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OPENSEQ.org
255
Genes: A B A+B
Length: 131 87 213
Sequences: 134 211 102
Seq/Len: 1.02 2.43 0.48
MirrorTree (Pazo et al. 2001) 0.55
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 0.01 0.27 0.46
2 0.03 0.31 0.47
5 0.03 0.33 0.47
10 0.03 0.33 0.47
20 0.03 0.33 0.47
100 0.03 0.33 0.47
∞ 0.06 0.36 0.47
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
86_T 52_D 2.02 0.86 0.21
94_T 39_E 1.71 0.70 0.10
72_N 56_Y 1.64 0.65 0.08
15_V 83_G 1.57 0.61 0.07
86_T 42_V 1.48 0.54 0.05
71_N 23_E 1.45 0.51 0.05
125_I 64_S 1.44 0.51 0.04
75_R 31_D 1.38 0.46 0.04
95_S 38_L 1.30 0.40 0.03
83_K 38_L 1.27 0.38 0.03
96_F 45_T 1.22 0.34 0.02
116_I 4_K 1.20 0.33 0.02
75_R 38_L 1.20 0.33 0.02
117_S 53_L 1.19 0.32 0.02
95_S 37_L 1.16 0.30 0.02
90_S 64_S 1.13 0.28 0.02
129_R 8_S 1.12 0.28 0.01
69_S 63_D 1.12 0.28 0.01
8_A 62_D 1.11 0.27 0.01
95_S 35_D 1.10 0.26 0.01
57_E 78_A 1.08 0.25 0.01
53_K 72_I 1.07 0.25 0.01
92_K 36_V 1.05 0.24 0.01
76_M 42_V 1.04 0.23 0.01
85_R 52_D 1.02 0.22 0.01
63_E 72_I 1.01 0.22 0.01
113_M 64_S 1.01 0.22 0.01
42_K 5_N 1.00 0.21 0.01
72_N 68_I 1.00 0.21 0.01
83_K 42_V 1.00 0.21 0.01
109_G 53_L 0.96 0.19 0.01
89_V 51_T 0.95 0.18 0.01
116_I 55_Y 0.94 0.18 0.01
97_E 64_S 0.94 0.18 0.01
97_E 67_G 0.94 0.18 0.01
106_Q 55_Y 0.94 0.18 0.01
21_N 74_E 0.93 0.18 0.01
15_V 86_Q 0.90 0.16 0.01
84_T 59_D 0.89 0.16 0.01
123_R 81_K 0.89 0.16 0.01
96_F 54_I 0.88 0.16 0.01
111_Y 57_P 0.88 0.16 0.01
14_P 78_A 0.88 0.16 0.01
103_P 18_L 0.88 0.15 0.01
37_N 10_Y 0.87 0.15 0.01
46_S 78_A 0.87 0.15 0.01
98_L 51_T 0.87 0.15 0.01
11_K 69_V 0.87 0.15 0.01
77_K 49_D 0.87 0.15 0.01
88_D 38_L 0.87 0.15 0.01
131_K 81_K 0.87 0.15 0.01
59_S 8_S 0.87 0.15 0.01
40_R 12_E 0.86 0.15 0.01
102_K 81_K 0.85 0.14 0.01
89_V 67_G 0.85 0.14 0.01
56_E 86_Q 0.85 0.14 0.01
110_V 10_Y 0.84 0.14 0.01
40_R 73_K 0.84 0.14 0.01
15_V 79_N 0.83 0.14 0.01
61_D 46_E 0.82 0.13 0.01
59_S 80_G 0.82 0.13 0.01
39_L 14_E 0.82 0.13 0.01
48_D 62_D 0.82 0.13 0.01
95_S 31_D 0.81 0.13 0.00
80_K 28_A 0.81 0.13 0.00
118_V 17_Q 0.81 0.13 0.00
118_V 13_A 0.81 0.13 0.00
9_T 40_H 0.81 0.13 0.00
59_S 53_L 0.81 0.13 0.00
24_G 9_D 0.81 0.13 0.00
67_Q 18_L 0.80 0.13 0.00
96_F 22_I 0.80 0.12 0.00
66_K 53_L 0.80 0.12 0.00
9_T 81_K 0.80 0.12 0.00
96_F 18_L 0.78 0.12 0.00
84_T 55_Y 0.78 0.12 0.00
79_G 54_I 0.78 0.12 0.00
9_T 37_L 0.78 0.12 0.00
109_G 55_Y 0.78 0.12 0.00
82_P 67_G 0.77 0.12 0.00
99_H 12_E 0.77 0.12 0.00
29_S 60_N 0.77 0.12 0.00
61_D 79_N 0.76 0.11 0.00
63_E 85_K 0.76 0.11 0.00
106_Q 18_L 0.76 0.11 0.00
92_K 39_E 0.76 0.11 0.00
88_D 19_L 0.76 0.11 0.00
57_E 46_E 0.75 0.11 0.00
41_D 60_N 0.75 0.11 0.00
109_G 51_T 0.75 0.11 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)
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