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OPENSEQ.org
2OT3
Genes: A B A+B
Length: 274 170 421
Sequences: 535 11557 56
Seq/Len: 1.95 67.98 0.13
MirrorTree (Pazo et al. 2001) 0.18
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 0.04 0.05 0.01
2 0.04 0.06 0.02
5 0.04 0.08 0.04
10 0.04 0.10 0.07
20 0.04 0.13 0.13
100 0.04 0.23 0.34
∞ 0.05 0.28 0.66
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
198_Y 104_L 1.57 0.27 0.00
198_Y 156_I 1.31 0.17 0.00
214_Y 53_K 1.29 0.17 0.00
152_I 134_A 1.25 0.16 0.00
125_V 90_D 1.23 0.15 0.00
198_Y 132_Q 1.20 0.14 0.00
198_Y 21_S 1.19 0.14 0.00
243_I 123_L 1.17 0.14 0.00
151_D 134_A 1.16 0.13 0.00
190_D 61_D 1.15 0.13 0.00
113_L 29_N 1.13 0.13 0.00
163_D 130_S 1.13 0.12 0.00
214_Y 163_L 1.13 0.12 0.00
152_I 104_L 1.09 0.12 0.00
256_E 83_I 1.07 0.11 0.00
175_I 22_L 1.06 0.11 0.00
112_D 19_K 1.05 0.11 0.00
159_R 41_A 1.03 0.10 0.00
215_I 22_L 1.02 0.10 0.00
152_I 51_G 1.02 0.10 0.00
118_R 23_V 1.01 0.10 0.00
125_V 23_V 1.01 0.10 0.00
215_I 7_F 1.01 0.10 0.00
126_T 103_E 1.00 0.10 0.00
234_T 53_K 1.00 0.10 0.00
201_L 17_V 0.99 0.10 0.00
54_E 66_E 0.99 0.10 0.00
119_I 116_I 0.99 0.10 0.00
158_K 51_G 0.98 0.09 0.00
112_D 13_G 0.98 0.09 0.00
201_L 94_F 0.98 0.09 0.00
259_D 115_C 0.98 0.09 0.00
190_D 64_G 0.98 0.09 0.00
255_Q 157_E 0.97 0.09 0.00
175_I 90_D 0.97 0.09 0.00
141_V 56_N 0.97 0.09 0.00
187_A 104_L 0.96 0.09 0.00
206_P 116_I 0.96 0.09 0.00
256_E 134_A 0.96 0.09 0.00
156_D 48_L 0.95 0.09 0.00
215_I 78_D 0.95 0.09 0.00
234_T 150_A 0.95 0.09 0.00
231_Y 39_L 0.95 0.09 0.00
190_D 38_T 0.94 0.09 0.00
50_L 14_E 0.94 0.09 0.00
224_L 156_I 0.94 0.09 0.00
164_K 120_K 0.93 0.09 0.00
127_P 68_F 0.93 0.09 0.00
161_P 122_D 0.93 0.09 0.00
41_L 22_L 0.93 0.09 0.00
155_M 53_K 0.93 0.09 0.00
160_V 12_L 0.93 0.09 0.00
112_D 18_G 0.92 0.08 0.00
204_N 8_K 0.92 0.08 0.00
189_A 61_D 0.91 0.08 0.00
108_D 64_G 0.91 0.08 0.00
54_E 100_W 0.91 0.08 0.00
164_K 122_D 0.91 0.08 0.00
125_V 97_V 0.91 0.08 0.00
95_R 78_D 0.91 0.08 0.00
198_Y 98_K 0.91 0.08 0.00
243_I 35_H 0.90 0.08 0.00
198_Y 145_H 0.90 0.08 0.00
51_S 49_N 0.90 0.08 0.00
159_R 48_L 0.89 0.08 0.00
224_L 34_K 0.89 0.08 0.00
191_D 118_G 0.89 0.08 0.00
198_Y 120_K 0.88 0.08 0.00
208_L 31_F 0.88 0.08 0.00
202_K 123_L 0.88 0.08 0.00
194_P 61_D 0.87 0.08 0.00
239_A 94_F 0.87 0.08 0.00
27_H 23_V 0.86 0.07 0.00
190_D 118_G 0.86 0.07 0.00
51_S 88_I 0.86 0.07 0.00
131_C 81_G 0.86 0.07 0.00
115_I 9_V 0.86 0.07 0.00
119_I 97_V 0.85 0.07 0.00
257_D 11_L 0.85 0.07 0.00
177_N 134_A 0.85 0.07 0.00
189_A 8_K 0.85 0.07 0.00
34_Y 82_A 0.85 0.07 0.00
178_A 10_V 0.84 0.07 0.00
192_F 71_L 0.84 0.07 0.00
51_S 29_N 0.84 0.07 0.00
23_L 155_G 0.84 0.07 0.00
51_S 55_V 0.84 0.07 0.00
214_Y 145_H 0.84 0.07 0.00
201_L 51_G 0.83 0.07 0.00
234_T 59_I 0.83 0.07 0.00
224_L 63_A 0.83 0.07 0.00
118_R 167_M 0.83 0.07 0.00
190_D 120_K 0.83 0.07 0.00
172_S 154_K 0.82 0.07 0.00
52_I 133_E 0.82 0.07 0.00
91_Y 48_L 0.82 0.07 0.00
246_L 90_D 0.82 0.07 0.00
112_D 20_T 0.82 0.07 0.00
236_L 29_N 0.82 0.07 0.00
97_Y 65_Q 0.82 0.07 0.00
131_C 23_V 0.82 0.07 0.00
152_I 138_A 0.81 0.07 0.00
200_V 10_V 0.81 0.07 0.00
54_E 88_I 0.81 0.07 0.00
112_D 120_K 0.81 0.07 0.00
229_D 95_Q 0.81 0.07 0.00
168_I 31_F 0.81 0.07 0.00
195_T 90_D 0.81 0.07 0.00
162_R 55_V 0.80 0.07 0.00
190_D 122_D 0.80 0.07 0.00
240_V 167_M 0.80 0.07 0.00
54_E 60_W 0.80 0.07 0.00
208_L 18_G 0.80 0.07 0.00
111_K 151_K 0.80 0.07 0.00
71_Q 165_K 0.80 0.07 0.00
152_I 116_I 0.80 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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