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OPENSEQ.org
gazunzunga1
Genes: A B A+B
Length: 382 226 525
Sequences: 1313 720 396
Seq/Len: 3.44 3.19 0.75
MirrorTree (Pazo et al. 2001) 0.56
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 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.00
10 0.00 0.00 0.00
20 0.00 0.00 0.01
100 0.01 0.00 0.06
∞ 0.03 0.00 0.65
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
308_V 107_S 1.57 0.74 0.01
22_G 18_L 1.43 0.63 0.01
39_E 189_K 1.41 0.61 0.01
39_E 136_V 1.37 0.59 0.01
151_I 159_N 1.29 0.52 0.01
119_Q 20_L 1.23 0.46 0.00
142_K 124_L 1.23 0.46 0.00
4_F 118_L 1.19 0.43 0.00
122_K 56_V 1.19 0.43 0.00
270_L 20_L 1.17 0.42 0.00
73_A 167_S 1.16 0.41 0.00
302_L 79_K 1.16 0.40 0.00
59_M 136_V 1.15 0.40 0.00
251_E 170_L 1.14 0.39 0.00
245_I 127_I 1.14 0.39 0.00
120_I 127_I 1.14 0.39 0.00
289_D 27_S 1.14 0.39 0.00
10_G 71_L 1.12 0.37 0.00
77_V 167_S 1.10 0.36 0.00
181_E 35_L 1.10 0.35 0.00
126_A 59_G 1.10 0.35 0.00
289_D 206_I 1.08 0.34 0.00
251_E 168_E 1.08 0.34 0.00
92_A 171_P 1.08 0.34 0.00
198_S 119_Q 1.07 0.33 0.00
309_T 177_N 1.07 0.33 0.00
209_L 159_N 1.07 0.33 0.00
254_I 184_P 1.05 0.32 0.00
234_E 126_L 1.05 0.32 0.00
277_E 162_A 1.05 0.32 0.00
34_E 110_K 1.04 0.31 0.00
92_A 13_G 1.04 0.31 0.00
58_K 13_G 1.04 0.31 0.00
134_R 134_G 1.03 0.30 0.00
35_V 50_Q 1.03 0.30 0.00
148_A 47_G 1.03 0.30 0.00
123_D 35_L 1.03 0.30 0.00
94_K 56_V 1.02 0.30 0.00
24_N 164_I 1.02 0.29 0.00
43_V 184_P 1.02 0.29 0.00
168_R 175_R 1.01 0.29 0.00
167_D 31_L 1.01 0.29 0.00
315_F 153_H 1.01 0.29 0.00
39_E 85_S 1.00 0.28 0.00
264_I 209_L 1.00 0.28 0.00
202_A 112_V 1.00 0.28 0.00
234_E 146_G 0.99 0.28 0.00
123_D 40_S 0.98 0.27 0.00
13_S 12_K 0.98 0.27 0.00
220_N 204_M 0.98 0.27 0.00
179_M 211_H 0.98 0.27 0.00
33_N 34_G 0.98 0.27 0.00
315_F 181_N 0.97 0.26 0.00
258_Q 124_L 0.97 0.26 0.00
101_V 208_R 0.97 0.26 0.00
116_V 179_V 0.97 0.26 0.00
282_V 7_Q 0.96 0.25 0.00
102_T 87_D 0.96 0.25 0.00
152_S 73_E 0.96 0.25 0.00
311_I 16_N 0.95 0.25 0.00
55_A 38_M 0.94 0.24 0.00
171_E 34_G 0.94 0.24 0.00
258_Q 149_K 0.94 0.24 0.00
177_T 18_L 0.94 0.24 0.00
209_L 139_G 0.94 0.24 0.00
122_K 49_G 0.94 0.24 0.00
272_L 76_A 0.93 0.24 0.00
73_A 209_L 0.93 0.24 0.00
76_E 69_E 0.93 0.24 0.00
124_L 156_F 0.93 0.23 0.00
53_S 144_V 0.93 0.23 0.00
302_L 122_G 0.93 0.23 0.00
217_I 171_P 0.93 0.23 0.00
39_E 35_L 0.93 0.23 0.00
221_K 145_L 0.92 0.23 0.00
294_F 129_D 0.92 0.23 0.00
41_I 187_I 0.92 0.23 0.00
120_I 157_N 0.92 0.23 0.00
192_Q 153_H 0.92 0.23 0.00
165_P 50_Q 0.92 0.23 0.00
