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OPENSEQ.org
cIV_C_60_cI_N_40_1_human
Genes: A B A+B
Length: 261 347 606
Sequences: 2363 3793 2401
Seq/Len: 9.05 10.93 3.96
MirrorTree (Pazo et al. 2001) 0.86
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 0.12
2 0.00 0.00 0.22
5 0.00 0.00 3.56
10 0.00 0.00 3.89
20 0.00 0.00 3.89
100 0.00 0.00 3.89
∞ 0.00 0.00 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
53_T 168_G 1.60 0.98 0.89
36_H 176_R 1.41 0.96 0.80
167_I 65_T 1.39 0.96 0.79
239_A 32_G 1.26 0.92 0.69
6_H 295_R 1.23 0.90 0.66
80_R 58_K 1.21 0.89 0.64
13_P 27_F 1.20 0.89 0.63
21_A 298_Y 1.13 0.85 0.56
80_R 56_A 1.12 0.84 0.55
42_L 257_L 1.12 0.83 0.55
209_I 190_M 1.11 0.83 0.54
26_L 181_Y 1.08 0.80 0.50
110_P 136_L 1.07 0.80 0.50
6_H 177_K 1.05 0.78 0.47
8_Y 297_I 1.04 0.77 0.46
112_L 15_A 1.03 0.76 0.45
120_G 118_V 1.03 0.76 0.45
189_S 9_I 1.01 0.74 0.42
127_L 117_E 1.00 0.73 0.41
104_S 170_L 0.98 0.71 0.40
172_Y 54_E 0.98 0.71 0.39
70_H 64_A 0.98 0.70 0.39
135_S 117_E 0.97 0.69 0.38
46_G 136_L 0.96 0.69 0.37
159_M 68_M 0.95 0.68 0.37
104_S 268_E 0.95 0.68 0.37
143_S 100_M 0.95 0.68 0.36
79_L 130_L 0.95 0.67 0.36
127_L 285_I 0.95 0.67 0.36
114_G 139_I 0.94 0.67 0.35
21_A 279_P 0.94 0.66 0.35
10_M 298_Y 0.94 0.66 0.35
8_Y 125_T 0.93 0.65 0.34
48_L 332_L 0.93 0.65 0.34
124_L 25_H 0.93 0.65 0.34
191_G 281_I 0.93 0.65 0.34
32_A 25_H 0.92 0.64 0.33
37_F 289_N 0.92 0.64 0.33
45_L 65_T 0.92 0.63 0.33
235_F 171_N 0.92 0.63 0.33
167_I 155_L 0.92 0.63 0.32
200_A 61_L 0.91 0.63 0.32
144_I 68_M 0.91 0.63 0.32
199_V 74_I 0.91 0.62 0.32
88_T 300_T 0.90 0.61 0.31
96_G 174_Q 0.89 0.60 0.30
125_N 274_N 0.89 0.59 0.29
61_V 4_L 0.88 0.59 0.29
217_I 61_L 0.88 0.58 0.28
151_L 285_I 0.87 0.57 0.28
255_S 117_E 0.87 0.57 0.27
96_G 120_Q 0.86 0.56 0.27
227_F 13_I 0.86 0.56 0.27
212_S 285_I 0.85 0.55 0.26
6_H 39_A 0.85 0.55 0.26
10_M 185_T 0.85 0.54 0.26
167_I 181_Y 0.85 0.54 0.26
195_S 74_I 0.85 0.54 0.26
179_S 289_N 0.85 0.54 0.25
61_V 209_I 0.84 0.54 0.25
144_I 119_T 0.84 0.53 0.25
162_A 11_S 0.84 0.53 0.25
100_A 165_G 0.84 0.53 0.25
212_S 191_M 0.83 0.53 0.24
55_Y 20_T 0.83 0.52 0.24
139_A 291_Y 0.83 0.52 0.24
56_Q 287_L 0.83 0.52 0.24
196_T 102_M 0.82 0.51 0.23
61_V 151_V 0.82 0.50 0.23
107_A 128_L 0.82 0.50 0.23
48_L 159_I 0.82 0.50 0.23
129_V 44_L 0.81 0.49 0.22
61_V 318_E 0.81 0.49 0.22
43_L 246_S 0.81 0.49 0.22
51_T 160_L 0.81 0.49 0.22
92_L 106_L 0.80 0.48 0.22
124_L 201_T 0.80 0.48 0.21
43_L 266_I 0.80 0.48 0.21
61_V 157_L 0.80 0.48 0.21
152_M 257_L 0.80 0.48 0.21
158_Q 109_A 0.80 0.48 0.21
250_L 111_F 0.80 0.48 0.21
139_A 117_E 0.80 0.47 0.21
21_A 247_T 0.80 0.47 0.21
67_Y 11_S 0.80 0.47 0.21
127_L 294_L 0.79 0.47 0.21
209_I 242_P 0.79 0.47 0.21
26_L 296_L 0.79 0.47 0.21
103_H 204_N 0.79 0.46 0.20
8_Y 333_T 0.79 0.46 0.20
142_V 298_Y 0.79 0.46 0.20
192_I 339_I 0.79 0.46 0.20
199_V 248_F 0.79 0.46 0.20
24_A 104_M 0.79 0.46 0.20
