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OPENSEQ.org
cIV_B_80_cI_H_60_human
Genes: A B A+B
Length: 227 318 539
Sequences: 1814 4127 1935
Seq/Len: 7.99 12.98 3.59
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 1.65
10 0.00 0.00 3.33
20 0.00 0.01 3.43
100 0.00 0.01 3.47
∞ 0.00 0.02 3.55
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 1.28 0.91 0.33
12_A 52_A 1.21 0.88 0.28
59_Q 185_W 1.18 0.85 0.26
13_T 83_L 1.12 0.81 0.22
160_L 109_S 1.10 0.80 0.20
76_I 97_N 1.10 0.80 0.20
83_I 67_T 1.09 0.79 0.20
61_M 119_S 1.07 0.77 0.19
223_P 237_L 1.07 0.77 0.19
33_L 118_W 1.06 0.76 0.18
192_Y 263_T 1.05 0.75 0.18
90_V 132_A 1.05 0.75 0.17
63_T 217_A 1.04 0.74 0.17
215_P 217_A 1.03 0.74 0.17
16_I 307_M 1.03 0.73 0.17
61_M 144_V 1.03 0.73 0.17
203_N 212_N 1.02 0.72 0.16
170_L 45_L 1.01 0.71 0.15
87_T 52_A 1.01 0.71 0.15
99_S 79_L 1.01 0.71 0.15
92_D 266_L 1.00 0.70 0.15
9_L 135_A 1.00 0.70 0.15
142_V 157_S 1.00 0.70 0.15
184_F 115_S 0.99 0.69 0.15
83_I 130_I 0.99 0.69 0.14
138_V 148_I 0.98 0.68 0.14
202_A 185_W 0.98 0.68 0.14
113_Y 147_A 0.96 0.66 0.13
205_S 203_G 0.95 0.65 0.13
87_T 303_W 0.95 0.65 0.13
74_V 261_T 0.95 0.64 0.12
216_L 102_L 0.95 0.64 0.12
186_A 302_M 0.94 0.64 0.12
38_V 193_T 0.94 0.63 0.12
205_S 209_S 0.94 0.63 0.12
192_Y 78_A 0.93 0.62 0.12
148_T 307_M 0.93 0.61 0.12
19_E 203_G 0.92 0.60 0.11
192_Y 106_L 0.92 0.60 0.11
168_L 89_L 0.92 0.60 0.11
11_D 231_I 0.92 0.60 0.11
152_M 240_T 0.92 0.60 0.11
162_S 217_A 0.91 0.60 0.11
29_M 165_L 0.91 0.59 0.11
142_V 225_M 0.91 0.59 0.11
160_L 132_A 0.90 0.58 0.11
51_T 71_Y 0.90 0.58 0.11
57_D 135_A 0.90 0.58 0.10
89_E 221_A 0.89 0.57 0.10
155_T 158_G 0.89 0.57 0.10
137_D 299_A 0.89 0.56 0.10
12_A 116_I 0.88 0.56 0.10
52_N 20_L 0.88 0.56 0.10
83_I 7_L 0.88 0.56 0.10
121_Y 82_A 0.88 0.56 0.10
118_F 273_I 0.87 0.55 0.10
155_T 69_T 0.87 0.55 0.10
206_F 144_V 0.86 0.53 0.09
34_I 302_M 0.86 0.53 0.09
154_I 272_W 0.86 0.53 0.09
34_I 17_M 0.86 0.53 0.09
82_R 225_M 0.86 0.53 0.09
224_V 162_L 0.85 0.52 0.09
223_P 222_L 0.85 0.51 0.09
23_F 209_S 0.85 0.51 0.09
74_V 29_G 0.84 0.51 0.09
167_T 240_T 0.84 0.51 0.09
179_L 213_I 0.84 0.50 0.08
175_I 126_N 0.84 0.50 0.08
45_T 46_L 0.84 0.50 0.08
25_D 205_S 0.83 0.49 0.08
22_T 200_L 0.83 0.49 0.08
97_I 260_V 0.83 0.49 0.08
213_L 74_A 0.83 0.49 0.08
38_V 273_I 0.83 0.49 0.08
116_L 172_F 0.82 0.48 0.08
205_S 201_A 0.82 0.48 0.08
215_P 160_F 0.82 0.48 0.08
152_M 157_S 0.82 0.48 0.08
182_T 20_L 0.82 0.48 0.08
32_F 266_L 0.82 0.47 0.08
191_V 167_T 0.82 0.47 0.08
86_M 232_I 0.82 0.47 0.08
219_F 146_L 0.81 0.47 0.07
150_I 133_L 0.81 0.47 0.07
132_D 128_A 0.81 0.47 0.07
113_Y 196_T 0.81 0.47 0.07
97_I 85_L 0.81 0.46 0.07
95_L 307_M 0.81 0.46 0.07
12_A 111_L 0.81 0.46 0.07
8_G 11_V 0.81 0.46 0.07
172_T 233_M 0.81 0.46 0.07
96_T 306_S 0.81 0.46 0.07
