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OPENSEQ.org
1buh_ab
Genes: A B A+B
Length: 298 79 367
Sequences: 61003 299 94
Seq/Len: 204.71 3.78 0.26
MirrorTree (Pazo et al. 2001) 0.17
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 0.04 0.03
2 0.12 0.04 0.04
5 0.16 0.04 0.08
10 0.20 0.04 0.15
20 0.24 0.04 0.25
100 0.31 0.06 0.63
∞ 0.34 0.06 0.76
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
114_G 66_I 1.56 0.41 0.00
81_E 15_E 1.22 0.23 0.00
114_G 73_L 1.21 0.23 0.00
67_L 73_L 1.18 0.21 0.00
146_F 18_E 1.18 0.21 0.00
215_I 67_L 1.17 0.21 0.00
263_L 36_H 1.17 0.21 0.00
63_I 4_K 1.15 0.20 0.00
14_T 48_V 1.14 0.19 0.00
168_Y 15_E 1.12 0.19 0.00
51_E 18_E 1.12 0.19 0.00
4_F 66_I 1.12 0.18 0.00
203_F 34_K 1.09 0.17 0.00
198_T 48_V 1.07 0.17 0.00
130_P 15_E 1.07 0.17 0.00
90_F 38_M 1.07 0.17 0.00
16_G 45_N 1.05 0.16 0.00
169_R 46_L 1.04 0.16 0.00
267_L 70_R 1.02 0.15 0.00
11_G 73_L 1.01 0.15 0.00
158_T 28_I 1.01 0.15 0.00
55_L 22_V 0.99 0.14 0.00
146_F 71_R 0.99 0.14 0.00
12_E 15_E 0.98 0.14 0.00
170_A 42_E 0.98 0.14 0.00
273_K 32_V 0.98 0.14 0.00
198_T 52_Q 0.98 0.14 0.00
51_E 51_S 0.97 0.14 0.00
62_N 66_I 0.97 0.13 0.00
23_N 30_K 0.97 0.13 0.00
60_H 15_E 0.96 0.13 0.00
18_V 50_Q 0.96 0.13 0.00
116_A 23_M 0.95 0.13 0.00
269_Y 38_M 0.95 0.13 0.00
170_A 67_L 0.94 0.12 0.00
237_K 67_L 0.94 0.12 0.00
160_T 55_V 0.93 0.12 0.00
52_I 66_I 0.93 0.12 0.00
187_W 33_P 0.93 0.12 0.00
98_G 10_D 0.93 0.12 0.00
62_N 13_D 0.91 0.12 0.00
275_I 74_P 0.91 0.12 0.00
122_R 39_S 0.91 0.12 0.00
250_K 73_L 0.90 0.12 0.00
119_H 69_F 0.90 0.12 0.00
118_C 56_H 0.90 0.12 0.00
83_L 48_V 0.90 0.11 0.00
82_F 50_Q 0.89 0.11 0.00
186_I 37_L 0.89 0.11 0.00
195_E 27_D 0.89 0.11 0.00
258_D 38_M 0.88 0.11 0.00
187_W 12_Y 0.88 0.11 0.00
174_L 55_V 0.88 0.11 0.00
287_Q 25_P 0.88 0.11 0.00
191_C 66_I 0.86 0.10 0.00
115_L 26_K 0.86 0.10 0.00
85_Q 37_L 0.86 0.10 0.00
135_I 52_Q 0.86 0.10 0.00
23_N 59_I 0.86 0.10 0.00
172_E 44_R 0.85 0.10 0.00
185_D 44_R 0.85 0.10 0.00
274_R 44_R 0.85 0.10 0.00
122_R 27_D 0.85 0.10 0.00
196_M 11_K 0.85 0.10 0.00
171_P 62_P 0.85 0.10 0.00
118_C 63_E 0.85 0.10 0.00
30_V 25_P 0.84 0.10 0.00
141_I 65_H 0.84 0.10 0.00
51_E 47_G 0.84 0.10 0.00
130_P 36_H 0.84 0.10 0.00
204_P 48_V 0.84 0.10 0.00
161_H 36_H 0.83 0.10 0.00
110_Q 36_H 0.83 0.10 0.00
76_L 33_P 0.82 0.10 0.00
276_S 38_M 0.82 0.10 0.00
174_L 5_Q 0.82 0.10 0.00
48_A 28_I 0.82 0.10 0.00
173_I 28_I 0.82 0.09 0.00
165_T 70_R 0.82 0.09 0.00
165_T 17_F 0.81 0.09 0.00
68_D 52_Q 0.81 0.09 0.00
45_P 36_H 0.81 0.09 0.00
60_H 42_E 0.81 0.09 0.00
202_L 70_R 0.80 0.09 0.00
197_V 17_F 0.80 0.09 0.00
45_P 32_V 0.80 0.09 0.00
181_S 30_K 0.80 0.09 0.00
13_G 46_L 0.80 0.09 0.00
198_T 73_L 0.80 0.09 0.00
125_H 18_E 0.80 0.09 0.00
256_D 55_V 0.80 0.09 0.00
121_H 39_S 0.79 0.09 0.00
200_R 58_M 0.79 0.09 0.00
29_V 27_D 0.79 0.09 0.00
206_D 28_I 0.79 0.09 0.00
132_N 44_R 0.79 0.09 0.00
3_N 39_S 0.79 0.09 0.00
122_R 17_F 0.79 0.09 0.00
57_E 10_D 0.78 0.09 0.00
269_Y 58_M 0.78 0.09 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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