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OPENSEQ.org
3sfs_E_H
Genes: A B A+B
Length: 167 130 289
Sequences: 2153 2935 1681
Seq/Len: 12.89 22.58 5.82
MirrorTree (Pazo et al. 2001) 0.85
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 0.07 0.09 0.01
2 0.07 0.09 0.13
5 0.07 0.09 5.66
10 0.07 0.09 5.64
20 0.07 0.09 5.66
100 0.07 0.09 5.76
∞ 0.08 0.09 6.04
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
148_N 73_E 1.41 0.98 0.75
129_G 78_V 1.29 0.96 0.66
156_K 73_E 1.24 0.95 0.61
91_G 10_M 1.03 0.85 0.39
29_R 97_A 1.01 0.84 0.38
7_Q 129_V 0.97 0.80 0.33
156_K 71_V 0.93 0.76 0.30
158_G 66_F 0.91 0.74 0.28
117_V 104_V 0.89 0.72 0.26
156_K 66_F 0.88 0.70 0.25
66_K 83_L 0.85 0.66 0.22
15_L 18_Q 0.85 0.66 0.22
123_V 85_I 0.81 0.60 0.19
132_N 127_C 0.80 0.59 0.18
156_K 69_K 0.80 0.59 0.18
153_V 99_L 0.79 0.58 0.18
84_P 97_A 0.78 0.56 0.17
13_E 93_P 0.76 0.53 0.15
128_Y 130_A 0.73 0.50 0.14
156_K 130_A 0.73 0.49 0.14
125_A 36_I 0.73 0.48 0.13
90_T 125_I 0.72 0.48 0.13
124_L 41_K 0.72 0.48 0.13
107_A 79_S 0.72 0.47 0.13
110_A 78_V 0.71 0.47 0.13
30_I 41_K 0.71 0.46 0.13
89_H 126_I 0.70 0.44 0.12
103_T 99_L 0.69 0.43 0.12
18_V 117_R 0.69 0.43 0.11
77_N 37_A 0.68 0.42 0.11
12_Q 80_R 0.67 0.41 0.10
117_V 80_R 0.67 0.40 0.10
123_V 31_K 0.67 0.40 0.10
83_H 96_M 0.66 0.39 0.10
125_A 88_R 0.66 0.39 0.10
159_K 45_F 0.66 0.39 0.10
32_S 97_A 0.66 0.38 0.10
92_S 89_K 0.66 0.38 0.10
11_L 85_I 0.65 0.38 0.09
105_I 25_V 0.65 0.38 0.09
143_G 27_M 0.65 0.37 0.09
67_A 30_S 0.65 0.37 0.09
8_A 121_L 0.65 0.37 0.09
164_I 21_N 0.65 0.37 0.09
90_T 111_M 0.64 0.36 0.09
60_I 67_Q 0.63 0.35 0.09
16_I 59_L 0.63 0.35 0.09
106_I 108_K 0.63 0.34 0.08
81_L 92_L 0.63 0.34 0.08
121_H 75_I 0.62 0.34 0.08
36_L 126_I 0.62 0.34 0.08
32_S 68_G 0.62 0.34 0.08
57_P 43_E 0.62 0.34 0.08
154_A 114_R 0.62 0.33 0.08
146_N 118_Q 0.62 0.33 0.08
54_R 50_K 0.62 0.33 0.08
86_K 120_G 0.61 0.33 0.08
25_V 50_K 0.61 0.33 0.08
83_H 82_G 0.61 0.33 0.08
63_A 32_L 0.61 0.32 0.08
131_T 130_A 0.61 0.32 0.08
55_E 87_K 0.61 0.32 0.07
134_I 19_A 0.61 0.32 0.07
10_E 47_E 0.60 0.31 0.07
15_L 97_A 0.60 0.31 0.07
148_N 45_F 0.60 0.31 0.07
72_I 90_D 0.60 0.31 0.07
122_N 8_A 0.60 0.30 0.07
130_S 112_T 0.60 0.30 0.07
17_A 45_F 0.60 0.30 0.07
48_F 120_G 0.59 0.30 0.07
44_G 85_I 0.59 0.30 0.07
22_S 112_T 0.59 0.29 0.07
72_I 120_G 0.59 0.29 0.07
46_V 76_Q 0.59 0.29 0.07
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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