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OPENSEQ.org
cIV_C_60_cI_J_20_human
Genes: A B A+B
Length: 261 174 426
Sequences: 2363 1614 1010
Seq/Len: 9.05 9.28 2.37
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 2.11
10 0.00 0.00 2.32
20 0.00 0.00 2.32
100 0.00 0.00 2.32
∞ 0.00 0.00 2.32
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 1.85 0.99 0.94
189_S 75_I 1.76 0.98 0.92
103_H 48_G 1.64 0.96 0.88
61_V 35_S 1.50 0.93 0.80
50_N 72_A 1.46 0.92 0.78
143_S 146_Y 1.43 0.91 0.76
103_H 41_V 1.40 0.90 0.74
114_G 139_P 1.38 0.89 0.72
195_S 11_G 1.37 0.88 0.71
114_G 48_G 1.36 0.88 0.70
189_S 73_M 1.33 0.86 0.68
212_S 159_T 1.31 0.85 0.67
150_S 156_T 1.30 0.84 0.65
103_H 139_P 1.29 0.84 0.65
125_N 9_S 1.27 0.82 0.62
104_S 139_P 1.23 0.80 0.58
127_L 164_V 1.22 0.79 0.58
162_A 145_L 1.22 0.79 0.57
114_G 41_V 1.21 0.79 0.57
112_L 64_M 1.20 0.78 0.56
144_I 29_G 1.19 0.77 0.55
125_N 11_G 1.18 0.76 0.54
103_H 8_L 1.17 0.75 0.52
217_I 64_M 1.17 0.75 0.52
229_S 11_G 1.16 0.74 0.51
25_L 74_A 1.15 0.73 0.50
123_P 157_G 1.13 0.71 0.48
65_S 110_D 1.13 0.71 0.47
153_E 41_V 1.12 0.70 0.46
103_H 81_A 1.11 0.69 0.46
212_S 135_I 1.09 0.67 0.43
8_Y 90_V 1.09 0.67 0.43
178_A 157_G 1.08 0.66 0.42
143_S 170_I 1.08 0.66 0.42
175_L 58_I 1.07 0.65 0.41
212_S 27_Y 1.06 0.65 0.41
62_T 64_M 1.06 0.64 0.40
158_Q 97_A 1.06 0.64 0.40
189_S 152_L 1.04 0.62 0.38
191_G 52_G 1.04 0.62 0.38
49_T 43_I 1.03 0.61 0.37
12_K 14_M 1.03 0.61 0.37
167_I 28_G 1.03 0.61 0.37
114_G 81_A 1.02 0.60 0.36
217_I 12_L 1.02 0.59 0.36
27_M 162_V 1.02 0.59 0.35
20_G 146_Y 1.02 0.59 0.35
46_G 19_F 1.01 0.59 0.35
225_F 124_W 1.01 0.59 0.35
167_I 162_V 1.01 0.58 0.34
143_S 37_V 1.00 0.58 0.34
65_S 8_L 1.00 0.58 0.34
8_Y 156_T 1.00 0.57 0.34
162_A 9_S 0.99 0.57 0.33
165_I 75_I 0.99 0.56 0.33
121_I 171_A 0.99 0.56 0.33
191_G 18_G 0.98 0.56 0.32
62_T 27_Y 0.98 0.55 0.31
213_T 64_M 0.97 0.54 0.31
253_Y 159_T 0.97 0.54 0.31
27_M 51_M 0.96 0.53 0.30
31_L 89_L 0.96 0.52 0.29
2_T 144_A 0.95 0.52 0.29
92_L 4_A 0.95 0.52 0.29
195_S 17_V 0.95 0.52 0.28
143_S 9_S 0.94 0.51 0.28
49_T 9_S 0.94 0.50 0.27
125_N 172_R 0.93 0.50 0.27
161_Q 69_Y 0.93 0.50 0.27
