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OPENSEQ.org
cIV_C_60_cI_N_60_1_human
Genes: A B A+B
Length: 261 347 607
Sequences: 2363 2495 1296
Seq/Len: 9.05 7.19 2.14
MirrorTree (Pazo et al. 2001) 0.78
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 0.00
2 0.00 0.00 0.00
5 0.00 0.00 2.08
10 0.00 0.00 2.13
20 0.00 0.00 2.13
100 0.00 0.00 2.13
∞ 0.00 0.00 2.13
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
143_S 267_I 1.60 0.95 0.69
168_L 179_L 1.33 0.84 0.46
112_L 170_L 1.26 0.80 0.40
104_S 170_L 1.26 0.80 0.40
112_L 264_W 1.23 0.77 0.36
8_Y 282_M 1.22 0.77 0.36
8_Y 333_T 1.20 0.74 0.34
182_F 209_I 1.20 0.74 0.34
229_S 196_Y 1.20 0.74 0.34
162_A 113_F 1.19 0.74 0.33
217_I 146_S 1.18 0.73 0.33
25_L 170_L 1.18 0.72 0.32
54_M 296_L 1.17 0.72 0.32
27_M 128_L 1.17 0.72 0.31
216_T 67_S 1.12 0.67 0.28
212_S 43_V 1.11 0.67 0.27
191_G 127_G 1.11 0.66 0.27
62_T 261_L 1.10 0.65 0.26
143_S 48_M 1.09 0.64 0.25
2_T 314_K 1.08 0.63 0.24
103_H 83_Q 1.08 0.63 0.24
154_N 286_T 1.08 0.63 0.24
103_H 257_L 1.07 0.62 0.23
112_L 271_T 1.06 0.61 0.23
2_T 155_L 1.06 0.61 0.23
114_G 139_I 1.06 0.60 0.22
8_Y 11_S 1.05 0.60 0.22
8_Y 99_M 1.05 0.60 0.22
38_H 304_L 1.05 0.60 0.22
49_T 104_M 1.04 0.59 0.21
189_S 147_P 1.04 0.59 0.21
192_I 45_T 1.04 0.59 0.21
162_A 22_L 1.03 0.58 0.21
158_Q 291_Y 1.03 0.58 0.20
254_V 45_T 1.01 0.56 0.19
31_L 98_I 1.01 0.56 0.19
165_I 9_I 1.00 0.55 0.19
220_I 226_T 1.00 0.55 0.19
150_S 229_L 1.00 0.55 0.19
10_M 16_G 1.00 0.54 0.18
12_K 320_T 1.00 0.54 0.18
112_L 195_P 0.98 0.53 0.17
224_M 343_M 0.98 0.53 0.17
212_S 130_L 0.98 0.53 0.17
153_E 181_Y 0.98 0.53 0.17
254_V 245_P 0.98 0.52 0.17
103_H 311_V 0.98 0.52 0.17
53_T 168_G 0.98 0.52 0.17
189_S 53_T 0.97 0.51 0.16
48_L 261_L 0.97 0.51 0.16
213_T 235_N 0.97 0.51 0.16
224_M 9_I 0.97 0.51 0.16
189_S 122_T 0.96 0.50 0.16
115_H 35_M 0.96 0.50 0.16
10_M 82_G 0.96 0.50 0.16
195_S 275_S 0.96 0.50 0.16
43_L 141_I 0.96 0.50 0.16
104_S 342_F 0.96 0.50 0.16
179_S 99_M 0.96 0.50 0.16
216_T 53_T 0.96 0.49 0.16
157_N 17_T 0.96 0.49 0.16
212_S 148_S 0.96 0.49 0.16
26_L 57_I 0.95 0.49 0.16
143_S 127_G 0.95 0.49 0.15
8_Y 205_L 0.95 0.49 0.15
192_I 242_P 0.95 0.49 0.15
125_N 4_L 0.95 0.48 0.15
67_Y 163_M 0.95 0.48 0.15
199_V 37_M 0.95 0.48 0.15
7_A 178_I 0.95 0.48 0.15
103_H 170_L 0.94 0.48 0.15
144_I 329_L 0.94 0.48 0.15
61_V 98_I 0.94 0.48 0.15
156_R 302_I 0.94 0.48 0.15
125_N 247_T 0.94 0.47 0.15
47_L 193_V 0.94 0.47 0.14
142_V 106_L 0.94 0.47 0.14
23_S 143_Y 0.94 0.47 0.14
212_S 73_A 0.94 0.47 0.14
