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OPENSEQ.org
Hcp-VipB
Genes: A B A+B
Length: 172 492 655
Sequences: 938 558 369
Seq/Len: 5.45 1.13 0.56
MirrorTree (Pazo et al. 2001) 0.74
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.04 0.07 0.33
2 0.05 0.08 0.38
5 0.07 0.08 0.47
10 0.08 0.09 0.52
20 0.13 0.10 0.56
100 0.14 0.11 0.57
∞ 0.19 0.16 0.61
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
41_V 163_Y 1.50 0.60 0.00
114_K 86_N 1.47 0.58 0.00
41_V 412_A 1.33 0.46 0.00
117_N 201_D 1.26 0.41 0.00
148_Y 420_E 1.25 0.40 0.00
150_K 440_D 1.24 0.39 0.00
115_L 420_E 1.21 0.37 0.00
27_I 233_A 1.20 0.36 0.00
6_Y 233_A 1.16 0.33 0.00
110_F 199_G 1.13 0.31 0.00
110_F 84_L 1.11 0.30 0.00
42_Q 114_V 1.08 0.28 0.00
37_D 160_I 1.07 0.27 0.00
101_T 333_D 1.05 0.27 0.00
72_V 118_H 1.05 0.26 0.00
68_F 46_F 1.04 0.26 0.00
7_I 170_P 1.03 0.25 0.00
38_E 333_D 1.02 0.25 0.00
148_Y 459_G 1.01 0.24 0.00
96_L 124_L 1.01 0.24 0.00
89_E 435_E 1.01 0.24 0.00
74_L 72_L 1.01 0.24 0.00
77_A 67_Q 1.01 0.24 0.00
146_L 44_A 1.01 0.24 0.00
119_S 114_V 1.00 0.23 0.00
41_V 168_S 0.99 0.23 0.00
96_L 193_V 0.99 0.23 0.00
72_V 130_F 0.99 0.23 0.00
147_S 365_Q 0.98 0.22 0.00
120_I 193_V 0.96 0.21 0.00
115_L 76_I 0.95 0.20 0.00
68_F 233_A 0.94 0.20 0.00
151_I 424_N 0.93 0.19 0.00
86_S 39_A 0.92 0.19 0.00
168_K 65_V 0.92 0.19 0.00
162_G 315_F 0.92 0.19 0.00
41_V 460_N 0.91 0.19 0.00
121_V 198_F 0.91 0.19 0.00
158_A 333_D 0.91 0.18 0.00
116_E 33_E 0.91 0.18 0.00
119_S 410_I 0.90 0.18 0.00
144_V 459_G 0.90 0.18 0.00
96_L 88_Q 0.90 0.18 0.00
60_S 332_T 0.90 0.18 0.00
122_D 456_D 0.90 0.18 0.00
100_R 432_A 0.90 0.18 0.00
120_I 230_S 0.90 0.18 0.00
81_L 74_K 0.89 0.18 0.00
161_S 420_E 0.89 0.17 0.00
104_E 195_P 0.89 0.17 0.00
146_L 264_N 0.89 0.17 0.00
108_E 410_I 0.89 0.17 0.00
116_E 427_I 0.88 0.17 0.00
116_E 389_L 0.88 0.17 0.00
79_P 344_F 0.88 0.17 0.00
133_P 86_N 0.88 0.17 0.00
159_G 218_S 0.88 0.17 0.00
43_Q 192_S 0.88 0.17 0.00
76_K 84_L 0.87 0.17 0.00
117_N 324_K 0.87 0.17 0.00
43_Q 159_I 0.87 0.17 0.00
68_F 424_N 0.87 0.17 0.00
53_D 405_L 0.87 0.17 0.00
9_I 267_A 0.87 0.17 0.00
66_K 216_F 0.86 0.16 0.00
155_H 259_F 0.86 0.16 0.00
120_I 453_E 0.86 0.16 0.00
115_L 74_K 0.86 0.16 0.00
57_G 282_A 0.85 0.16 0.00
80_L 288_S 0.85 0.16 0.00
158_A 432_A 0.85 0.16 0.00
6_Y 234_R 0.85 0.16 0.00
83_N 344_F 0.85 0.16 0.00
96_L 37_D 0.85 0.16 0.00
60_S 471_R 0.84 0.16 0.00
39_M 201_D 0.84 0.16 0.00
61_G 90_Q 0.84 0.16 0.00
48_V 239_T 0.84 0.15 0.00
122_D 257_K 0.84 0.15 0.00
157_N 432_A 0.84 0.15 0.00
117_N 231_E 0.84 0.15 0.00
10_E 161_G 0.83 0.15 0.00
9_I 67_Q 0.83 0.15 0.00
146_L 87_S 0.83 0.15 0.00
11_G 201_D 0.83 0.15 0.00
156_V 261_Y 0.83 0.15 0.00
45_D 222_T 0.83 0.15 0.00
63_R 434_Q 0.82 0.15 0.00
70_F 219_P 0.82 0.15 0.00
28_G 379_A 0.82 0.15 0.00
2_P 133_E 0.82 0.14 0.00
104_E 69_L 0.82 0.14 0.00
122_D 405_L 0.82 0.14 0.00
9_I 440_D 0.82 0.14 0.00
156_V 143_V 0.81 0.14 0.00
162_G 333_D 0.81 0.14 0.00
51_P 424_N 0.81 0.14 0.00
120_I 270_E 0.81 0.14 0.00
145_S 169_T 0.81 0.14 0.00
161_S 178_M 0.81 0.14 0.00
7_I 133_E 0.81 0.14 0.00
84_A 199_G 0.81 0.14 0.00
43_Q 190_I 0.81 0.14 0.00
53_D 288_S 0.81 0.14 0.00
46_H 80_M 0.81 0.14 0.00
82_Y 282_A 0.81 0.14 0.00
155_H 317_S 0.81 0.14 0.00
152_T 329_V 0.80 0.14 0.00
113_T 119_V 0.80 0.14 0.00
118_A 363_S 0.80 0.14 0.00
155_H 333_D 0.80 0.14 0.00
120_I 77_S 0.80 0.14 0.00
35_H 333_D 0.80 0.14 0.00
143_T 185_A 0.80 0.14 0.00
39_M 185_A 0.80 0.14 0.00
44_F 218_S 0.79 0.14 0.00
143_T 83_I 0.79 0.14 0.00
70_F 123_E 0.79 0.14 0.00
11_G 279_F 0.79 0.13 0.00
120_I 271_H 0.79 0.13 0.00
7_I 124_L 0.79 0.13 0.00
60_S 289_F 0.79 0.13 0.00
146_L 215_T 0.78 0.13 0.00
15_G 150_Q 0.78 0.13 0.00
7_I 421_R 0.78 0.13 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
4272 0.48 HCP_VipB Δgene:(1, 5) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4271 0.16 HCP_VipB Δgene:(1, 5) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4225 0.22 HCP_VipB Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4224 0.56 Hcp-VipB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done
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