31_I 179_V 0.92 0.23 0.00
187_D 43_Q 0.92 0.23 0.00
89_I 123_D 0.91 0.23 0.00
87_E 69_E 0.91 0.22 0.00
89_I 73_E 0.91 0.22 0.00
87_E 209_L 0.91 0.22 0.00
29_R 129_D 0.91 0.22 0.00
47_A 148_L 0.90 0.22 0.00
175_K 13_G 0.90 0.22 0.00
176_N 13_G 0.90 0.22 0.00
93_L 52_I 0.90 0.22 0.00
228_I 9_V 0.90 0.22 0.00
103_A 12_K 0.90 0.21 0.00
35_V 45_T 0.90 0.21 0.00
54_K 159_N 0.90 0.21 0.00
265_T 108_V 0.90 0.21 0.00
124_L 47_G 0.89 0.21 0.00
117_I 45_T 0.89 0.21 0.00
34_E 122_G 0.89 0.21 0.00
165_P 112_V 0.88 0.21 0.00
43_V 38_M 0.88 0.21 0.00
134_R 126_L 0.88 0.21 0.00
145_L 30_E 0.88 0.21 0.00
145_L 73_E 0.88 0.21 0.00
116_V 56_V 0.87 0.20 0.00
61_I 208_R 0.87 0.20 0.00
28_N 128_G 0.87 0.20 0.00
184_R 130_V 0.87 0.20 0.00
137_T 67_Q 0.87 0.20 0.00
124_L 56_V 0.87 0.20 0.00
122_K 147_S 0.86 0.20 0.00
94_K 127_I 0.86 0.20 0.00
167_D 144_V 0.86 0.20 0.00
261_L 209_L 0.86 0.20 0.00
223_S 153_H 0.86 0.19 0.00
188_N 27_S 0.85 0.19 0.00
61_I 184_P 0.85 0.19 0.00
182_A 18_L 0.85 0.19 0.00
180_L 112_V 0.85 0.19 0.00
116_V 89_E 0.84 0.19 0.00
97_D 38_M 0.84 0.19 0.00
43_V 123_D 0.84 0.19 0.00
225_L 173_Q 0.84 0.19 0.00
122_K 83_V 0.84 0.18 0.00
163_V 13_G 0.84 0.18 0.00
272_L 22_L 0.84 0.18 0.00
206_L 206_I 0.84 0.18 0.00
304_D 81_L 0.84 0.18 0.00
76_E 48_K 0.84 0.18 0.00
180_L 124_L 0.84 0.18 0.00
152_S 71_L 0.84 0.18 0.00
9_D 64_Y 0.84 0.18 0.00
267_G 112_V 0.84 0.18 0.00
24_N 171_P 0.84 0.18 0.00
262_M 151_I 0.84 0.18 0.00
163_V 148_L 0.83 0.18 0.00
254_I 194_E 0.83 0.18 0.00
35_V 59_G 0.83 0.18 0.00
153_A 108_V 0.83 0.18 0.00
94_K 68_E 0.83 0.18 0.00
261_L 116_Q 0.83 0.18 0.00
3_E 204_M 0.83 0.18 0.00
187_D 51_K 0.82 0.18 0.00
141_R 199_D 0.82 0.18 0.00
39_E 75_I 0.82 0.18 0.00
134_R 47_G 0.82 0.18 0.00
65_L 85_S 0.82 0.17 0.00
302_L 134_G 0.82 0.17 0.00
81_A 49_G 0.82 0.17 0.00
228_I 152_A 0.82 0.17 0.00
134_R 61_R 0.81 0.17 0.00
32_E 24_D 0.81 0.17 0.00
187_D 88_S 0.81 0.17 0.00
37_G 152_A 0.81 0.17 0.00
59_M 81_L 0.81 0.17 0.00
207_I 188_Q 0.81 0.17 0.00
277_E 57_K 0.81 0.17 0.00
200_L 13_G 0.81 0.17 0.00
59_M 35_L 0.81 0.17 0.00
47_A 107_S 0.81 0.17 0.00
174_D 20_L 0.81 0.17 0.00
309_T 78_K 0.81 0.17 0.00
289_D 99_I 0.80 0.17 0.00
111_T 130_V 0.80 0.17 0.00
96_A 37_N 0.80 0.17 0.00
91_E 29_D 0.80 0.17 0.00
53_S 138_A 0.80 0.16 0.00
296_S 120_V 0.80 0.16 0.00
262_M 120_V 0.80 0.16 0.00
245_I 146_G 0.80 0.16 0.00
33_N 11_I 0.80 0.16 0.00
123_D 152_A 0.80 0.16 0.00
178_P 61_R 0.80 0.16 0.00
251_E 183_S 0.80 0.16 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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