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OPENSEQ.org
1DKG_AD_real
Genes: A B A+B
Length: 376 158 511
Sequences: 8317 3521 1344
Seq/Len: 22.12 22.28 2.63
MirrorTree (Pazo et al. 2001) 0.43
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 0.06 2.25
2 0.07 0.06 2.32
5 0.07 0.06 2.39
10 0.08 0.06 2.44
20 0.08 0.06 2.52
100 0.11 0.07 2.91
∞ 0.20 0.07 3.96
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
58_T 117_A 0.92 0.51 0.00
119_K 45_L 0.88 0.46 0.00
375_L 54_A 0.84 0.42 0.00
57_V 91_M 0.84 0.41 0.00
123_K 52_K 0.82 0.39 0.00
307_N 146_I 0.81 0.39 0.00
50_Q 71_R 0.81 0.38 0.00
162_E 125_D 0.80 0.37 0.00
357_D 120_M 0.79 0.36 0.00
24_V 40_R 0.79 0.36 0.00
290_N 86_L 0.77 0.34 0.00
187_I 19_A 0.77 0.33 0.00
213_A 73_L 0.76 0.33 0.00
325_S 96_R 0.76 0.33 0.00
257_E 97_K 0.76 0.32 0.00
2_I 86_L 0.75 0.31 0.00
135_E 88_L 0.75 0.31 0.00
13_C 58_F 0.75 0.31 0.00
23_R 36_M 0.73 0.30 0.00
355_R 148_A 0.73 0.30 0.00
331_I 80_M 0.73 0.29 0.00
255_L 69_L 0.73 0.29 0.00
201_I 153_V 0.71 0.28 0.00
347_A 45_L 0.71 0.28 0.00
203_E 145_T 0.71 0.27 0.00
330_V 134_I 0.71 0.27 0.00
204_I 35_E 0.71 0.27 0.00
42_Q 128_P 0.70 0.27 0.00
133_V 35_E 0.70 0.27 0.00
145_N 49_K 0.70 0.27 0.00
190_Y 69_L 0.70 0.27 0.00
370_V 37_E 0.69 0.26 0.00
350_F 49_K 0.69 0.26 0.00
2_I 80_M 0.69 0.26 0.00
46_T 134_I 0.69 0.26 0.00
33_T 149_A 0.69 0.26 0.00
344_K 35_E 0.69 0.26 0.00
323_S 146_I 0.69 0.26 0.00
190_Y 75_V 0.68 0.25 0.00
117_V 139_Y 0.68 0.25 0.00
124_T 36_M 0.68 0.24 0.00
51_P 112_P 0.68 0.24 0.00
346_V 69_L 0.67 0.24 0.00
331_I 128_P 0.67 0.24 0.00
51_P 129_G 0.67 0.24 0.00
348_E 69_L 0.67 0.24 0.00
121_M 40_R 0.67 0.24 0.00
278_Y 74_E 0.66 0.23 0.00
215_N 100_V 0.66 0.23 0.00
22_P 145_T 0.66 0.23 0.00
70_L 39_L 0.65 0.22 0.00
257_E 76_A 0.65 0.22 0.00
54_R 148_A 0.65 0.22 0.00
213_A 109_P 0.64 0.21 0.00
264_I 40_R 0.64 0.21 0.00
257_E 121_V 0.64 0.21 0.00
322_L 131_V 0.64 0.21 0.00
112_Q 36_M 0.64 0.21 0.00
330_V 152_T 0.64 0.21 0.00
363_A 85_E 0.64 0.21 0.00
187_I 132_L 0.64 0.21 0.00
23_R 39_L 0.63 0.21 0.00
293_V 19_A 0.62 0.20 0.00
190_Y 100_V 0.62 0.20 0.00
207_K 71_R 0.62 0.20 0.00
157_R 128_P 0.62 0.20 0.00
357_D 134_I 0.62 0.20 0.00
315_V 98_F 0.61 0.20 0.00
190_Y 25_E 0.61 0.19 0.00
132_P 62_L 0.61 0.19 0.00
77_D 68_S 0.61 0.19 0.00
164_K 120_M 0.61 0.19 0.00
282_D 54_A 0.60 0.19 0.00
13_C 40_R 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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