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OPENSEQ.org
cIV_B_60_cI_J_60_human
Genes: A B A+B
Length: 227 174 400
Sequences: 2677 184 118
Seq/Len: 11.79 1.06 0.29
MirrorTree (Pazo et al. 2001) 0.33
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 0.01
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
223_P 51_M 1.80 0.61 0.00
64_V 93_L 1.59 0.47 0.00
192_Y 64_M 1.55 0.44 0.00
149_P 138_D 1.53 0.42 0.00
213_L 3_Y 1.46 0.38 0.00
127_F 34_V 1.46 0.38 0.00
97_I 51_M 1.42 0.36 0.00
202_A 93_L 1.36 0.32 0.00
43_F 19_F 1.35 0.32 0.00
9_L 89_L 1.35 0.32 0.00
63_T 92_V 1.32 0.30 0.00
149_P 156_T 1.31 0.29 0.00
149_P 105_W 1.29 0.28 0.00
192_Y 31_V 1.28 0.28 0.00
164_A 51_M 1.26 0.27 0.00
64_V 7_L 1.26 0.27 0.00
142_V 170_I 1.25 0.26 0.00
33_L 137_E 1.24 0.26 0.00
125_P 5_L 1.22 0.25 0.00
182_T 106_V 1.22 0.25 0.00
9_L 136_R 1.21 0.24 0.00
63_T 31_V 1.21 0.24 0.00
37_L 35_S 1.20 0.23 0.00
187_T 41_V 1.19 0.23 0.00
149_P 168_I 1.18 0.23 0.00
185_T 156_T 1.17 0.22 0.00
100_I 17_V 1.16 0.22 0.00
164_A 55_V 1.16 0.22 0.00
149_P 164_V 1.15 0.21 0.00
147_E 90_V 1.15 0.21 0.00
114_G 137_E 1.15 0.21 0.00
191_V 51_M 1.13 0.20 0.00
152_M 121_V 1.12 0.20 0.00
71_I 4_A 1.11 0.20 0.00
123_L 51_M 1.11 0.20 0.00
202_A 51_M 1.10 0.19 0.00
213_L 7_L 1.10 0.19 0.00
115_G 106_V 1.09 0.19 0.00
164_A 14_M 1.09 0.19 0.00
95_L 1_M 1.09 0.19 0.00
213_L 86_V 1.08 0.18 0.00
22_T 135_I 1.07 0.18 0.00
186_A 30_L 1.07 0.18 0.00
13_T 107_K 1.07 0.18 0.00
150_I 90_V 1.06 0.18 0.00
202_A 30_L 1.06 0.17 0.00
107_T 12_L 1.05 0.17 0.00
22_T 126_I 1.05 0.17 0.00
95_L 15_G 1.05 0.17 0.00
27_A 153_V 1.05 0.17 0.00
47_S 21_S 1.04 0.17 0.00
146_I 30_L 1.04 0.17 0.00
182_T 42_I 1.03 0.17 0.00
226_T 91_S 1.03 0.16 0.00
182_T 88_V 1.02 0.16 0.00
182_T 107_K 1.01 0.16 0.00
164_A 43_I 1.01 0.16 0.00
170_L 51_M 1.01 0.16 0.00
149_P 86_V 1.00 0.15 0.00
147_E 38_V 1.00 0.15 0.00
21_I 159_T 1.00 0.15 0.00
9_L 122_G 1.00 0.15 0.00
47_S 98_M 1.00 0.15 0.00
27_A 165_Y 0.99 0.15 0.00
187_T 149_G 0.99 0.15 0.00
192_Y 123_S 0.99 0.15 0.00
44_L 168_I 0.99 0.15 0.00
47_S 143_G 0.98 0.15 0.00
149_P 130_E 0.98 0.15 0.00
61_M 71_T 0.98 0.15 0.00
217_K 10_V 0.97 0.14 0.00
92_D 165_Y 0.97 0.14 0.00
221_M 86_V 0.97 0.14 0.00
165_V 85_G 0.96 0.14 0.00
182_T 111_G 0.96 0.14 0.00
184_F 167_V 0.96 0.14 0.00
54_N 132_S 0.96 0.14 0.00
92_D 51_M 0.96 0.14 0.00
213_L 91_S 0.96 0.14 0.00
117_I 45_N 0.95 0.14 0.00
224_V 7_L 0.95 0.14 0.00
165_V 107_K 0.95 0.14 0.00
90_V 6_F 0.94 0.13 0.00
111_T 162_V 0.93 0.13 0.00
154_I 33_I 0.93 0.13 0.00
221_M 138_D 0.92 0.13 0.00
165_V 128_E 0.92 0.13 0.00
157_Q 50_Y 0.92 0.13 0.00
94_S 14_M 0.92 0.13 0.00
64_V 109_Y 0.92 0.13 0.00
71_I 125_M 0.92 0.13 0.00
220_E 1_M 0.92 0.13 0.00
100_I 100_V 0.92 0.13 0.00
92_D 4_A 0.91 0.12 0.00
115_G 145_L 0.91 0.12 0.00
182_T 163_G 0.91 0.12 0.00
187_T 89_L 0.91 0.12 0.00
184_F 37_V 0.91 0.12 0.00
186_A 104_L 0.91 0.12 0.00
