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OPENSEQ.org
ecadh
Genes: A B A+B
Length: 116 136 246
Sequences: 5250 966 53
Seq/Len: 45.26 7.1 0.22
MirrorTree (Pazo et al. 2001) 0.33
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 0.15 0.11 0.00
2 0.18 0.13 0.01
5 0.20 0.17 0.01
10 0.22 0.17 0.01
20 0.22 0.17 0.04
100 0.25 0.17 0.08
∞ 0.26 0.18 0.21
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
55_V 110_F 1.87 0.56 0.00
107_V 102_V 1.42 0.30 0.00
105_V 49_L 1.35 0.27 0.00
28_V 124_V 1.33 0.26 0.00
86_V 87_F 1.23 0.21 0.00
48_D 68_G 1.21 0.20 0.00
101_A 13_G 1.19 0.19 0.00
14_V 32_R 1.18 0.19 0.00
82_L 49_L 1.10 0.16 0.00
23_I 97_G 1.10 0.16 0.00
74_F 67_Q 1.09 0.16 0.00
105_V 105_A 1.07 0.15 0.00
72_L 32_R 1.06 0.15 0.00
40_E 133_V 1.06 0.15 0.00
28_V 35_V 1.05 0.15 0.00
53_F 55_L 1.05 0.14 0.00
3_P 63_N 1.05 0.14 0.00
62_N 46_D 1.03 0.14 0.00
28_V 103_G 1.03 0.14 0.00
100_T 33_F 1.03 0.14 0.00
72_L 55_L 1.00 0.13 0.00
32_D 70_W 0.98 0.13 0.00
32_D 33_F 0.98 0.12 0.00
38_A 110_F 0.97 0.12 0.00
69_A 119_V 0.97 0.12 0.00
105_V 26_V 0.96 0.12 0.00
28_V 50_H 0.96 0.12 0.00
45_I 98_F 0.95 0.12 0.00
63_D 68_G 0.95 0.12 0.00
23_I 14_I 0.95 0.12 0.00
99_S 124_V 0.94 0.12 0.00
53_F 37_L 0.94 0.11 0.00
68_T 71_G 0.94 0.11 0.00
82_L 107_Y 0.93 0.11 0.00
84_V 103_G 0.92 0.11 0.00
64_G 70_W 0.92 0.11 0.00
18_E 60_V 0.92 0.11 0.00
40_E 49_L 0.92 0.11 0.00
65_I 111_R 0.91 0.11 0.00
107_V 51_F 0.91 0.11 0.00
84_V 42_E 0.91 0.11 0.00
82_L 115_P 0.91 0.11 0.00
103_V 124_V 0.91 0.11 0.00
103_V 51_F 0.90 0.10 0.00
22_V 12_E 0.90 0.10 0.00
5_F 70_W 0.89 0.10 0.00
30_D 33_F 0.88 0.10 0.00
14_V 99_K 0.88 0.10 0.00
113_A 23_R 0.88 0.10 0.00
84_V 14_I 0.88 0.10 0.00
17_N 112_H 0.88 0.10 0.00
30_D 70_W 0.88 0.10 0.00
53_F 91_I 0.88 0.10 0.00
108_L 102_V 0.87 0.10 0.00
94_V 100_A 0.87 0.10 0.00
28_V 63_N 0.86 0.10 0.00
66_L 87_F 0.86 0.10 0.00
45_I 20_L 0.86 0.10 0.00
101_A 86_P 0.85 0.09 0.00
24_T 135_I 0.85 0.09 0.00
5_F 61_V 0.85 0.09 0.00
87_T 60_V 0.85 0.09 0.00
72_L 91_I 0.85 0.09 0.00
77_K 92_I 0.84 0.09 0.00
79_Q 5_P 0.84 0.09 0.00
53_F 126_G 0.84 0.09 0.00
88_N 63_N 0.83 0.09 0.00
84_V 91_I 0.83 0.09 0.00
15_P 96_D 0.83 0.09 0.00
45_I 112_H 0.82 0.09 0.00
84_V 37_L 0.82 0.09 0.00
66_L 130_L 0.82 0.09 0.00
80_Y 88_E 0.82 0.09 0.00
3_P 70_W 0.82 0.09 0.00
3_P 50_H 0.82 0.09 0.00
101_A 75_R 0.82 0.09 0.00
94_V 53_P 0.81 0.09 0.00
28_V 55_L 0.81 0.09 0.00
53_F 5_P 0.81 0.09 0.00
55_V 18_T 0.81 0.09 0.00
5_F 33_F 0.81 0.09 0.00
63_D 29_N 0.81 0.09 0.00
107_V 124_V 0.81 0.09 0.00
28_V 113_R 0.81 0.09 0.00
110_V 18_T 0.80 0.08 0.00
90_V 37_L 0.80 0.08 0.00
86_V 14_I 0.80 0.08 0.00
21_V 120_R 0.80 0.08 0.00
105_V 96_D 0.80 0.08 0.00
23_I 81_F 0.80 0.08 0.00
2_P 103_G 0.80 0.08 0.00
64_G 61_V 0.79 0.08 0.00
107_V 57_T 0.79 0.08 0.00
82_L 47_A 0.79 0.08 0.00
14_V 58_S 0.78 0.08 0.00
99_S 51_F 0.78 0.08 0.00
78_Q 130_L 0.78 0.08 0.00
67_K 64_S 0.78 0.08 0.00
62_N 118_R 0.78 0.08 0.00
103_V 47_A 0.78 0.08 0.00
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
9440 0.22 ecadh Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9439 0.04 ecadh Δgene:(1, 20) A:(1E-06, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
9438 0.04 ecadh Δgene:(1, 20) A:(1E-10, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
9437 0.03 gal Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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