123_P 36_N 0.93 0.47 0.14
147_A 159_I 0.93 0.47 0.14
104_S 268_E 0.93 0.46 0.14
229_S 70_L 0.93 0.46 0.14
121_I 15_A 0.93 0.46 0.14
125_N 228_L 0.93 0.46 0.14
61_V 151_V 0.92 0.46 0.14
217_I 125_T 0.92 0.45 0.14
209_I 254_L 0.92 0.45 0.14
168_L 8_V 0.92 0.45 0.14
103_H 204_N 0.92 0.45 0.14
45_L 191_M 0.92 0.45 0.13
62_T 80_L 0.92 0.45 0.13
175_L 247_T 0.91 0.45 0.13
53_T 137_A 0.91 0.44 0.13
92_L 106_L 0.91 0.44 0.13
12_K 128_L 0.91 0.44 0.13
8_Y 308_S 0.90 0.43 0.13
12_K 213_T 0.90 0.43 0.13
229_S 229_L 0.90 0.43 0.12
187_T 75_L 0.90 0.43 0.12
212_S 6_Q 0.89 0.42 0.12
223_L 102_M 0.89 0.42 0.12
185_P 240_L 0.89 0.41 0.12
8_Y 243_L 0.88 0.41 0.12
103_H 24_S 0.88 0.41 0.12
151_L 94_S 0.88 0.41 0.12
192_I 296_L 0.88 0.41 0.12
155_N 88_N 0.88 0.41 0.12
8_Y 195_P 0.88 0.41 0.12
103_H 100_M 0.88 0.41 0.12
254_V 305_L 0.88 0.41 0.12
136_V 316_Q 0.88 0.41 0.12
110_P 136_L 0.88 0.41 0.12
38_H 83_Q 0.88 0.41 0.12
49_T 144_Q 0.88 0.40 0.12
192_I 280_T 0.88 0.40 0.12
224_M 245_P 0.88 0.40 0.11
78_G 108_M 0.87 0.40 0.11
88_T 37_M 0.87 0.40 0.11
19_T 286_T 0.87 0.40 0.11
67_Y 85_T 0.87 0.40 0.11
196_T 167_W 0.87 0.40 0.11
103_H 5_A 0.87 0.40 0.11
165_I 141_I 0.87 0.40 0.11
144_I 273_N 0.87 0.39 0.11
216_T 158_S 0.87 0.39 0.11
22_L 111_F 0.86 0.39 0.11
88_T 187_M 0.86 0.39 0.11
67_Y 44_L 0.86 0.39 0.11
171_L 258_T 0.86 0.39 0.11
223_L 330_I 0.86 0.39 0.11
125_N 97_M 0.86 0.39 0.11
119_T 268_E 0.86 0.38 0.11
103_H 139_I 0.86 0.38 0.11
179_S 119_T 0.86 0.38 0.11
143_S 219_L 0.86 0.38 0.11
65_S 35_M 0.86 0.38 0.11
61_V 173_T 0.85 0.38 0.10
216_T 207_I 0.85 0.38 0.10
223_L 197_N 0.85 0.38 0.10
22_L 154_L 0.85 0.38 0.10
22_L 158_S 0.85 0.37 0.10
225_F 206_T 0.84 0.37 0.10
143_S 283_A 0.84 0.37 0.10
49_T 111_F 0.84 0.37 0.10
127_L 79_M 0.84 0.37 0.10
2_T 153_L 0.84 0.37 0.10
223_L 333_T 0.84 0.37 0.10
220_I 224_S 0.84 0.37 0.10
26_L 179_L 0.84 0.37 0.10
37_F 207_I 0.84 0.36 0.10
42_L 144_Q 0.84 0.36 0.10
5_S 200_M 0.84 0.36 0.10
103_H 205_L 0.84 0.36 0.10
161_Q 28_F 0.84 0.36 0.10
55_Y 181_Y 0.84 0.36 0.10
81_Y 237_L 0.84 0.36 0.10
191_G 236_K 0.84 0.36 0.10
104_S 87_T 0.84 0.36 0.10
162_A 11_S 0.83 0.36 0.10
8_Y 103_A 0.83 0.36 0.10
23_S 19_I 0.83 0.35 0.10
62_T 333_T 0.83 0.35 0.09
29_S 136_L 0.83 0.35 0.09
199_V 307_M 0.83 0.35 0.09
229_S 155_L 0.83 0.35 0.09
217_I 185_T 0.83 0.35 0.09
95_A 307_M 0.82 0.35 0.09
65_S 56_A 0.82 0.35 0.09
25_L 205_L 0.82 0.35 0.09
73_P 53_T 0.82 0.35 0.09
50_N 27_F 0.82 0.35 0.09
162_A 213_T 0.82 0.35 0.09
156_R 130_L 0.82 0.34 0.09
199_V 163_M 0.82 0.34 0.09
