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OPENSEQ.org
test
Genes: A B A+B
Length: 202 156 347
Sequences: 3674 3481 2378
Seq/Len: 18.19 22.31 6.85
MirrorTree (Pazo et al. 2001) 0.56
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 0.19 0.22
2 0.04 0.19 6.49
5 0.04 0.19 6.63
10 0.04 0.19 6.63
20 0.04 0.19 6.64
100 0.04 0.19 6.72
∞ 0.04 0.19 6.86
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
5_K 34_E 2.70 1.00 1.00
8_T 33_I 2.07 1.00 0.99
83_S 7_I 2.04 1.00 0.99
80_V 10_Q 1.75 1.00 0.97
30_K 34_E 1.63 1.00 0.96
37_L 26_W 1.30 0.98 0.85
15_G 33_I 1.29 0.97 0.85
14_I 29_L 1.27 0.97 0.84
42_W 10_Q 1.21 0.96 0.80
170_V 16_L 1.19 0.95 0.78
18_N 30_M 1.14 0.94 0.74
5_K 37_Q 1.08 0.91 0.68
79_N 4_N 1.04 0.89 0.64
168_L 13_A 1.01 0.87 0.61
14_I 30_M 1.00 0.86 0.60
174_I 20_F 0.98 0.85 0.58
83_S 11_A 0.96 0.83 0.55
43_V 16_L 0.96 0.83 0.55
170_V 13_A 0.93 0.80 0.51
169_N 13_A 0.93 0.80 0.51
174_I 17_F 0.91 0.78 0.49
10_I 29_L 0.89 0.76 0.47
79_N 7_I 0.84 0.70 0.40
128_G 53_D 0.81 0.66 0.36
11_E 36_R 0.79 0.64 0.34
18_N 37_Q 0.79 0.63 0.34
39_I 14_F 0.78 0.62 0.33
148_A 128_A 0.78 0.61 0.32
38_T 17_F 0.75 0.57 0.29
194_Y 6_T 0.74 0.55 0.27
137_S 128_A 0.71 0.52 0.25
85_A 60_S 0.71 0.51 0.25
148_A 68_A 0.70 0.49 0.23
122_V 103_A 0.70 0.49 0.23
43_V 56_L 0.68 0.47 0.21
5_K 33_I 0.68 0.46 0.21
46_M 86_I 0.67 0.45 0.21
49_M 33_I 0.67 0.45 0.21
191_T 25_V 0.67 0.45 0.20
11_E 40_I 0.67 0.45 0.20
139_G 102_V 0.67 0.44 0.20
79_N 6_T 0.67 0.44 0.20
126_L 29_L 0.67 0.44 0.20
193_V 26_W 0.67 0.44 0.20
136_V 11_A 0.66 0.43 0.19
7_Q 32_A 0.65 0.42 0.19
107_K 153_V 0.65 0.42 0.19
75_S 116_A 0.65 0.42 0.18
81_T 86_I 0.65 0.41 0.18
100_K 40_I 0.65 0.41 0.18
172_W 25_V 0.65 0.41 0.18
52_L 153_V 0.64 0.41 0.18
56_L 11_A 0.64 0.41 0.18
39_I 146_S 0.64 0.40 0.18
23_D 124_V 0.64 0.40 0.17
80_V 7_I 0.64 0.40 0.17
185_F 150_D 0.63 0.39 0.17
140_L 50_A 0.63 0.39 0.17
8_T 39_E 0.62 0.38 0.16
78_V 7_I 0.62 0.37 0.16
196_S 33_I 0.62 0.37 0.16
103_G 115_R 0.61 0.36 0.15
43_V 122_K 0.61 0.36 0.15
132_L 137_E 0.61 0.35 0.15
150_E 14_F 0.61 0.35 0.15
22_K 66_K 0.60 0.35 0.15
82_L 3_L 0.60 0.34 0.14
192_I 37_Q 0.60 0.34 0.14
9_A 89_E 0.60 0.34 0.14
172_W 14_F 0.60 0.34 0.14
76_A 10_Q 0.60 0.34 0.14
41_V 106_Q 0.60 0.34 0.14
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
9395 6.85 test Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done
0070 4.03 ATP6 - ATPF (A, 70-271) Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) (2013_03) 1.00 Done - Shared
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