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OPENSEQ.org
2HQS-2
Genes: A B A+B
Length: 404 112 509
Sequences: 973 11341 843
Seq/Len: 2.41 101.26 1.66
MirrorTree (Pazo et al. 2001) 0.78
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 0.08 0.02 1.55
2 0.08 0.02 1.58
5 0.08 0.03 1.61
10 0.08 0.05 1.63
20 0.08 0.07 1.63
100 0.08 0.13 1.67
∞ 0.08 0.21 1.76
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
313_Q 51_T 1.48 0.87 0.21
225_G 56_I 1.38 0.82 0.16
178_Q 89_K 1.33 0.78 0.14
239_A 87_K 1.25 0.72 0.11
217_V 71_Q 1.24 0.71 0.11
303_Q 101_S 1.22 0.69 0.10
380_N 75_V 1.16 0.63 0.08
181_M 56_I 1.16 0.63 0.08
59_G 8_V 1.14 0.62 0.08
250_V 20_D 1.13 0.61 0.08
392_L 65_A 1.13 0.60 0.07
88_G 80_I 1.12 0.60 0.07
148_V 14_K 1.12 0.59 0.07
229_F 77_A 1.12 0.59 0.07
401_F 52_P 1.09 0.57 0.07
241_S 60_E 1.08 0.56 0.07
234_S 39_K 1.08 0.56 0.07
344_G 29_A 1.06 0.54 0.06
266_S 20_D 1.05 0.52 0.06
36_V 101_S 1.02 0.49 0.05
90_Y 85_Y 1.01 0.48 0.05
148_V 8_V 1.00 0.47 0.05
292_V 76_S 0.99 0.46 0.05
39_D 95_H 0.99 0.46 0.05
21_Q 41_T 0.98 0.45 0.04
240_L 105_R 0.96 0.43 0.04
74_I 23_Q 0.96 0.42 0.04
173_V 17_I 0.95 0.42 0.04
266_S 100_Y 0.95 0.42 0.04
281_A 12_L 0.95 0.42 0.04
247_N 60_E 0.95 0.42 0.04
268_N 17_I 0.95 0.41 0.04
371_S 8_V 0.95 0.41 0.04
266_S 68_M 0.94 0.41 0.04
155_Q 12_L 0.94 0.40 0.04
33_G 46_A 0.93 0.40 0.04
263_D 96_D 0.93 0.40 0.04
229_F 69_Y 0.93 0.40 0.04
132_E 11_D 0.93 0.39 0.04
315_A 82_I 0.92 0.39 0.04
280_L 19_S 0.92 0.39 0.04
259_R 78_D 0.91 0.38 0.04
214_V 67_K 0.91 0.38 0.04
283_T 28_H 0.91 0.38 0.04
7_S 40_V 0.91 0.37 0.03
383_S 28_H 0.90 0.37 0.03
159_E 8_V 0.90 0.36 0.03
172_V 65_A 0.89 0.36 0.03
132_E 13_D 0.89 0.36 0.03
269_T 66_V 0.89 0.35 0.03
79_V 9_Y 0.88 0.34 0.03
5_I 87_K 0.87 0.34 0.03
192_L 96_D 0.87 0.34 0.03
45_K 67_K 0.87 0.33 0.03
144_R 19_S 0.86 0.33 0.03
361_A 43_E 0.86 0.33 0.03
200_G 61_R 0.86 0.33 0.03
370_S 42_V 0.85 0.32 0.03
245_S 60_E 0.85 0.32 0.03
148_V 13_D 0.85 0.32 0.03
336_I 43_E 0.85 0.32 0.03
6_D 109_V 0.84 0.31 0.03
216_Q 83_V 0.84 0.31 0.03
305_I 101_S 0.84 0.31 0.03
129_E 11_D 0.84 0.31 0.03
346_V 87_K 0.84 0.31 0.03
226_A 19_S 0.84 0.31 0.03
222_R 56_I 0.84 0.31 0.03
251_M 85_Y 0.83 0.30 0.03
148_V 56_I 0.83 0.30 0.03
72_L 82_I 0.83 0.30 0.03
