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OPENSEQ.org
L20-vs-S7
Genes: A B A+B
Length: 118 179 271
Sequences: 1984 1685 1027
Seq/Len: 16.81 9.41 3.79
MirrorTree (Pazo et al. 2001) 0.74
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 0.10 0.11 0.00
2 0.10 0.11 0.06
5 0.10 0.11 0.15
10 0.10 0.11 0.19
20 0.10 0.11 0.36
100 0.10 0.11 1.12
∞ 0.10 0.11 3.46
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
14_H 22_L 1.25 0.90 0.28
51_R 80_V 1.09 0.80 0.18
2_A 43_V 1.07 0.79 0.17
91_D 70_R 1.06 0.78 0.17
75_S 76_K 1.01 0.73 0.14
42_A 4_R 0.99 0.71 0.13
60_L 139_E 0.98 0.69 0.13
40_I 131_K 0.93 0.63 0.11
97_D 40_E 0.92 0.62 0.10
91_D 40_E 0.90 0.60 0.10
98_I 18_F 0.90 0.60 0.10
99_A 99_L 0.89 0.58 0.09
42_A 36_K 0.85 0.53 0.08
51_R 105_V 0.85 0.53 0.08
37_Q 91_V 0.84 0.52 0.08
98_I 107_A 0.84 0.52 0.08
53_R 93_P 0.83 0.51 0.07
101_F 83_S 0.81 0.48 0.07
30_R 138_R 0.81 0.48 0.07
28_R 31_M 0.81 0.48 0.07
77_S 149_K 0.81 0.47 0.07
28_R 101_M 0.80 0.47 0.07
45_Y 83_S 0.80 0.47 0.07
31_V 129_E 0.79 0.46 0.06
83_L 143_R 0.79 0.45 0.06
63_A 125_S 0.79 0.45 0.06
38_A 17_K 0.77 0.43 0.06
15_K 31_M 0.77 0.42 0.06
27_A 119_R 0.76 0.42 0.06
30_R 22_L 0.76 0.41 0.06
77_S 41_S 0.75 0.40 0.05
94_I 51_A 0.75 0.40 0.05
73_G 108_A 0.75 0.40 0.05
34_V 29_I 0.75 0.40 0.05
2_A 33_D 0.74 0.39 0.05
69_A 81_G 0.74 0.38 0.05
31_V 18_F 0.73 0.38 0.05
53_R 137_K 0.73 0.38 0.05
7_G 66_L 0.73 0.38 0.05
30_R 84_T 0.72 0.37 0.05
14_H 27_V 0.72 0.37 0.05
67_A 81_G 0.72 0.37 0.05
109_L 5_R 0.72 0.36 0.05
89_E 140_D 0.71 0.36 0.05
14_H 146_E 0.71 0.35 0.04
28_R 104_I 0.70 0.34 0.04
47_Y 80_V 0.70 0.34 0.04
69_A 107_A 0.70 0.34 0.04
77_S 111_R 0.70 0.34 0.04
31_V 29_I 0.70 0.34 0.04
87_S 18_F 0.70 0.34 0.04
38_A 101_M 0.70 0.34 0.04
28_R 2_P 0.70 0.34 0.04
37_Q 2_P 0.70 0.34 0.04
108_A 72_T 0.70 0.34 0.04
32_Y 130_N 0.69 0.33 0.04
8_V 28_N 0.69 0.33 0.04
57_F 87_V 0.69 0.33 0.04
81_N 104_I 0.69 0.33 0.04
49_D 80_V 0.69 0.33 0.04
80_I 128_A 0.69 0.33 0.04
6_R 138_R 0.69 0.33 0.04
15_K 138_R 0.69 0.32 0.04
107_T 45_S 0.69 0.32 0.04
67_A 153_H 0.68 0.32 0.04
48_R 115_S 0.68 0.32 0.04
91_D 29_I 0.68 0.32 0.04
11_R 146_E 0.68 0.32 0.04
86_A 87_V 0.68 0.31 0.04
38_A 18_F 0.67 0.31 0.04
27_A 26_F 0.67 0.31 0.04
75_S 129_E 0.67 0.30 0.04
41_K 130_N 0.67 0.30 0.04
91_D 24_A 0.67 0.30 0.04
96_A 25_K 0.67 0.30 0.04
33_R 117_A 0.66 0.30 0.04
85_K 18_F 0.66 0.29 0.04
25_Y 40_E 0.66 0.29 0.04
80_I 129_E 0.66 0.29 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)
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