84_I 0.87 0.10 0.00
128_V 93_I 0.87 0.10 0.00
160_I 55_I 0.87 0.10 0.00
143_V 138_G 0.87 0.10 0.00
185_G 148_T 0.86 0.10 0.00
49_H 97_R 0.86 0.10 0.00
142_L 109_V 0.86 0.10 0.00
177_T 82_F 0.86 0.10 0.00
96_F 46_I 0.85 0.10 0.00
154_P 117_K 0.85 0.10 0.00
233_F 115_G 0.85 0.09 0.00
64_E 115_G 0.85 0.09 0.00
184_S 134_A 0.85 0.09 0.00
164_L 53_L 0.85 0.09 0.00
16_L 44_V 0.85 0.09 0.00
170_H 113_L 0.84 0.09 0.00
204_I 99_Q 0.84 0.09 0.00
119_P 142_I 0.84 0.09 0.00
105_I 138_G 0.84 0.09 0.00
171_K 153_E 0.84 0.09 0.00
220_V 78_F 0.84 0.09 0.00
217_L 5_K 0.83 0.09 0.00
108_I 158_T 0.83 0.09 0.00
244_N 157_Y 0.82 0.09 0.00
64_E 15_G 0.82 0.09 0.00
64_E 16_K 0.82 0.09 0.00
261_L 77_G 0.82 0.09 0.00
139_L 17_S 0.82 0.09 0.00
310_L 93_I 0.81 0.09 0.00
103_D 138_G 0.81 0.09 0.00
154_P 57_D 0.81 0.09 0.00
103_D 112_V 0.81 0.09 0.00
292_H 138_G 0.81 0.09 0.00
217_L 28_F 0.81 0.09 0.00
144_E 129_Q 0.81 0.09 0.00
40_A 116_N 0.80 0.08 0.00
199_P 15_G 0.80 0.08 0.00
199_P 16_K 0.80 0.08 0.00
252_H 5_K 0.80 0.08 0.00
296_L 136_S 0.80 0.08 0.00
140_S 133_L 0.80 0.08 0.00
190_R 119_D 0.80 0.08 0.00
83_T 72_M 0.80 0.08 0.00
145_K 8_V 0.80 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)
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