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OPENSEQ.org
LEUC - LEUD
Genes: A B A+B
Length: 466 201 639
Sequences: 5246 3384 1504
Seq/Len: 11.26 16.84 2.35
MirrorTree (Pazo et al. 2001) 0.81
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 1.49 0.93 0.55
52_R 193_E 1.37 0.88 0.44
15_V 188_A 1.36 0.88 0.44
160_Q 112_G 1.36 0.88 0.43
53_Q 193_E 1.31 0.85 0.39
76_G 32_Q 1.21 0.78 0.30
148_E 112_G 1.18 0.76 0.28
36_T 88_H 1.17 0.75 0.27
15_V 185_H 1.16 0.74 0.27
151_H 182_T 1.13 0.71 0.24
33_H 26_I 1.07 0.65 0.21
433_E 47_W 1.07 0.65 0.20
149_V 108_D 1.02 0.60 0.17
411_L 88_H 1.00 0.57 0.16
132_A 106_F 0.96 0.53 0.14
64_N 32_Q 0.94 0.50 0.13
85_E 34_V 0.91 0.47 0.12
226_M 116_N 0.90 0.46 0.11
443_H 182_T 0.89 0.45 0.11
52_R 190_A 0.88 0.44 0.10
81_I 34_V 0.87 0.42 0.10
159_K 171_C 0.83 0.38 0.08
36_T 107_A 0.81 0.35 0.07
197_T 82_C 0.80 0.34 0.07
293_N 19_N 0.79 0.33 0.07
388_A 59_P 0.79 0.33 0.07
423_R 182_T 0.78 0.33 0.07
47_H 180_G 0.78 0.33 0.07
79_A 32_Q 0.78 0.32 0.07
150_E 179_I 0.77 0.32 0.07
56_K 196_Q 0.77 0.32 0.07
82_Q 91_W 0.77 0.31 0.06
412_A 95_D 0.77 0.31 0.06
39_Q 88_H 0.76 0.31 0.06
146_T 88_H 0.76 0.30 0.06
64_N 39_F 0.76 0.30 0.06
37_S 88_H 0.76 0.30 0.06
81_I 35_T 0.74 0.29 0.06
318_S 18_A 0.74 0.28 0.06
411_L 28_K 0.73 0.28 0.05
280_Q 125_S 0.73 0.28 0.05
445_V 47_W 0.72 0.27 0.05
433_E 91_W 0.72 0.27 0.05
149_V 26_I 0.72 0.26 0.05
29_R 119_L 0.71 0.26 0.05
79_A 178_S 0.71 0.26 0.05
150_E 91_W 0.71 0.26 0.05
455_V 195_K 0.70 0.25 0.05
6_Y 178_S 0.70 0.25 0.05
333_P 185_H 0.69 0.24 0.04
368_A 145_D 0.69 0.24 0.04
370_G 39_F 0.69 0.24 0.04
66_S 32_Q 0.69 0.24 0.04
79_A 42_H 0.69 0.24 0.04
91_K 134_A 0.69 0.24 0.04
61_M 121_P 0.68 0.23 0.04
455_V 102_I 0.68 0.23 0.04
175_A 164_I 0.68 0.23 0.04
368_A 166_A 0.68 0.23 0.04
114_E 79_N 0.67 0.23 0.04
264_T 199_F 0.67 0.22 0.04
231_G 108_D 0.67 0.22 0.04
261_Y 198_A 0.66 0.22 0.04
197_T 79_N 0.66 0.21 0.04
208_I 6_I 0.66 0.21 0.04
301_N 191_A 0.65 0.21 0.04
411_L 107_A 0.65 0.21 0.04
438_R 28_K 0.65 0.21 0.04
29_R 33_K 0.65 0.21 0.04
411_L 32_Q 0.65 0.21 0.04
269_E 127_A 0.65 0.20 0.04
83_M 146_V 0.64 0.20 0.04
82_Q 36_R 0.64 0.20 0.03
344_I 104_P 0.64 0.20 0.03
193_S 5_F 0.64 0.20 0.03
50_P 150_A 0.63 0.19 0.03
38_P 31_L 0.63 0.19 0.03
155_T 183_L 0.63 0.19 0.03
287_Q 8_H 0.62 0.19 0.03
23_P 65_F 0.62 0.19 0.03
393_K 11_L 0.62 0.18 0.03
35_V 88_H 0.62 0.18 0.03
78_M 39_F 0.62 0.18 0.03
281_A 164_I 0.62 0.18 0.03
7_E 178_S 0.62 0.18 0.03
281_A 15_L 0.61 0.18 0.03
148_E 116_N 0.61 0.18 0.03
273_F 90_P 0.61 0.18 0.03
229_K 107_A 0.61 0.18 0.03
91_K 149_E 0.61 0.18 0.03
293_N 82_C 0.61 0.18 0.03
287_Q 75_L 0.61 0.18 0.03
197_T 107_A 0.60 0.17 0.03
24_L 182_T 0.60 0.17 0.03
388_A 194_A 0.60 0.17 0.03
38_P 88_H 0.60 0.17 0.03
98_Y 78_E 0.60 0.17 0.03
260_A 127_A 0.60 0.17 0.03
373_A 105_S 0.60 0.17 0.03
3_K 65_F 0.60 0.17 0.03
433_E 38_G 0.59 0.17 0.03
290_W 182_T 0.59 0.17 0.03
25_L 145_D 0.59 0.17 0.03
36_T 32_Q 0.59 0.17 0.03
153_L 90_P 0.59 0.17 0.03
459_F 39_F 0.59 0.16 0.03
272_T 137_K 0.58 0.16 0.03
464_N 101_V 0.58 0.16 0.03
183_I 154_K 0.58 0.16 0.03
404_L 116_N 0.58 0.16 0.03
119_L 41_A 0.58 0.16 0.03
37_S 32_Q 0.58 0.16 0.03
160_Q 95_D 0.58 0.16 0.03
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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