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OPENSEQ.org
HCP_VipB
Genes: A B A+B
Length: 172 492 654
Sequences: 490 556 143
Seq/Len: 2.85 1.13 0.22
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 0.05 0.07 0.05
2 0.06 0.08 0.09
5 0.07 0.08 0.16
10 0.08 0.09 0.19
20 0.16 0.10 0.22
100 0.18 0.11 0.23
∞ 0.21 0.16 0.30
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
99_Y 460_N 2.03 0.66 0.02
68_F 46_F 1.85 0.55 0.01
154_D 332_T 1.52 0.35 0.01
110_F 465_Q 1.49 0.34 0.01
118_A 445_R 1.48 0.33 0.01
155_H 333_D 1.47 0.33 0.01
160_T 333_D 1.36 0.27 0.00
39_M 160_I 1.35 0.27 0.00
72_V 130_F 1.32 0.25 0.00
111_F 331_I 1.31 0.24 0.00
168_K 65_V 1.30 0.24 0.00
144_V 384_K 1.26 0.22 0.00
78_V 240_A 1.26 0.22 0.00
78_V 130_F 1.23 0.21 0.00
43_Q 192_S 1.23 0.21 0.00
45_D 222_T 1.23 0.21 0.00
50_V 148_Y 1.22 0.20 0.00
161_S 133_E 1.21 0.20 0.00
160_T 434_Q 1.20 0.20 0.00
68_F 86_N 1.19 0.20 0.00
78_V 332_T 1.19 0.19 0.00
43_Q 190_I 1.19 0.19 0.00
123_I 283_T 1.18 0.19 0.00
161_S 136_Q 1.16 0.18 0.00
101_T 333_D 1.16 0.18 0.00
67_P 214_S 1.15 0.18 0.00
153_W 244_L 1.14 0.17 0.00
27_I 27_T 1.13 0.17 0.00
121_V 60_V 1.12 0.17 0.00
2_P 83_I 1.09 0.16 0.00
140_Q 147_G 1.08 0.16 0.00
75_N 130_F 1.08 0.15 0.00
155_H 112_N 1.07 0.15 0.00
75_N 332_T 1.07 0.15 0.00
10_E 161_G 1.07 0.15 0.00
77_A 237_G 1.06 0.15 0.00
127_M 197_F 1.06 0.15 0.00
111_F 482_E 1.05 0.14 0.00
44_F 58_E 1.04 0.14 0.00
28_G 379_A 1.03 0.14 0.00
9_I 81_D 1.02 0.14 0.00
107_Q 396_N 1.01 0.13 0.00
116_E 194_G 1.01 0.13 0.00
9_I 261_Y 1.01 0.13 0.00
42_Q 441_V 1.01 0.13 0.00
118_A 285_L 1.00 0.13 0.00
67_P 148_Y 1.00 0.13 0.00
162_G 315_F 1.00 0.13 0.00
58_Q 333_D 1.00 0.13 0.00
44_F 48_E 1.00 0.13 0.00
32_V 72_L 1.00 0.13 0.00
2_P 65_V 1.00 0.13 0.00
116_E 159_I 0.99 0.13 0.00
101_T 439_A 0.99 0.13 0.00
72_V 332_T 0.98 0.13 0.00
129_H 465_Q 0.98 0.13 0.00
160_T 303_S 0.98 0.13 0.00
99_Y 54_Q 0.98 0.12 0.00
114_K 412_A 0.98 0.12 0.00
140_Q 465_Q 0.98 0.12 0.00
43_Q 261_Y 0.98 0.12 0.00
52_T 168_S 0.97 0.12 0.00
120_I 23_I 0.97 0.12 0.00
78_V 193_V 0.97 0.12 0.00
47_V 308_E 0.97 0.12 0.00
161_S 332_T 0.97 0.12 0.00
121_V 190_I 0.97 0.12 0.00
117_N 170_P 0.97 0.12 0.00
3_T 101_L 0.96 0.12 0.00
165_D 396_N 0.96 0.12 0.00
2_P 72_L 0.96 0.12 0.00
80_L 39_A 0.96 0.12 0.00
153_W 329_V 0.95 0.12 0.00
26_S 333_D 0.95 0.12 0.00
52_T 488_R 0.95 0.12 0.00
120_I 205_E 0.95 0.12 0.00
71_T 261_Y 0.95 0.12 0.00
2_P 132_P 0.94 0.12 0.00
47_V 86_N 0.94 0.12 0.00
17_I 355_N 0.94 0.12 0.00
18_T 409_Q 0.94 0.12 0.00
120_I 112_N 0.94 0.11 0.00
82_Y 269_H 0.93 0.11 0.00
56_S 47_I 0.93 0.11 0.00
71_T 81_D 0.93 0.11 0.00
52_T 191_S 0.93 0.11 0.00
135_K 92_M 0.93 0.11 0.00
62_Q 373_T 0.93 0.11 0.00
111_F 193_V 0.93 0.11 0.00
71_T 418_D 0.93 0.11 0.00
160_T 296_P 0.93 0.11 0.00
