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OPENSEQ.org
HCP_VipB
Genes: A B A+B
Length: 172 492 648
Sequences: 938 558 310
Seq/Len: 5.45 1.13 0.48
MirrorTree (Pazo et al. 2001) 0.77
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
27_I 233_A 1.41 0.48 0.00
41_V 163_Y 1.39 0.47 0.00
110_F 84_L 1.33 0.42 0.00
74_L 72_L 1.28 0.39 0.00
43_Q 190_I 1.22 0.34 0.00
6_Y 233_A 1.21 0.34 0.00
41_V 412_A 1.21 0.33 0.00
115_L 420_E 1.19 0.32 0.00
43_Q 159_I 1.17 0.31 0.00
150_K 440_D 1.16 0.30 0.00
114_K 86_N 1.15 0.30 0.00
42_Q 114_V 1.15 0.29 0.00
72_V 118_H 1.12 0.28 0.00
146_L 44_A 1.10 0.27 0.00
108_E 410_I 1.10 0.27 0.00
7_I 170_P 1.09 0.26 0.00
117_N 231_E 1.09 0.26 0.00
110_F 158_A 1.09 0.26 0.00
113_T 288_S 1.08 0.25 0.00
96_L 88_Q 1.08 0.25 0.00
84_A 199_G 1.06 0.24 0.00
148_Y 420_E 1.05 0.24 0.00
61_G 90_Q 1.05 0.24 0.00
120_I 230_S 1.04 0.23 0.00
68_F 46_F 1.04 0.23 0.00
98_W 340_A 1.02 0.22 0.00
115_L 76_I 1.01 0.22 0.00
144_V 252_I 1.00 0.21 0.00
105_G 191_S 0.99 0.21 0.00
120_I 100_K 0.99 0.21 0.00
98_W 233_A 0.99 0.20 0.00
37_D 160_I 0.99 0.20 0.00
68_F 424_N 0.98 0.20 0.00
157_N 432_A 0.98 0.20 0.00
95_E 49_N 0.98 0.20 0.00
38_E 333_D 0.97 0.20 0.00
70_F 160_I 0.97 0.19 0.00
5_C 340_A 0.96 0.19 0.00
70_F 193_V 0.96 0.19 0.00
143_T 83_I 0.96 0.19 0.00
77_A 257_K 0.96 0.19 0.00
72_V 130_F 0.96 0.19 0.00
91_L 288_S 0.96 0.19 0.00
158_A 432_A 0.95 0.19 0.00
45_D 412_A 0.95 0.19 0.00
41_V 384_K 0.95 0.19 0.00
82_Y 84_L 0.95 0.18 0.00
153_W 148_Y 0.94 0.18 0.00
160_T 128_F 0.94 0.18 0.00
65_H 217_E 0.94 0.18 0.00
53_D 405_L 0.94 0.18 0.00
119_S 410_I 0.94 0.18 0.00
101_T 333_D 0.93 0.18 0.00
144_V 459_G 0.93 0.18 0.00
89_E 435_E 0.93 0.18 0.00
10_E 161_G 0.93 0.18 0.00
70_F 219_P 0.93 0.18 0.00
57_G 282_A 0.93 0.18 0.00
94_V 157_G 0.93 0.18 0.00
81_L 174_L 0.93 0.18 0.00
151_I 424_N 0.93 0.17 0.00
56_S 236_L 0.93 0.17 0.00
54_P 257_K 0.92 0.17 0.00
145_S 416_R 0.92 0.17 0.00
100_R 432_A 0.92 0.17 0.00
37_D 78_A 0.92 0.17 0.00
97_K 420_E 0.92 0.17 0.00
158_A 333_D 0.92 0.17 0.00
93_T 410_I 0.91 0.17 0.00
60_S 471_R 0.91 0.17 0.00
133_P 86_N 0.91 0.17 0.00
156_V 143_V 0.91 0.17 0.00
52_T 24_M 0.90 0.17 0.00
115_L 74_K 0.90 0.16 0.00
156_V 261_Y 0.90 0.16 0.00
159_G 218_S 0.89 0.16 0.00
118_A 370_F 0.89 0.16 0.00
27_I 364_I 0.89 0.16 0.00
76_K 84_L 0.89 0.16 0.00
53_D 288_S 0.88 0.16 0.00
11_G 436_N 0.88 0.16 0.00
162_G 333_D 0.88 0.16 0.00
48_V 239_T 0.88 0.16 0.00
120_I 453_E 0.88 0.15 0.00
6_Y 164_A 0.88 0.15 0.00
71_T 261_Y 0.87 0.15 0.00
