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OPENSEQ.org
FiFFliE
Genes: A B A+B
Length: 220 104 312
Sequences: 3836 1768 1410
Seq/Len: 17.44 17 4.52
MirrorTree (Pazo et al. 2001) 0.63
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 4.21
2 0.00 0.00 4.25
5 0.00 0.00 4.35
10 0.00 0.00 4.35
20 0.00 0.00 4.35
100 0.01 0.00 4.36
∞ 0.06 0.01 4.46
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
191_I 58_K 1.44 0.97 0.75
78_R 104_V 1.32 0.95 0.66
215_Q 76_Q 1.09 0.84 0.43
85_A 80_V 1.05 0.81 0.40
90_A 40_A 1.05 0.81 0.39
147_L 71_V 1.02 0.79 0.37
122_G 72_M 1.01 0.78 0.36
35_A 99_V 1.01 0.77 0.35
125_Q 93_V 0.98 0.75 0.33
106_P 77_K 0.98 0.74 0.32
92_K 91_K 0.97 0.73 0.31
216_S 81_S 0.97 0.73 0.31
199_S 24_Q 0.95 0.71 0.30
105_L 101_S 0.93 0.69 0.28
191_I 80_V 0.93 0.69 0.28
135_A 83_Q 0.93 0.68 0.27
212_L 101_S 0.91 0.67 0.26
161_K 91_K 0.91 0.66 0.26
137_E 46_S 0.91 0.66 0.26
138_G 87_Q 0.90 0.65 0.25
195_V 104_V 0.90 0.65 0.25
123_I 69_N 0.89 0.64 0.24
68_A 51_A 0.88 0.63 0.24
141_A 79_S 0.88 0.62 0.23
130_V 104_V 0.87 0.62 0.23
197_L 76_Q 0.87 0.61 0.23
51_Y 70_D 0.87 0.61 0.23
21_R 74_D 0.87 0.61 0.22
30_V 45_I 0.87 0.61 0.22
150_V 102_M 0.86 0.61 0.22
108_G 56_A 0.86 0.60 0.22
57_N 54_V 0.86 0.60 0.22
164_L 87_Q 0.85 0.59 0.21
124_S 92_L 0.85 0.59 0.21
54_L 39_H 0.85 0.58 0.21
24_P 63_E 0.84 0.58 0.20
167_R 60_T 0.84 0.58 0.20
66_I 45_I 0.84 0.57 0.20
199_S 100_M 0.84 0.57 0.20
196_H 100_M 0.84 0.57 0.20
25_R 58_K 0.83 0.56 0.20
86_I 59_F 0.83 0.56 0.20
163_S 97_Q 0.82 0.55 0.19
21_R 85_G 0.82 0.54 0.18
128_E 56_A 0.82 0.54 0.18
166_V 54_V 0.82 0.54 0.18
40_V 36_G 0.81 0.53 0.18
211_T 100_M 0.81 0.53 0.18
32_G 78_A 0.81 0.53 0.18
32_G 84_M 0.81 0.53 0.18
195_V 26_T 0.81 0.53 0.18
173_S 10_V 0.81 0.53 0.18
63_G 87_Q 0.80 0.52 0.17
94_H 99_V 0.80 0.51 0.17
218_H 80_V 0.80 0.51 0.17
131_N 85_G 0.79 0.51 0.17
150_V 26_T 0.79 0.51 0.17
127_S 69_N 0.79 0.51 0.17
215_Q 72_M 0.79 0.50 0.17
132_Y 39_H 0.79 0.50 0.16
151_K 42_L 0.79 0.50 0.16
97_R 89_R 0.79 0.50 0.16
201_A 13_Q 0.79 0.50 0.16
201_A 90_N 0.79 0.50 0.16
173_S 85_G 0.79 0.50 0.16
127_S 41_A 0.78 0.49 0.16
201_A 89_R 0.78 0.48 0.16
212_L 98_E 0.77 0.47 0.15
219_L 92_L 0.77 0.47 0.15
46_A 85_G 0.77 0.47 0.15
218_H 38_L 0.77 0.47 0.15
121_F 89_R 0.77 0.47 0.15
193_A 9_G 0.76 0.47 0.15
204_G 12_S 0.76 0.46 0.15
216_S 80_V 0.76 0.46 0.14
153_A 103_Q 0.76 0.46 0.14
100_L 68_L 0.76 0.46 0.14
153_A 45_I 0.76 0.46 0.14
192_S 33_S 0.75 0.45 0.14
153_A 92_L 0.75 0.45 0.14
214_D 32_V 0.75 0.45 0.14
119_E 86_I 0.75 0.44 0.14
55_F 10_V 0.74 0.44 0.14
218_H 51_A 0.74 0.44 0.14
50_D 35_A 0.74 0.44 0.14
95_E 42_L 0.74 0.44 0.14
212_L 22_R 0.74 0.44 0.14
45_W 77_K 0.74 0.43 0.13
78_R 91_K 0.74 0.43 0.13
133_Q 59_F 0.74 0.43 0.13
206_P 6_G 0.74 0.43 0.13
198_V 42_L 0.74 0.43 0.13
166_V 60_T 0.73 0.43 0.13
102_Q 17_T 0.73 0.43 0.13
43_V 26_T 0.73 0.42 0.13
206_P 23_G 0.73 0.42 0.13
133_Q 92_L 0.73 0.42 0.13
54_L 56_A 0.73 0.42 0.13
72_Q 93_V 0.73 0.42 0.12
34_A 36_G 0.72 0.41 0.12
179_T 51_A 0.72 0.41 0.12
172_P 57_E 0.72 0.41 0.12
150_V 57_E 0.72 0.41 0.12
56_S 78_A 0.72 0.41 0.12
92_K 33_S 0.72 0.41 0.12
66_I 17_T 0.72 0.40 0.12
66_I 69_N 0.71 0.40 0.12
84_G 49_Q 0.71 0.40 0.12
98_L 92_L 0.71 0.40 0.12
165_F 72_M 0.71 0.40 0.12
43_V 17_T 0.71 0.40 0.12
25_R 6_G 0.71 0.40 0.12
104_G 92_L 0.71 0.40 0.12
38_I 43_D 0.71 0.39 0.12
29_I 46_S 0.71 0.39 0.12
52_R 80_V 0.71 0.39 0.11
218_H 43_D 0.71 0.39 0.11
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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