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OPENSEQ.org
XF
Genes: A B A+B
Length: 307 253 504
Sequences: 1803 81320 87
Seq/Len: 5.87 321.42 0.17
MirrorTree (Pazo et al. 2001) 0.63
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 0.03 0.11 0.01
2 0.03 0.12 0.02
5 0.03 0.15 0.16
10 0.03 0.20 0.30
20 0.03 0.25 0.52
100 0.03 0.35 1.26
∞ 0.08 0.37 1.74
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
51_D 45_G 1.70 0.39 0.00
15_G 23_L 1.51 0.29 0.00
27_E 242_V 1.24 0.18 0.00
156_V 189_M 1.23 0.18 0.00
105_Q 180_Q 1.21 0.17 0.00
42_D 214_V 1.20 0.17 0.00
130_T 184_K 1.15 0.15 0.00
172_N 173_A 1.14 0.15 0.00
212_F 47_T 1.14 0.15 0.00
101_A 171_T 1.13 0.15 0.00
211_V 173_A 1.12 0.14 0.00
9_G 40_G 1.12 0.14 0.00
9_G 46_K 1.12 0.14 0.00
9_G 145_S 1.12 0.14 0.00
9_G 147_G 1.12 0.14 0.00
9_G 168_D 1.12 0.14 0.00
9_G 169_E 1.12 0.14 0.00
9_G 175_D 1.12 0.14 0.00
66_D 64_I 1.12 0.14 0.00
189_V 197_I 1.11 0.14 0.00
264_L 16_K 1.10 0.14 0.00
52_I 135_D 1.10 0.14 0.00
110_I 102_V 1.10 0.14 0.00
52_I 173_A 1.10 0.14 0.00
25_D 158_F 1.09 0.14 0.00
11_T 96_L 1.09 0.14 0.00
27_E 64_I 1.09 0.14 0.00
48_I 158_F 1.08 0.13 0.00
182_G 149_R 1.08 0.13 0.00
102_A 57_D 1.07 0.13 0.00
15_G 47_T 1.07 0.13 0.00
163_V 30_I 1.06 0.13 0.00
105_Q 64_I 1.06 0.13 0.00
19_S 196_T 1.05 0.13 0.00
260_Y 53_L 1.05 0.13 0.00
242_L 164_I 1.05 0.12 0.00
183_Y 196_T 1.05 0.12 0.00
15_G 49_L 1.03 0.12 0.00
68_A 154_A 1.02 0.12 0.00
203_K 30_I 1.02 0.12 0.00
43_V 197_I 1.01 0.12 0.00
56_E 233_H 1.01 0.12 0.00
28_L 221_I 1.01 0.11 0.00
9_G 43_G 1.00 0.11 0.00
256_H 197_I 1.00 0.11 0.00
51_D 40_G 1.00 0.11 0.00
51_D 46_K 1.00 0.11 0.00
51_D 145_S 1.00 0.11 0.00
51_D 147_G 1.00 0.11 0.00
51_D 168_D 1.00 0.11 0.00
51_D 169_E 1.00 0.11 0.00
51_D 175_D 1.00 0.11 0.00
7_L 68_G 1.00 0.11 0.00
254_Y 135_D 0.99 0.11 0.00
148_L 9_L 0.99 0.11 0.00
12_G 40_G 0.99 0.11 0.00
12_G 46_K 0.99 0.11 0.00
12_G 145_S 0.99 0.11 0.00
12_G 147_G 0.99 0.11 0.00
12_G 168_D 0.99 0.11 0.00
12_G 169_E 0.99 0.11 0.00
12_G 175_D 0.99 0.11 0.00
10_G 196_T 0.99 0.11 0.00
27_E 221_I 0.98 0.11 0.00
3_P 221_I 0.97 0.11 0.00
248_K 38_I 0.97 0.11 0.00
249_E 232_K 0.97 0.11 0.00
10_G 128_A 0.97 0.10 0.00
141_R 101_T 0.96 0.10 0.00
109_V 23_L 0.96 0.10 0.00
15_G 40_G 0.96 0.10 0.00
15_G 46_K 0.96 0.10 0.00
15_G 145_S 0.96 0.10 0.00
15_G 147_G 0.96 0.10 0.00
15_G 168_D 0.96 0.10 0.00
15_G 169_E 0.96 0.10 0.00
15_G 175_D 0.96 0.10 0.00
50_C 122_N 0.96 0.10 0.00
24_N 232_K 0.96 0.10 0.00
190_K 5_E 0.95 0.10 0.00
62_M 148_Q 0.95 0.10 0.00
33_K 26_I 0.95 0.10 0.00
166_K 101_T 0.95 0.10 0.00
159_T 53_L 0.94 0.10 0.00
174_V 148_Q 0.94 0.10 0.00
27_E 232_K 0.94 0.10 0.00
107_K 64_I 0.94 0.10 0.00
18_L 150_Q 0.94 0.10 0.00
18_L 64_I 0.94 0.10 0.00
27_E 23_L 0.94 0.10 0.00
141_R 39_M 0.93 0.10 0.00
203_K 240_I 0.93 0.10 0.00
251_A 232_K 0.93 0.10 0.00
11_T 159_I 0.93 0.10 0.00
39_K 242_V 0.93 0.10 0.00
19_S 9_L 0.93 0.10 0.00
182_G 3_I 0.92 0.10 0.00
107_K 36_I 0.92 0.10 0.00
37_N 138_D 0.92 0.10 0.00
55_Y 101_T 0.92 0.10 0.00
45_M 30_I 0.92 0.10 0.00
247_I 242_V 0.92 0.10 0.00
251_A 180_Q 0.92 0.10 0.00
84_S 198_I 0.91 0.09 0.00
22_I 132_N 0.91 0.09 0.00
189_V 221_I 0.91 0.09 0.00
31_I 4_L 0.91 0.09 0.00
7_L 217_K 0.91 0.09 0.00
256_H 140_Y 0.91 0.09 0.00
9_G 62_G 0.91 0.09 0.00
