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OPENSEQ.org
A3DK20vsA3dk19at-20
Genes: A B A+B
Length: 256 328 564
Sequences: 1297 909 459
Seq/Len: 5.07 2.77 0.81
MirrorTree (Pazo et al. 2001) 0.49
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 0.28 0.66
2 0.02 0.29 0.74
5 0.03 0.30 0.77
10 0.03 0.30 0.78
20 0.04 0.31 0.79
100 0.06 0.31 0.80
∞ 0.13 0.34 0.82
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
125_A 49_R 2.27 0.97 0.90
79_L 321_A 1.64 0.80 0.53
166_S 313_Q 1.34 0.58 0.26
188_S 14_V 1.29 0.53 0.23
194_K 297_G 1.24 0.49 0.19
83_T 150_W 1.22 0.47 0.18
219_E 243_I 1.21 0.47 0.17
199_R 107_Y 1.19 0.45 0.16
105_S 49_R 1.17 0.43 0.15
192_R 49_R 1.16 0.42 0.14
125_A 278_Y 1.14 0.41 0.13
197_I 19_G 1.13 0.40 0.13
77_L 43_E 1.12 0.39 0.13
230_V 276_I 1.12 0.39 0.12
110_V 266_Q 1.10 0.38 0.12
114_K 295_E 1.09 0.36 0.11
217_L 294_K 1.08 0.36 0.11
140_G 161_H 1.08 0.36 0.11
250_E 276_I 1.07 0.35 0.10
13_V 245_E 1.06 0.34 0.10
130_R 223_V 1.05 0.34 0.10
120_L 317_L 1.05 0.33 0.10
215_K 297_G 1.05 0.33 0.09
194_K 124_S 1.03 0.32 0.09
203_E 263_I 1.03 0.32 0.09
222_K 190_K 1.01 0.30 0.08
161_A 293_R 0.99 0.29 0.07
130_R 71_L 0.99 0.29 0.07
166_S 44_N 0.98 0.28 0.07
97_L 18_A 0.97 0.27 0.07
176_Y 117_F 0.96 0.27 0.07
89_Q 275_V 0.95 0.26 0.06
226_D 181_L 0.94 0.26 0.06
17_D 220_D 0.94 0.25 0.06
116_A 190_K 0.93 0.25 0.06
115_M 321_A 0.93 0.25 0.06
184_G 201_G 0.92 0.24 0.05
132_L 170_F 0.91 0.24 0.05
145_E 4_I 0.91 0.23 0.05
14_V 103_S 0.91 0.23 0.05
157_N 260_L 0.91 0.23 0.05
98_L 92_K 0.91 0.23 0.05
141_I 223_V 0.90 0.23 0.05
192_R 179_R 0.90 0.23 0.05
95_F 27_N 0.90 0.23 0.05
50_L 292_I 0.89 0.23 0.05
117_D 293_R 0.88 0.22 0.04
112_N 271_K 0.88 0.21 0.04
130_R 205_V 0.88 0.21 0.04
133_E 322_F 0.88 0.21 0.04
149_Y 197_S 0.88 0.21 0.04
157_N 117_F 0.88 0.21 0.04
222_K 141_R 0.87 0.21 0.04
177_G 121_F 0.87 0.21 0.04
177_G 190_K 0.87 0.21 0.04
221_I 241_E 0.87 0.21 0.04
158_S 153_N 0.86 0.20 0.04
234_E 131_V 0.86 0.20 0.04
223_S 186_S 0.86 0.20 0.04
189_L 153_N 0.86 0.20 0.04
221_I 272_I 0.86 0.20 0.04
142_G 225_Y 0.85 0.20 0.04
199_R 298_V 0.85 0.20 0.04
208_C 117_F 0.85 0.20 0.04
97_L 228_V 0.85 0.20 0.04
58_V 295_E 0.85 0.20 0.04
176_Y 241_E 0.85 0.20 0.04
223_S 133_K 0.85 0.20 0.04
211_V 278_Y 0.85 0.20 0.04
174_E 313_Q 0.84 0.20 0.04
60_S 319_I 0.84 0.20 0.04
230_V 119_S 0.84 0.20 0.04
92_L 189_E 0.84 0.20 0.04
55_F 326_L 0.84 0.20 0.04
148_G 272_I 0.84 0.19 0.04
28_T 267_V 0.84 0.19 0.04
107_V 243_I 0.84 0.19 0.04
215_K 186_S 0.84 0.19 0.04
22_N 190_K 0.83 0.19 0.04
86_A 248_R 0.83 0.19 0.04
35_F 61_A 0.83 0.19 0.04
218_L 245_E 0.83 0.19 0.04
253_K 130_K 0.83 0.19 0.04
115_M 323_I 0.83 0.19 0.04
196_I 90_E 0.83 0.19 0.04
234_E 108_D 0.82 0.18 0.04
179_R 127_E 0.82 0.18 0.03
144_E 301_L 0.82 0.18 0.03
81_A 213_Y 0.82 0.18 0.03
225_L 148_L 0.82 0.18 0.03
237_Q 277_H 0.82 0.18 0.03
128_C 314_R 0.82 0.18 0.03
20_F 297_G 0.82 0.18 0.03
181_L 250_F 0.82 0.18 0.03
113_G 194_K 0.82 0.18 0.03
192_R 300_V 0.81 0.18 0.03
181_L 303_L 0.81 0.18 0.03
136_A 155_A 0.81 0.18 0.03
180_E 21_R 0.81 0.18 0.03
77_L 248_R 0.81 0.18 0.03
97_L 31_T 0.81 0.18 0.03
119_V 22_P 0.81 0.18 0.03
18_G 155_A 0.81 0.18 0.03
26_Y 4_I 0.81 0.18 0.03
222_K 261_E 0.81 0.18 0.03
166_S 231_Q 0.81 0.17 0.03
161_A 317_L 0.81 0.17 0.03
192_R 186_S 0.80 0.17 0.03
43_I 320_E 0.80 0.17 0.03
168_L 165_V 0.80 0.17 0.03
77_L 321_A 0.80 0.17 0.03
120_L 324_D 0.80 0.17 0.03
93_D 18_A 0.80 0.17 0.03
144_E 223_V 0.79 0.17 0.03
180_E 295_E 0.79 0.17 0.03
229_R 119_S 0.79 0.17 0.03
57_S 63_A 0.79 0.17 0.03
14_V 150_W 0.79 0.17 0.03
187_Y 221_A 0.79 0.17 0.03
161_A 97_F 0.78 0.16 0.03
20_F 214_E 0.78 0.16 0.03
248_R 58_I 0.78 0.16 0.03
133_E 200_I 0.78 0.16 0.03
137_N 49_R 0.78 0.16 0.03
226_D 265_V 0.78 0.16 0.03
28_T 135_L 0.78 0.16 0.03
130_R 246_E 0.78 0.16 0.03
169_I 94_V 0.78 0.16 0.03
219_E 127_E 0.78 0.16 0.03
107_V 116_R 0.77 0.16 0.03
130_R 318_R 0.77 0.16 0.03
44_N 116_R 0.77 0.16 0.03
180_E 152_H 0.77 0.16 0.03
130_R 85_L 0.77 0.16 0.03
185_V 242_D 0.77 0.16 0.03
246_A 295_E 0.77 0.16 0.03
245_C 279_T 0.77 0.16 0.03
16_E 268_K 0.77 0.16 0.03
211_V 213_Y 0.77 0.16 0.03
191_K 114_I 0.77 0.16 0.03
157_N 123_V 0.77 0.16 0.03
81_A 278_Y 0.76 0.15 0.03
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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