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OPENSEQ.org
cIV_C_60_cI_J_60_human
Genes: A B A+B
Length: 261 174 435
Sequences: 2363 184 126
Seq/Len: 9.05 1.06 0.29
MirrorTree (Pazo et al. 2001) 0.46
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 0.29
10 0.00 0.00 0.29
20 0.00 0.00 0.29
100 0.00 0.00 0.29
∞ 0.00 0.00 0.29
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 142_A 1.96 0.70 0.02
219_F 133_G 1.87 0.65 0.02
45_L 35_S 1.51 0.41 0.01
199_V 64_M 1.49 0.40 0.01
62_T 64_M 1.46 0.38 0.01
224_M 102_L 1.45 0.38 0.01
62_T 105_W 1.41 0.35 0.01
115_H 126_I 1.41 0.35 0.01
155_N 149_G 1.41 0.35 0.01
155_N 37_V 1.40 0.34 0.01
187_T 148_Y 1.39 0.34 0.01
192_I 98_M 1.36 0.32 0.01
65_S 38_V 1.33 0.30 0.00
62_T 43_I 1.32 0.30 0.00
175_L 20_S 1.31 0.30 0.00
8_Y 3_Y 1.31 0.29 0.00
62_T 14_M 1.31 0.29 0.00
27_M 3_Y 1.31 0.29 0.00
184_S 89_L 1.29 0.28 0.00
61_V 168_I 1.26 0.27 0.00
65_S 167_V 1.26 0.27 0.00
182_F 109_Y 1.24 0.26 0.00
219_F 132_S 1.24 0.26 0.00
61_V 2_M 1.21 0.24 0.00
164_L 98_M 1.20 0.24 0.00
110_P 136_R 1.19 0.23 0.00
110_P 10_V 1.19 0.23 0.00
219_F 44_L 1.17 0.22 0.00
73_P 33_I 1.17 0.22 0.00
8_Y 16_F 1.17 0.22 0.00
155_N 3_Y 1.16 0.22 0.00
192_I 163_G 1.16 0.22 0.00
179_S 30_L 1.15 0.21 0.00
182_F 156_T 1.15 0.21 0.00
155_N 148_Y 1.15 0.21 0.00
92_L 54_M 1.14 0.21 0.00
61_V 55_V 1.14 0.21 0.00
67_Y 31_V 1.13 0.21 0.00
7_A 15_G 1.13 0.20 0.00
95_A 54_M 1.13 0.20 0.00
199_V 105_W 1.13 0.20 0.00
47_L 1_M 1.12 0.20 0.00
67_Y 87_E 1.12 0.20 0.00
143_S 136_R 1.12 0.20 0.00
84_I 33_I 1.10 0.19 0.00
27_M 93_L 1.10 0.19 0.00
212_S 171_A 1.10 0.19 0.00
67_Y 44_L 1.09 0.19 0.00
8_Y 167_V 1.08 0.18 0.00
111_Q 136_R 1.08 0.18 0.00
92_L 121_V 1.08 0.18 0.00
159_M 75_I 1.07 0.18 0.00
213_T 43_I 1.07 0.18 0.00
67_Y 41_V 1.06 0.18 0.00
224_M 126_I 1.06 0.18 0.00
119_T 30_L 1.06 0.17 0.00
115_H 75_I 1.06 0.17 0.00
111_Q 168_I 1.06 0.17 0.00
121_I 54_M 1.05 0.17 0.00
122_T 113_V 1.05 0.17 0.00
27_M 21_S 1.05 0.17 0.00
27_M 87_E 1.04 0.17 0.00
155_N 167_V 1.04 0.17 0.00
127_L 44_L 1.03 0.17 0.00
7_A 92_V 1.03 0.17 0.00
185_P 83_G 1.03 0.16 0.00
67_Y 12_L 1.03 0.16 0.00
65_S 15_G 1.03 0.16 0.00
179_S 161_F 1.02 0.16 0.00
224_M 87_E 1.02 0.16 0.00
37_F 144_A 1.02 0.16 0.00
199_V 10_V 1.02 0.16 0.00
230_K 136_R 1.01 0.16 0.00
168_L 45_N 1.01 0.16 0.00
65_S 155_V 1.01 0.16 0.00
213_T 64_M 1.01 0.16 0.00
185_P 85_G 1.01 0.15 0.00
155_N 139_P 1.00 0.15 0.00
52_L 10_V 1.00 0.15 0.00
155_N 16_F 1.00 0.15 0.00
