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OPENSEQ.org
L14-vs-S4
Genes: A B A+B
Length: 123 206 327
Sequences: 1778 1236 731
Seq/Len: 14.46 6 2.24
MirrorTree (Pazo et al. 2001) 0.68
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 0.09 0.09 0.00
2 0.09 0.09 0.01
5 0.09 0.09 0.02
10 0.09 0.09 0.11
20 0.09 0.09 1.02
100 0.09 0.09 1.58
∞ 0.10 0.09 2.22
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
103_V 142_V 1.15 0.71 0.02
39_I 123_I 1.08 0.64 0.01
78_R 80_A 1.05 0.61 0.01
93_Q 206_K 1.01 0.56 0.01
31_R 48_L 1.01 0.56 0.01
93_Q 86_T 0.99 0.55 0.01
84_C 43_A 0.93 0.47 0.01
109_S 10_K 0.89 0.42 0.01
107_L 135_Y 0.88 0.42 0.01
55_G 186_P 0.87 0.41 0.01
14_S 136_Q 0.86 0.40 0.01
104_T 105_M 0.84 0.38 0.01
14_S 74_N 0.84 0.38 0.01
35_V 140_N 0.83 0.37 0.01
112_F 67_V 0.83 0.36 0.01
45_E 129_V 0.83 0.36 0.01
86_L 37_A 0.83 0.36 0.01
72_P 74_N 0.83 0.36 0.01
86_L 62_R 0.82 0.36 0.01
107_L 62_R 0.82 0.36 0.01
68_G 48_L 0.81 0.35 0.01
57_V 118_V 0.81 0.35 0.01
31_R 10_K 0.81 0.34 0.01
39_I 93_L 0.80 0.34 0.01
99_I 74_N 0.80 0.33 0.01
9_N 53_V 0.79 0.32 0.01
78_R 151_K 0.78 0.32 0.01
34_G 101_V 0.78 0.31 0.01
6_T 174_D 0.78 0.31 0.01
32_Y 118_V 0.77 0.30 0.01
20_M 132_I 0.76 0.30 0.01
57_V 45_K 0.76 0.29 0.01
99_I 163_E 0.76 0.29 0.01
67_K 90_L 0.76 0.29 0.01
6_T 175_A 0.76 0.29 0.01
59_K 128_R 0.75 0.29 0.01
6_T 113_E 0.75 0.28 0.01
103_V 190_D 0.74 0.28 0.01
84_C 20_F 0.74 0.28 0.01
106_E 99_D 0.73 0.27 0.01
66_K 10_K 0.73 0.26 0.01
23_K 80_A 0.73 0.26 0.01
55_G 76_Y 0.72 0.26 0.01
4_E 61_V 0.72 0.26 0.01
114_K 191_L 0.72 0.26 0.01
87_L 33_K 0.72 0.25 0.01
111_K 154_R 0.71 0.25 0.01
80_D 69_E 0.71 0.25 0.01
21_C 49_S 0.71 0.25 0.01
70_R 93_L 0.71 0.25 0.01
56_D 43_A 0.71 0.25 0.01
4_E 93_L 0.71 0.25 0.01
45_E 181_T 0.71 0.25 0.01
52_V 163_E 0.71 0.24 0.01
17_R 136_Q 0.70 0.24 0.00
73_D 140_N 0.70 0.24 0.00
23_K 77_K 0.70 0.24 0.00
14_S 206_K 0.69 0.24 0.00
22_I 51_Y 0.69 0.23 0.00
22_I 115_R 0.69 0.23 0.00
113_M 124_M 0.69 0.23 0.00
95_I 74_N 0.69 0.23 0.00
5_Q 124_M 0.69 0.23 0.00
23_K 153_S 0.69 0.23 0.00
43_I 147_E 0.69 0.23 0.00
35_V 102_V 0.68 0.23 0.00
14_S 80_A 0.68 0.22 0.00
99_I 156_K 0.68 0.22 0.00
53_K 69_E 0.68 0.22 0.00
56_D 129_V 0.67 0.22 0.00
35_V 96_G 0.67 0.22 0.00
35_V 181_T 0.67 0.22 0.00
99_I 20_F 0.67 0.22 0.00
20_M 7_P 0.67 0.21 0.00
114_K 40_Q 0.67 0.21 0.00
14_S 162_A 0.67 0.21 0.00
91_S 47_R 0.66 0.21 0.00
110_E 181_T 0.66 0.21 0.00
104_T 180_G 0.66 0.21 0.00
87_L 119_S 0.66 0.21 0.00
72_P 130_V 0.66 0.21 0.00
83_A 88_E 0.66 0.21 0.00
6_T 200_I 0.65 0.20 0.00
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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