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OPENSEQ.org
MFDRNAPbeta
Genes: A B A+B
Length: 150 140 289
Sequences: 2267 2998 1107
Seq/Len: 15.11 21.41 3.83
MirrorTree (Pazo et al. 2001) 0.70
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 0.01
2 0.00 0.00 0.01
5 0.00 0.00 0.01
10 0.00 0.00 0.03
20 0.00 0.00 0.10
100 0.00 0.00 0.66
∞ 0.00 0.00 3.82
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
120_Q 47_A 2.08 1.00 0.99
101_R 29_L 1.98 1.00 0.98
149_L 97_E 1.59 0.98 0.93
117_I 29_L 1.51 0.97 0.91
71_V 29_L 1.40 0.95 0.86
119_E 50_Y 1.39 0.95 0.86
35_F 60_S 1.38 0.95 0.86
28_L 56_L 1.26 0.91 0.78
35_F 123_F 1.19 0.87 0.72
93_S 99_L 1.15 0.85 0.68
65_N 47_A 1.14 0.84 0.67
36_Q 23_Y 1.12 0.83 0.65
117_I 38_Y 1.09 0.81 0.63
19_P 17_E 1.07 0.79 0.61
81_D 31_A 1.05 0.77 0.58
127_I 35_T 1.05 0.77 0.58
145_I 27_T 1.01 0.73 0.54
119_E 48_K 0.99 0.70 0.51
124_M 103_A 0.98 0.70 0.50
14_D 13_V 0.98 0.70 0.50
122_V 91_V 0.98 0.70 0.50
134_G 98_L 0.97 0.68 0.48
127_I 63_A 0.96 0.68 0.48
30_I 106_A 0.95 0.67 0.46
17_K 85_Q 0.94 0.66 0.46
91_T 41_L 0.94 0.65 0.45
18_R 99_L 0.92 0.62 0.42
135_T 14_V 0.91 0.61 0.41
103_V 88_A 0.91 0.61 0.41
117_I 128_P 0.90 0.61 0.41
103_V 31_A 0.90 0.60 0.40
124_M 64_G 0.89 0.59 0.39
8_K 28_T 0.89 0.59 0.39
57_F 53_V 0.89 0.59 0.39
82_V 92_R 0.89 0.58 0.38
49_L 106_A 0.89 0.58 0.38
70_Y 123_F 0.89 0.58 0.38
80_F 61_R 0.89 0.58 0.38
50_E 20_V 0.88 0.57 0.37
99_K 73_H 0.88 0.57 0.37
78_P 89_E 0.87 0.57 0.37
102_L 25_G 0.87 0.57 0.37
118_K 18_H 0.87 0.56 0.37
141_T 61_R 0.87 0.56 0.36
27_L 14_V 0.86 0.55 0.35
131_T 43_Y 0.86 0.55 0.35
141_T 120_Y 0.86 0.55 0.35
145_I 80_W 0.85 0.54 0.34
149_L 54_S 0.85 0.54 0.34
118_K 3_N 0.85 0.54 0.34
75_L 60_S 0.84 0.52 0.33
7_E 96_A 0.83 0.52 0.32
91_T 23_Y 0.83 0.51 0.32
67_E 32_G 0.83 0.51 0.32
118_K 49_L 0.83 0.51 0.31
127_I 53_V 0.83 0.51 0.31
98_V 128_P 0.82 0.50 0.31
17_K 140_N 0.82 0.50 0.30
118_K 52_P 0.82 0.50 0.30
56_V 34_I 0.82 0.49 0.30
88_R 28_T 0.81 0.49 0.30
71_V 83_A 0.81 0.49 0.30
49_L 102_Y 0.81 0.49 0.30
76_G 40_M 0.81 0.48 0.30
51_A 137_Q 0.81 0.48 0.29
99_K 51_V 0.80 0.47 0.29
100_L 50_Y 0.80 0.47 0.29
35_F 37_E 0.80 0.47 0.29
16_G 39_L 0.80 0.47 0.28
75_L 64_G 0.80 0.47 0.28
81_D 81_S 0.80 0.47 0.28
66_S 17_E 0.80 0.47 0.28
28_L 53_V 0.80 0.47 0.28
104_I 120_Y 0.80 0.47 0.28
33_D 86_K 0.80 0.47 0.28
88_R 49_L 0.80 0.47 0.28
15_F 56_L 0.80 0.46 0.28
69_Q 20_V 0.79 0.46 0.28
83_Q 59_I 0.79 0.46 0.27
117_I 31_A 0.79 0.46 0.27
124_M 5_A 0.79 0.45 0.27
27_L 58_L 0.79 0.45 0.27
100_L 60_S 0.79 0.45 0.27
85_C 5_A 0.79 0.45 0.27
71_V 84_R 0.78 0.45 0.27
99_K 130_E 0.78 0.45 0.26
60_Q 81_S 0.78 0.44 0.26
118_K 75_L 0.78 0.44 0.26
60_Q 92_R 0.78 0.44 0.26
124_M 97_E 0.77 0.43 0.25
29_S 39_L 0.77 0.43 0.25
147_S 98_L 0.76 0.41 0.24
125_G 127_F 0.76 0.41 0.24
53_F 37_E 0.76 0.41 0.24
120_Q 31_A 0.76 0.41 0.24
26_Y 93_D 0.75 0.41 0.23
75_L 56_L 0.75 0.41 0.23
124_M 58_L 0.75 0.41 0.23
38_F 123_F 0.75 0.41 0.23
119_E 49_L 0.75 0.41 0.23
132_D 114_K 0.75 0.40 0.23
82_V 39_L 0.75 0.40 0.23
49_L 32_G 0.75 0.40 0.23
14_D 90_K 0.75 0.40 0.23
75_L 123_F 0.75 0.40 0.23
28_L 22_R 0.75 0.40 0.23
141_T 94_V 0.75 0.40 0.23
23_D 9_I 0.75 0.40 0.23
17_K 24_A 0.74 0.39 0.22
125_G 98_L 0.74 0.39 0.22
145_I 84_R 0.74 0.39 0.22
33_D 66_A 0.74 0.39 0.22
76_G 48_K 0.73 0.39 0.22
53_F 77_G 0.73 0.38 0.21
77_E 28_T 0.73 0.38 0.21
23_D 33_G 0.73 0.38 0.21
75_L 27_T 0.73 0.38 0.21
35_F 139_I 0.73 0.38 0.21
27_L 72_L 0.73 0.38 0.21
54_R 32_G 0.73 0.38 0.21
104_I 18_H 0.73 0.38 0.21
119_E 103_A 0.73 0.38 0.21
93_S 40_M 0.72 0.37 0.20
54_R 69_N 0.72 0.37 0.20
98_V 65_G 0.72 0.37 0.20
22_L 77_G 0.72 0.36 0.20
73_Y 95_A 0.72 0.36 0.20
56_V 41_L 0.72 0.36 0.20
100_L 90_K 0.71 0.36 0.20
124_M 80_W 0.71 0.36 0.20
132_D 75_L 0.71 0.36 0.20
99_K 25_G 0.71 0.36 0.20
89_G 56_L 0.71 0.36 0.20
29_S 82_R 0.71 0.36 0.20
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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