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OPENSEQ.org
NDBs
Genes: A B A+B
Length: 245 191 416
Sequences: 29219 9344 67
Seq/Len: 119.26 48.92 0.16
MirrorTree (Pazo et al. 2001) 0.28
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 0.12 0.02 0.05
2 0.14 0.03 0.06
5 0.15 0.04 0.08
10 0.17 0.05 0.11
20 0.19 0.06 0.15
100 0.24 0.09 0.44
∞ 0.27 0.18 0.67
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
206_L 48_K 1.44 0.25 0.00
199_V 176_I 1.38 0.23 0.00
147_I 176_I 1.29 0.19 0.00
30_T 173_G 1.26 0.18 0.00
91_Y 163_L 1.26 0.18 0.00
24_E 113_S 1.25 0.18 0.00
46_G 74_G 1.23 0.17 0.00
46_G 79_G 1.23 0.17 0.00
46_G 80_K 1.23 0.17 0.00
220_R 88_A 1.21 0.17 0.00
49_G 74_G 1.20 0.16 0.00
49_G 79_G 1.20 0.16 0.00
49_G 80_K 1.20 0.16 0.00
51_G 74_G 1.20 0.16 0.00
51_G 79_G 1.20 0.16 0.00
51_G 80_K 1.20 0.16 0.00
169_F 55_R 1.20 0.16 0.00
174_V 171_G 1.12 0.14 0.00
205_A 81_T 1.10 0.13 0.00
212_L 142_V 1.08 0.13 0.00
44_L 43_Q 1.07 0.13 0.00
56_I 88_A 1.07 0.12 0.00
46_G 146_D 1.04 0.12 0.00
117_I 173_G 1.04 0.12 0.00
44_L 70_F 1.03 0.12 0.00
178_S 34_R 1.02 0.11 0.00
168_R 146_D 1.01 0.11 0.00
49_G 146_D 1.00 0.11 0.00
51_G 146_D 1.00 0.11 0.00
55_I 21_L 1.00 0.11 0.00
52_K 81_T 1.00 0.11 0.00
44_L 16_I 1.00 0.11 0.00
52_K 74_G 0.98 0.11 0.00
52_K 79_G 0.98 0.11 0.00
52_K 80_K 0.98 0.11 0.00
20_V 143_L 0.98 0.10 0.00
46_G 77_G 0.98 0.10 0.00
192_K 33_E 0.97 0.10 0.00
185_I 62_A 0.97 0.10 0.00
16_K 58_R 0.96 0.10 0.00
175_A 183_V 0.95 0.10 0.00
94_D 101_V 0.95 0.10 0.00
120_I 145_F 0.95 0.10 0.00
138_A 65_R 0.95 0.10 0.00
235_A 101_V 0.95 0.10 0.00
119_E 74_G 0.95 0.10 0.00
119_E 79_G 0.95 0.10 0.00
119_E 80_K 0.95 0.10 0.00
163_G 45_D 0.94 0.10 0.00
236_G 145_F 0.94 0.10 0.00
99_F 178_C 0.94 0.10 0.00
49_G 77_G 0.94 0.10 0.00
51_G 77_G 0.94 0.10 0.00
46_G 81_T 0.94 0.10 0.00
74_G 148_V 0.93 0.09 0.00
44_L 44_M 0.92 0.09 0.00
114_V 129_G 0.92 0.09 0.00
80_L 134_Q 0.92 0.09 0.00
60_A 91_L 0.91 0.09 0.00
20_V 88_A 0.90 0.09 0.00
57_E 42_G 0.89 0.09 0.00
49_G 81_T 0.89 0.09 0.00
51_G 81_T 0.89 0.09 0.00
165_F 102_D 0.89 0.09 0.00
56_I 108_E 0.89 0.09 0.00
119_E 163_L 0.89 0.09 0.00
119_E 81_T 0.88 0.09 0.00
180_R 47_I 0.88 0.09 0.00
20_V 100_R 0.88 0.09 0.00
64_I 108_E 0.88 0.09 0.00
223_P 152_H 0.87 0.08 0.00
123_L 116_L 0.87 0.08 0.00
198_G 180_N 0.87 0.08 0.00
207_V 24_S 0.87 0.08 0.00
237_V 34_R 0.86 0.08 0.00
16_K 50_V 0.85 0.08 0.00
149_A 115_L 0.85 0.08 0.00
143_Q 32_M 0.84 0.08 0.00
144_L 49_A 0.84 0.08 0.00
114_V 56_L 0.84 0.08 0.00
18_D 77_G 0.84 0.08 0.00
212_L 164_D 0.84 0.08 0.00
222_L 88_A 0.83 0.08 0.00
28_R 143_L 0.83 0.08 0.00
120_I 91_L 0.83 0.08 0.00
24_E 78_S 0.83 0.08 0.00
34_L 171_G 0.82 0.07 0.00
62_R 154_D 0.82 0.07 0.00
178_S 41_V 0.82 0.07 0.00
186_L 88_A 0.81 0.07 0.00
149_A 146_D 0.81 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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