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OPENSEQ.org
1efv_1_A_B
Genes: A B A+B
Length: 315 255 566
Sequences: 3098 2620 2382
Seq/Len: 9.83 10.27 4.21
MirrorTree (Pazo et al. 2001) 0.91
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 0.01 4.13
2 0.01 0.01 4.15
5 0.01 0.01 4.17
10 0.01 0.01 4.18
20 0.02 0.01 4.18
100 0.03 0.03 4.19
∞ 0.09 0.08 4.23
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
180_E 174_R 4.37 1.00 1.00
108_K 140_G 3.29 1.00 1.00
140_K 223_S 3.15 1.00 1.00
104_R 140_G 2.91 1.00 1.00
311_I 243_E 2.33 1.00 1.00
110_E 106_R 2.04 1.00 0.99
279_V 245_L 1.86 1.00 0.98
113_P 133_Q 1.77 0.99 0.97
127_V 228_E 1.73 0.99 0.97
107_A 137_M 1.70 0.99 0.96
184_Q 171_E 1.69 0.99 0.96
104_R 146_Q 1.68 0.99 0.96
138_T 226_S 1.67 0.99 0.96
178_I 143_D 1.61 0.99 0.95
311_I 246_V 1.46 0.97 0.91
183_D 172_T 1.44 0.97 0.90
71_P 146_Q 1.33 0.95 0.85
178_I 145_P 1.30 0.94 0.84
295_Y 245_L 1.30 0.94 0.83
182_L 172_T 1.23 0.91 0.79
182_L 174_R 1.22 0.91 0.78
315_K 250_K 1.21 0.90 0.78
107_A 141_F 1.12 0.85 0.70
112_A 100_G 1.11 0.84 0.68
297_I 242_T 1.11 0.84 0.68
297_I 239_V 1.07 0.81 0.65
142_D 223_S 1.07 0.81 0.64
135_A 22_V 1.07 0.81 0.64
76_P 143_D 1.04 0.79 0.61
135_A 227_V 1.04 0.79 0.61
108_K 143_D 1.01 0.76 0.57
100_N 146_Q 0.96 0.70 0.52
179_S 173_L 0.96 0.70 0.52
140_K 225_I 0.96 0.70 0.52
103_P 132_N 0.94 0.68 0.49
277_T 252_I 0.94 0.68 0.49
315_K 247_A 0.93 0.67 0.48
115_S 133_Q 0.93 0.66 0.47
115_S 131_C 0.88 0.60 0.41
299_A 119_L 0.87 0.59 0.40
110_E 141_F 0.86 0.58 0.39
216_L 20_I 0.83 0.53 0.35
103_P 39_N 0.82 0.52 0.34
125_T 225_I 0.81 0.52 0.33
185_K 172_T 0.81 0.51 0.33
100_N 148_T 0.80 0.50 0.32
308_M 246_V 0.79 0.49 0.31
112_A 222_L 0.78 0.47 0.30
178_I 176_K 0.77 0.46 0.28
199_V 214_L 0.77 0.45 0.28
131_Y 28_G 0.76 0.45 0.27
276_K 252_I 0.76 0.44 0.27
296_G 201_A 0.74 0.41 0.25
177_E 143_D 0.74 0.41 0.25
149_S 27_T 0.74 0.41 0.24
200_V 134_T 0.73 0.41 0.24
182_L 161_K 0.73 0.40 0.24
113_P 131_C 0.72 0.39 0.23
103_P 147_G 0.71 0.38 0.22
180_E 176_K 0.71 0.37 0.21
234_V 130_D 0.70 0.37 0.21
238_F 9_A 0.70 0.36 0.21
281_I 64_V 0.69 0.36 0.20
98_G 45_A 0.68 0.34 0.19
71_P 173_L 0.68 0.34 0.19
156_D 254_R 0.68 0.34 0.19
284_D 202_K 0.68 0.34 0.19
206_G 61_V 0.68 0.33 0.18
75_T 140_G 0.67 0.33 0.18
136_L 228_E 0.67 0.33 0.18
175_P 145_P 0.67 0.32 0.18
151_R 39_N 0.67 0.32 0.18
248_T 183_A 0.66 0.32 0.17
138_T 225_I 0.66 0.31 0.17
248_T 17_A 0.65 0.31 0.17
19_T 50_V 0.65 0.31 0.17
276_K 205_K 0.65 0.30 0.16
305_V 108_L 0.65 0.30 0.16
150_V 9_A 0.65 0.30 0.16
138_T 228_E 0.65 0.30 0.16
129_T 130_D 0.64 0.29 0.16
22_T 91_V 0.64 0.29 0.15
97_F 173_L 0.64 0.29 0.15
99_K 149_F 0.64 0.29 0.15
230_S 198_I 0.64 0.29 0.15
231_R 47_E 0.64 0.29 0.15
269_L 80_A 0.63 0.28 0.15
112_A 221_K 0.63 0.28 0.15
283_K 202_K 0.63 0.28 0.15
278_I 233_R 0.63 0.28 0.15
137_C 227_V 0.62 0.27 0.14
110_E 102_L 0.62 0.27 0.14
185_K 163_E 0.62 0.27 0.14
200_V 121_L 0.62 0.27 0.14
105_V 223_S 0.61 0.26 0.14
71_P 140_G 0.61 0.26 0.14
57_K 159_K 0.61 0.26 0.14
228_G 112_A 0.61 0.26 0.13
245_V 234_T 0.61 0.26 0.13
128_R 130_D 0.61 0.26 0.13
200_V 247_A 0.60 0.25 0.13
143_E 223_S 0.60 0.25 0.13
235_D 41_F 0.60 0.25 0.13
64_D 250_K 0.60 0.25 0.13
166_S 144_W 0.60 0.25 0.13
279_V 163_E 0.60 0.25 0.12
103_P 133_Q 0.60 0.25 0.12
283_K 167_D 0.60 0.24 0.12
153_T 227_V 0.60 0.24 0.12
315_K 246_V 0.59 0.24 0.12
312_L 153_V 0.59 0.24 0.12
192_P 167_D 0.59 0.24 0.12
94_A 130_D 0.59 0.24 0.12
305_V 76_R 0.59 0.24 0.12
245_V 185_L 0.59 0.24 0.12
132_A 29_V 0.59 0.24 0.12
235_D 191_R 0.59 0.24 0.12
215_L 74_T 0.59 0.23 0.12
78_I 252_I 0.58 0.23 0.12
5_L 46_V 0.58 0.23 0.11
310_E 181_V 0.58 0.23 0.11
279_V 248_K 0.58 0.23 0.11
285_P 121_L 0.58 0.23 0.11
248_T 188_N 0.58 0.23 0.11
312_L 250_K 0.58 0.23 0.11
94_A 31_T 0.58 0.23 0.11
247_Q 127_I 0.57 0.22 0.11
304_V 160_L 0.57 0.22 0.11
277_T 246_V 0.57 0.22 0.11
103_P 162_V 0.57 0.22 0.11
308_M 38_M 0.57 0.22 0.11
81_T 108_L 0.57 0.22 0.10
290_F 245_L 0.57 0.22 0.10
241_N 138_T 0.57 0.22 0.10
79_L 143_D 0.57 0.22 0.10
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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