111_F 408_E 0.87 0.15 0.00
78_V 164_A 0.87 0.15 0.00
28_G 379_A 0.87 0.15 0.00
50_V 84_L 0.87 0.15 0.00
100_R 198_F 0.87 0.15 0.00
110_F 457_V 0.87 0.15 0.00
9_I 67_Q 0.87 0.15 0.00
120_I 271_H 0.87 0.15 0.00
9_I 267_A 0.86 0.15 0.00
51_P 71_E 0.86 0.15 0.00
35_H 333_D 0.86 0.15 0.00
121_V 198_F 0.86 0.15 0.00
72_V 371_P 0.86 0.15 0.00
63_R 434_Q 0.86 0.15 0.00
11_G 68_M 0.86 0.15 0.00
146_L 264_N 0.86 0.15 0.00
90_K 402_V 0.85 0.14 0.00
78_V 52_G 0.85 0.14 0.00
41_V 460_N 0.85 0.14 0.00
100_R 419_L 0.85 0.14 0.00
88_G 331_I 0.85 0.14 0.00
118_A 363_S 0.85 0.14 0.00
68_F 269_H 0.85 0.14 0.00
94_V 252_I 0.85 0.14 0.00
107_Q 333_D 0.85 0.14 0.00
77_A 191_S 0.84 0.14 0.00
148_Y 459_G 0.84 0.14 0.00
81_L 114_V 0.84 0.14 0.00
51_P 424_N 0.84 0.14 0.00
110_F 114_V 0.84 0.14 0.00
118_A 293_R 0.84 0.14 0.00
146_L 83_I 0.84 0.14 0.00
3_T 201_D 0.84 0.14 0.00
153_W 344_F 0.84 0.14 0.00
98_W 215_T 0.84 0.14 0.00
150_K 49_N 0.84 0.14 0.00
83_N 344_F 0.83 0.14 0.00
56_S 288_S 0.83 0.14 0.00
107_Q 445_R 0.83 0.14 0.00
147_S 363_S 0.83 0.14 0.00
165_D 333_D 0.83 0.14 0.00
45_D 141_K 0.83 0.14 0.00
49_T 313_H 0.82 0.14 0.00
45_D 222_T 0.82 0.13 0.00
80_L 197_F 0.82 0.13 0.00
41_V 16_Q 0.82 0.13 0.00
38_E 117_L 0.82 0.13 0.00
81_L 74_K 0.81 0.13 0.00
62_Q 156_V 0.81 0.13 0.00
61_G 235_Y 0.81 0.13 0.00
41_V 168_S 0.81 0.13 0.00
55_Q 148_Y 0.81 0.13 0.00
160_T 227_L 0.81 0.13 0.00
51_P 229_E 0.81 0.13 0.00
88_G 211_D 0.81 0.13 0.00
5_C 129_E 0.81 0.13 0.00
110_F 199_G 0.81 0.13 0.00
77_A 67_Q 0.81 0.13 0.00
63_R 292_Y 0.81 0.13 0.00
120_I 321_L 0.81 0.13 0.00
66_K 216_F 0.81 0.13 0.00
44_F 218_S 0.81 0.13 0.00
144_V 414_K 0.80 0.13 0.00
155_H 222_T 0.80 0.13 0.00
77_A 16_Q 0.80 0.13 0.00
81_L 292_Y 0.80 0.13 0.00
96_L 201_D 0.80 0.13 0.00
146_L 78_A 0.80 0.13 0.00
161_S 410_I 0.80 0.13 0.00
68_F 392_M 0.80 0.13 0.00
46_H 80_M 0.80 0.13 0.00
116_E 119_V 0.80 0.13 0.00
135_K 209_I 0.80 0.12 0.00
91_L 243_F 0.80 0.12 0.00
60_S 332_T 0.80 0.12 0.00
43_Q 192_S 0.80 0.12 0.00
129_H 240_A 0.80 0.12 0.00
120_I 270_E 0.79 0.12 0.00
78_V 354_D 0.79 0.12 0.00
89_E 429_Q 0.79 0.12 0.00
81_L 217_E 0.79 0.12 0.00
90_K 160_I 0.79 0.12 0.00
122_D 415_E 0.79 0.12 0.00
120_I 341_E 0.79 0.12 0.00
96_L 369_V 0.79 0.12 0.00
163_S 314_V 0.79 0.12 0.00
28_G 102_F 0.79 0.12 0.00
58_Q 360_S 0.79 0.12 0.00
80_L 288_S 0.79 0.12 0.00
122_D 220_K 0.79 0.12 0.00
71_T 348_T 0.79 0.12 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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