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OPENSEQ.org
ExP
Genes: A B A+B
Length: 98 244 326
Sequences: 888 1471 576
Seq/Len: 9.06 6.03 1.77
MirrorTree (Pazo et al. 2001) 0.69
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.00
2 0.00 0.00 0.00
5 0.00 0.01 0.03
10 0.00 0.01 0.24
20 0.00 0.02 1.59
100 0.01 0.03 1.68
∞ 0.01 0.07 1.92
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
93_I 57_V 1.77 0.96 0.82
79_M 41_L 1.65 0.94 0.74
98_I 85_N 1.48 0.89 0.62
78_F 212_P 1.44 0.86 0.57
83_R 241_S 1.39 0.83 0.53
87_I 96_T 1.38 0.83 0.53
67_I 134_K 1.38 0.83 0.53
54_I 194_V 1.38 0.83 0.52
72_A 188_I 1.36 0.82 0.51
98_I 88_L 1.32 0.79 0.46
48_E 234_L 1.30 0.78 0.44
81_E 215_M 1.28 0.76 0.42
92_E 212_P 1.27 0.75 0.41
55_A 197_M 1.26 0.75 0.41
70_T 68_V 1.25 0.73 0.39
78_F 75_Q 1.24 0.72 0.38
36_E 115_Y 1.22 0.71 0.37
50_A 212_P 1.18 0.67 0.33
33_L 233_L 1.17 0.66 0.32
81_E 59_V 1.14 0.63 0.29
84_N 241_S 1.10 0.60 0.26
94_T 209_M 1.10 0.60 0.26
85_K 50_L 1.09 0.59 0.25
80_L 55_S 1.07 0.56 0.23
74_S 39_T 1.07 0.56 0.23
92_E 151_R 1.06 0.56 0.23
83_R 198_V 1.06 0.56 0.23
81_E 190_L 1.06 0.55 0.23
81_E 205_A 1.05 0.54 0.22
72_A 45_I 1.04 0.53 0.21
49_A 164_V 1.02 0.51 0.20
40_L 212_P 1.01 0.50 0.19
85_K 119_K 0.99 0.48 0.18
95_R 212_P 0.99 0.47 0.18
64_Q 166_L 0.98 0.47 0.17
46_S 163_D 0.98 0.47 0.17
70_T 189_Y 0.97 0.46 0.17
43_A 170_V 0.97 0.46 0.17
54_I 51_A 0.97 0.45 0.16
81_E 194_V 0.97 0.45 0.16
36_E 187_L 0.96 0.44 0.16
63_H 47_L 0.96 0.44 0.16
46_S 205_A 0.95 0.44 0.15
96_T 74_R 0.95 0.43 0.15
41_N 41_L 0.93 0.41 0.14
86_A 53_A 0.93 0.41 0.14
57_G 217_S 0.93 0.41 0.14
93_I 134_K 0.93 0.41 0.14
37_I 234_L 0.92 0.41 0.14
63_H 214_T 0.92 0.40 0.14
94_T 86_T 0.92 0.40 0.14
91_K 190_L 0.92 0.40 0.13
45_E 92_A 0.91 0.40 0.13
40_L 41_L 0.91 0.40 0.13
39_D 110_E 0.91 0.39 0.13
77_K 197_M 0.90 0.38 0.13
47_G 184_I 0.90 0.38 0.13
22_S 222_L 0.90 0.38 0.12
76_M 75_Q 0.89 0.37 0.12
43_A 205_A 0.89 0.37 0.12
68_A 99_I 0.89 0.37 0.12
68_A 37_L 0.89 0.37 0.12
83_R 126_F 0.88 0.36 0.11
88_S 108_Y 0.88 0.36 0.11
63_H 212_P 0.87 0.35 0.11
62_L 226_V 0.87 0.35 0.11
54_I 60_M 0.87 0.35 0.11
95_R 89_V 0.87 0.35 0.11
75_S 41_L 0.86 0.34 0.11
42_K 169_L 0.86 0.34 0.11
76_M 212_P 0.86 0.34 0.11
76_M 73_L 0.86 0.34 0.10
61_D 80_Q 0.85 0.33 0.10
85_K 53_A 0.85 0.33 0.10
85_K 110_E 0.85 0.33 0.10
74_S 133_F 0.85 0.33 0.10
17_N 119_K 0.85 0.33 0.10
71_K 223_L 0.84 0.33 0.10
55_A 148_L 0.84 0.33 0.10
77_K 77_M 0.84 0.33 0.10
91_K 240_E 0.84 0.32 0.10
47_G 56_I 0.83 0.32 0.09
44_Q 51_A 0.83 0.32 0.09
61_D 232_N 0.83 0.31 0.09
87_I 52_L 0.83 0.31 0.09
66_A 111_G 0.83 0.31 0.09
45_E 51_A 0.83 0.31 0.09
93_I 62_S 0.82 0.31 0.09
97_Q 135_D 0.82 0.31 0.09
65_A 143_E 0.82 0.31 0.09
73_E 139_K 0.82 0.30 0.09
80_L 77_M 0.82 0.30 0.09
98_I 70_F 0.82 0.30 0.09
92_E 96_T 0.82 0.30 0.09
62_L 129_G 0.81 0.30 0.09
84_N 184_I 0.81 0.30 0.09
73_E 38_V 0.81 0.30 0.08
32_M 215_M 0.81 0.29 0.08
64_Q 223_L 0.80 0.29 0.08
25_I 51_A 0.80 0.29 0.08
37_I 112_I 0.80 0.28 0.08
76_M 56_I 0.80 0.28 0.08
67_I 131_K 0.80 0.28 0.08
63_H 239_V 0.80 0.28 0.08
98_I 133_F 0.80 0.28 0.08
67_I 101_E 0.79 0.28 0.08
86_A 197_M 0.79 0.28 0.08
37_I 24_V 0.79 0.28 0.08
91_K 119_K 0.79 0.28 0.08
80_L 184_I 0.79 0.27 0.07
81_E 90_T 0.78 0.27 0.07
36_E 211_L 0.78 0.27 0.07
97_Q 124_E 0.78 0.27 0.07
93_I 121_G 0.78 0.27 0.07
63_H 223_L 0.78 0.27 0.07
91_K 118_E 0.78 0.27 0.07
21_N 119_K 0.78 0.26 0.07
47_G 128_K 0.78 0.26 0.07
60_K 143_E 0.77 0.26 0.07
85_K 222_L 0.77 0.26 0.07
55_A 232_N 0.77 0.26 0.07
61_D 179_K 0.77 0.26 0.07
50_A 71_S 0.77 0.26 0.07
61_D 223_L 0.77 0.26 0.07
56_T 105_T 0.77 0.26 0.07
81_E 60_M 0.77 0.26 0.07
58_Q 212_P 0.76 0.25 0.07
93_I 70_F 0.76 0.25 0.07
79_M 239_V 0.76 0.25 0.07
77_K 145_D 0.76 0.25 0.07
33_L 198_V 0.75 0.25 0.06
78_F 239_V 0.75 0.24 0.06
62_L 126_F 0.75 0.24 0.06
63_H 197_M 0.75 0.24 0.06
76_M 240_E 0.75 0.24 0.06
35_N 226_V 0.75 0.24 0.06
54_I 58_F 0.75 0.24 0.06
40_L 49_I 0.75 0.24 0.06
85_K 168_V 0.74 0.24 0.06
92_E 58_F 0.74 0.24 0.06
97_Q 79_T 0.74 0.24 0.06
75_S 118_E 0.74 0.23 0.06
41_N 44_V 0.74 0.23 0.06
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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