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OPENSEQ.org
PulG-PulM
Genes: A B A+B
Length: 134 161 286
Sequences: 1175 457 381
Seq/Len: 8.77 2.84 1.33
MirrorTree (Pazo et al. 2001) 0.59
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 0.01 0.01
2 0.09 0.01 0.04
5 0.09 0.01 0.17
10 0.09 0.01 1.29
20 0.09 0.01 1.29
100 0.09 0.01 1.31
∞ 0.13 0.01 1.33
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
59_T 90_A 1.55 0.86 0.16
23_N 46_W 1.54 0.86 0.16
109_V 70_L 1.33 0.72 0.09
69_S 88_R 1.21 0.62 0.06
6_I 95_L 1.18 0.58 0.06
51_K 130_G 1.18 0.58 0.06
10_I 150_V 1.15 0.56 0.05
6_I 116_F 1.14 0.55 0.05
112_F 120_M 1.14 0.55 0.05
51_K 31_V 1.14 0.55 0.05
55_S 130_G 1.13 0.54 0.05
10_I 55_A 1.09 0.50 0.04
51_K 92_R 1.07 0.48 0.04
113_S 11_R 1.07 0.48 0.04
72_S 109_L 1.07 0.48 0.04
106_H 138_V 1.07 0.48 0.04
39_D 8_W 1.07 0.48 0.04
87_R 87_M 1.07 0.47 0.04
108_Q 35_L 1.06 0.47 0.04
29_E 53_E 1.05 0.46 0.04
35_K 7_L 1.04 0.45 0.04
61_E 139_T 1.03 0.44 0.03
23_N 37_Q 1.03 0.44 0.03
76_H 110_T 1.02 0.43 0.03
91_Q 56_S 1.01 0.42 0.03
61_E 110_T 1.00 0.41 0.03
10_I 112_Q 1.00 0.41 0.03
116_P 122_W 0.99 0.40 0.03
6_I 35_L 0.98 0.39 0.03
38_S 105_S 0.97 0.39 0.03
101_L 100_L 0.97 0.38 0.03
14_G 123_L 0.97 0.38 0.03
15_V 69_Q 0.96 0.38 0.03
40_L 29_G 0.96 0.37 0.03
2_T 60_M 0.96 0.37 0.03
51_K 132_T 0.95 0.36 0.03
80_Y 95_L 0.95 0.36 0.03
131_I 23_A 0.95 0.36 0.03
113_S 66_L 0.94 0.36 0.02
44_E 130_G 0.94 0.35 0.02
109_V 19_L 0.93 0.34 0.02
59_T 106_R 0.93 0.34 0.02
6_I 111_V 0.93 0.34 0.02
59_T 145_P 0.92 0.34 0.02
109_V 13_R 0.92 0.34 0.02
72_S 86_I 0.92 0.34 0.02
79_N 23_A 0.91 0.33 0.02
83_G 12_T 0.91 0.32 0.02
111_I 7_L 0.91 0.32 0.02
48_D 135_T 0.90 0.32 0.02
125_D 97_I 0.90 0.32 0.02
59_T 136_L 0.90 0.32 0.02
11_V 119_L 0.90 0.31 0.02
105_Q 39_W 0.90 0.31 0.02
48_D 152_T 0.89 0.31 0.02
13_L 21_G 0.88 0.30 0.02
2_T 61_R 0.88 0.30 0.02
78_R 102_P 0.88 0.30 0.02
51_K 62_Q 0.88 0.30 0.02
65_Q 138_V 0.88 0.30 0.02
124_D 151_N 0.88 0.30 0.02
6_I 89_E 0.87 0.29 0.02
25_M 110_T 0.87 0.29 0.02
126_I 115_D 0.87 0.29 0.02
56_R 60_M 0.87 0.29 0.02
37_V 39_W 0.87 0.29 0.02
44_E 126_L 0.86 0.28 0.02
24_L 33_Y 0.86 0.28 0.02
59_T 49_T 0.86 0.28 0.02
40_L 133_T 0.86 0.28 0.02
101_L 131_M 0.86 0.28 0.02
10_I 22_M 0.86 0.28 0.02
118_G 127_G 0.86 0.28 0.02
126_I 130_G 0.85 0.28 0.02
13_L 43_E 0.85 0.28 0.02
77_A 128_Q 0.84 0.27 0.02
73_A 28_I 0.84 0.27 0.02
97_D 144_Q 0.84 0.27 0.02
61_E 102_P 0.83 0.26 0.02
95_G 122_W 0.83 0.26 0.02
83_G 7_L 0.83 0.26 0.02
61_E 97_I 0.83 0.26 0.02
15_V 37_Q 0.83 0.26 0.02
89_L 84_T 0.83 0.26 0.01
4_L 83_S 0.82 0.26 0.01
42_A 42_R 0.82 0.26 0.01
35_K 63_Q 0.82 0.26 0.01
36_V 86_I 0.82 0.25 0.01
127_G 100_L 0.82 0.25 0.01
102_S 34_T 0.81 0.25 0.01
112_F 100_L 0.81 0.25 0.01
19_L 138_V 0.81 0.25 0.01
102_S 105_S 0.81 0.24 0.01
17_A 129_A 0.81 0.24 0.01
73_A 86_I 0.80 0.24 0.01
131_I 105_S 0.80 0.24 0.01
36_V 81_E 0.80 0.24 0.01
111_I 19_L 0.79 0.23 0.01
21_V 8_W 0.79 0.23 0.01
24_L 82_P 0.79 0.23 0.01
18_S 12_T 0.79 0.23 0.01
35_K 130_G 0.79 0.23 0.01
44_E 101_Q 0.78 0.23 0.01
45_G 83_S 0.78 0.22 0.01
111_I 27_L 0.78 0.22 0.01
82_E 27_L 0.78 0.22 0.01
82_E 86_I 0.78 0.22 0.01
108_Q 85_V 0.77 0.21 0.01
17_A 32_Y 0.77 0.21 0.01
114_L 134_A 0.77 0.21 0.01
97_D 11_R 0.77 0.21 0.01
6_I 32_Y 0.77 0.21 0.01
35_K 114_A 0.77 0.21 0.01
113_S 151_N 0.76 0.21 0.01
94_W 122_W 0.76 0.21 0.01
24_L 116_F 0.76 0.21 0.01
20_V 80_E 0.76 0.21 0.01
19_L 143_Q 0.76 0.21 0.01
113_S 133_T 0.75 0.20 0.01
20_V 99_R 0.75 0.20 0.01
97_D 23_A 0.75 0.20 0.01
45_G 30_L 0.75 0.20 0.01
113_S 54_Q 0.75 0.20 0.01
29_E 93_H 0.75 0.20 0.01
123_N 79_P 0.74 0.20 0.01
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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