39_K 68_G 0.91 0.09 0.00
212_F 137_S 0.90 0.09 0.00
108_K 228_G 0.90 0.09 0.00
41_D 88_G 0.90 0.09 0.00
257_L 53_L 0.90 0.09 0.00
18_L 25_D 0.90 0.09 0.00
230_S 188_R 0.90 0.09 0.00
243_E 141_P 0.89 0.09 0.00
110_I 88_G 0.89 0.09 0.00
182_G 87_I 0.89 0.09 0.00
23_E 27_N 0.89 0.09 0.00
251_A 38_I 0.89 0.09 0.00
68_A 70_K 0.89 0.09 0.00
208_P 53_L 0.88 0.09 0.00
112_I 34_E 0.88 0.09 0.00
162_V 8_Q 0.88 0.09 0.00
32_S 150_Q 0.88 0.09 0.00
46_T 129_E 0.88 0.09 0.00
110_I 118_E 0.88 0.09 0.00
30_T 29_S 0.88 0.09 0.00
202_I 9_L 0.88 0.09 0.00
51_D 43_G 0.88 0.09 0.00
111_Y 164_I 0.88 0.09 0.00
251_A 158_F 0.87 0.09 0.00
56_E 242_V 0.87 0.09 0.00
176_H 51_N 0.87 0.09 0.00
251_A 186_L 0.87 0.09 0.00
12_G 196_T 0.87 0.09 0.00
254_Y 192_A 0.87 0.09 0.00
13_Y 64_I 0.87 0.09 0.00
45_M 150_Q 0.87 0.09 0.00
224_L 27_N 0.87 0.09 0.00
265_F 27_N 0.87 0.09 0.00
15_G 174_L 0.86 0.09 0.00
206_V 221_I 0.86 0.09 0.00
249_E 49_L 0.86 0.09 0.00
26_A 129_E 0.86 0.09 0.00
146_V 6_V 0.86 0.09 0.00
255_I 154_A 0.86 0.09 0.00
12_G 43_G 0.86 0.08 0.00
131_P 186_L 0.86 0.08 0.00
218_A 198_I 0.86 0.08 0.00
31_I 131_L 0.86 0.08 0.00
217_T 198_I 0.86 0.08 0.00
195_H 2_A 0.86 0.08 0.00
256_H 36_I 0.86 0.08 0.00
51_D 196_T 0.86 0.08 0.00
180_W 239_I 0.86 0.08 0.00
183_Y 238_E 0.85 0.08 0.00
224_L 77_K 0.85 0.08 0.00
29_F 9_L 0.85 0.08 0.00
7_L 33_G 0.85 0.08 0.00
206_V 232_K 0.85 0.08 0.00
254_Y 186_L 0.85 0.08 0.00
218_A 128_A 0.85 0.08 0.00
161_K 8_Q 0.85 0.08 0.00
264_L 70_K 0.85 0.08 0.00
202_I 187_T 0.85 0.08 0.00
67_I 101_T 0.84 0.08 0.00
27_E 38_I 0.84 0.08 0.00
265_F 234_T 0.84 0.08 0.00
91_L 128_A 0.84 0.08 0.00
101_A 202_H 0.84 0.08 0.00
174_V 88_G 0.84 0.08 0.00
15_G 45_G 0.84 0.08 0.00
28_L 38_I 0.84 0.08 0.00
252_V 180_Q 0.84 0.08 0.00
18_L 205_V 0.84 0.08 0.00
31_I 130_A 0.84 0.08 0.00
169_T 34_E 0.84 0.08 0.00
107_K 12_I 0.83 0.08 0.00
24_N 171_T 0.83 0.08 0.00
160_M 132_N 0.83 0.08 0.00
44_E 77_K 0.83 0.08 0.00
45_M 103_K 0.83 0.08 0.00
113_P 32_E 0.83 0.08 0.00
15_G 43_G 0.83 0.08 0.00
263_R 225_L 0.83 0.08 0.00
240_G 47_T 0.83 0.08 0.00
25_D 79_L 0.83 0.08 0.00
163_V 42_S 0.83 0.08 0.00
159_T 87_I 0.83 0.08 0.00
255_I 30_I 0.83 0.08 0.00
100_A 201_T 0.83 0.08 0.00
129_G 189_M 0.83 0.08 0.00
56_E 232_K 0.82 0.08 0.00
251_A 198_I 0.82 0.08 0.00
218_A 31_E 0.82 0.08 0.00
62_M 47_T 0.82 0.08 0.00
256_H 48_T 0.82 0.08 0.00
103_I 189_M 0.82 0.08 0.00
245_R 44_S 0.82 0.08 0.00
125_L 106_I 0.82 0.08 0.00
231_L 57_D 0.82 0.08 0.00
63_N 135_D 0.82 0.08 0.00
209_L 22_V 0.81 0.08 0.00
9_G 45_G 0.81 0.08 0.00
25_D 220_Q 0.81 0.08 0.00
169_T 165_I 0.81 0.08 0.00
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)
ID Seq/Len Name Options I_Prob Status
10756 0.17 XF Δgene:(1, 5) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10193 1.83 Gx-Vf2 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-60, 4) msa: HHblits (2015_06) 0.00 Done - Shared
10190 1.93 Gx-Vf1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 4) msa: HHblits (2015_06) 0.00 Done - Shared
10147 1.86 Gx-Vf Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 4) msa: HHblits (2015_06) 0.01 Done - Shared
10139 1.95 X-F1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.04 Done - Shared
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