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OPENSEQ.org
Gazunga3 (A, 1-315) (B, 5-82)
Genes: A B A+B
Length: 315 78 391
Sequences: 1313 999 450
Seq/Len: 4.17 12.81 1.15
MirrorTree (Pazo et al. 2001) 0.67
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 0.01
5 0.00 0.00 0.01
10 0.00 0.00 0.01
20 0.00 0.00 0.02
100 0.01 0.00 0.15
∞ 0.03 0.01 1.15
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
311_I 54_L 1.74 0.91 0.40
292_M 40_N 1.28 0.64 0.13
177_T 28_V 1.27 0.62 0.12
187_D 61_H 1.20 0.56 0.10
292_M 55_T 1.19 0.55 0.09
315_F 49_N 1.18 0.55 0.09
76_E 9_I 1.16 0.53 0.09
311_I 18_G 1.14 0.50 0.08
29_R 24_H 1.06 0.43 0.06
306_I 71_E 1.01 0.38 0.05
310_V 9_I 1.01 0.38 0.05
29_R 28_V 1.00 0.38 0.05
153_A 16_I 0.99 0.36 0.04
299_N 12_Q 0.97 0.35 0.04
245_I 11_G 0.97 0.35 0.04
29_R 18_G 0.95 0.33 0.04
278_A 54_L 0.95 0.33 0.04
188_N 60_V 0.93 0.31 0.04
2_L 18_G 0.92 0.31 0.04
254_I 21_S 0.92 0.30 0.03
93_L 34_D 0.91 0.30 0.03
160_T 28_V 0.91 0.29 0.03
29_R 61_H 0.90 0.29 0.03
315_F 36_M 0.90 0.29 0.03
308_V 61_H 0.90 0.28 0.03
167_D 25_M 0.90 0.28 0.03
207_I 57_V 0.89 0.28 0.03
286_S 5_T 0.89 0.28 0.03
173_V 61_H 0.88 0.27 0.03
309_T 48_I 0.87 0.27 0.03
236_R 51_L 0.87 0.27 0.03
148_A 15_T 0.87 0.26 0.03
35_V 19_E 0.86 0.26 0.03
299_N 54_L 0.86 0.26 0.03
292_M 60_V 0.85 0.25 0.03
99_V 73_L 0.85 0.25 0.03
119_Q 13_H 0.85 0.25 0.03
254_I 28_V 0.85 0.25 0.03
289_D 33_D 0.85 0.25 0.03
13_S 61_H 0.83 0.24 0.02
209_L 45_Y 0.83 0.24 0.02
182_A 16_I 0.83 0.24 0.02
36_Q 50_K 0.83 0.24 0.02
129_V 54_L 0.83 0.23 0.02
217_I 52_A 0.83 0.23 0.02
160_T 49_N 0.83 0.23 0.02
289_D 72_K 0.82 0.23 0.02
165_P 61_H 0.82 0.23 0.02
254_I 18_G 0.81 0.22 0.02
124_L 40_N 0.81 0.22 0.02
311_I 47_D 0.81 0.22 0.02
31_I 8_D 0.81 0.22 0.02
258_Q 4_K 0.80 0.22 0.02
266_G 10_Y 0.80 0.21 0.02
243_K 14_F 0.80 0.21 0.02
155_K 50_K 0.79 0.21 0.02
101_V 26_R 0.79 0.21 0.02
158_V 11_G 0.79 0.21 0.02
91_E 47_D 0.79 0.21 0.02
311_I 15_T 0.79 0.21 0.02
95_G 62_D 0.78 0.20 0.02
27_V 51_L 0.78 0.20 0.02
192_Q 54_L 0.78 0.20 0.02
292_M 36_M 0.78 0.20 0.02
289_D 37_R 0.78 0.20 0.02
60_Q 14_F 0.78 0.20 0.02
193_G 49_N 0.78 0.20 0.02
229_G 16_I 0.78 0.20 0.02
300_E 31_I 0.77 0.20 0.02
266_G 28_V 0.77 0.20 0.02
185_E 23_A 0.77 0.20 0.02
101_V 16_I 0.77 0.19 0.02
282_V 70_C 0.76 0.19 0.02
54_K 26_R 0.76 0.19 0.02
264_I 12_Q 0.76 0.19 0.02
196_G 52_A 0.76 0.19 0.02
102_T 14_F 0.76 0.19 0.02
287_D 25_M 0.76 0.19 0.02
94_K 21_S 0.76 0.19 0.02
56_E 16_I 0.75 0.19 0.02
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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