154_I 84_L 0.80 0.46 0.07
12_A 88_P 0.80 0.45 0.07
23_F 56_F 0.80 0.45 0.07
33_L 222_L 0.80 0.45 0.07
128_L 116_I 0.80 0.45 0.07
144_L 237_L 0.80 0.45 0.07
59_Q 113_V 0.80 0.44 0.07
95_L 108_T 0.80 0.44 0.07
37_L 232_I 0.79 0.44 0.07
18_E 280_F 0.79 0.44 0.07
83_I 179_W 0.79 0.44 0.07
203_N 282_Y 0.79 0.43 0.07
133_L 110_S 0.79 0.43 0.07
72_I 42_P 0.79 0.43 0.07
167_T 182_A 0.79 0.43 0.07
102_H 100_L 0.79 0.43 0.07
154_I 264_L 0.78 0.43 0.07
190_G 151_L 0.78 0.43 0.07
95_L 266_L 0.78 0.43 0.07
100_I 7_L 0.78 0.42 0.07
92_D 259_F 0.78 0.42 0.07
164_A 45_L 0.78 0.42 0.07
139_D 79_L 0.78 0.42 0.07
95_L 150_L 0.78 0.42 0.06
131_G 88_P 0.77 0.42 0.06
105_Y 150_L 0.77 0.42 0.06
87_T 177_P 0.77 0.41 0.06
22_T 223_F 0.77 0.41 0.06
213_L 180_P 0.77 0.41 0.06
123_L 225_M 0.77 0.41 0.06
55_I 154_L 0.77 0.41 0.06
189_P 270_F 0.76 0.41 0.06
11_D 223_F 0.76 0.41 0.06
2_A 97_N 0.76 0.40 0.06
19_E 277_Y 0.76 0.40 0.06
144_L 108_T 0.76 0.40 0.06
99_S 95_L 0.76 0.40 0.06
143_V 257_T 0.76 0.40 0.06
107_T 22_L 0.76 0.40 0.06
33_L 176_L 0.76 0.40 0.06
224_V 107_A 0.76 0.40 0.06
42_L 223_F 0.76 0.40 0.06
41_A 81_I 0.76 0.40 0.06
179_L 266_L 0.76 0.40 0.06
140_N 90_P 0.76 0.39 0.06
86_M 101_G 0.76 0.39 0.06
193_Y 135_A 0.76 0.39 0.06
54_N 277_Y 0.76 0.39 0.06
35_C 271_L 0.75 0.39 0.06
222_G 219_P 0.75 0.39 0.06
95_L 11_V 0.75 0.39 0.06
146_I 13_I 0.75 0.39 0.06
222_G 268_S 0.75 0.39 0.06
105_Y 273_I 0.75 0.39 0.06
214_I 83_L 0.75 0.39 0.06
156_S 293_F 0.75 0.39 0.06
93_P 216_A 0.75 0.39 0.06
13_T 45_L 0.75 0.38 0.06
160_L 154_L 0.75 0.38 0.06
218_I 128_A 0.75 0.38 0.06
217_K 15_I 0.75 0.38 0.06
21_I 247_Y 0.74 0.38 0.06
20_L 280_F 0.74 0.38 0.06
147_E 42_P 0.74 0.38 0.06
68_L 81_I 0.74 0.38 0.06
127_F 309_I 0.74 0.38 0.06
46_L 159_S 0.74 0.38 0.06
146_I 45_L 0.74 0.38 0.06
150_I 242_F 0.74 0.38 0.06
83_I 297_T 0.74 0.38 0.06
165_V 291_K 0.74 0.38 0.06
7_V 90_P 0.74 0.38 0.06
127_F 226_A 0.74 0.38 0.06
138_V 25_R 0.74 0.38 0.06
211_L 226_A 0.74 0.38 0.06
186_A 98_L 0.74 0.38 0.06
10_Q 272_W 0.74 0.37 0.06
63_T 66_S 0.74 0.37 0.06
125_P 43_Y 0.74 0.37 0.06
167_T 82_A 0.74 0.37 0.06
220_E 162_L 0.74 0.37 0.06
156_S 118_W 0.74 0.37 0.06
157_Q 50_A 0.74 0.37 0.06
34_I 46_L 0.74 0.37 0.06
81_L 48_P 0.74 0.37 0.05
99_S 257_T 0.73 0.37 0.05
192_Y 222_L 0.73 0.37 0.05
86_M 288_L 0.73 0.37 0.05
188_R 196_T 0.73 0.37 0.05
163_W 58_K 0.73 0.36 0.05
64_V 133_L 0.73 0.36 0.05
7_V 53_M 0.73 0.36 0.05
157_Q 193_T 0.73 0.36 0.05
119_N 114_Y 0.73 0.36 0.05
170_L 81_I 0.73 0.36 0.05
43_F 151_L 0.73 0.36 0.05
153_M 277_Y 0.73 0.36 0.05
57_D 28_L 0.73 0.36 0.05
76_I 9_L 0.73 0.36 0.05
111_T 271_L 0.72 0.36 0.05
214_I 115_S 0.72 0.36 0.05
168_L 132_A 0.72 0.36 0.05
78_L 58_K 0.72 0.36 0.05
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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