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OPENSEQ.org
f_c
Genes: A B A+B
Length: 406 226 614
Sequences: 245 132 78
Seq/Len: 0.6 0.58 0.13
MirrorTree (Pazo et al. 2001) 0.61
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 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.01 0.00 0.12
10 0.01 0.00 0.12
20 0.01 0.00 0.12
100 0.01 0.00 0.12
∞ 0.03 0.00 0.12
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
297_D 122_V 1.48 0.23 0.00
310_K 107_L 1.42 0.21 0.00
297_D 208_T 1.37 0.19 0.00
321_V 144_V 1.32 0.18 0.00
365_G 134_L 1.29 0.17 0.00
194_E 122_V 1.27 0.16 0.00
391_D 133_N 1.26 0.16 0.00
170_V 26_S 1.24 0.15 0.00
186_G 196_A 1.23 0.15 0.00
203_I 43_N 1.22 0.15 0.00
170_V 175_V 1.19 0.14 0.00
353_G 26_S 1.19 0.14 0.00
5_D 109_N 1.17 0.14 0.00
352_G 26_S 1.16 0.13 0.00
118_R 151_E 1.15 0.13 0.00
357_I 134_L 1.13 0.13 0.00
353_G 120_V 1.13 0.12 0.00
42_A 124_A 1.08 0.11 0.00
186_G 197_A 1.08 0.11 0.00
160_L 20_V 1.07 0.11 0.00
243_L 123_A 1.07 0.11 0.00
239_F 50_K 1.06 0.11 0.00
267_I 200_G 1.06 0.11 0.00
401_K 74_S 1.06 0.11 0.00
116_Y 56_N 1.05 0.11 0.00
67_S 43_N 1.05 0.11 0.00
330_R 207_L 1.04 0.11 0.00
117_A 31_F 1.04 0.11 0.00
168_V 110_S 1.03 0.10 0.00
362_A 52_N 1.03 0.10 0.00
187_G 114_S 1.03 0.10 0.00
401_K 129_Q 1.02 0.10 0.00
9_L 115_S 1.02 0.10 0.00
323_V 154_S 1.01 0.10 0.00
313_L 7_K 0.99 0.10 0.00
83_K 110_S 0.99 0.10 0.00
147_A 182_N 0.99 0.10 0.00
349_P 43_N 0.98 0.10 0.00
397_T 107_L 0.98 0.09 0.00
168_V 118_V 0.98 0.09 0.00
40_Q 141_G 0.97 0.09 0.00
400_L 62_G 0.96 0.09 0.00
386_A 73_S 0.96 0.09 0.00
80_Q 55_A 0.96 0.09 0.00
348_K 72_T 0.95 0.09 0.00
185_S 106_L 0.95 0.09 0.00
9_L 94_N 0.95 0.09 0.00
245_R 43_N 0.95 0.09 0.00
399_S 136_I 0.95 0.09 0.00
218_S 135_A 0.95 0.09 0.00
121_A 100_G 0.95 0.09 0.00
389_M 126_Q 0.95 0.09 0.00
73_T 20_V 0.95 0.09 0.00
313_L 149_N 0.95 0.09 0.00
359_S 192_G 0.94 0.09 0.00
363_N 18_A 0.94 0.09 0.00
308_G 113_N 0.94 0.09 0.00
116_Y 51_G 0.94 0.09 0.00
304_N 153_V 0.94 0.09 0.00
185_S 87_I 0.94 0.09 0.00
289_T 22_D 0.94 0.09 0.00
158_Y 194_N 0.93 0.09 0.00
350_D 43_N 0.93 0.09 0.00
177_S 80_T 0.93 0.09 0.00
361_D 161_N 0.92 0.08 0.00
302_D 148_S 0.92 0.08 0.00
308_G 160_L 0.92 0.08 0.00
330_R 203_Q 0.91 0.08 0.00
237_E 186_N 0.91 0.08 0.00
37_V 107_L 0.90 0.08 0.00
6_I 77_D 0.90 0.08 0.00
362_A 117_N 0.90 0.08 0.00
358_V 41_G 0.90 0.08 0.00
