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OPENSEQ.org
cIV_B_60_cI_H_80_human
Genes: A B A+B
Length: 227 318 541
Sequences: 2677 3641 2155
Seq/Len: 11.79 11.45 3.98
MirrorTree (Pazo et al. 2001) 0.79
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 0.10
2 0.00 0.00 0.22
5 0.00 0.00 1.75
10 0.00 0.00 3.39
20 0.00 0.00 3.52
100 0.00 0.01 3.57
∞ 0.00 0.02 3.95
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
162_S 217_A 1.24 0.91 0.28
144_L 237_L 1.16 0.86 0.23
95_L 11_V 1.09 0.82 0.19
83_I 67_T 1.05 0.78 0.17
192_Y 78_A 1.04 0.77 0.16
61_M 144_V 1.04 0.77 0.16
23_F 209_S 1.04 0.77 0.16
76_I 97_N 1.03 0.76 0.16
203_N 35_K 1.02 0.75 0.15
99_S 79_L 1.00 0.73 0.14
127_F 87_T 0.99 0.72 0.14
105_Y 81_I 0.99 0.72 0.14
33_L 118_W 0.98 0.71 0.13
63_T 217_A 0.98 0.71 0.13
160_L 132_A 0.97 0.70 0.13
188_R 269_L 0.95 0.67 0.12
90_V 132_A 0.95 0.67 0.12
12_A 116_I 0.93 0.65 0.11
192_Y 263_T 0.92 0.63 0.10
184_F 115_S 0.92 0.63 0.10
155_T 128_A 0.91 0.63 0.10
105_Y 273_I 0.91 0.63 0.10
51_T 71_Y 0.91 0.62 0.10
156_S 293_F 0.90 0.61 0.10
87_T 52_A 0.90 0.61 0.10
213_L 74_A 0.90 0.61 0.10
37_L 232_I 0.90 0.61 0.10
205_S 203_G 0.90 0.61 0.10
57_D 135_A 0.89 0.60 0.10
222_G 219_P 0.89 0.60 0.10
59_Q 185_W 0.88 0.59 0.09
38_V 193_T 0.88 0.59 0.09
19_E 203_G 0.88 0.59 0.09
175_I 126_N 0.88 0.59 0.09
155_T 158_G 0.87 0.58 0.09
77_A 133_L 0.87 0.57 0.09
12_A 52_A 0.86 0.56 0.09
99_S 95_L 0.86 0.56 0.09
92_D 266_L 0.86 0.56 0.09
8_G 11_V 0.85 0.55 0.08
223_P 222_L 0.85 0.55 0.08
43_F 151_L 0.85 0.54 0.08
88_D 225_M 0.85 0.54 0.08
76_I 9_L 0.85 0.54 0.08
87_T 182_A 0.84 0.54 0.08
225_F 77_L 0.84 0.54 0.08
29_M 165_L 0.83 0.53 0.08
59_Q 113_V 0.83 0.53 0.08
122_M 13_I 0.83 0.52 0.08
142_V 157_S 0.83 0.52 0.08
215_P 217_A 0.83 0.52 0.08
39_L 188_S 0.83 0.52 0.07
122_M 22_L 0.82 0.51 0.07
168_L 89_L 0.82 0.51 0.07
116_L 53_M 0.82 0.51 0.07
11_D 231_I 0.82 0.51 0.07
34_I 17_M 0.82 0.50 0.07
34_I 302_M 0.82 0.50 0.07
89_E 221_A 0.82 0.50 0.07
25_D 205_S 0.81 0.50 0.07
34_I 46_L 0.81 0.49 0.07
152_M 157_S 0.81 0.49 0.07
42_L 223_F 0.81 0.49 0.07
215_P 160_F 0.81 0.49 0.07
153_M 277_Y 0.80 0.48 0.07
139_D 79_L 0.80 0.48 0.07
52_N 216_A 0.80 0.48 0.07
10_Q 272_W 0.80 0.48 0.07
224_V 162_L 0.80 0.48 0.07
131_G 88_P 0.80 0.48 0.07
51_T 119_S 0.80 0.48 0.07
154_I 84_L 0.80 0.48 0.07
167_T 182_A 0.80 0.48 0.07
49_K 229_T 0.80 0.48 0.07
160_L 109_S 0.79 0.47 0.07
