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OPENSEQ.org
cIV_C_40_cI_J_20_human
Genes: A B A+B
Length: 261 174 426
Sequences: 2457 1614 1005
Seq/Len: 9.41 9.28 2.36
MirrorTree (Pazo et al. 2001) 0.67
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 0.01
5 0.00 0.00 2.13
10 0.00 0.00 2.31
20 0.00 0.00 2.31
100 0.00 0.00 2.31
∞ 0.00 0.00 2.31
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
125_N 28_G 1.95 0.99 0.96
189_S 75_I 1.75 0.98 0.92
103_H 48_G 1.61 0.96 0.88
50_N 72_A 1.44 0.91 0.79
143_S 146_Y 1.40 0.90 0.76
61_V 35_S 1.39 0.89 0.75
103_H 41_V 1.38 0.89 0.75
189_S 73_M 1.38 0.89 0.74
114_G 139_P 1.34 0.87 0.71
212_S 159_T 1.33 0.86 0.70
195_S 11_G 1.32 0.86 0.70
150_S 156_T 1.29 0.84 0.67
114_G 48_G 1.29 0.84 0.67
103_H 139_P 1.27 0.83 0.66
162_A 145_L 1.26 0.82 0.64
127_L 164_V 1.25 0.81 0.63
104_S 139_P 1.24 0.80 0.62
125_N 11_G 1.23 0.80 0.61
217_I 64_M 1.23 0.79 0.61
125_N 9_S 1.22 0.79 0.60
123_P 157_G 1.21 0.79 0.59
212_S 135_I 1.21 0.78 0.59
114_G 41_V 1.20 0.77 0.58
112_L 64_M 1.17 0.75 0.55
25_L 74_A 1.15 0.73 0.52
103_H 8_L 1.14 0.72 0.52
143_S 170_I 1.13 0.71 0.50
229_S 11_G 1.13 0.71 0.50
153_E 41_V 1.13 0.71 0.50
65_S 110_D 1.11 0.69 0.48
103_H 81_A 1.11 0.69 0.48
8_Y 90_V 1.10 0.68 0.47
178_A 157_G 1.09 0.68 0.46
144_I 29_G 1.09 0.67 0.46
165_I 75_I 1.07 0.66 0.44
217_I 12_L 1.07 0.65 0.43
167_I 162_V 1.07 0.65 0.43
212_S 27_Y 1.06 0.64 0.43
62_T 64_M 1.06 0.64 0.43
191_G 52_G 1.04 0.62 0.41
213_T 64_M 1.03 0.61 0.40
20_G 146_Y 1.03 0.61 0.40
49_T 43_I 1.03 0.61 0.39
162_A 9_S 1.03 0.61 0.39
158_Q 97_A 1.03 0.61 0.39
189_S 152_L 1.03 0.61 0.39
65_S 8_L 1.02 0.60 0.39
46_G 19_F 1.02 0.60 0.38
114_G 81_A 1.02 0.60 0.38
41_T 96_L 1.01 0.59 0.37
167_I 28_G 1.01 0.58 0.37
27_M 162_V 1.01 0.58 0.37
12_K 14_M 1.01 0.58 0.37
143_S 37_V 1.00 0.58 0.36
62_T 27_Y 1.00 0.58 0.36
2_T 144_A 1.00 0.57 0.36
192_I 34_V 1.00 0.57 0.35
121_I 171_A 0.99 0.56 0.35
175_L 58_I 0.99 0.56 0.35
191_G 18_G 0.99 0.56 0.34
43_L 146_Y 0.98 0.55 0.34
143_S 9_S 0.96 0.52 0.31
253_Y 159_T 0.95 0.52 0.31
151_L 161_F 0.95 0.52 0.31
38_H 27_Y 0.95 0.52 0.31
161_Q 69_Y 0.95 0.51 0.30
31_L 89_L 0.94 0.50 0.29
27_M 72_A 0.93 0.50 0.29
49_T 9_S 0.93 0.49 0.28
48_L 147_D 0.92 0.48 0.28
8_Y 156_T 0.92 0.48 0.27
216_T 58_I 0.92 0.48 0.27
7_A 170_I 0.91 0.47 0.27
195_S 17_V 0.91 0.47 0.27
125_N 172_R 0.91 0.47 0.27
23_S 36_G 0.91 0.47 0.27
127_L 36_G 0.91 0.47 0.26
213_T 9_S 0.91 0.46 0.26
21_A 153_V 0.91 0.46 0.26
