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OPENSEQ.org
L4-vs-
Genes: A B A+B
Length: 201 206 406
Sequences: 3177 1236 671
Seq/Len: 15.81 6 1.65
MirrorTree (Pazo et al. 2001) 0.63
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 0.08 0.09 0.00
2 0.08 0.09 0.00
5 0.08 0.09 0.00
10 0.09 0.09 0.05
20 0.09 0.09 0.10
100 0.09 0.09 0.94
∞ 0.09 0.09 1.65
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
18_T 143_V 1.64 0.93 0.57
61_R 139_P 1.49 0.88 0.45
31_V 62_R 1.21 0.68 0.22
188_M 143_V 1.11 0.58 0.16
164_L 145_I 1.05 0.52 0.13
170_R 150_K 0.97 0.43 0.10
196_V 195_I 0.96 0.43 0.10
50_A 138_S 0.89 0.35 0.07
79_R 76_Y 0.87 0.34 0.07
33_V 206_K 0.87 0.34 0.07
191_D 150_K 0.86 0.33 0.06
90_Q 201_V 0.86 0.32 0.06
193_V 135_Y 0.85 0.32 0.06
196_V 128_R 0.84 0.31 0.06
90_Q 125_V 0.83 0.30 0.06
61_R 129_V 0.83 0.30 0.05
116_D 137_V 0.83 0.30 0.05
183_F 52_G 0.82 0.29 0.05
98_K 169_T 0.81 0.28 0.05
196_V 62_R 0.81 0.28 0.05
102_R 158_A 0.81 0.28 0.05
121_V 148_K 0.80 0.28 0.05
54_G 15_E 0.80 0.28 0.05
113_V 67_V 0.80 0.28 0.05
64_G 69_E 0.79 0.27 0.05
97_N 129_V 0.79 0.26 0.04
29_H 75_Y 0.79 0.26 0.04
76_P 188_R 0.78 0.26 0.04
106_K 73_R 0.78 0.25 0.04
199_M 50_D 0.77 0.25 0.04
70_S 15_E 0.77 0.25 0.04
28_V 88_E 0.76 0.24 0.04
190_A 155_V 0.76 0.24 0.04
36_A 90_L 0.75 0.24 0.04
119_I 178_M 0.75 0.23 0.04
97_N 159_L 0.75 0.23 0.04
11_A 145_I 0.74 0.23 0.04
149_I 178_M 0.74 0.22 0.04
65_T 171_L 0.73 0.22 0.04
77_I 103_Y 0.73 0.22 0.04
38_G 158_A 0.73 0.22 0.04
161_A 190_D 0.73 0.22 0.04
55_S 50_D 0.73 0.22 0.03
73_I 125_V 0.73 0.21 0.03
7_D 67_V 0.72 0.21 0.03
15_S 131_N 0.72 0.21 0.03
48_T 75_Y 0.72 0.21 0.03
106_K 128_R 0.72 0.21 0.03
190_A 37_A 0.71 0.21 0.03
134_L 51_Y 0.71 0.21 0.03
191_D 62_R 0.71 0.21 0.03
77_I 8_K 0.71 0.20 0.03
118_L 49_S 0.70 0.20 0.03
194_K 146_R 0.70 0.20 0.03
148_I 70_R 0.70 0.20 0.03
186_V 169_T 0.70 0.20 0.03
98_K 12_S 0.70 0.20 0.03
46_Q 151_K 0.70 0.20 0.03
85_F 113_E 0.70 0.20 0.03
85_F 130_V 0.70 0.20 0.03
170_R 125_V 0.70 0.20 0.03
46_Q 206_K 0.70 0.19 0.03
102_R 142_V 0.69 0.19 0.03
134_L 123_I 0.69 0.19 0.03
53_T 137_V 0.69 0.19 0.03
92_H 57_E 0.69 0.19 0.03
75_S 76_Y 0.69 0.19 0.03
79_R 62_R 0.69 0.19 0.03
27_L 75_Y 0.69 0.19 0.03
164_L 40_Q 0.69 0.19 0.03
116_D 81_R 0.68 0.19 0.03
102_R 117_L 0.68 0.18 0.03
14_V 47_R 0.68 0.18 0.03
168_D 53_V 0.68 0.18 0.03
120_V 128_R 0.68 0.18 0.03
200_L 61_V 0.68 0.18 0.03
161_A 10_K 0.67 0.18 0.03
26_A 6_G 0.67 0.18 0.03
124_F 53_V 0.67 0.18 0.03
92_H 100_N 0.67 0.18 0.03
59_P 188_R 0.67 0.18 0.03
56_G 11_L 0.67 0.17 0.03
176_D 52_G 0.67 0.17 0.03
45_A 158_A 0.66 0.17 0.03
53_T 46_P 0.66 0.17 0.03
140_D 181_T 0.66 0.17 0.03
10_S 146_R 0.66 0.17 0.03
120_V 151_K 0.66 0.17 0.02
152_E 143_V 0.66 0.17 0.02
164_L 101_V 0.66 0.17 0.02
16_E 54_Q 0.66 0.17 0.02
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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