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OPENSEQ.org
Wzc_wzb
Genes: A B A+B
Length: 259 147 398
Sequences: 4260 5421 523
Seq/Len: 16.45 36.88 1.31
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 0.01 0.02 0.92
2 0.02 0.02 1.02
5 0.03 0.02 1.08
10 0.03 0.02 1.14
20 0.04 0.03 1.29
100 0.07 0.04 1.83
∞ 0.15 0.13 3.74
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
116_I 117_Y 1.46 0.81 0.06
15_E 82_M 1.34 0.73 0.04
198_T 124_F 1.30 0.69 0.04
175_L 35_A 1.13 0.53 0.02
87_T 75_N 1.11 0.51 0.02
25_I 143_N 1.08 0.49 0.02
93_I 24_Q 1.06 0.47 0.02
140_I 90_L 1.05 0.46 0.02
20_S 46_D 1.05 0.45 0.02
226_N 79_I 1.02 0.42 0.01
210_V 117_Y 1.02 0.42 0.01
187_A 90_L 1.02 0.42 0.01
8_I 101_V 1.02 0.42 0.01
93_I 73_C 1.02 0.42 0.01
7_G 124_F 1.00 0.41 0.01
198_T 21_R 0.99 0.40 0.01
207_A 22_L 0.99 0.39 0.01
196_I 125_A 0.97 0.38 0.01
78_Q 130_L 0.97 0.38 0.01
124_Y 104_F 0.97 0.37 0.01
96_T 141_A 0.97 0.37 0.01
238_F 13_I 0.96 0.37 0.01
252_S 10_V 0.96 0.37 0.01
87_T 38_G 0.96 0.37 0.01
45_R 32_V 0.96 0.37 0.01
31_Q 10_V 0.95 0.36 0.01
161_L 37_L 0.94 0.35 0.01
17_H 114_P 0.94 0.35 0.01
102_L 131_L 0.92 0.33 0.01
64_A 81_T 0.91 0.32 0.01
127_E 131_L 0.91 0.32 0.01
13_V 106_H 0.91 0.32 0.01
107_S 76_Y 0.91 0.32 0.01
115_L 18_T 0.91 0.32 0.01
129_L 134_S 0.90 0.31 0.01
211_G 103_L 0.90 0.31 0.01
55_G 131_L 0.90 0.31 0.01
141_L 7_V 0.89 0.31 0.01
105_V 18_T 0.89 0.30 0.01
196_I 129_T 0.89 0.30 0.01
229_K 127_V 0.88 0.30 0.01
13_V 127_V 0.88 0.29 0.01
4_F 129_T 0.87 0.29 0.01
31_Q 73_C 0.87 0.29 0.01
76_M 79_I 0.86 0.28 0.01
47_K 26_Y 0.86 0.28 0.01
209_I 101_V 0.85 0.28 0.01
214_V 77_D 0.85 0.28 0.01
130_G 24_Q 0.85 0.27 0.01
20_S 73_C 0.85 0.27 0.01
130_G 104_F 0.85 0.27 0.01
182_E 81_T 0.85 0.27 0.01
214_V 119_K 0.84 0.27 0.01
141_L 101_V 0.84 0.26 0.01
127_E 135_A 0.83 0.26 0.01
130_G 22_L 0.82 0.25 0.01
150_A 53_A 0.82 0.25 0.01
18_G 52_V 0.82 0.25 0.01
111_K 111_C 0.81 0.24 0.01
40_I 91_C 0.81 0.24 0.01
123_G 138_W 0.81 0.24 0.01
192_D 100_K 0.81 0.24 0.01
13_V 135_A 0.81 0.24 0.01
195_L 88_E 0.81 0.24 0.01
48_Q 139_A 0.81 0.24 0.01
248_V 141_A 0.81 0.24 0.01
115_L 38_G 0.81 0.24 0.01
19_I 46_D 0.80 0.23 0.01
236_S 87_I 0.80 0.23 0.01
152_K 79_I 0.80 0.23 0.01
36_S 37_L 0.80 0.23 0.01
112_R 78_L 0.80 0.23 0.01
112_R 131_L 0.80 0.23 0.01
6_R 94_A 0.79 0.23 0.01
8_I 64_C 0.79 0.23 0.01
141_L 66_R 0.79 0.23 0.01
240_Q 83_E 0.79 0.23 0.01
118_S 77_D 0.79 0.23 0.01
130_G 44_G 0.79 0.23 0.01
19_I 99_G 0.79 0.23 0.01
96_T 7_V 0.78 0.22 0.01
141_L 53_A 0.78 0.22 0.01
182_E 61_E 0.78 0.22 0.01
93_I 68_I 0.78 0.22 0.01
36_S 134_S 0.77 0.22 0.01
123_G 99_G 0.77 0.21 0.01
10_S 131_L 0.77 0.21 0.01
187_A 93_M 0.77 0.21 0.01
67_S 10_V 0.77 0.21 0.01
118_S 22_L 0.77 0.21 0.01
27_L 90_L 0.77 0.21 0.01
47_K 66_R 0.77 0.21 0.01
36_S 26_Y 0.77 0.21 0.01
228_L 37_L 0.77 0.21 0.01
36_S 25_R 0.76 0.21 0.01
236_S 90_L 0.76 0.21 0.01
120_M 42_G 0.76 0.21 0.01
212_R 32_V 0.76 0.21 0.01
68_L 39_A 0.76 0.20 0.01
67_S 63_H 0.76 0.20 0.01
9_E 128_Y 0.76 0.20 0.01
151_A 126_A 0.75 0.20 0.01
129_L 90_L 0.75 0.20 0.01
39_T 26_Y 0.75 0.20 0.01
67_S 99_G 0.75 0.20 0.01
172_S 68_I 0.75 0.20 0.01
30_W 32_V 0.75 0.20 0.01
207_A 103_L 0.75 0.20 0.01
109_T 119_K 0.75 0.20 0.01
21_V 23_L 0.75 0.20 0.01
150_A 23_L 0.75 0.20 0.01
128_L 86_H 0.75 0.20 0.01
231_V 106_H 0.75 0.20 0.01
255_R 113_I 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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