403_A 51_T 0.82 0.29 0.03
360_L 46_A 0.82 0.29 0.02
150_Q 52_P 0.81 0.29 0.02
72_L 61_R 0.81 0.29 0.02
152_N 101_S 0.81 0.28 0.02
304_R 60_E 0.81 0.28 0.02
11_S 78_D 0.81 0.28 0.02
208_T 92_V 0.81 0.28 0.02
130_V 100_Y 0.81 0.28 0.02
211_N 70_L 0.81 0.28 0.02
350_S 46_A 0.81 0.28 0.02
210_A 65_A 0.80 0.28 0.02
192_L 68_M 0.80 0.28 0.02
93_A 27_A 0.80 0.28 0.02
105_T 67_K 0.80 0.27 0.02
353_F 100_Y 0.80 0.27 0.02
377_S 52_P 0.79 0.27 0.02
24_G 96_D 0.79 0.27 0.02
191_K 17_I 0.79 0.26 0.02
3_I 9_Y 0.78 0.26 0.02
260_Q 42_V 0.78 0.26 0.02
318_S 103_N 0.78 0.26 0.02
360_L 69_Y 0.78 0.26 0.02
149_V 97_E 0.78 0.26 0.02
3_I 41_T 0.78 0.26 0.02
213_A 97_E 0.77 0.25 0.02
19_P 42_V 0.77 0.25 0.02
43_S 16_D 0.77 0.25 0.02
108_A 83_V 0.77 0.25 0.02
292_V 16_D 0.77 0.25 0.02
65_Q 80_I 0.77 0.25 0.02
398_Q 40_V 0.76 0.24 0.02
5_I 99_A 0.76 0.24 0.02
339_Q 102_K 0.76 0.24 0.02
180_L 46_A 0.76 0.24 0.02
370_S 99_A 0.76 0.24 0.02
12_G 109_V 0.76 0.24 0.02
336_I 61_R 0.76 0.24 0.02
87_D 78_D 0.75 0.24 0.02
367_V 110_Y 0.75 0.23 0.02
243_T 64_N 0.75 0.23 0.02
65_Q 39_K 0.75 0.23 0.02
83_T 23_Q 0.75 0.23 0.02
327_V 51_T 0.75 0.23 0.02
102_A 65_A 0.75 0.23 0.02
217_V 85_Y 0.75 0.23 0.02
236_L 6_N 0.75 0.23 0.02
114_V 101_S 0.75 0.23 0.02
297_I 35_N 0.75 0.23 0.02
255_S 60_E 0.74 0.23 0.02
15_I 26_D 0.74 0.23 0.02
369_Y 65_A 0.74 0.23 0.02
381_L 52_P 0.74 0.23 0.02
278_Q 42_V 0.74 0.23 0.02
306_T 38_Y 0.74 0.23 0.02
161_R 108_L 0.74 0.22 0.02
145_I 96_D 0.74 0.22 0.02
48_P 107_V 0.74 0.22 0.02
327_V 83_V 0.73 0.22 0.02
305_I 63_A 0.73 0.22 0.02
352_T 91_A 0.73 0.22 0.02
379_L 75_V 0.73 0.22 0.02
87_D 31_F 0.73 0.22 0.02
393_P 67_K 0.73 0.22 0.02
73_G 100_Y 0.73 0.22 0.02
32_I 32_L 0.73 0.22 0.02
305_I 69_Y 0.73 0.22 0.02
367_V 77_A 0.73 0.22 0.02
360_L 45_H 0.72 0.21 0.02
133_K 65_A 0.72 0.21 0.02
403_A 33_R 0.72 0.21 0.02
70_S 43_E 0.72 0.21 0.02
2_R 83_V 0.72 0.21 0.02
137_I 63_A 0.72 0.21 0.02
244_G 60_E 0.72 0.21 0.02
4_V 41_T 0.72 0.21 0.02
236_L 31_F 0.72 0.21 0.02
15_I 41_T 0.72 0.21 0.02
165_Y 100_Y 0.72 0.21 0.02
200_G 40_V 0.71 0.21 0.01
217_V 29_A 0.71 0.21 0.01
149_V 65_A 0.71 0.21 0.01
292_V 78_D 0.71 0.21 0.01
322_K 45_H 0.71 0.21 0.01
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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