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OPENSEQ.org
WzcWzb
Genes: A B A+B
Length: 147 256 396
Sequences: 5421 4371 523
Seq/Len: 36.88 17.07 1.32
MirrorTree (Pazo et al. 2001) 0.78
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 0.02 0.01 0.94
2 0.02 0.02 1.03
5 0.02 0.03 1.09
10 0.02 0.03 1.15
20 0.03 0.04 1.30
100 0.04 0.07 1.84
∞ 0.13 0.16 3.82
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
117_Y 113_I 1.60 0.89 0.25
124_F 195_T 1.29 0.69 0.11
82_M 12_E 1.28 0.68 0.10
35_A 172_L 1.13 0.53 0.06
143_N 22_I 1.12 0.52 0.06
75_N 84_T 1.11 0.51 0.06
101_V 5_I 1.11 0.51 0.06
79_I 223_N 1.08 0.49 0.05
38_G 84_T 1.07 0.48 0.05
21_R 195_T 1.06 0.47 0.05
24_Q 90_I 1.05 0.46 0.05
117_Y 207_V 1.04 0.45 0.05
90_L 184_A 1.03 0.44 0.04
90_L 137_I 1.02 0.42 0.04
73_C 90_I 1.02 0.42 0.04
46_D 17_S 1.01 0.41 0.04
10_V 249_S 1.01 0.41 0.04
127_V 226_K 0.97 0.38 0.04
141_A 93_T 0.97 0.38 0.04
125_A 193_I 0.97 0.38 0.04
106_H 10_V 0.97 0.38 0.04
77_D 211_V 0.97 0.38 0.04
114_P 14_H 0.96 0.37 0.04
81_T 61_A 0.96 0.37 0.04
131_L 124_E 0.96 0.37 0.04
32_V 42_R 0.96 0.37 0.04
103_L 208_G 0.95 0.36 0.03
24_Q 59_I 0.95 0.36 0.03
22_L 204_A 0.95 0.36 0.03
124_F 4_G 0.95 0.36 0.03
13_I 235_F 0.95 0.36 0.03
131_L 52_G 0.94 0.35 0.03
130_L 75_Q 0.93 0.34 0.03
104_F 127_G 0.92 0.33 0.03
119_K 106_T 0.92 0.33 0.03
18_T 112_L 0.92 0.33 0.03
26_Y 44_K 0.91 0.32 0.03
141_A 245_V 0.90 0.32 0.03
139_A 45_Q 0.90 0.32 0.03
131_L 99_L 0.90 0.32 0.03
134_S 80_V 0.87 0.29 0.03
113_I 62_I 0.87 0.29 0.02
119_K 211_V 0.87 0.29 0.02
76_Y 104_S 0.86 0.29 0.02
88_E 192_L 0.86 0.28 0.02
66_R 138_L 0.86 0.28 0.02
76_Y 81_L 0.86 0.28 0.02
46_D 16_I 0.85 0.28 0.02
75_N 250_I 0.85 0.28 0.02
38_G 112_L 0.85 0.27 0.02
122_E 95_V 0.85 0.27 0.02
7_V 138_L 0.85 0.27 0.02
10_V 28_Q 0.84 0.27 0.02
37_L 158_L 0.84 0.27 0.02
104_F 121_Y 0.84 0.27 0.02
66_R 44_K 0.84 0.27 0.02
114_P 85_G 0.84 0.27 0.02
23_L 18_V 0.84 0.27 0.02
127_V 10_V 0.84 0.26 0.02
106_H 48_L 0.83 0.26 0.02
61_E 179_E 0.83 0.26 0.02
93_M 243_K 0.83 0.26 0.02
122_E 246_I 0.83 0.26 0.02
73_C 17_S 0.83 0.26 0.02
131_L 109_R 0.83 0.26 0.02
81_T 179_E 0.83 0.26 0.02
25_R 149_K 0.82 0.25 0.02
37_L 33_S 0.82 0.25 0.02
90_L 126_L 0.82 0.25 0.02
103_L 204_A 0.82 0.25 0.02
129_T 1_F 0.82 0.25 0.02
44_G 184_A 0.82 0.25 0.02
32_V 209_R 0.82 0.25 0.02
101_V 138_L 0.82 0.25 0.02
111_C 108_K 0.82 0.25 0.02
109_N 142_G 0.82 0.25 0.02
86_H 10_V 0.81 0.25 0.02
32_V 27_W 0.81 0.24 0.02
79_I 154_A 0.81 0.24 0.02
13_I 193_I 0.81 0.24 0.02
91_C 37_I 0.81 0.24 0.02
78_L 109_R 0.80 0.24 0.02
52_V 228_V 0.80 0.24 0.02
53_A 147_A 0.80 0.24 0.02
52_V 15_G 0.80 0.23 0.02
7_V 93_T 0.80 0.23 0.02
79_I 73_M 0.79 0.23 0.02
90_L 160_P 0.79 0.23 0.02
83_E 237_Q 0.79 0.23 0.02
129_T 193_I 0.79 0.23 0.02
133_R 159_I 0.79 0.23 0.02
88_E 184_A 0.79 0.23 0.02
101_V 206_I 0.79 0.23 0.02
54_A 195_T 0.79 0.23 0.02
79_I 42_R 0.78 0.22 0.02
113_I 30_A 0.78 0.22 0.02
90_L 24_L 0.78 0.22 0.02
71_R 90_I 0.78 0.22 0.02
18_T 2_N 0.78 0.22 0.02
32_V 179_E 0.78 0.22 0.02
100_K 189_D 0.78 0.22 0.02
138_W 188_Y 0.78 0.22 0.02
37_L 137_I 0.78 0.22 0.02
23_L 95_V 0.78 0.22 0.02
87_I 233_S 0.77 0.22 0.02
73_C 28_Q 0.77 0.22 0.02
117_Y 221_A 0.77 0.21 0.02
62_G 109_R 0.77 0.21 0.02
26_Y 33_S 0.77 0.21 0.02
5_I 82_M 0.77 0.21 0.02
89_R 247_L 0.77 0.21 0.02
134_S 126_L 0.77 0.21 0.02
42_G 10_V 0.76 0.21 0.01
138_W 120_G 0.76 0.21 0.01
46_D 206_I 0.76 0.21 0.01
18_T 102_V 0.76 0.21 0.01
24_Q 147_A 0.76 0.21 0.01
64_C 5_I 0.76 0.21 0.01
24_Q 127_G 0.76 0.21 0.01
138_W 215_L 0.76 0.21 0.01
10_V 64_S 0.76 0.21 0.01
125_A 218_A 0.76 0.21 0.01
113_I 154_A 0.76 0.20 0.01
135_A 10_V 0.75 0.20 0.01
74_R 207_V 0.75 0.20 0.01
22_L 127_G 0.75 0.20 0.01
95_P 86_V 0.75 0.20 0.01
86_H 119_K 0.75 0.20 0.01
127_V 20_A 0.75 0.20 0.01
53_A 138_L 0.75 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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