148_T 307_M 0.79 0.47 0.07
12_A 111_L 0.79 0.47 0.07
172_T 233_M 0.79 0.47 0.06
170_L 45_L 0.79 0.46 0.06
113_Y 147_A 0.79 0.46 0.06
202_A 185_W 0.79 0.46 0.06
82_R 225_M 0.79 0.46 0.06
93_P 216_A 0.79 0.46 0.06
16_I 307_M 0.79 0.46 0.06
95_L 150_L 0.78 0.46 0.06
83_I 297_T 0.78 0.46 0.06
20_L 280_F 0.78 0.45 0.06
45_T 46_L 0.78 0.45 0.06
78_L 154_L 0.77 0.44 0.06
9_L 135_A 0.77 0.44 0.06
31_I 119_S 0.77 0.44 0.06
111_T 149_I 0.77 0.44 0.06
15_P 211_F 0.77 0.43 0.06
74_V 184_M 0.77 0.43 0.06
35_C 271_L 0.76 0.43 0.06
219_F 30_Y 0.76 0.43 0.06
150_I 276_A 0.76 0.43 0.06
123_L 296_L 0.76 0.43 0.06
72_I 3_M 0.76 0.43 0.06
192_Y 106_L 0.76 0.43 0.06
74_V 29_G 0.76 0.43 0.06
67_I 225_M 0.76 0.42 0.06
206_F 144_V 0.76 0.42 0.06
86_M 232_I 0.76 0.42 0.06
219_F 146_L 0.76 0.42 0.06
186_A 302_M 0.75 0.42 0.06
127_F 309_I 0.75 0.42 0.06
199_I 209_S 0.75 0.41 0.06
191_V 229_T 0.75 0.41 0.06
143_V 269_L 0.75 0.41 0.06
140_N 90_P 0.75 0.41 0.06
217_K 15_I 0.75 0.41 0.06
22_T 223_F 0.75 0.41 0.06
179_L 213_I 0.75 0.41 0.06
50_L 8_L 0.75 0.41 0.05
19_E 277_Y 0.75 0.41 0.05
175_I 118_W 0.75 0.41 0.05
86_M 101_G 0.74 0.41 0.05
24_H 114_Y 0.74 0.41 0.05
121_Y 82_A 0.74 0.40 0.05
190_G 151_L 0.74 0.40 0.05
203_N 282_Y 0.74 0.40 0.05
97_I 166_I 0.74 0.40 0.05
18_E 280_F 0.74 0.40 0.05
37_L 18_A 0.74 0.40 0.05
223_P 237_L 0.74 0.40 0.05
193_Y 135_A 0.74 0.40 0.05
61_M 104_F 0.74 0.40 0.05
205_S 209_S 0.73 0.39 0.05
32_F 266_L 0.73 0.39 0.05
7_V 90_P 0.73 0.39 0.05
99_S 33_L 0.73 0.39 0.05
32_F 183_M 0.73 0.39 0.05
224_V 107_A 0.73 0.39 0.05
114_G 155_L 0.73 0.39 0.05
64_V 15_I 0.72 0.38 0.05
92_D 188_S 0.72 0.38 0.05
11_D 151_L 0.72 0.38 0.05
219_F 174_L 0.72 0.38 0.05
2_A 29_G 0.72 0.38 0.05
223_P 7_L 0.72 0.38 0.05
9_L 97_N 0.72 0.38 0.05
81_L 48_P 0.72 0.37 0.05
224_V 140_I 0.72 0.37 0.05
37_L 14_L 0.71 0.37 0.05
224_V 305_V 0.71 0.37 0.05
116_L 172_F 0.71 0.37 0.05
110_Y 87_T 0.71 0.37 0.05
102_H 100_L 0.71 0.37 0.05
191_V 167_T 0.71 0.36 0.05
11_D 223_F 0.71 0.36 0.05
97_I 260_V 0.71 0.36 0.05
119_N 114_Y 0.71 0.36 0.05
18_E 41_G 0.71 0.36 0.05
151_R 272_W 0.71 0.36 0.05
102_H 212_N 0.71 0.36 0.05
119_N 196_T 0.71 0.36 0.05
87_T 303_W 0.71 0.36 0.04
76_I 89_L 0.70 0.36 0.04
189_P 238_T 0.70 0.35 0.04
9_L 140_I 0.70 0.35 0.04
32_F 297_T 0.70 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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