135_S 58_K 0.78 0.46 0.20
192_I 45_T 0.78 0.46 0.20
2_T 61_L 0.78 0.45 0.20
103_H 5_A 0.78 0.45 0.20
28_T 158_S 0.78 0.45 0.20
8_Y 246_S 0.78 0.45 0.20
163_L 179_L 0.78 0.45 0.20
92_L 133_W 0.78 0.45 0.19
216_T 136_L 0.77 0.44 0.19
96_G 25_H 0.77 0.44 0.19
80_R 197_N 0.77 0.44 0.19
195_S 33_L 0.77 0.44 0.19
142_V 108_M 0.77 0.44 0.19
192_I 242_P 0.77 0.44 0.19
165_I 13_I 0.77 0.43 0.18
91_V 296_L 0.77 0.43 0.18
74_P 44_L 0.76 0.43 0.18
136_V 316_Q 0.76 0.43 0.18
7_A 178_I 0.76 0.43 0.18
107_A 58_K 0.76 0.42 0.18
48_L 271_T 0.76 0.42 0.18
42_L 131_L 0.76 0.42 0.18
22_L 199_N 0.76 0.42 0.18
128_E 113_F 0.76 0.42 0.18
110_P 98_I 0.76 0.42 0.18
23_S 188_G 0.76 0.42 0.18
67_Y 275_S 0.75 0.42 0.17
28_T 187_M 0.75 0.41 0.17
62_T 286_T 0.75 0.41 0.17
48_L 335_L 0.75 0.41 0.17
196_T 187_M 0.75 0.41 0.17
50_N 342_F 0.75 0.41 0.17
109_T 97_M 0.75 0.41 0.17
53_T 108_M 0.75 0.41 0.17
79_L 24_S 0.75 0.41 0.17
22_L 4_L 0.75 0.41 0.17
216_T 207_I 0.75 0.41 0.17
171_L 265_A 0.74 0.41 0.17
27_M 8_V 0.74 0.40 0.17
255_S 71_L 0.74 0.40 0.17
70_H 173_T 0.74 0.40 0.17
250_L 62_T 0.74 0.40 0.17
8_Y 180_A 0.74 0.40 0.17
6_H 57_I 0.74 0.40 0.16
121_I 31_V 0.74 0.40 0.16
21_A 162_I 0.74 0.40 0.16
189_S 13_I 0.74 0.40 0.16
151_L 79_M 0.74 0.40 0.16
144_I 246_S 0.74 0.39 0.16
28_T 100_M 0.74 0.39 0.16
112_L 215_A 0.73 0.39 0.16
128_E 198_P 0.73 0.39 0.16
47_L 150_N 0.73 0.39 0.16
151_L 309_N 0.73 0.39 0.16
24_A 186_H 0.73 0.39 0.16
44_M 153_L 0.73 0.39 0.16
184_S 56_A 0.73 0.39 0.16
103_H 139_I 0.73 0.39 0.16
29_S 252_G 0.73 0.38 0.16
233_F 259_G 0.73 0.38 0.16
109_T 68_M 0.73 0.38 0.16
41_T 97_M 0.72 0.38 0.15
34_W 176_R 0.72 0.38 0.15
195_S 162_I 0.72 0.38 0.15
189_S 229_L 0.72 0.37 0.15
158_Q 288_L 0.72 0.37 0.15
178_A 55_A 0.72 0.37 0.15
261_S 137_A 0.72 0.37 0.15
124_L 174_Q 0.72 0.37 0.15
121_I 228_L 0.72 0.37 0.15
127_L 104_M 0.72 0.37 0.15
183_E 262_P 0.72 0.37 0.15
80_R 25_H 0.72 0.37 0.15
165_I 9_I 0.72 0.37 0.15
229_S 156_T 0.72 0.37 0.15
159_M 69_I 0.71 0.36 0.14
182_F 193_V 0.71 0.36 0.14
230_K 24_S 0.71 0.36 0.14
128_E 193_V 0.71 0.36 0.14
209_I 154_L 0.71 0.36 0.14
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
4561 3.97 cIV_C_40_cI_N_20_1_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.89 Done - Shared
4560 4.43 cIV_C_60_cI_N_20_8_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
4559 3.96 cIV_C_60_cI_N_40_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.89 Done - Shared
4558 3.29 cIV_C_60_cI_N_40_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.80 Done - Shared
4557 2.14 cIV_C_60_cI_N_60_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.69 Done - Shared
4555 1.79 cIV_C_80_cI_N_80_1_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.36 Done - Shared
4554 1.79 cIV_C_80_cI_N_80_1_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 1) msa: Jackhmmer (2015_06) 0.23 Done - Shared
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