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OPENSEQ.org
62
Genes: A B A+B
Length: 290 178 446
Sequences: 61736 2617 61
Seq/Len: 212.88 14.7 0.14
MirrorTree (Pazo et al. 2001) 0.11
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 0.10 0.02 0.01
2 0.13 0.02 0.02
5 0.16 0.03 0.05
10 0.20 0.03 0.08
20 0.24 0.03 0.13
100 0.31 0.07 0.42
∞ 0.34 0.11 0.85
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
141_A 144_Q 1.45 0.23 0.00
262_D 111_Y 1.25 0.17 0.00
43_E 117_H 1.10 0.12 0.00
43_E 121_G 1.10 0.12 0.00
137_D 117_H 1.10 0.12 0.00
137_D 121_G 1.10 0.12 0.00
163_P 117_H 1.10 0.12 0.00
163_P 121_G 1.10 0.12 0.00
177_D 117_H 1.10 0.12 0.00
177_D 121_G 1.10 0.12 0.00
182_G 123_G 1.08 0.12 0.00
162_A 53_I 1.08 0.12 0.00
53_P 134_L 1.08 0.12 0.00
32_L 84_H 1.08 0.12 0.00
263_P 102_E 1.07 0.12 0.00
127_I 52_D 1.06 0.11 0.00
47_L 134_L 1.05 0.11 0.00
111_H 114_T 1.04 0.11 0.00
103_L 166_Y 1.03 0.11 0.00
118_R 124_R 1.02 0.11 0.00
115_V 82_H 1.02 0.11 0.00
11_G 49_G 1.02 0.10 0.00
172_Y 135_Y 0.99 0.10 0.00
195_F 153_R 0.99 0.10 0.00
69_Y 114_T 0.99 0.10 0.00
117_H 117_H 0.99 0.10 0.00
117_H 121_G 0.99 0.10 0.00
124_N 117_H 0.98 0.10 0.00
124_N 121_G 0.98 0.10 0.00
173_S 120_G 0.97 0.10 0.00
127_I 106_T 0.97 0.10 0.00
191_R 132_L 0.96 0.09 0.00
139_G 117_H 0.96 0.09 0.00
139_G 121_G 0.96 0.09 0.00
4_F 145_A 0.95 0.09 0.00
33_K 117_H 0.94 0.09 0.00
33_K 121_G 0.94 0.09 0.00
164_E 117_H 0.94 0.09 0.00
164_E 121_G 0.94 0.09 0.00
10_I 54_F 0.93 0.09 0.00
193_A 126_C 0.93 0.09 0.00
166_L 167_L 0.93 0.09 0.00
91_I 97_C 0.92 0.09 0.00
43_E 88_D 0.92 0.09 0.00
137_D 88_D 0.92 0.09 0.00
163_P 88_D 0.92 0.09 0.00
177_D 88_D 0.92 0.09 0.00
56_V 28_G 0.92 0.09 0.00
91_I 54_F 0.92 0.09 0.00
254_L 145_A 0.91 0.09 0.00
70_L 45_L 0.90 0.08 0.00
199_S 10_L 0.90 0.08 0.00
70_L 53_I 0.90 0.08 0.00
30_V 131_C 0.90 0.08 0.00
58_L 145_A 0.89 0.08 0.00
35_I 116_I 0.89 0.08 0.00
53_P 167_L 0.89 0.08 0.00
182_G 163_Q 0.88 0.08 0.00
136_A 146_I 0.88 0.08 0.00
255_L 48_C 0.87 0.08 0.00
165_I 57_C 0.86 0.08 0.00
21_A 86_I 0.86 0.08 0.00
136_A 167_L 0.86 0.08 0.00
141_A 45_L 0.85 0.08 0.00
43_E 118_S 0.85 0.07 0.00
137_D 118_S 0.85 0.07 0.00
163_P 118_S 0.85 0.07 0.00
177_D 118_S 0.85 0.07 0.00
82_F 84_H 0.85 0.07 0.00
121_K 124_R 0.85 0.07 0.00
61_V 52_D 0.84 0.07 0.00
128_N 143_E 0.84 0.07 0.00
119_D 117_H 0.84 0.07 0.00
119_D 121_G 0.84 0.07 0.00
273_L 46_K 0.84 0.07 0.00
23_N 98_C 0.83 0.07 0.00
157_T 52_D 0.83 0.07 0.00
69_Y 58_T 0.83 0.07 0.00
182_G 117_H 0.82 0.07 0.00
182_G 121_G 0.82 0.07 0.00
138_F 8_S 0.82 0.07 0.00
143_A 141_S 0.82 0.07 0.00
266_R 117_H 0.82 0.07 0.00
266_R 121_G 0.82 0.07 0.00
193_A 149_L 0.81 0.07 0.00
195_F 174_L 0.81 0.07 0.00
34_K 85_P 0.81 0.07 0.00
123_Q 142_P 0.81 0.07 0.00
262_D 25_A 0.81 0.07 0.00
43_E 124_R 0.80 0.07 0.00
137_D 124_R 0.80 0.07 0.00
163_P 124_R 0.80 0.07 0.00
177_D 124_R 0.80 0.07 0.00
31_A 88_D 0.80 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)
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