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OPENSEQ.org
fliQflhA
Genes: A B A+B
Length: 89 335 401
Sequences: 1330 1331 827
Seq/Len: 14.94 3.97 2.06
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 0.10
2 0.00 0.01 0.26
5 0.00 0.01 1.63
10 0.01 0.01 1.79
20 0.01 0.02 1.95
100 0.02 0.03 2.21
∞ 0.05 0.07 2.52
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
54_K 121_F 1.47 0.90 0.38
35_I 132_I 1.29 0.81 0.25
47_M 263_I 1.19 0.73 0.19
7_V 306_I 1.15 0.69 0.17
8_A 91_S 1.12 0.66 0.15
6_L 164_M 1.11 0.66 0.15
38_F 104_G 1.10 0.64 0.14
67_P 266_T 1.08 0.62 0.14
36_S 269_A 1.07 0.61 0.13
50_S 96_T 1.05 0.59 0.12
43_Q 214_V 1.04 0.58 0.12
14_F 145_V 1.03 0.57 0.11
45_N 257_S 1.03 0.56 0.11
64_F 46_P 1.02 0.56 0.11
7_V 57_A 1.02 0.56 0.11
19_L 304_L 1.02 0.56 0.11
38_F 298_L 1.02 0.55 0.11
68_W 119_G 1.00 0.54 0.10
33_L 69_I 1.00 0.53 0.10
23_P 121_F 0.99 0.52 0.10
2_D 43_L 0.98 0.51 0.09
30_I 295_R 0.97 0.50 0.09
10_G 140_I 0.97 0.50 0.09
44_I 246_Y 0.96 0.49 0.09
25_L 121_F 0.96 0.49 0.09
43_Q 179_L 0.96 0.49 0.09
85_P 234_Q 0.95 0.48 0.09
58_V 152_V 0.94 0.47 0.08
29_L 137_L 0.94 0.47 0.08
88_I 58_L 0.94 0.46 0.08
45_N 106_N 0.94 0.46 0.08
73_M 113_E 0.94 0.46 0.08
14_F 243_A 0.93 0.46 0.08
41_T 313_L 0.92 0.44 0.08
30_I 128_V 0.92 0.44 0.07
35_I 80_T 0.92 0.44 0.07
58_V 319_G 0.91 0.43 0.07
26_L 184_T 0.90 0.42 0.07
43_Q 136_I 0.90 0.42 0.07
66_M 55_S 0.90 0.41 0.07
55_I 145_V 0.89 0.41 0.07
43_Q 74_D 0.89 0.41 0.07
85_P 308_A 0.89 0.41 0.07
40_A 214_V 0.89 0.41 0.07
53_P 198_F 0.89 0.40 0.07
11_V 149_S 0.88 0.40 0.06
38_F 36_L 0.88 0.40 0.06
54_K 100_I 0.88 0.40 0.06
76_F 65_I 0.87 0.39 0.06
6_L 98_R 0.87 0.39 0.06
36_S 28_I 0.87 0.39 0.06
81_L 201_A 0.86 0.38 0.06
34_V 22_K 0.86 0.38 0.06
40_A 118_F 0.86 0.38 0.06
17_T 261_G 0.86 0.37 0.06
43_Q 210_K 0.85 0.37 0.06
75_D 251_I 0.85 0.37 0.06
84_I 146_T 0.84 0.36 0.06
55_I 52_L 0.84 0.36 0.06
46_E 173_A 0.84 0.36 0.06
3_E 95_A 0.84 0.36 0.06
26_L 115_I 0.84 0.35 0.05
9_L 57_A 0.84 0.35 0.05
58_V 140_I 0.83 0.35 0.05
58_V 182_E 0.83 0.34 0.05
45_N 249_L 0.83 0.34 0.05
60_V 58_L 0.82 0.34 0.05
40_A 208_F 0.82 0.34 0.05
77_T 122_V 0.81 0.33 0.05
61_I 66_S 0.81 0.33 0.05
59_V 308_A 0.81 0.33 0.05
13_T 163_A 0.81 0.33 0.05
20_L 50_F 0.81 0.33 0.05
25_L 133_V 0.81 0.33 0.05
25_L 250_T 0.81 0.32 0.05
20_L 239_L 0.81 0.32 0.05
56_I 184_T 0.80 0.32 0.05
73_M 286_T 0.80 0.32 0.05
56_I 81_L 0.80 0.32 0.05
29_L 114_I 0.80 0.32 0.05
38_F 164_M 0.80 0.32 0.05
85_P 312_G 0.80 0.32 0.05
19_L 177_A 0.80 0.32 0.05
7_V 117_A 0.80 0.32 0.05
14_F 69_I 0.79 0.31 0.04
68_W 51_F 0.79 0.31 0.04
20_L 216_G 0.79 0.31 0.04
36_S 87_L 0.79 0.30 0.04
69_M 245_T 0.79 0.30 0.04
28_G 317_S 0.79 0.30 0.04
47_M 95_A 0.78 0.30 0.04
6_L 322_A 0.78 0.30 0.04
74_I 250_T 0.78 0.30 0.04
37_I 282_F 0.78 0.30 0.04
88_I 28_I 0.78 0.29 0.04
26_L 190_Q 0.78 0.29 0.04
80_I 325_F 0.77 0.29 0.04
79_N 323_L 0.77 0.29 0.04
37_I 266_T 0.77 0.29 0.04
73_M 329_G 0.77 0.29 0.04
22_L 319_G 0.77 0.29 0.04
61_I 319_G 0.77 0.28 0.04
7_V 218_I 0.76 0.28 0.04
62_L 270_I 0.76 0.28 0.04
43_Q 294_Y 0.76 0.28 0.04
33_L 225_I 0.76 0.28 0.04
87_F 311_P 0.76 0.28 0.04
52_V 84_I 0.76 0.28 0.04
40_A 177_A 0.76 0.28 0.04
23_P 100_I 0.76 0.28 0.04
40_A 65_I 0.76 0.28 0.04
55_I 129_I 0.75 0.27 0.04
75_D 31_F 0.75 0.27 0.04
19_L 181_D 0.75 0.27 0.04
49_L 248_I 0.75 0.27 0.04
67_P 142_F 0.75 0.27 0.04
74_I 63_I 0.75 0.27 0.04
53_P 176_N 0.75 0.27 0.04
53_P 206_S 0.74 0.27 0.04
31_A 117_A 0.74 0.26 0.04
43_Q 35_I 0.74 0.26 0.04
9_L 222_I 0.74 0.26 0.04
41_T 292_S 0.74 0.26 0.04
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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