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OPENSEQ.org
n1t26
Genes: A B A+B
Length: 238 299 517
Sequences: 83808 23509 641
Seq/Len: 352.13 78.63 1.24
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 0.15 0.11 0.70
2 0.16 0.12 0.79
5 0.19 0.12 0.87
10 0.23 0.13 0.96
20 0.27 0.15 1.19
100 0.35 0.22 1.75
∞ 0.38 0.28 1.96
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
49_S 225_A 1.65 0.89 0.28
108_C 297_Y 1.25 0.63 0.10
8_I 82_L 1.23 0.61 0.09
174_V 71_G 1.14 0.52 0.07
90_V 256_S 1.11 0.49 0.06
122_H 113_V 1.09 0.48 0.06
8_I 55_L 1.09 0.48 0.06
37_L 181_V 1.04 0.42 0.05
109_A 121_L 1.00 0.39 0.04
30_L 167_S 0.98 0.38 0.04
174_V 54_C 0.97 0.36 0.04
110_L 116_D 0.95 0.35 0.03
73_A 197_A 0.94 0.34 0.03
80_W 191_G 0.94 0.34 0.03
205_L 129_F 0.94 0.33 0.03
81_V 295_Q 0.92 0.32 0.03
154_L 46_G 0.91 0.31 0.03
38_L 76_R 0.90 0.30 0.03
37_L 54_C 0.90 0.30 0.03
150_A 265_S 0.90 0.30 0.03
30_L 16_Q 0.89 0.29 0.03
120_G 277_V 0.89 0.29 0.03
18_S 124_L 0.89 0.29 0.03
140_L 167_S 0.89 0.29 0.03
83_N 195_V 0.88 0.29 0.03
137_K 274_L 0.88 0.29 0.03
152_V 66_A 0.88 0.29 0.03
51_L 134_V 0.87 0.28 0.02
145_A 79_F 0.87 0.28 0.02
63_E 224_V 0.87 0.28 0.02
82_Q 251_S 0.86 0.27 0.02
86_V 233_V 0.86 0.27 0.02
189_V 96_R 0.86 0.27 0.02
53_S 14_C 0.86 0.27 0.02
125_I 280_N 0.86 0.27 0.02
170_V 236_L 0.85 0.27 0.02
170_V 110_T 0.85 0.26 0.02
69_E 247_C 0.85 0.26 0.02
186_R 225_A 0.85 0.26 0.02
130_M 94_F 0.84 0.26 0.02
217_Q 277_V 0.84 0.26 0.02
40_V 201_Q 0.84 0.25 0.02
132_L 71_G 0.84 0.25 0.02
92_F 255_L 0.83 0.25 0.02
29_N 70_G 0.83 0.25 0.02
12_S 151_P 0.83 0.25 0.02
189_V 125_L 0.83 0.25 0.02
92_F 198_F 0.82 0.24 0.02
188_L 200_T 0.82 0.24 0.02
139_R 106_F 0.82 0.24 0.02
30_L 240_L 0.81 0.24 0.02
189_V 134_V 0.81 0.23 0.02
28_I 264_V 0.81 0.23 0.02
86_V 60_L 0.81 0.23 0.02
110_L 245_A 0.81 0.23 0.02
29_N 221_P 0.81 0.23 0.02
39_A 285_E 0.80 0.23 0.02
88_E 150_L 0.80 0.23 0.02
26_H 254_H 0.80 0.23 0.02
154_L 191_G 0.80 0.23 0.02
46_A 74_A 0.80 0.23 0.02
215_S 142_T 0.80 0.22 0.02
155_L 173_L 0.80 0.22 0.02
210_I 17_V 0.79 0.22 0.02
28_I 65_A 0.79 0.22 0.02
152_V 219_S 0.79 0.22 0.02
155_L 164_V 0.79 0.22 0.02
189_V 72_A 0.78 0.21 0.02
55_L 288_I 0.78 0.21 0.02
161_A 118_P 0.78 0.21 0.02
218_E 148_A 0.78 0.21 0.02
21_S 151_P 0.78 0.21 0.02
9_T 146_T 0.78 0.21 0.02
38_L 154_L 0.78 0.21 0.02
82_Q 284_L 0.77 0.21 0.02
24_C 21_C 0.77 0.21 0.02
14_T 192_S 0.77 0.21 0.02
122_H 249_V 0.77 0.21 0.02
152_V 242_F 0.77 0.20 0.01
85_S 113_V 0.77 0.20 0.01
25_L 67_V 0.77 0.20 0.01
55_L 69_L 0.77 0.20 0.01
217_Q 235_L 0.76 0.20 0.01
211_A 50_G 0.76 0.20 0.01
187_I 231_A 0.76 0.20 0.01
10_I 214_E 0.76 0.20 0.01
65_F 136_L 0.76 0.20 0.01
145_A 51_L 0.75 0.20 0.01
62_V 58_I 0.75 0.20 0.01
141_S 163_Y 0.75 0.20 0.01
114_V 116_D 0.75 0.19 0.01
29_N 253_A 0.75 0.19 0.01
51_L 180_S 0.75 0.19 0.01
49_S 115_V 0.75 0.19 0.01
106_E 239_G 0.75 0.19 0.01
146_V 265_S 0.74 0.19 0.01
24_C 253_A 0.74 0.19 0.01
197_P 292_E 0.74 0.19 0.01
36_C 59_G 0.74 0.19 0.01
26_H 96_R 0.74 0.19 0.01
137_K 103_L 0.74 0.19 0.01
157_D 171_R 0.74 0.19 0.01
49_S 202_A 0.74 0.19 0.01
140_L 195_V 0.74 0.19 0.01
55_L 21_C 0.74 0.18 0.01
188_L 147_V 0.74 0.18 0.01
149_K 181_V 0.74 0.18 0.01
160_A 195_V 0.73 0.18 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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