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OPENSEQ.org
cIV_B_80_cI_H_60_human
Genes: A B A+B
Length: 227 318 539
Sequences: 1814 3920 1939
Seq/Len: 7.99 12.33 3.6
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 0.19
5 0.00 0.00 1.69
10 0.00 0.00 3.30
20 0.00 0.00 3.44
100 0.00 0.01 3.49
∞ 0.00 0.02 3.56
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
59_Q 185_W 1.23 0.88 0.21
127_F 87_T 1.22 0.88 0.21
12_A 52_A 1.15 0.84 0.17
223_P 237_L 1.12 0.81 0.16
215_P 217_A 1.11 0.81 0.15
160_L 109_S 1.11 0.80 0.15
76_I 97_N 1.10 0.80 0.15
83_I 67_T 1.07 0.77 0.13
203_N 212_N 1.06 0.77 0.13
13_T 83_L 1.06 0.77 0.13
16_I 307_M 1.06 0.76 0.13
192_Y 263_T 1.06 0.76 0.13
61_M 144_V 1.04 0.74 0.12
33_L 118_W 1.03 0.74 0.12
83_I 130_I 1.03 0.74 0.12
90_V 132_A 1.03 0.73 0.12
63_T 217_A 1.02 0.73 0.12
205_S 209_S 1.02 0.72 0.11
61_M 119_S 1.02 0.72 0.11
9_L 135_A 1.02 0.72 0.11
87_T 52_A 1.01 0.71 0.11
38_V 193_T 1.00 0.70 0.10
216_L 102_L 1.00 0.70 0.10
34_I 17_M 0.99 0.69 0.10
184_F 115_S 0.98 0.68 0.10
92_D 266_L 0.98 0.67 0.10
87_T 303_W 0.97 0.67 0.10
57_D 135_A 0.97 0.67 0.10
142_V 157_S 0.97 0.66 0.10
113_Y 147_A 0.97 0.66 0.10
205_S 203_G 0.96 0.66 0.09
83_I 7_L 0.96 0.65 0.09
89_E 221_A 0.95 0.65 0.09
99_S 79_L 0.95 0.64 0.09
19_E 203_G 0.94 0.64 0.09
170_L 45_L 0.94 0.63 0.09
192_Y 78_A 0.94 0.63 0.09
138_V 148_I 0.93 0.62 0.09
162_S 217_A 0.93 0.62 0.08
148_T 307_M 0.93 0.62 0.08
11_D 231_I 0.93 0.61 0.08
202_A 185_W 0.93 0.61 0.08
168_L 89_L 0.92 0.61 0.08
155_T 158_G 0.92 0.61 0.08
192_Y 106_L 0.92 0.61 0.08
160_L 154_L 0.92 0.60 0.08
175_I 126_N 0.91 0.59 0.08
51_T 71_Y 0.91 0.59 0.08
167_T 240_T 0.91 0.59 0.08
34_I 302_M 0.90 0.58 0.08
29_M 165_L 0.90 0.58 0.07
99_S 95_L 0.89 0.57 0.07
160_L 132_A 0.89 0.57 0.07
137_D 299_A 0.89 0.57 0.07
205_S 201_A 0.89 0.57 0.07
82_R 225_M 0.89 0.57 0.07
152_M 240_T 0.89 0.56 0.07
23_F 209_S 0.88 0.56 0.07
121_Y 82_A 0.88 0.56 0.07
45_T 46_L 0.88 0.56 0.07
186_A 302_M 0.88 0.55 0.07
37_L 232_I 0.87 0.55 0.07
93_P 216_A 0.87 0.54 0.07
213_L 180_P 0.86 0.53 0.06
223_P 222_L 0.85 0.52 0.06
25_D 205_S 0.85 0.52 0.06
52_N 20_L 0.85 0.52 0.06
95_L 108_T 0.85 0.52 0.06
142_V 225_M 0.85 0.51 0.06
8_G 11_V 0.85 0.51 0.06
128_L 116_I 0.85 0.51 0.06
118_F 273_I 0.85 0.51 0.06
83_I 179_W 0.84 0.51 0.06
12_A 116_I 0.84 0.51 0.06
12_A 111_L 0.84 0.51 0.06
86_M 232_I 0.84 0.50 0.06
100_I 7_L 0.84 0.50 0.06
97_I 85_L 0.84 0.50 0.06
113_Y 196_T 0.84 0.50 0.06
34_I 64_A 0.83 0.49 0.06
213_L 74_A 0.82 0.48 0.06
7_V 90_P 0.82 0.48 0.06
191_V 167_T 0.82 0.48 0.06
155_T 69_T 0.82 0.48 0.06
133_L 110_S 0.82 0.48 0.06
22_T 200_L 0.82 0.47 0.06
123_L 225_M 0.82 0.47 0.06
224_V 162_L 0.81 0.47 0.05
217_K 15_I 0.81 0.47 0.05
144_L 237_L 0.81 0.47 0.05
116_L 53_M 0.81 0.47 0.05
172_T 233_M 0.81 0.46 0.05
92_D 259_F 0.81 0.46 0.05
12_A 88_P 0.81 0.46 0.05
74_V 29_G 0.81 0.46 0.05
