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OPENSEQ.org
LEUC - LEUD
Genes: A B A+B
Length: 466 201 639
Sequences: 5246 3384 1655
Seq/Len: 11.26 16.84 2.59
MirrorTree (Pazo et al. 2001) 0.80
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 2.25
2 0.05 0.05 2.39
5 0.05 0.05 2.45
10 0.05 0.05 2.46
20 0.06 0.06 2.48
100 0.09 0.06 2.49
∞ 0.20 0.11 2.59
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
26_Y 193_E 1.42 0.92 0.48
15_V 188_A 1.40 0.91 0.45
160_Q 112_G 1.38 0.90 0.44
52_R 193_E 1.28 0.85 0.35
53_Q 193_E 1.26 0.84 0.34
76_G 32_Q 1.20 0.80 0.29
15_V 185_H 1.18 0.78 0.27
36_T 88_H 1.18 0.78 0.27
148_E 112_G 1.16 0.76 0.26
151_H 182_T 1.09 0.70 0.21
33_H 26_I 1.06 0.67 0.19
433_E 47_W 1.06 0.67 0.19
411_L 88_H 0.99 0.59 0.15
149_V 108_D 0.98 0.58 0.14
52_R 190_A 0.92 0.51 0.12
64_N 32_Q 0.92 0.50 0.11
226_M 116_N 0.90 0.49 0.11
85_E 34_V 0.90 0.48 0.11
443_H 182_T 0.89 0.48 0.10
81_I 34_V 0.87 0.45 0.10
159_K 171_C 0.86 0.43 0.09
36_T 107_A 0.82 0.39 0.08
56_K 196_Q 0.80 0.36 0.07
197_T 82_C 0.79 0.35 0.07
47_H 180_G 0.78 0.35 0.07
293_N 19_N 0.77 0.34 0.06
132_A 106_F 0.77 0.34 0.06
150_E 179_I 0.77 0.33 0.06
39_Q 88_H 0.77 0.33 0.06
146_T 88_H 0.77 0.33 0.06
423_R 182_T 0.77 0.33 0.06
445_V 47_W 0.76 0.33 0.06
29_R 119_L 0.76 0.32 0.06
412_A 95_D 0.75 0.32 0.06
79_A 178_S 0.75 0.31 0.06
82_Q 91_W 0.75 0.31 0.06
37_S 88_H 0.74 0.30 0.06
388_A 59_P 0.74 0.30 0.06
281_A 15_L 0.72 0.28 0.05
150_E 91_W 0.72 0.28 0.05
79_A 32_Q 0.71 0.28 0.05
81_I 35_T 0.71 0.27 0.05
66_S 32_Q 0.71 0.27 0.05
264_T 199_F 0.71 0.27 0.05
433_E 91_W 0.71 0.27 0.05
318_S 18_A 0.71 0.27 0.05
411_L 28_K 0.70 0.26 0.04
455_V 195_K 0.70 0.26 0.04
438_R 28_K 0.69 0.26 0.04
6_Y 178_S 0.69 0.26 0.04
368_A 166_A 0.68 0.25 0.04
64_N 39_F 0.68 0.25 0.04
149_V 26_I 0.68 0.25 0.04
269_E 127_A 0.68 0.24 0.04
114_E 79_N 0.67 0.24 0.04
231_G 108_D 0.67 0.24 0.04
333_P 185_H 0.67 0.23 0.04
368_A 145_D 0.66 0.23 0.04
175_A 164_I 0.66 0.23 0.04
261_Y 198_A 0.66 0.23 0.04
78_M 39_F 0.66 0.22 0.04
197_T 107_A 0.65 0.22 0.04
280_Q 125_S 0.65 0.22 0.04
162_R 90_P 0.65 0.22 0.04
197_T 79_N 0.64 0.21 0.03
91_K 134_A 0.64 0.21 0.03
79_A 42_H 0.64 0.21 0.03
82_Q 36_R 0.63 0.21 0.03
29_R 33_K 0.63 0.20 0.03
23_P 65_F 0.63 0.20 0.03
219_L 145_D 0.63 0.20 0.03
301_N 191_A 0.63 0.20 0.03
320_E 180_G 0.62 0.20 0.03
411_L 32_Q 0.62 0.20 0.03
344_I 104_P 0.62 0.20 0.03
293_N 82_C 0.62 0.20 0.03
226_M 196_Q 0.61 0.19 0.03
36_T 32_Q 0.61 0.19 0.03
373_A 105_S 0.61 0.19 0.03
311_A 134_A 0.61 0.19 0.03
260_A 191_A 0.61 0.19 0.03
148_E 116_N 0.61 0.19 0.03
35_V 88_H 0.61 0.19 0.03
155_T 183_L 0.60 0.18 0.03
404_L 116_N 0.60 0.18 0.03
209_R 99_K 0.60 0.18 0.03
411_L 107_A 0.60 0.18 0.03
370_G 15_L 0.60 0.18 0.03
193_S 5_F 0.59 0.18 0.03
299_S 125_S 0.59 0.18 0.03
38_P 31_L 0.59 0.18 0.03
24_L 182_T 0.59 0.18 0.03
95_V 130_D 0.59 0.17 0.03
61_M 121_P 0.59 0.17 0.03
183_I 154_K 0.59 0.17 0.03
438_R 46_D 0.59 0.17 0.03
287_Q 75_L 0.59 0.17 0.03
287_Q 8_H 0.59 0.17 0.03
199_H 101_V 0.59 0.17 0.03
38_P 88_H 0.59 0.17 0.03
150_E 182_T 0.59 0.17 0.03
153_L 90_P 0.59 0.17 0.03
280_Q 11_L 0.58 0.17 0.03
142_F 40_G 0.58 0.17 0.03
290_W 182_T 0.58 0.17 0.03
308_A 195_K 0.58 0.17 0.03
455_V 163_T 0.58 0.17 0.03
279_L 192_Y 0.58 0.17 0.03
91_K 149_E 0.58 0.17 0.03
393_K 11_L 0.58 0.17 0.03
334_L 94_T 0.58 0.17 0.03
329_K 149_E 0.58 0.17 0.03
25_L 145_D 0.58 0.17 0.03
159_K 167_F 0.58 0.17 0.03
376_V 44_F 0.58 0.17 0.03
153_L 123_K 0.58 0.17 0.03
368_A 74_L 0.58 0.17 0.03
412_A 55_Q 0.58 0.17 0.03
433_E 38_G 0.58 0.17 0.03
370_G 39_F 0.58 0.17 0.03
50_P 150_A 0.57 0.16 0.02
281_A 164_I 0.57 0.16 0.02
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)
ID Seq/Len Name Options I_Prob Status
2735 1.93 LEUC - LEUD Δgene:(0, 0) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.92 Done
2734 4.05 LEUC - LEUD Δgene:(0, 1) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.47 Done
2733 2.35 LEUC - LEUD Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.55 Done
2729 2.7 LEUC - LEUD Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.29 Done - Shared
2728 2.59 LEUC - LEUD Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.48 Done - Shared
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