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OPENSEQ.org
haidai
Genes: A B A+B
Length: 253 86 313
Sequences: 1735 97 101
Seq/Len: 6.86 1.13 0.32
MirrorTree (Pazo et al. 2001) 0.88
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 0.01 0.29
2 0.00 0.01 0.30
5 0.00 0.01 0.30
10 0.01 0.01 0.30
20 0.02 0.01 0.30
100 0.03 0.01 0.30
∞ 0.12 0.01 0.30
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
215_R 44_V 1.38 0.35 0.00
177_P 22_F 1.37 0.35 0.00
46_V 20_G 1.36 0.34 0.00
170_D 43_D 1.27 0.29 0.00
163_V 37_L 1.25 0.28 0.00
233_V 31_C 1.24 0.27 0.00
75_D 5_D 1.22 0.26 0.00
39_V 41_E 1.22 0.26 0.00
158_T 21_T 1.21 0.26 0.00
117_D 68_D 1.18 0.24 0.00
46_V 19_M 1.13 0.22 0.00
100_I 38_S 1.12 0.21 0.00
219_M 60_V 1.12 0.21 0.00
213_L 63_Q 1.10 0.20 0.00
84_A 79_E 1.09 0.20 0.00
48_M 16_P 1.09 0.20 0.00
45_V 47_F 1.09 0.20 0.00
46_V 14_G 1.09 0.20 0.00
98_M 69_I 1.09 0.20 0.00
35_I 6_N 1.06 0.19 0.00
213_L 23_A 1.06 0.19 0.00
144_R 16_P 1.06 0.19 0.00
198_F 15_L 1.06 0.19 0.00
174_A 12_P 1.05 0.18 0.00
222_V 50_I 1.05 0.18 0.00
29_F 35_L 1.05 0.18 0.00
89_K 34_V 1.04 0.18 0.00
86_A 67_K 1.03 0.17 0.00
226_Q 78_Q 1.03 0.17 0.00
125_L 58_F 1.03 0.17 0.00
179_M 21_T 1.03 0.17 0.00
173_K 39_F 1.02 0.17 0.00
39_V 6_N 1.00 0.17 0.00
163_V 48_K 1.00 0.16 0.00
87_A 58_F 1.00 0.16 0.00
46_V 15_L 1.00 0.16 0.00
233_V 26_M 0.99 0.16 0.00
58_A 54_M 0.99 0.16 0.00
95_L 32_F 0.99 0.16 0.00
155_M 21_T 0.99 0.16 0.00
185_T 21_T 0.99 0.16 0.00
42_S 4_E 0.98 0.16 0.00
112_L 74_S 0.98 0.16 0.00
29_F 69_I 0.98 0.15 0.00
115_G 33_F 0.98 0.15 0.00
60_K 31_C 0.97 0.15 0.00
184_L 48_K 0.97 0.15 0.00
242_L 35_L 0.97 0.15 0.00
214_N 70_P 0.97 0.15 0.00
39_V 16_P 0.96 0.15 0.00
52_M 12_P 0.96 0.15 0.00
35_I 7_K 0.96 0.15 0.00
52_M 67_K 0.96 0.15 0.00
49_K 5_D 0.96 0.15 0.00
26_I 11_P 0.96 0.15 0.00
158_T 30_M 0.96 0.15 0.00
160_V 16_P 0.96 0.15 0.00
34_S 21_T 0.96 0.15 0.00
68_F 62_N 0.95 0.15 0.00
101_N 42_M 0.95 0.15 0.00
131_L 66_V 0.95 0.14 0.00
244_E 83_G 0.95 0.14 0.00
130_A 50_I 0.95 0.14 0.00
100_I 51_A 0.95 0.14 0.00
118_A 75_I 0.95 0.14 0.00
28_M 37_L 0.94 0.14 0.00
112_L 80_F 0.94 0.14 0.00
103_T 44_V 0.93 0.14 0.00
232_R 32_F 0.93 0.14 0.00
175_I 50_I 0.93 0.14 0.00
58_A 69_I 0.93 0.14 0.00
35_I 66_V 0.93 0.14 0.00
169_M 66_V 0.93 0.14 0.00
183_L 21_T 0.93 0.14 0.00
52_M 17_L 0.92 0.14 0.00
78_A 5_D 0.92 0.14 0.00
245_G 67_K 0.92 0.14 0.00
196_V 61_Q 0.92 0.14 0.00
238_L 28_L 0.92 0.14 0.00
121_V 31_C 0.92 0.13 0.00
36_L 62_N 0.92 0.13 0.00
217_L 42_M 0.91 0.13 0.00
106_Q 27_S 0.91 0.13 0.00
159_L 21_T 0.91 0.13 0.00
24_G 68_D 0.90 0.13 0.00
233_V 78_Q 0.90 0.13 0.00
113_V 29_L 0.90 0.13 0.00
163_V 20_G 0.90 0.13 0.00
100_I 81_R 0.90 0.13 0.00
33_T 75_I 0.89 0.13 0.00
250_E 57_A 0.89 0.12 0.00
73_P 69_I 0.88 0.12 0.00
61_I 68_D 0.88 0.12 0.00
251_I 67_K 0.87 0.12 0.00
39_V 12_P 0.87 0.12 0.00
76_L 6_N 0.87 0.12 0.00
168_N 45_L 0.87 0.12 0.00
48_M 49_Q 0.87 0.12 0.00
214_N 57_A 0.87 0.12 0.00
228_G 32_F 0.86 0.12 0.00
137_T 37_L 0.86 0.12 0.00
248_A 51_A 0.86 0.12 0.00
165_M 21_T 0.86 0.12 0.00
169_M 57_A 0.86 0.12 0.00
174_A 10_C 0.86 0.12 0.00
29_F 22_F 0.86 0.12 0.00
57_G 69_I 0.86 0.12 0.00
249_L 7_K 0.85 0.12 0.00
57_G 55_K 0.85 0.11 0.00
65_A 57_A 0.85 0.11 0.00
117_D 69_I 0.85 0.11 0.00
51_T 12_P 0.84 0.11 0.00
231_P 28_L 0.84 0.11 0.00
52_M 19_M 0.84 0.11 0.00
184_L 4_E 0.84 0.11 0.00
195_M 78_Q 0.84 0.11 0.00
176_G 32_F 0.84 0.11 0.00
133_D 23_A 0.84 0.11 0.00
144_R 14_G 0.84 0.11 0.00
172_P 50_I 0.83 0.11 0.00
149_V 75_I 0.83 0.11 0.00
123_A 62_N 0.83 0.11 0.00
191_I 15_L 0.83 0.11 0.00
220_D 85_P 0.82 0.11 0.00
43_I 75_I 0.82 0.11 0.00
201_A 86_E 0.82 0.11 0.00
60_K 43_D 0.82 0.11 0.00
76_L 11_P 0.81 0.10 0.00
42_S 68_D 0.81 0.10 0.00
101_N 41_E 0.81 0.10 0.00
169_M 6_N 0.81 0.10 0.00
66_F 57_A 0.81 0.10 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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