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OPENSEQ.org
cIV_B_80_cI_H_80_human
Genes: A B A+B
Length: 227 318 539
Sequences: 1814 3641 1903
Seq/Len: 7.99 11.45 3.53
MirrorTree (Pazo et al. 2001) 0.83
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 0.00 0.00 0.07
2 0.00 0.00 0.18
5 0.00 0.00 1.68
10 0.00 0.00 3.26
20 0.00 0.00 3.40
100 0.00 0.01 3.44
∞ 0.00 0.02 3.49
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
127_F 87_T 1.22 0.88 0.19
192_Y 263_T 1.19 0.86 0.18
12_A 52_A 1.19 0.86 0.18
59_Q 185_W 1.15 0.83 0.16
215_P 217_A 1.14 0.82 0.15
90_V 132_A 1.13 0.82 0.15
87_T 52_A 1.12 0.81 0.15
63_T 217_A 1.12 0.81 0.14
76_I 97_N 1.09 0.79 0.13
113_Y 147_A 1.07 0.76 0.12
57_D 135_A 1.06 0.75 0.12
162_S 217_A 1.05 0.75 0.12
144_L 237_L 1.05 0.74 0.12
160_L 109_S 1.05 0.74 0.11
192_Y 78_A 1.04 0.74 0.11
61_M 119_S 1.04 0.73 0.11
16_I 307_M 1.03 0.73 0.11
23_F 209_S 1.02 0.72 0.11
9_L 135_A 1.02 0.72 0.11
138_V 148_I 1.02 0.71 0.10
142_V 157_S 1.00 0.70 0.10
33_L 118_W 1.00 0.70 0.10
205_S 209_S 1.00 0.69 0.10
13_T 83_L 0.99 0.69 0.10
38_V 193_T 0.97 0.67 0.09
184_F 115_S 0.97 0.66 0.09
89_E 221_A 0.97 0.66 0.09
95_L 11_V 0.97 0.66 0.09
51_T 71_Y 0.96 0.65 0.09
83_I 67_T 0.96 0.65 0.09
175_I 126_N 0.96 0.65 0.09
205_S 203_G 0.95 0.63 0.08
83_I 130_I 0.94 0.63 0.08
153_M 277_Y 0.94 0.63 0.08
61_M 144_V 0.94 0.62 0.08
223_P 237_L 0.93 0.62 0.08
87_T 303_W 0.93 0.61 0.08
148_T 307_M 0.93 0.61 0.08
137_D 299_A 0.93 0.61 0.08
160_L 132_A 0.93 0.61 0.08
167_T 240_T 0.93 0.61 0.08
19_E 203_G 0.92 0.60 0.07
59_Q 113_V 0.92 0.60 0.07
202_A 185_W 0.92 0.60 0.07
111_T 149_I 0.92 0.60 0.07
172_T 233_M 0.91 0.59 0.07
170_L 45_L 0.91 0.59 0.07
189_P 270_F 0.91 0.58 0.07
82_R 225_M 0.91 0.58 0.07
86_M 101_G 0.90 0.58 0.07
118_F 273_I 0.90 0.58 0.07
74_V 29_G 0.90 0.57 0.07
45_T 46_L 0.89 0.56 0.07
92_D 266_L 0.89 0.56 0.07
99_S 95_L 0.89 0.56 0.07
116_L 53_M 0.88 0.56 0.07
67_I 9_L 0.88 0.55 0.07
168_L 89_L 0.88 0.55 0.06
22_T 223_F 0.88 0.55 0.06
7_V 90_P 0.88 0.55 0.06
18_E 280_F 0.88 0.54 0.06
83_I 7_L 0.88 0.54 0.06
25_D 205_S 0.87 0.54 0.06
37_L 232_I 0.87 0.54 0.06
29_M 165_L 0.87 0.54 0.06
34_I 302_M 0.87 0.54 0.06
186_A 302_M 0.87 0.54 0.06
203_N 282_Y 0.87 0.54 0.06
203_N 212_N 0.87 0.53 0.06
167_T 182_A 0.87 0.53 0.06
167_T 82_A 0.86 0.53 0.06
7_V 53_M 0.86 0.53 0.06
213_L 74_A 0.86 0.52 0.06
216_L 102_L 0.86 0.52 0.06
205_S 201_A 0.85 0.52 0.06
12_A 116_I 0.85 0.51 0.06
37_L 14_L 0.84 0.50 0.06
224_V 162_L 0.84 0.50 0.06
121_Y 82_A 0.84 0.50 0.06
152_M 240_T 0.84 0.50 0.06
222_G 219_P 0.84 0.50 0.06
19_E 277_Y 0.84 0.50 0.06
33_L 222_L 0.84 0.49 0.06
93_P 216_A 0.84 0.49 0.06
191_V 167_T 0.83 0.49 0.05
97_I 260_V 0.83 0.49 0.05
95_L 307_M 0.83 0.49 0.05
87_T 177_P 0.83 0.49 0.05
105_Y 273_I 0.83 0.48 0.05
97_I 109_S 0.82 0.47 0.05
31_I 53_M 0.82 0.47 0.05
122_M 13_I 0.81 0.47 0.05
99_S 79_L 0.81 0.46 0.05
131_G 88_P 0.81 0.46 0.05
8_G 11_V 0.81 0.46 0.05
157_Q 50_A 0.81 0.46 0.05
95_L 150_L 0.81 0.46 0.05
155_T 158_G 0.81 0.46 0.05
224_V 107_A 0.81 0.46 0.05
156_S 118_W 0.81 0.46 0.05
76_I 9_L 0.81 0.45 0.05
11_D 231_I 0.81 0.45 0.05
215_P 160_F 0.80 0.45 0.05
193_Y 135_A 0.80 0.45 0.05
97_I 85_L 0.80 0.45 0.05
34_I 17_M 0.80 0.45 0.05
42_L 223_F 0.80 0.44 0.05
156_S 293_F 0.79 0.44 0.05
151_R 272_W 0.79 0.44 0.05
223_P 222_L 0.79 0.44 0.05
