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OPENSEQ.org
HscBIscX
Genes: A B A+B
Length: 171 66 235
Sequences: 2875 324 277
Seq/Len: 16.81 4.91 1.18
MirrorTree (Pazo et al. 2001) 0.60
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 0.01 0.00 0.01
2 0.01 0.00 0.06
5 0.01 0.00 1.17
10 0.01 0.00 1.19
20 0.02 0.00 1.20
100 0.02 0.00 1.22
∞ 0.05 0.00 1.35
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
28_Q 31_D 1.45 0.78 0.03
28_Q 40_E 1.40 0.74 0.02
49_Q 40_E 1.26 0.63 0.02
39_G 32_M 1.25 0.62 0.01
57_A 56_A 1.24 0.61 0.01
152_R 28_R 1.20 0.57 0.01
101_E 52_K 1.19 0.56 0.01
72_L 13_E 1.17 0.54 0.01
110_D 53_I 1.16 0.53 0.01
156_K 26_T 1.15 0.52 0.01
93_M 11_I 1.14 0.51 0.01
108_A 2_G 1.13 0.51 0.01
47_A 4_K 1.13 0.50 0.01
127_T 66_E 1.12 0.49 0.01
160_S 32_M 1.12 0.49 0.01
47_A 36_I 1.11 0.48 0.01
86_V 57_I 1.10 0.47 0.01
106_E 49_S 1.08 0.46 0.01
167_K 48_A 1.07 0.45 0.01
47_A 17_D 1.05 0.43 0.01
120_R 30_T 1.05 0.43 0.01
145_A 63_D 1.05 0.42 0.01
104_E 66_E 1.03 0.41 0.01
120_R 8_S 1.03 0.41 0.01
115_E 14_A 1.03 0.41 0.01
21_S 2_G 1.03 0.41 0.01
82_E 17_D 1.03 0.41 0.01
2_D 40_E 1.01 0.39 0.01
153_F 24_P 1.01 0.39 0.01
106_E 50_N 0.99 0.37 0.01
8_G 13_E 0.99 0.37 0.01
3_Y 33_H 0.99 0.37 0.01
5_T 62_L 0.99 0.37 0.01
56_Q 6_T 0.99 0.37 0.01
113_R 40_E 0.98 0.36 0.01
35_K 18_A 0.97 0.35 0.01
91_F 24_P 0.97 0.35 0.01
29_R 53_I 0.96 0.34 0.01
71_L 48_A 0.95 0.34 0.01
56_Q 36_I 0.95 0.33 0.01
6_L 24_P 0.95 0.33 0.01
21_S 3_L 0.94 0.33 0.01
128_R 14_A 0.94 0.33 0.01
13_Y 62_L 0.94 0.33 0.01
25_Q 12_G 0.93 0.32 0.01
56_Q 8_S 0.93 0.32 0.01
46_A 33_H 0.92 0.31 0.01
69_E 30_T 0.92 0.31 0.01
151_L 31_D 0.92 0.31 0.01
47_A 45_D 0.92 0.30 0.01
51_S 62_L 0.91 0.30 0.01
135_Q 27_V 0.90 0.29 0.01
24_F 37_C 0.90 0.29 0.01
56_Q 58_L 0.90 0.29 0.01
164_L 1_M 0.89 0.28 0.01
109_K 28_R 0.89 0.28 0.01
88_D 46_P 0.88 0.28 0.01
113_R 36_I 0.87 0.27 0.01
105_I 3_L 0.87 0.27 0.01
8_G 10_E 0.87 0.27 0.01
13_Y 50_N 0.87 0.27 0.01
137_D 41_D 0.87 0.27 0.01
73_S 8_S 0.87 0.27 0.01
69_E 8_S 0.86 0.26 0.01
13_Y 12_G 0.85 0.26 0.01
106_E 33_H 0.85 0.26 0.01
54_I 62_L 0.85 0.26 0.01
82_E 40_E 0.85 0.25 0.00
147_T 59_L 0.84 0.25 0.00
66_M 21_D 0.84 0.24 0.00
28_Q 35_W 0.84 0.24 0.00
56_Q 50_N 0.84 0.24 0.00
39_G 38_D 0.82 0.23 0.00
126_D 34_Q 0.82 0.23 0.00
85_T 52_K 0.82 0.23 0.00
145_A 28_R 0.81 0.23 0.00
14_Q 40_E 0.81 0.22 0.00
131_L 34_Q 0.80 0.22 0.00
53_T 13_E 0.80 0.22 0.00
96_L 58_L 0.80 0.22 0.00
166_E 19_Y 0.80 0.22 0.00
113_R 28_R 0.80 0.22 0.00
72_L 10_E 0.80 0.22 0.00
40_S 11_I 0.80 0.22 0.00
43_E 13_E 0.79 0.21 0.00
71_L 32_M 0.79 0.21 0.00
154_L 48_A 0.79 0.21 0.00
127_T 45_D 0.79 0.21 0.00
104_E 41_D 0.79 0.21 0.00
112_A 25_K 0.78 0.21 0.00
164_L 52_K 0.78 0.21 0.00
138_N 53_I 0.78 0.21 0.00
86_V 27_V 0.78 0.21 0.00
5_T 17_D 0.78 0.20 0.00
158_R 36_I 0.77 0.20 0.00
41_Q 30_T 0.77 0.20 0.00
166_E 58_L 0.77 0.20 0.00
137_D 63_D 0.77 0.20 0.00
21_S 1_M 0.76 0.19 0.00
65_L 53_I 0.75 0.19 0.00
102_L 21_D 0.75 0.19 0.00
58_W 52_K 0.75 0.19 0.00
47_A 29_F 0.75 0.19 0.00
141_W 9_R 0.75 0.19 0.00
151_L 59_L 0.75 0.18 0.00
90_A 49_S 0.74 0.18 0.00
116_S 38_D 0.74 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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