153_E 8_L 0.91 0.46 0.26
42_L 139_P 0.90 0.46 0.25
187_T 56_F 0.90 0.45 0.25
27_M 51_M 0.88 0.44 0.24
125_N 140_I 0.88 0.44 0.24
150_S 79_P 0.88 0.43 0.24
229_S 165_Y 0.88 0.43 0.23
22_L 55_V 0.88 0.43 0.23
189_S 48_G 0.87 0.43 0.23
195_S 41_V 0.87 0.43 0.23
103_H 156_T 0.87 0.42 0.23
228_T 20_S 0.87 0.42 0.23
213_T 41_V 0.87 0.42 0.23
135_S 164_V 0.87 0.42 0.23
225_F 124_W 0.87 0.42 0.23
229_S 71_T 0.87 0.42 0.23
160_I 37_V 0.86 0.41 0.22
88_T 70_T 0.86 0.41 0.22
248_V 151_W 0.86 0.41 0.22
178_A 31_V 0.85 0.40 0.21
40_M 43_I 0.85 0.40 0.21
23_S 85_G 0.85 0.40 0.21
67_Y 7_L 0.84 0.39 0.21
92_L 47_G 0.84 0.39 0.20
178_A 150_R 0.84 0.39 0.20
213_T 17_V 0.84 0.39 0.20
23_S 55_V 0.84 0.38 0.20
154_N 150_R 0.83 0.38 0.20
23_S 95_G 0.83 0.38 0.20
38_H 28_G 0.83 0.38 0.20
18_L 36_G 0.83 0.38 0.19
8_Y 46_F 0.83 0.38 0.19
182_F 27_Y 0.82 0.37 0.19
155_N 157_G 0.82 0.37 0.19
191_G 159_T 0.82 0.37 0.19
73_P 52_G 0.82 0.37 0.19
123_P 110_D 0.82 0.37 0.19
107_A 74_A 0.82 0.36 0.18
53_T 153_V 0.81 0.36 0.18
121_I 101_G 0.81 0.36 0.18
150_S 51_M 0.81 0.36 0.18
127_L 153_V 0.81 0.36 0.18
144_I 163_G 0.81 0.36 0.18
216_T 64_M 0.81 0.36 0.18
18_L 76_E 0.81 0.35 0.18
229_S 30_L 0.81 0.35 0.17
62_T 151_W 0.81 0.35 0.17
225_F 11_G 0.80 0.35 0.17
48_L 93_L 0.80 0.34 0.17
73_P 107_K 0.80 0.34 0.17
156_R 37_V 0.80 0.34 0.17
84_I 79_P 0.80 0.34 0.17
151_L 124_W 0.80 0.34 0.17
104_S 56_F 0.79 0.34 0.17
175_L 9_S 0.79 0.34 0.17
136_V 58_I 0.79 0.34 0.16
152_M 44_L 0.79 0.34 0.16
23_S 70_T 0.79 0.34 0.16
171_L 123_S 0.79 0.34 0.16
179_S 49_G 0.79 0.33 0.16
187_T 99_E 0.79 0.33 0.16
8_Y 1_M 0.79 0.33 0.16
165_I 129_G 0.79 0.33 0.16
29_S 40_C 0.79 0.33 0.16
92_L 149_G 0.79 0.33 0.16
125_N 169_E 0.79 0.33 0.16
212_S 125_M 0.79 0.33 0.16
217_I 91_S 0.79 0.33 0.16
56_Q 167_V 0.79 0.33 0.16
212_S 133_G 0.78 0.33 0.16
199_V 26_I 0.78 0.33 0.16
158_Q 153_V 0.78 0.33 0.16
92_L 156_T 0.78 0.33 0.16
223_L 163_G 0.78 0.32 0.16
153_E 64_M 0.78 0.32 0.15
92_L 4_A 0.78 0.32 0.15
43_L 5_L 0.78 0.32 0.15
192_I 18_G 0.78 0.32 0.15
112_L 170_I 0.77 0.32 0.15
32_A 72_A 0.77 0.32 0.15
222_Q 64_M 0.77 0.32 0.15
162_A 162_V 0.77 0.32 0.15
33_M 163_G 0.77 0.32 0.15
73_P 138_D 0.77 0.31 0.15
216_T 97_A 0.77 0.31 0.15
103_H 170_I 0.77 0.31 0.15
27_M 85_G 0.76 0.31 0.14
3_H 23_P 0.76 0.31 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
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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