22_T 223_F 0.81 0.46 0.05
18_E 280_F 0.80 0.46 0.05
59_Q 113_V 0.80 0.46 0.05
37_L 14_L 0.80 0.46 0.05
189_P 270_F 0.80 0.45 0.05
215_P 160_F 0.80 0.45 0.05
23_F 56_F 0.80 0.45 0.05
11_D 223_F 0.80 0.45 0.05
203_N 282_Y 0.80 0.45 0.05
2_A 97_N 0.80 0.45 0.05
10_Q 272_W 0.80 0.45 0.05
154_I 272_W 0.80 0.45 0.05
35_C 271_L 0.79 0.44 0.05
131_G 88_P 0.79 0.44 0.05
193_Y 135_A 0.79 0.44 0.05
97_I 260_V 0.79 0.44 0.05
102_H 100_L 0.79 0.44 0.05
19_E 277_Y 0.79 0.44 0.05
206_F 144_V 0.79 0.44 0.05
33_L 222_L 0.79 0.43 0.05
132_D 128_A 0.79 0.43 0.05
42_L 223_F 0.79 0.43 0.05
32_F 266_L 0.79 0.43 0.05
72_I 42_P 0.78 0.43 0.05
179_L 266_L 0.78 0.43 0.05
95_L 150_L 0.78 0.43 0.05
222_G 268_S 0.78 0.43 0.05
190_G 151_L 0.78 0.42 0.05
222_G 219_P 0.78 0.42 0.05
143_V 257_T 0.78 0.42 0.05
219_F 146_L 0.78 0.42 0.05
188_R 196_T 0.78 0.42 0.05
86_M 101_G 0.78 0.42 0.05
156_S 118_W 0.78 0.42 0.05
95_L 307_M 0.77 0.42 0.05
170_L 81_I 0.77 0.42 0.05
150_I 133_L 0.77 0.42 0.05
87_T 177_P 0.77 0.42 0.05
96_T 306_S 0.77 0.42 0.05
83_I 297_T 0.77 0.42 0.05
179_L 213_I 0.77 0.42 0.05
156_S 293_F 0.77 0.41 0.05
57_D 28_L 0.77 0.41 0.05
218_I 128_A 0.77 0.41 0.04
182_T 20_L 0.77 0.41 0.04
54_N 277_Y 0.76 0.41 0.04
38_V 273_I 0.76 0.40 0.04
68_L 81_I 0.76 0.40 0.04
77_A 132_A 0.76 0.40 0.04
41_A 81_I 0.76 0.40 0.04
81_L 48_P 0.76 0.40 0.04
139_D 79_L 0.76 0.40 0.04
95_L 11_V 0.76 0.40 0.04
34_I 46_L 0.76 0.40 0.04
139_D 148_I 0.76 0.39 0.04
144_L 260_V 0.76 0.39 0.04
25_D 211_F 0.76 0.39 0.04
63_T 66_S 0.76 0.39 0.04
138_V 25_R 0.75 0.39 0.04
157_Q 193_T 0.75 0.39 0.04
154_I 84_L 0.75 0.39 0.04
143_V 269_L 0.75 0.39 0.04
95_L 266_L 0.75 0.39 0.04
175_I 118_W 0.75 0.38 0.04
127_F 226_A 0.75 0.38 0.04
167_T 82_A 0.75 0.38 0.04
164_A 45_L 0.75 0.38 0.04
192_Y 222_L 0.74 0.38 0.04
164_A 276_A 0.74 0.38 0.04
74_V 261_T 0.74 0.38 0.04
105_Y 150_L 0.74 0.38 0.04
107_T 22_L 0.74 0.38 0.04
131_G 76_T 0.74 0.38 0.04
186_A 98_L 0.74 0.38 0.04
116_L 172_F 0.74 0.38 0.04
223_P 6_L 0.74 0.38 0.04
146_I 13_I 0.74 0.38 0.04
43_F 151_L 0.74 0.38 0.04
151_R 272_W 0.74 0.38 0.04
64_V 133_L 0.74 0.38 0.04
24_H 114_Y 0.74 0.37 0.04
57_D 56_F 0.74 0.37 0.04
163_W 58_K 0.74 0.37 0.04
13_T 45_L 0.74 0.37 0.04
149_P 186_F 0.73 0.37 0.04
167_T 182_A 0.73 0.37 0.04
2_A 29_G 0.73 0.37 0.04
153_M 277_Y 0.73 0.37 0.04
97_I 109_S 0.73 0.36 0.04
163_W 212_N 0.73 0.36 0.04
125_P 53_M 0.73 0.36 0.04
21_I 247_Y 0.73 0.36 0.04
9_L 97_N 0.73 0.36 0.04
55_I 154_L 0.73 0.36 0.04
92_D 265_L 0.73 0.36 0.04
82_R 66_S 0.73 0.36 0.04
20_L 280_F 0.72 0.36 0.04
114_G 305_V 0.72 0.36 0.04
144_L 108_T 0.72 0.35 0.04
219_F 30_Y 0.72 0.35 0.04
11_D 151_L 0.72 0.35 0.04
111_T 271_L 0.72 0.35 0.04
119_N 114_Y 0.72 0.35 0.04
82_R 211_F 0.72 0.35 0.04
6_Q 117_L 0.72 0.35 0.04
4_A 105_I 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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