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OPENSEQ.org
1DKG_AD_DMPmodel
Genes: A B A+B
Length: 376 171 520
Sequences: 8317 3620 1374
Seq/Len: 22.12 21.17 2.64
MirrorTree (Pazo et al. 2001) 0.42
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 0.07 0.03 2.24
2 0.07 0.03 2.32
5 0.07 0.03 2.39
10 0.08 0.03 2.43
20 0.08 0.03 2.51
100 0.11 0.03 2.91
∞ 0.20 0.04 3.97
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
307_N 162_I 0.88 0.46 0.00
58_T 133_A 0.87 0.45 0.00
119_K 56_Q 0.86 0.44 0.00
24_V 51_R 0.82 0.40 0.00
201_I 169_V 0.82 0.40 0.00
13_C 69_L 0.80 0.37 0.00
357_D 136_Q 0.78 0.34 0.00
190_Y 80_F 0.77 0.34 0.00
50_Q 82_R 0.77 0.34 0.00
375_L 65_R 0.77 0.34 0.00
330_V 168_K 0.77 0.33 0.00
331_I 96_I 0.76 0.33 0.00
162_E 141_N 0.76 0.33 0.00
330_V 150_E 0.76 0.33 0.00
290_N 102_M 0.76 0.32 0.00
190_Y 86_I 0.74 0.31 0.00
123_K 63_K 0.74 0.30 0.00
190_Y 116_V 0.73 0.30 0.00
57_V 107_L 0.72 0.29 0.00
344_K 46_D 0.71 0.28 0.00
278_Y 85_K 0.71 0.28 0.00
346_V 80_F 0.71 0.28 0.00
135_E 104_Y 0.71 0.27 0.00
347_A 56_Q 0.70 0.27 0.00
203_E 161_V 0.70 0.27 0.00
23_R 47_F 0.70 0.26 0.00
54_R 164_P 0.69 0.26 0.00
257_E 113_K 0.69 0.26 0.00
164_K 136_Q 0.69 0.26 0.00
321_G 23_N 0.69 0.26 0.00
235_E 85_K 0.69 0.25 0.00
350_F 60_A 0.68 0.25 0.00
204_I 46_D 0.68 0.25 0.00
355_R 164_P 0.68 0.25 0.00
145_N 60_A 0.68 0.25 0.00
46_T 150_E 0.67 0.24 0.00
325_S 112_K 0.67 0.24 0.00
51_P 128_P 0.67 0.24 0.00
330_V 46_D 0.66 0.23 0.00
315_V 114_E 0.65 0.23 0.00
213_A 84_L 0.65 0.23 0.00
42_Q 144_P 0.65 0.22 0.00
353_E 56_Q 0.65 0.22 0.00
331_I 144_P 0.65 0.22 0.00
31_D 107_L 0.65 0.22 0.00
215_N 116_V 0.65 0.22 0.00
255_L 80_F 0.65 0.22 0.00
51_P 145_N 0.65 0.22 0.00
117_V 155_Y 0.65 0.22 0.00
2_I 102_M 0.64 0.22 0.00
207_K 82_R 0.64 0.22 0.00
124_T 47_F 0.64 0.21 0.00
132_P 157_L 0.64 0.21 0.00
301_L 23_N 0.64 0.21 0.00
307_N 23_N 0.64 0.21 0.00
33_T 165_A 0.63 0.21 0.00
40_Y 29_L 0.63 0.21 0.00
2_I 96_I 0.63 0.20 0.00
133_V 46_D 0.62 0.20 0.00
323_S 162_I 0.62 0.20 0.00
264_I 51_R 0.62 0.20 0.00
306_V 148_V 0.61 0.20 0.00
187_I 148_V 0.61 0.20 0.00
234_V 32_K 0.61 0.19 0.00
67_I 102_M 0.61 0.19 0.00
134_T 27_A 0.61 0.19 0.00
121_M 51_R 0.61 0.19 0.00
77_D 79_N 0.61 0.19 0.00
363_A 101_E 0.60 0.19 0.00
282_D 65_R 0.60 0.19 0.00
167_I 171_Q 0.60 0.19 0.00
37_I 90_N 0.60 0.18 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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