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OPENSEQ.org
LEUC - LEUD
Genes: A B A+B
Length: 466 201 640
Sequences: 5246 3384 1727
Seq/Len: 11.26 16.84 2.7
MirrorTree (Pazo et al. 2001) 0.59
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
160_Q 112_G 1.33 0.89 0.29
15_V 188_A 1.33 0.89 0.29
26_Y 193_E 1.30 0.87 0.27
76_G 32_Q 1.23 0.83 0.22
52_R 193_E 1.22 0.82 0.21
53_Q 193_E 1.20 0.81 0.20
15_V 185_H 1.17 0.79 0.19
148_E 112_G 1.14 0.76 0.17
36_T 88_H 1.11 0.73 0.16
151_H 182_T 1.03 0.65 0.12
33_H 26_I 1.02 0.64 0.12
433_E 47_W 1.02 0.64 0.12
149_V 108_D 0.95 0.56 0.09
411_L 88_H 0.91 0.51 0.08
85_E 34_V 0.89 0.49 0.07
226_M 116_N 0.89 0.48 0.07
52_R 190_A 0.88 0.47 0.07
159_K 171_C 0.86 0.45 0.07
81_I 34_V 0.85 0.43 0.06
64_N 32_Q 0.84 0.43 0.06
443_H 182_T 0.83 0.42 0.06
47_H 180_G 0.78 0.35 0.05
293_N 19_N 0.77 0.35 0.05
56_K 196_Q 0.76 0.33 0.04
197_T 82_C 0.76 0.33 0.04
146_T 88_H 0.75 0.32 0.04
132_A 106_F 0.75 0.32 0.04
36_T 107_A 0.74 0.32 0.04
150_E 179_I 0.73 0.30 0.04
39_Q 88_H 0.73 0.30 0.04
412_A 95_D 0.72 0.29 0.04
79_A 178_S 0.72 0.29 0.04
423_R 182_T 0.72 0.29 0.04
150_E 91_W 0.71 0.29 0.04
37_S 88_H 0.71 0.28 0.04
269_E 127_A 0.71 0.28 0.04
388_A 59_P 0.70 0.27 0.03
149_V 26_I 0.70 0.27 0.03
183_I 154_K 0.70 0.27 0.03
81_I 35_T 0.70 0.27 0.03
6_Y 178_S 0.69 0.27 0.03
445_V 47_W 0.68 0.26 0.03
155_T 183_L 0.68 0.26 0.03
281_A 15_L 0.68 0.25 0.03
411_L 28_K 0.67 0.25 0.03
29_R 119_L 0.67 0.25 0.03
438_R 28_K 0.67 0.24 0.03
329_K 149_E 0.67 0.24 0.03
23_P 65_F 0.66 0.24 0.03
455_V 102_I 0.66 0.24 0.03
334_L 94_T 0.66 0.23 0.03
333_P 185_H 0.66 0.23 0.03
264_T 199_F 0.66 0.23 0.03
79_A 32_Q 0.65 0.23 0.03
36_T 32_Q 0.65 0.23 0.03
433_E 91_W 0.65 0.23 0.03
318_S 18_A 0.64 0.22 0.03
64_N 39_F 0.64 0.22 0.03
66_S 32_Q 0.64 0.21 0.03
197_T 79_N 0.64 0.21 0.03
82_Q 91_W 0.63 0.21 0.02
160_Q 95_D 0.63 0.21 0.02
78_M 39_F 0.63 0.21 0.02
404_L 116_N 0.62 0.21 0.02
360_E 161_R 0.62 0.20 0.02
226_M 196_Q 0.62 0.20 0.02
29_R 33_K 0.62 0.20 0.02
320_E 180_G 0.62 0.20 0.02
61_M 121_P 0.62 0.20 0.02
438_R 46_D 0.61 0.20 0.02
301_N 191_A 0.61 0.19 0.02
197_T 107_A 0.61 0.19 0.02
279_L 192_Y 0.61 0.19 0.02
175_A 164_I 0.61 0.19 0.02
199_H 101_V 0.60 0.19 0.02
209_R 99_K 0.60 0.19 0.02
91_K 134_A 0.60 0.19 0.02
368_A 145_D 0.60 0.19 0.02
287_Q 8_H 0.60 0.19 0.02
231_G 108_D 0.60 0.19 0.02
261_Y 198_A 0.60 0.19 0.02
368_A 166_A 0.60 0.19 0.02
219_L 145_D 0.59 0.18 0.02
79_A 42_H 0.59 0.18 0.02
281_A 164_I 0.59 0.18 0.02
55_G 20_V 0.59 0.18 0.02
411_L 32_Q 0.59 0.18 0.02
339_I 135_L 0.59 0.18 0.02
455_V 195_K 0.59 0.18 0.02
30_H 10_G 0.58 0.18 0.02
293_N 82_C 0.58 0.17 0.02
95_V 130_D 0.58 0.17 0.02
148_E 116_N 0.58 0.17 0.02
338_A 195_K 0.58 0.17 0.02
82_Q 36_R 0.58 0.17 0.02
35_V 88_H 0.58 0.17 0.02
142_F 40_G 0.58 0.17 0.02
370_G 15_L 0.58 0.17 0.02
422_E 192_Y 0.58 0.17 0.02
412_A 55_Q 0.58 0.17 0.02
193_S 5_F 0.57 0.17 0.02
411_L 107_A 0.57 0.17 0.02
1_M 188_A 0.57 0.17 0.02
267_T 11_L 0.57 0.17 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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