95_A 104_L 1.00 0.15 0.00
185_P 101_G 1.00 0.15 0.00
61_V 91_S 0.99 0.15 0.00
61_V 33_I 0.99 0.15 0.00
119_T 126_I 0.99 0.15 0.00
32_A 113_V 0.99 0.15 0.00
61_V 17_V 0.99 0.15 0.00
7_A 19_F 0.98 0.15 0.00
110_P 135_I 0.98 0.15 0.00
171_L 85_G 0.98 0.15 0.00
192_I 155_V 0.97 0.14 0.00
230_K 3_Y 0.97 0.14 0.00
44_M 11_G 0.97 0.14 0.00
184_S 14_M 0.97 0.14 0.00
199_V 130_E 0.97 0.14 0.00
219_F 87_E 0.97 0.14 0.00
84_I 97_A 0.97 0.14 0.00
199_V 101_G 0.97 0.14 0.00
225_F 134_L 0.97 0.14 0.00
27_M 34_V 0.97 0.14 0.00
110_P 2_M 0.96 0.14 0.00
67_Y 126_I 0.96 0.14 0.00
155_N 4_A 0.96 0.14 0.00
65_S 137_E 0.96 0.14 0.00
165_I 117_N 0.96 0.14 0.00
187_T 13_V 0.95 0.14 0.00
111_Q 75_I 0.95 0.14 0.00
171_L 129_G 0.95 0.14 0.00
199_V 131_G 0.95 0.14 0.00
48_L 8_L 0.95 0.14 0.00
219_F 18_G 0.95 0.14 0.00
216_T 11_G 0.95 0.14 0.00
143_S 130_E 0.94 0.13 0.00
160_I 102_L 0.94 0.13 0.00
213_T 35_S 0.94 0.13 0.00
119_T 111_G 0.94 0.13 0.00
47_L 6_F 0.94 0.13 0.00
8_Y 37_V 0.93 0.13 0.00
49_T 95_G 0.93 0.13 0.00
37_F 120_S 0.93 0.13 0.00
143_S 159_T 0.93 0.13 0.00
178_A 33_I 0.93 0.13 0.00
192_I 41_V 0.93 0.13 0.00
199_V 142_A 0.93 0.13 0.00
135_S 129_G 0.93 0.13 0.00
159_M 165_Y 0.93 0.13 0.00
55_Y 20_S 0.93 0.13 0.00
44_M 3_Y 0.92 0.13 0.00
62_T 31_V 0.92 0.13 0.00
185_P 35_S 0.92 0.13 0.00
38_H 142_A 0.92 0.13 0.00
157_N 20_S 0.92 0.13 0.00
42_L 82_W 0.92 0.13 0.00
192_I 37_V 0.92 0.13 0.00
48_L 2_M 0.92 0.13 0.00
179_S 54_M 0.92 0.13 0.00
157_N 135_I 0.92 0.13 0.00
135_S 126_I 0.91 0.13 0.00
8_Y 75_I 0.91 0.13 0.00
84_I 34_V 0.91 0.12 0.00
158_Q 120_S 0.91 0.12 0.00
54_M 18_G 0.91 0.12 0.00
160_I 2_M 0.91 0.12 0.00
84_I 143_G 0.91 0.12 0.00
122_T 120_S 0.90 0.12 0.00
67_Y 163_G 0.90 0.12 0.00
212_S 170_I 0.90 0.12 0.00
121_I 46_F 0.90 0.12 0.00
111_Q 135_I 0.89 0.12 0.00
37_F 7_L 0.89 0.12 0.00
143_S 5_L 0.89 0.12 0.00
38_H 64_M 0.89 0.12 0.00
8_Y 117_N 0.89 0.12 0.00
122_T 108_E 0.88 0.12 0.00
182_F 139_P 0.88 0.12 0.00
44_M 38_V 0.88 0.12 0.00
49_T 127_Y 0.88 0.12 0.00
158_Q 167_V 0.88 0.12 0.00
41_T 164_V 0.88 0.12 0.00
8_Y 149_G 0.88 0.12 0.00
223_L 78_Y 0.88 0.12 0.00
111_Q 2_M 0.88 0.12 0.00
37_F 14_M 0.87 0.11 0.00
43_L 92_V 0.87 0.11 0.00
187_T 41_V 0.87 0.11 0.00
32_A 58_I 0.87 0.11 0.00
187_T 86_V 0.87 0.11 0.00
31_L 18_G 0.86 0.11 0.00
37_F 139_P 0.86 0.11 0.00
62_T 130_E 0.86 0.11 0.00
50_N 105_W 0.86 0.11 0.00
199_V 7_L 0.86 0.11 0.00
155_N 138_D 0.86 0.11 0.00
187_T 42_I 0.86 0.11 0.00
37_F 58_I 0.85 0.11 0.00