153_E 170_L 0.82 0.34 0.09
123_P 334_T 0.82 0.34 0.09
65_S 233_T 0.82 0.34 0.09
115_H 286_T 0.82 0.34 0.09
151_L 309_N 0.82 0.34 0.09
222_Q 159_I 0.82 0.34 0.09
159_M 68_M 0.82 0.34 0.09
48_L 335_L 0.82 0.34 0.09
229_S 225_T 0.81 0.34 0.09
25_L 48_M 0.81 0.34 0.09
27_M 8_V 0.81 0.34 0.09
153_E 219_L 0.81 0.34 0.09
65_S 99_M 0.81 0.34 0.09
167_I 187_M 0.81 0.34 0.09
209_I 32_G 0.81 0.34 0.09
84_I 332_L 0.81 0.34 0.09
212_S 229_L 0.81 0.34 0.09
84_I 199_N 0.81 0.34 0.09
253_Y 310_N 0.81 0.34 0.09
171_L 159_I 0.81 0.33 0.09
165_I 56_A 0.81 0.33 0.09
18_L 44_L 0.81 0.33 0.09
184_S 246_S 0.81 0.33 0.09
12_K 275_S 0.81 0.33 0.09
127_L 139_I 0.81 0.33 0.09
84_I 27_F 0.81 0.33 0.09
114_G 83_Q 0.80 0.33 0.08
179_S 79_M 0.80 0.33 0.08
213_T 209_I 0.80 0.33 0.08
115_H 185_T 0.80 0.33 0.08
143_S 31_V 0.80 0.33 0.08
229_S 309_N 0.80 0.33 0.08
10_M 39_A 0.80 0.33 0.08
253_Y 331_A 0.80 0.33 0.08
104_S 205_L 0.80 0.33 0.08
51_T 265_A 0.80 0.32 0.08
189_S 113_F 0.80 0.32 0.08
175_L 19_I 0.80 0.32 0.08
195_S 240_L 0.80 0.32 0.08
199_V 69_I 0.80 0.32 0.08
230_K 196_Y 0.80 0.32 0.08
33_M 201_T 0.80 0.32 0.08
187_T 316_Q 0.80 0.32 0.08
31_L 142_M 0.80 0.32 0.08
191_G 281_I 0.80 0.32 0.08
147_A 124_L 0.80 0.32 0.08
123_P 61_L 0.80 0.32 0.08
37_F 157_L 0.79 0.32 0.08
164_L 28_F 0.79 0.32 0.08
216_T 8_V 0.79 0.32 0.08
150_S 204_N 0.79 0.32 0.08
213_T 258_T 0.79 0.32 0.08
127_L 7_P 0.79 0.31 0.08
127_L 119_T 0.79 0.31 0.08
122_T 284_T 0.79 0.31 0.08
37_F 201_T 0.79 0.31 0.08
112_L 2_N 0.79 0.31 0.08
125_N 192_A 0.79 0.31 0.08
49_T 159_I 0.79 0.31 0.08
50_N 342_F 0.78 0.31 0.08
189_S 9_I 0.78 0.31 0.08
122_T 323_T 0.78 0.31 0.08
110_P 308_S 0.78 0.31 0.08
12_K 74_I 0.78 0.31 0.08
123_P 149_L 0.78 0.31 0.08
189_S 312_K 0.78 0.30 0.08
92_L 20_T 0.78 0.30 0.08
103_H 104_M 0.78 0.30 0.07
182_F 271_T 0.78 0.30 0.07
112_L 280_T 0.78 0.30 0.07
185_P 15_A 0.78 0.30 0.07
225_F 226_T 0.78 0.30 0.07
213_T 45_T 0.78 0.30 0.07
73_P 122_T 0.78 0.30 0.07
95_A 103_A 0.78 0.30 0.07
162_A 244_I 0.78 0.30 0.07
5_S 187_M 0.78 0.30 0.07
164_L 233_T 0.78 0.30 0.07
51_T 10_Y 0.78 0.30 0.07
151_L 24_S 0.77 0.30 0.07
229_S 151_V 0.77 0.30 0.07
23_S 49_N 0.77 0.30 0.07
114_G 5_A 0.77 0.30 0.07
55_Y 323_T 0.77 0.30 0.07
61_V 4_L 0.77 0.30 0.07
2_T 79_M 0.77 0.29 0.07
62_T 153_L 0.77 0.29 0.07
121_I 74_I 0.77 0.29 0.07
12_K 307_M 0.77 0.29 0.07
142_V 167_W 0.77 0.29 0.07
38_H 123_P 0.77 0.29 0.07
38_H 179_L 0.77 0.29 0.07
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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