8_T 138_T 0.90 0.08 0.00
67_S 41_G 0.90 0.08 0.00
386_A 155_L 0.90 0.08 0.00
389_M 182_N 0.90 0.08 0.00
316_S 107_L 0.89 0.08 0.00
84_D 112_N 0.89 0.08 0.00
335_F 141_G 0.89 0.08 0.00
187_G 122_V 0.89 0.08 0.00
144_R 133_N 0.89 0.08 0.00
399_S 176_N 0.89 0.08 0.00
308_G 42_A 0.88 0.08 0.00
307_V 109_N 0.88 0.08 0.00
5_D 71_I 0.88 0.08 0.00
374_A 58_A 0.88 0.08 0.00
285_S 80_T 0.88 0.08 0.00
227_S 175_V 0.88 0.08 0.00
207_N 80_T 0.88 0.08 0.00
54_A 49_S 0.87 0.08 0.00
116_Y 67_N 0.87 0.08 0.00
376_S 62_G 0.87 0.08 0.00
290_H 134_L 0.87 0.08 0.00
179_Y 202_Q 0.87 0.08 0.00
122_R 111_A 0.87 0.08 0.00
391_D 126_Q 0.87 0.07 0.00
73_T 134_L 0.87 0.07 0.00
66_S 28_D 0.87 0.07 0.00
313_L 153_V 0.87 0.07 0.00
376_S 28_D 0.87 0.07 0.00
154_L 98_N 0.86 0.07 0.00
329_E 195_V 0.86 0.07 0.00
109_S 137_V 0.86 0.07 0.00
8_T 156_D 0.86 0.07 0.00
385_L 18_A 0.86 0.07 0.00
303_V 57_I 0.86 0.07 0.00
158_Y 189_G 0.86 0.07 0.00
107_K 156_D 0.86 0.07 0.00
304_N 20_V 0.86 0.07 0.00
372_T 58_A 0.86 0.07 0.00
395_D 98_N 0.85 0.07 0.00
330_R 100_G 0.85 0.07 0.00
362_A 154_S 0.85 0.07 0.00
345_S 85_A 0.85 0.07 0.00
313_L 192_G 0.85 0.07 0.00
97_N 157_N 0.85 0.07 0.00
328_N 89_Q 0.85 0.07 0.00
311_V 124_A 0.85 0.07 0.00
91_S 56_N 0.85 0.07 0.00
187_G 57_I 0.85 0.07 0.00
118_R 113_N 0.85 0.07 0.00
102_F 129_Q 0.84 0.07 0.00
182_G 47_S 0.84 0.07 0.00
369_V 55_A 0.84 0.07 0.00
187_G 90_E 0.84 0.07 0.00
6_I 138_T 0.84 0.07 0.00
330_R 193_V 0.84 0.07 0.00
243_L 163_A 0.84 0.07 0.00
83_K 109_N 0.84 0.07 0.00
282_L 141_G 0.84 0.07 0.00
186_G 44_G 0.84 0.07 0.00
70_G 19_A 0.84 0.07 0.00
70_G 7_K 0.84 0.07 0.00
218_S 197_A 0.84 0.07 0.00
143_D 94_N 0.84 0.07 0.00
389_M 11_A 0.84 0.07 0.00
391_D 102_Q 0.83 0.07 0.00
311_V 200_G 0.83 0.07 0.00
198_S 25_V 0.83 0.07 0.00
160_L 188_S 0.83 0.07 0.00
221_M 138_T 0.83 0.07 0.00
141_N 133_N 0.83 0.07 0.00
305_Q 96_F 0.83 0.07 0.00
53_P 175_V 0.83 0.07 0.00
357_I 79_A 0.83 0.07 0.00
172_V 50_K 0.83 0.07 0.00
327_L 146_A 0.83 0.07 0.00
250_D 81_V 0.83 0.07 0.00
117_A 75_A 0.82 0.07 0.00
81_S 100_G 0.82 0.07 0.00
164_W 71_I 0.82 0.07 0.00
220_T 148_S 0.82 0.07 0.00
231_K 139_A 0.82 0.07 0.00
53_P 66_D 0.82 0.07 0.00
80_Q 182_N 0.82 0.07 0.00
206_V 106_L 0.82 0.07 0.00
256_E 148_S 0.82 0.07 0.00
365_G 42_A 0.82 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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