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OPENSEQ.org
LEUC - LEUD
Genes: A B A+B
Length: 466 201 662
Sequences: 5246 3384 2682
Seq/Len: 11.26 16.84 4.05
MirrorTree (Pazo et al. 2001) 0.95
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 4.02
2 0.05 0.05 4.20
5 0.05 0.05 4.25
10 0.05 0.05 4.25
20 0.06 0.06 4.26
100 0.09 0.06 4.29
∞ 0.20 0.11 4.37
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
36_T 88_H 1.31 0.94 0.47
15_V 188_A 1.31 0.94 0.47
26_Y 193_E 1.30 0.93 0.45
160_Q 112_G 1.26 0.92 0.42
52_R 193_E 1.17 0.87 0.34
53_Q 193_E 1.16 0.87 0.33
33_H 26_I 1.15 0.86 0.33
15_V 185_H 1.14 0.85 0.31
35_V 28_K 1.09 0.82 0.28
76_G 32_Q 1.09 0.82 0.27
151_H 182_T 1.05 0.78 0.24
148_E 112_G 1.04 0.77 0.24
36_T 107_A 0.97 0.70 0.19
318_S 18_A 0.96 0.69 0.18
411_L 88_H 0.95 0.68 0.18
149_V 108_D 0.93 0.66 0.17
438_R 28_K 0.92 0.64 0.16
433_E 47_W 0.89 0.61 0.14
35_V 29_Q 0.87 0.57 0.13
159_K 171_C 0.87 0.57 0.13
52_R 190_A 0.85 0.56 0.12
226_M 116_N 0.82 0.52 0.11
443_H 182_T 0.81 0.49 0.10
146_T 88_H 0.81 0.49 0.10
173_K 131_E 0.80 0.49 0.10
56_K 196_Q 0.80 0.48 0.10
64_N 32_Q 0.80 0.48 0.10
301_N 191_A 0.78 0.46 0.09
280_Q 125_S 0.77 0.45 0.09
293_N 19_N 0.77 0.45 0.09
85_E 34_V 0.75 0.42 0.08
86_L 28_K 0.74 0.41 0.08
36_T 36_R 0.74 0.41 0.08
81_I 34_V 0.74 0.41 0.08
140_L 119_L 0.74 0.41 0.08
324_A 195_K 0.74 0.40 0.08
197_T 82_C 0.73 0.40 0.08
228_A 107_A 0.73 0.40 0.07
150_E 179_I 0.73 0.39 0.07
79_A 178_S 0.72 0.37 0.07
64_N 39_F 0.71 0.37 0.07
39_Q 88_H 0.71 0.37 0.07
47_H 180_G 0.71 0.37 0.07
269_E 127_A 0.71 0.37 0.07
308_A 195_K 0.70 0.36 0.07
36_T 85_S 0.70 0.35 0.06
79_A 42_H 0.70 0.35 0.06
183_I 154_K 0.69 0.35 0.06
159_K 167_F 0.69 0.34 0.06
261_Y 198_A 0.69 0.34 0.06
197_T 79_N 0.69 0.34 0.06
59_A 48_R 0.69 0.34 0.06
114_E 79_N 0.69 0.34 0.06
79_A 32_Q 0.69 0.34 0.06
333_P 185_H 0.68 0.34 0.06
368_A 145_D 0.68 0.33 0.06
7_E 178_S 0.68 0.33 0.06
3_K 65_F 0.68 0.33 0.06
438_R 29_Q 0.67 0.32 0.06
423_R 182_T 0.67 0.32 0.06
66_S 32_Q 0.67 0.32 0.06
433_E 91_W 0.67 0.32 0.06
59_A 94_T 0.66 0.31 0.06
404_L 116_N 0.66 0.31 0.05
82_Q 91_W 0.66 0.30 0.05
35_V 42_H 0.66 0.30 0.05
279_L 192_Y 0.66 0.30 0.05
455_V 195_K 0.66 0.30 0.05
273_F 90_P 0.65 0.30 0.05
194_A 78_E 0.65 0.29 0.05
433_E 61_F 0.65 0.29 0.05
395_F 103_A 0.64 0.29 0.05
6_Y 178_S 0.64 0.29 0.05
150_E 91_W 0.64 0.29 0.05
1_M 188_A 0.64 0.28 0.05
303_N 191_A 0.64 0.28 0.05
395_F 148_L 0.63 0.28 0.05
358_A 103_A 0.63 0.28 0.05
422_E 192_Y 0.63 0.28 0.05
23_P 65_F 0.63 0.27 0.05
82_Q 36_R 0.63 0.27 0.05
344_I 104_P 0.63 0.27 0.05
153_L 90_P 0.63 0.27 0.05
228_A 79_N 0.63 0.27 0.05
343_F 21_D 0.62 0.27 0.04
231_G 108_D 0.62 0.26 0.04
314_V 77_R 0.62 0.26 0.04
314_V 184_Q 0.61 0.26 0.04
444_L 92_A 0.61 0.26 0.04
98_Y 78_E 0.61 0.26 0.04
29_R 33_K 0.61 0.26 0.04
388_A 59_P 0.61 0.25 0.04
170_V 180_G 0.61 0.25 0.04
397_E 134_A 0.60 0.25 0.04
81_I 35_T 0.60 0.25 0.04
348_T 27_P 0.60 0.25 0.04
151_H 177_D 0.60 0.24 0.04
64_N 88_H 0.60 0.24 0.04
455_V 102_I 0.60 0.24 0.04
388_A 194_A 0.60 0.24 0.04
37_S 88_H 0.59 0.24 0.04
132_A 116_N 0.59 0.24 0.04
466_K 194_A 0.59 0.23 0.04
35_V 88_H 0.59 0.23 0.04
362_A 25_I 0.59 0.23 0.04
393_K 11_L 0.59 0.23 0.04
200_V 33_K 0.59 0.23 0.04
186_A 3_E 0.59 0.23 0.04
308_A 197_P 0.59 0.23 0.04
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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