136_V 143_G 0.85 0.11 0.00
225_F 87_E 0.85 0.11 0.00
182_F 120_S 0.85 0.11 0.00
107_A 138_D 0.85 0.11 0.00
157_N 21_S 0.85 0.11 0.00
160_I 148_Y 0.85 0.11 0.00
160_I 41_V 0.85 0.11 0.00
184_S 148_Y 0.85 0.11 0.00
22_L 37_V 0.84 0.11 0.00
55_Y 11_G 0.84 0.11 0.00
42_L 1_M 0.84 0.11 0.00
74_P 14_M 0.84 0.11 0.00
95_A 7_L 0.84 0.10 0.00
182_F 87_E 0.84 0.10 0.00
230_K 145_L 0.84 0.10 0.00
219_F 21_S 0.83 0.10 0.00
192_I 64_M 0.83 0.10 0.00
220_I 150_R 0.83 0.10 0.00
67_Y 6_F 0.83 0.10 0.00
136_V 58_I 0.83 0.10 0.00
199_V 88_V 0.83 0.10 0.00
182_F 83_G 0.83 0.10 0.00
45_L 152_L 0.82 0.10 0.00
115_H 148_Y 0.82 0.10 0.00
135_S 127_Y 0.82 0.10 0.00
136_V 7_L 0.82 0.10 0.00
74_P 4_A 0.82 0.10 0.00
122_T 2_M 0.82 0.10 0.00
225_F 126_I 0.82 0.10 0.00
2_T 168_I 0.81 0.10 0.00
223_L 123_S 0.81 0.10 0.00
111_Q 122_G 0.81 0.10 0.00
74_P 135_I 0.81 0.10 0.00
187_T 167_V 0.81 0.10 0.00
187_T 16_F 0.81 0.10 0.00
213_T 130_E 0.81 0.10 0.00
216_T 113_V 0.81 0.10 0.00
199_V 8_L 0.81 0.10 0.00
160_I 166_I 0.81 0.10 0.00
95_A 129_G 0.81 0.10 0.00
223_L 85_G 0.80 0.10 0.00
135_S 120_S 0.80 0.10 0.00
107_A 10_V 0.80 0.10 0.00
213_T 42_I 0.80 0.10 0.00
7_A 101_G 0.80 0.10 0.00
52_L 127_Y 0.80 0.10 0.00
39_S 82_W 0.80 0.10 0.00
91_V 50_Y 0.80 0.10 0.00
92_L 114_V 0.80 0.10 0.00
25_L 153_V 0.80 0.10 0.00
217_I 143_G 0.79 0.10 0.00
62_T 138_D 0.79 0.09 0.00
44_M 96_L 0.79 0.09 0.00
91_V 114_V 0.79 0.09 0.00
184_S 136_R 0.79 0.09 0.00
254_V 12_L 0.79 0.09 0.00
224_M 164_V 0.79 0.09 0.00
199_V 26_I 0.79 0.09 0.00
185_P 17_V 0.79 0.09 0.00
38_H 159_T 0.79 0.09 0.00
155_N 19_F 0.79 0.09 0.00
191_G 132_S 0.79 0.09 0.00
217_I 102_L 0.79 0.09 0.00
45_L 93_L 0.79 0.09 0.00
216_T 129_G 0.79 0.09 0.00
41_T 34_V 0.78 0.09 0.00
48_L 152_L 0.78 0.09 0.00
192_I 14_M 0.78 0.09 0.00
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
4640 4.8 cIV_C_40_cI_J_10_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.95 Done - Shared
4628 2.37 cIV_C_60_cI_J_20_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.94 Done - Shared
4627 2.36 cIV_C_40_cI_J_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.96 Done - Shared
4626 2.35 cIV_C_20_cI_J_20_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.90 Done - Shared
4625 0.29 cIV_C_60_cI_J_60_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4624 0.36 cIV_C_40_cI_J_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.04 Done - Shared
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