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OPENSEQ.org
1w85_A_B
Genes: A B A+B
Length: 358 324 630
Sequences: 3237 10927 1672
Seq/Len: 9.04 33.73 2.65
MirrorTree (Pazo et al. 2001) 0.74
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 0.03 2.39
2 0.01 0.03 2.41
5 0.02 0.03 2.43
10 0.02 0.05 2.45
20 0.02 0.07 2.45
100 0.04 0.12 2.55
∞ 0.12 0.22 2.87
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
154_G 72_Q 3.11 1.00 1.00
157_M 74_F 2.22 1.00 0.99
158_R 22_N 2.17 1.00 0.99
158_R 74_F 1.68 0.98 0.94
153_L 65_L 1.36 0.90 0.81
334_L 307_W 1.36 0.90 0.81
156_K 53_F 1.36 0.90 0.81
328_K 301_A 1.30 0.87 0.77
188_F 53_F 1.27 0.85 0.74
151_V 72_Q 1.20 0.81 0.69
156_K 50_D 1.11 0.73 0.59
337_I 101_R 1.05 0.67 0.53
203_I 36_V 1.04 0.66 0.51
339_F 239_Q 1.04 0.65 0.51
175_Q 88_E 1.02 0.63 0.48
126_N 102_Y 0.99 0.59 0.45
153_L 53_F 0.98 0.58 0.43
124_H 105_G 0.98 0.58 0.43
146_I 60_S 0.96 0.57 0.42
138_Q 96_Q 0.96 0.56 0.41
157_M 50_D 0.95 0.56 0.40
337_I 105_G 0.93 0.53 0.38
190_A 69_L 0.92 0.52 0.37
153_L 69_L 0.92 0.51 0.36
184_F 65_L 0.90 0.49 0.34
157_M 53_F 0.90 0.49 0.34
154_G 69_L 0.90 0.49 0.34
334_L 306_V 0.90 0.48 0.33
203_I 81_Q 0.86 0.45 0.30
340_E 164_N 0.86 0.44 0.30
143_A 96_Q 0.85 0.43 0.29
331_V 306_V 0.82 0.40 0.26
204_S 81_Q 0.79 0.37 0.23
270_M 124_T 0.77 0.34 0.20
134_V 104_T 0.77 0.34 0.20
310_E 244_E 0.76 0.32 0.19
205_T 57_L 0.76 0.32 0.19
339_F 274_A 0.74 0.31 0.18
204_S 82_F 0.74 0.31 0.18
335_I 294_P 0.73 0.30 0.17
153_L 24_L 0.73 0.30 0.17
308_V 75_R 0.73 0.30 0.17
257_L 230_A 0.73 0.29 0.17
203_I 29_D 0.72 0.28 0.16
209_K 49_E 0.71 0.28 0.16
277_L 219_A 0.71 0.28 0.15
270_M 82_F 0.70 0.27 0.15
78_Q 33_N 0.70 0.27 0.15
136_P 104_T 0.70 0.27 0.15
204_S 29_D 0.68 0.25 0.13
337_I 102_Y 0.68 0.25 0.13
127_Q 103_R 0.67 0.24 0.13
78_Q 25_I 0.67 0.24 0.13
116_F 17_L 0.67 0.24 0.13
275_K 21_P 0.67 0.24 0.13
141_I 127_L 0.67 0.24 0.12
149_A 65_L 0.66 0.24 0.12
141_I 113_T 0.66 0.23 0.12
139_I 84_G 0.66 0.23 0.12
267_P 57_L 0.66 0.23 0.12
273_D 261_E 0.65 0.23 0.12
96_L 96_Q 0.65 0.22 0.11
95_I 104_T 0.65 0.22 0.11
273_D 79_E 0.65 0.22 0.11
52_Y 235_L 0.64 0.22 0.11
203_I 295_D 0.64 0.22 0.11
181_G 45_A 0.64 0.21 0.11
71_F 124_T 0.64 0.21 0.11
330_K 314_V 0.64 0.21 0.11
94_F 72_Q 0.64 0.21 0.11
140_I 96_Q 0.64 0.21 0.11
173_T 58_A 0.64 0.21 0.11
267_P 267_G 0.63 0.21 0.10
242_V 277_N 0.63 0.21 0.10
204_S 117_P 0.63 0.21 0.10
140_I 127_L 0.63 0.21 0.10
226_P 45_A 0.63 0.21 0.10
246_R 318_A 0.62 0.20 0.10
311_Q 257_I 0.62 0.20 0.10
184_F 7_Q 0.62 0.20 0.10
195_V 207_I 0.62 0.20 0.10
157_M 24_L 0.61 0.19 0.09
144_Q 132_L 0.61 0.19 0.09
119_S 156_L 0.61 0.19 0.09
177_D 88_E 0.61 0.19 0.09
74_P 130_D 0.61 0.19 0.09
329_Q 303_A 0.60 0.19 0.09
114_Q 107_R 0.60 0.19 0.09
337_I 91_D 0.60 0.19 0.09
71_F 82_F 0.60 0.18 0.09
41_E 222_E 0.60 0.18 0.09
174_S 126_E 0.59 0.18 0.08
180_E 85_F 0.59 0.18 0.08
85_S 23_V 0.59 0.18 0.08
190_A 24_L 0.59 0.18 0.08
294_L 17_L 0.59 0.18 0.08
140_I 88_E 0.59 0.17 0.08
71_F 83_F 0.58 0.17 0.08
137_P 84_G 0.58 0.17 0.08
219_K 321_V 0.58 0.17 0.08
182_I 164_N 0.58 0.17 0.08
143_A 95_G 0.58 0.17 0.07
292_K 109_H 0.58 0.17 0.07
156_K 74_F 0.58 0.17 0.07
219_K 126_E 0.57 0.17 0.07
293_F 320_K 0.57 0.17 0.07
269_T 300_F 0.57 0.17 0.07
203_I 117_P 0.57 0.16 0.07
183_N 58_A 0.57 0.16 0.07
142_G 52_V 0.57 0.16 0.07
204_S 122_V 0.57 0.16 0.07
154_G 74_F 0.56 0.16 0.07
40_D 272_V 0.56 0.16 0.07
157_M 67_I 0.56 0.16 0.07
139_I 126_E 0.56 0.16 0.07
176_G 140_P 0.56 0.16 0.07
139_I 103_R 0.56 0.16 0.07
197_Q 33_N 0.56 0.16 0.07
140_I 132_L 0.56 0.16 0.07
328_K 302_Q 0.56 0.16 0.07
171_G 270_A 0.56 0.16 0.07
52_Y 66_A 0.56 0.16 0.07
339_F 142_L 0.56 0.16 0.07
142_G 212_M 0.56 0.15 0.07
331_V 168_I 0.56 0.15 0.07
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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