47_S 58_I 0.91 0.12 0.00
71_I 167_V 0.91 0.12 0.00
115_G 43_I 0.91 0.12 0.00
94_S 148_Y 0.90 0.12 0.00
182_T 135_I 0.90 0.12 0.00
54_N 31_V 0.90 0.12 0.00
192_Y 134_L 0.90 0.12 0.00
152_M 54_M 0.90 0.12 0.00
5_A 51_M 0.90 0.12 0.00
115_G 89_L 0.90 0.12 0.00
94_S 86_V 0.90 0.12 0.00
150_I 85_G 0.89 0.12 0.00
43_F 159_T 0.89 0.12 0.00
7_V 97_A 0.89 0.12 0.00
64_V 51_M 0.89 0.12 0.00
21_I 147_D 0.89 0.12 0.00
225_F 110_D 0.89 0.12 0.00
202_A 44_L 0.89 0.12 0.00
7_V 152_L 0.88 0.12 0.00
226_T 89_L 0.88 0.12 0.00
213_L 21_S 0.88 0.12 0.00
41_A 3_Y 0.88 0.12 0.00
87_T 64_M 0.88 0.12 0.00
164_A 85_G 0.88 0.12 0.00
184_F 138_D 0.88 0.12 0.00
202_A 21_S 0.88 0.12 0.00
127_F 86_V 0.87 0.11 0.00
123_L 41_V 0.87 0.11 0.00
220_E 82_W 0.87 0.11 0.00
224_V 144_A 0.86 0.11 0.00
146_I 51_M 0.86 0.11 0.00
5_A 45_N 0.86 0.11 0.00
186_A 21_S 0.86 0.11 0.00
2_A 4_A 0.86 0.11 0.00
6_Q 163_G 0.86 0.11 0.00
71_I 108_E 0.86 0.11 0.00
125_P 165_Y 0.86 0.11 0.00
21_I 37_V 0.86 0.11 0.00
185_T 94_V 0.86 0.11 0.00
218_I 120_S 0.85 0.11 0.00
142_V 143_G 0.85 0.11 0.00
185_T 165_Y 0.85 0.11 0.00
44_L 33_I 0.85 0.11 0.00
64_V 114_V 0.85 0.11 0.00
165_V 143_G 0.85 0.11 0.00
132_D 34_V 0.84 0.11 0.00
218_I 121_V 0.84 0.11 0.00
95_L 102_L 0.84 0.11 0.00
149_P 161_F 0.84 0.11 0.00
92_D 152_L 0.84 0.10 0.00
164_A 147_D 0.84 0.10 0.00
117_I 11_G 0.84 0.10 0.00
186_A 106_V 0.83 0.10 0.00
5_A 2_M 0.83 0.10 0.00
149_P 64_M 0.83 0.10 0.00
187_T 21_S 0.83 0.10 0.00
21_I 50_Y 0.83 0.10 0.00
21_I 135_I 0.82 0.10 0.00
47_S 6_F 0.82 0.10 0.00
143_V 71_T 0.82 0.10 0.00
111_T 121_V 0.82 0.10 0.00
22_T 100_V 0.82 0.10 0.00
115_G 14_M 0.82 0.10 0.00
182_T 168_I 0.82 0.10 0.00
91_N 173_G 0.81 0.10 0.00
47_S 85_G 0.81 0.10 0.00
148_T 170_I 0.81 0.10 0.00
94_S 46_F 0.81 0.10 0.00
75_L 11_G 0.81 0.10 0.00
71_I 100_V 0.81 0.10 0.00
149_P 134_L 0.81 0.10 0.00
211_L 90_V 0.81 0.10 0.00
57_D 43_I 0.80 0.10 0.00
32_F 82_W 0.80 0.10 0.00
146_I 93_L 0.80 0.10 0.00
6_Q 161_F 0.80 0.10 0.00
63_T 115_V 0.80 0.10 0.00
164_A 12_L 0.80 0.10 0.00
192_Y 93_L 0.80 0.10 0.00
152_M 30_L 0.80 0.10 0.00
97_I 3_Y 0.80 0.10 0.00
27_A 137_E 0.80 0.10 0.00
64_V 171_A 0.80 0.10 0.00
224_V 14_M 0.79 0.10 0.00
185_T 83_G 0.79 0.10 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
4649 7.41 cIV_B_40_cI_J_6_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.47 Done - Shared
4648 2.8 cIV_B_40_cI_J_10_4_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 4) msa: Jackhmmer (2015_06) 0.57 Done - Shared
4647 5.35 cIV_B_40_cI_J_10_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.85 Done - Shared
4646 2.7 cIV_B_60_cI_J_20_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.31 Done - Shared
4645 0.29 cIV_B_60_cI_J_60_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4644 2.71 cIV_B_40_cI_J_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.47 Done - Shared
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