143_V 257_T 0.79 0.44 0.05
190_G 151_L 0.79 0.43 0.05
2_A 29_G 0.79 0.43 0.04
128_L 116_I 0.79 0.43 0.04
72_I 42_P 0.79 0.43 0.04
55_I 15_I 0.79 0.43 0.04
143_V 269_L 0.78 0.43 0.04
43_F 151_L 0.78 0.42 0.04
155_T 69_T 0.78 0.42 0.04
20_L 79_L 0.78 0.42 0.04
83_I 179_W 0.78 0.42 0.04
179_L 213_I 0.78 0.42 0.04
154_I 84_L 0.78 0.42 0.04
219_F 146_L 0.78 0.42 0.04
2_A 97_N 0.78 0.42 0.04
9_L 88_P 0.78 0.41 0.04
81_L 48_P 0.78 0.41 0.04
92_D 188_S 0.77 0.41 0.04
105_Y 150_L 0.77 0.41 0.04
10_Q 272_W 0.77 0.41 0.04
189_P 117_L 0.77 0.41 0.04
127_F 309_I 0.77 0.41 0.04
219_F 30_Y 0.77 0.41 0.04
188_R 269_L 0.77 0.41 0.04
142_V 225_M 0.77 0.41 0.04
113_Y 196_T 0.77 0.41 0.04
83_I 297_T 0.77 0.40 0.04
38_V 273_I 0.77 0.40 0.04
9_L 97_N 0.77 0.40 0.04
123_L 296_L 0.76 0.40 0.04
154_I 272_W 0.76 0.40 0.04
152_M 157_S 0.76 0.40 0.04
86_M 232_I 0.76 0.40 0.04
191_V 229_T 0.76 0.40 0.04
192_Y 222_L 0.76 0.40 0.04
116_L 172_F 0.76 0.40 0.04
8_G 73_T 0.76 0.40 0.04
119_N 114_Y 0.76 0.40 0.04
57_D 28_L 0.76 0.40 0.04
160_L 154_L 0.76 0.40 0.04
114_G 305_V 0.76 0.40 0.04
34_I 46_L 0.76 0.40 0.04
16_I 139_T 0.76 0.39 0.04
146_I 110_S 0.76 0.39 0.04
92_D 49_F 0.76 0.39 0.04
97_I 112_A 0.76 0.39 0.04
140_N 269_L 0.76 0.39 0.04
163_W 212_N 0.75 0.39 0.04
182_T 20_L 0.75 0.39 0.04
35_C 271_L 0.75 0.39 0.04
70_A 56_F 0.75 0.39 0.04
132_D 128_A 0.75 0.39 0.04
144_L 108_T 0.75 0.38 0.04
49_K 229_T 0.75 0.38 0.04
96_T 222_L 0.75 0.38 0.04
203_N 35_K 0.75 0.38 0.04
125_P 43_Y 0.75 0.38 0.04
82_R 211_F 0.75 0.38 0.04
170_L 81_I 0.75 0.38 0.04
40_Y 270_F 0.74 0.38 0.04
37_L 82_A 0.74 0.38 0.04
139_D 79_L 0.74 0.38 0.04
95_L 108_T 0.74 0.38 0.04
218_I 128_A 0.74 0.37 0.04
111_T 271_L 0.74 0.37 0.04
77_A 132_A 0.74 0.37 0.04
96_T 306_S 0.74 0.37 0.04
54_N 79_L 0.74 0.37 0.04
46_L 159_S 0.74 0.37 0.04
164_A 276_A 0.74 0.37 0.04
127_F 310_T 0.74 0.37 0.04
146_I 13_I 0.74 0.37 0.04
133_L 110_S 0.74 0.37 0.04
31_I 151_L 0.74 0.37 0.04
223_P 311_I 0.74 0.37 0.04
92_D 259_F 0.74 0.37 0.04
206_F 144_V 0.73 0.36 0.04
142_V 165_L 0.73 0.36 0.04
149_P 186_F 0.73 0.36 0.04
170_L 296_L 0.73 0.36 0.04
156_S 101_G 0.73 0.36 0.04
175_I 17_M 0.73 0.36 0.04
175_I 118_W 0.73 0.36 0.04
189_P 238_T 0.73 0.36 0.04
107_T 22_L 0.73 0.35 0.04
223_P 151_L 0.73 0.35 0.04
11_D 223_F 0.73 0.35 0.04
32_F 130_I 0.72 0.35 0.04
214_I 83_L 0.72 0.35 0.04
72_I 3_M 0.72 0.35 0.04
140_N 90_P 0.72 0.35 0.04
150_I 242_F 0.72 0.35 0.04
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
4579 4.19 cIV_B_60_cI_H_20_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.21 Done - Shared
4574 4.21 cIV_B_60_cI_H_40_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.36 Done - Shared
4573 3.59 cIV_B_80_cI_H_60_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.33 Done - Shared
4568 3.98 cIV_B_60_cI_H_80_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.28 Done - Shared
4567 3.6 cIV_B_80_cI_H_60_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.21 Done - Shared
4565 4.2 cIV_B_60_cI_H_60_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.12 Done - Shared
4564 5.01 cIV_B_40_cI_H_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4563 3.53 cIV_B_80_cI_H_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (2015_06) 0.19 Done - Shared
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