96_L 309_D 0.92 0.11 0.00
27_I 260_N 0.92 0.11 0.00
70_F 80_M 0.92 0.11 0.00
11_G 487_G 0.92 0.11 0.00
125_C 209_I 0.92 0.11 0.00
154_D 115_E 0.91 0.11 0.00
75_N 381_T 0.91 0.11 0.00
118_A 284_R 0.91 0.11 0.00
48_V 267_A 0.91 0.11 0.00
123_I 180_A 0.90 0.11 0.00
77_A 46_F 0.90 0.10 0.00
47_V 84_L 0.90 0.10 0.00
53_D 23_I 0.90 0.10 0.00
64_V 119_V 0.90 0.10 0.00
9_I 189_F 0.90 0.10 0.00
59_P 415_E 0.90 0.10 0.00
33_E 182_G 0.90 0.10 0.00
102_S 439_A 0.90 0.10 0.00
94_V 135_A 0.90 0.10 0.00
156_V 332_T 0.90 0.10 0.00
127_M 179_G 0.89 0.10 0.00
50_V 221_Y 0.89 0.10 0.00
38_E 333_D 0.89 0.10 0.00
154_D 145_S 0.89 0.10 0.00
155_H 303_S 0.89 0.10 0.00
135_K 329_V 0.88 0.10 0.00
165_D 333_D 0.88 0.10 0.00
7_I 130_F 0.88 0.10 0.00
87_S 181_L 0.88 0.10 0.00
138_F 393_M 0.88 0.10 0.00
9_I 226_S 0.88 0.10 0.00
133_P 309_D 0.88 0.10 0.00
40_L 98_G 0.88 0.10 0.00
40_L 233_A 0.88 0.10 0.00
120_I 179_G 0.88 0.10 0.00
43_Q 81_D 0.87 0.10 0.00
159_G 433_D 0.87 0.10 0.00
120_I 136_Q 0.87 0.10 0.00
33_E 98_G 0.87 0.10 0.00
72_V 318_M 0.87 0.10 0.00
90_K 280_A 0.87 0.10 0.00
61_G 363_S 0.87 0.10 0.00
25_D 467_S 0.87 0.10 0.00
80_L 40_K 0.87 0.10 0.00
134_A 134_T 0.86 0.10 0.00
140_Q 227_L 0.86 0.10 0.00
99_Y 190_I 0.86 0.10 0.00
121_V 29_I 0.86 0.10 0.00
5_C 77_S 0.86 0.10 0.00
48_V 221_Y 0.86 0.10 0.00
66_K 216_F 0.86 0.10 0.00
133_P 86_N 0.86 0.10 0.00
94_V 157_G 0.86 0.10 0.00
146_L 154_E 0.85 0.09 0.00
77_A 158_A 0.85 0.09 0.00
6_Y 234_R 0.85 0.09 0.00
26_S 434_Q 0.85 0.09 0.00
25_D 392_M 0.85 0.09 0.00
127_M 402_V 0.85 0.09 0.00
162_G 352_G 0.85 0.09 0.00
87_S 216_F 0.85 0.09 0.00
39_M 133_E 0.85 0.09 0.00
10_E 262_A 0.84 0.09 0.00
135_K 146_A 0.84 0.09 0.00
41_V 133_E 0.84 0.09 0.00
52_T 123_E 0.84 0.09 0.00
158_A 333_D 0.84 0.09 0.00
125_C 332_T 0.84 0.09 0.00
72_V 227_L 0.84 0.09 0.00
44_F 160_I 0.84 0.09 0.00
60_S 147_G 0.84 0.09 0.00
127_M 269_H 0.84 0.09 0.00
6_Y 278_A 0.84 0.09 0.00
39_M 193_V 0.84 0.09 0.00
70_F 183_A 0.84 0.09 0.00
80_L 333_D 0.84 0.09 0.00
5_C 72_L 0.84 0.09 0.00
6_Y 46_F 0.84 0.09 0.00
68_F 425_S 0.84 0.09 0.00
96_L 318_M 0.84 0.09 0.00
150_K 108_F 0.84 0.09 0.00
159_G 432_A 0.84 0.09 0.00
135_K 468_L 0.84 0.09 0.00
25_D 46_F 0.83 0.09 0.00
169_P 179_G 0.83 0.09 0.00
160_T 39_A 0.83 0.09 0.00
141_N 168_S 0.83 0.09 0.00
14_Q 487_G 0.83 0.09 0.00
60_S 250_D 0.83 0.09 0.00
121_V 425_S 0.83 0.09 0.00
77_A 72_L 0.83 0.09 0.00
158_A 61_N 0.83 0.09 0.00
26_S 303_S 0.83 0.09 0.00
90_K 313_H 0.83 0.09 0.00
28_G 102_F 0.83 0.09 0.00
133_P 453_E 0.83 0.09 0.00
41_V 335_K 0.82 0.09 0.00
163_S 46_F 0.82 0.09 0.00
143_T 222_T 0.82 0.09 0.00
93_T 329_V 0.82 0.09 0.00
120_I 470_V 0.82 0.09 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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