38_H 27_Y 0.93 0.49 0.27
48_L 147_D 0.93 0.49 0.27
153_E 8_L 0.93 0.49 0.26
187_T 56_F 0.92 0.48 0.26
127_L 36_G 0.91 0.47 0.25
229_S 165_Y 0.91 0.47 0.25
27_M 72_A 0.91 0.47 0.25
21_A 153_V 0.90 0.46 0.24
41_T 96_L 0.90 0.46 0.24
23_S 36_G 0.90 0.46 0.24
7_A 170_I 0.90 0.46 0.24
123_P 110_D 0.90 0.46 0.24
43_L 146_Y 0.90 0.45 0.23
151_L 161_F 0.89 0.45 0.23
223_L 163_G 0.89 0.45 0.23
195_S 41_V 0.89 0.44 0.23
150_S 79_P 0.88 0.43 0.22
8_Y 46_F 0.88 0.43 0.22
154_N 150_R 0.87 0.43 0.21
213_T 9_S 0.87 0.42 0.21
92_L 47_G 0.87 0.42 0.21
22_L 55_V 0.87 0.42 0.21
23_S 55_V 0.87 0.42 0.21
43_L 44_L 0.86 0.42 0.21
55_Y 135_I 0.86 0.41 0.21
229_S 71_T 0.86 0.41 0.20
42_L 139_P 0.86 0.41 0.20
178_A 150_R 0.86 0.41 0.20
88_T 70_T 0.86 0.41 0.20
189_S 48_G 0.86 0.41 0.20
213_T 41_V 0.85 0.41 0.20
192_I 34_V 0.85 0.40 0.20
125_N 140_I 0.85 0.40 0.20
38_H 28_G 0.85 0.40 0.20
213_T 17_V 0.85 0.40 0.20
103_H 156_T 0.85 0.40 0.20
104_S 56_F 0.85 0.40 0.19
73_P 107_K 0.84 0.39 0.19
191_G 159_T 0.84 0.39 0.19
153_E 64_M 0.84 0.39 0.19
135_S 164_V 0.84 0.39 0.19
248_V 72_A 0.84 0.39 0.19
228_T 20_S 0.84 0.39 0.19
92_L 156_T 0.84 0.39 0.18
229_S 30_L 0.83 0.38 0.18
62_T 131_G 0.83 0.38 0.18
178_A 31_V 0.83 0.38 0.18
62_T 151_W 0.83 0.38 0.18
18_L 36_G 0.82 0.37 0.18
144_I 35_S 0.82 0.37 0.17
18_L 76_E 0.81 0.36 0.17
107_A 74_A 0.81 0.36 0.17
46_G 64_M 0.81 0.36 0.17
187_T 99_E 0.81 0.36 0.17
23_S 70_T 0.81 0.36 0.17
152_M 44_L 0.81 0.36 0.17
54_M 142_A 0.81 0.35 0.16
179_S 49_G 0.81 0.35 0.16
192_I 18_G 0.80 0.35 0.16
7_A 2_M 0.80 0.35 0.16
84_I 79_P 0.80 0.35 0.16
160_I 37_V 0.80 0.35 0.16
150_S 51_M 0.80 0.35 0.16
50_N 48_G 0.80 0.35 0.16
103_H 170_I 0.80 0.35 0.16
184_S 122_G 0.80 0.34 0.16
27_M 136_R 0.80 0.34 0.16
67_Y 7_L 0.80 0.34 0.16
171_L 123_S 0.80 0.34 0.15
199_V 26_I 0.79 0.34 0.15
73_P 52_G 0.79 0.34 0.15
53_T 153_V 0.79 0.34 0.15
25_L 128_E 0.79 0.34 0.15
103_H 18_G 0.79 0.33 0.15
212_S 133_G 0.79 0.33 0.15
191_G 70_T 0.79 0.33 0.15
8_Y 1_M 0.78 0.33 0.15
162_A 12_L 0.78 0.33 0.15
23_S 95_G 0.78 0.33 0.15
3_H 23_P 0.78 0.33 0.15
23_S 85_G 0.78 0.33 0.15
92_L 149_G 0.78 0.33 0.15
29_S 40_C 0.78 0.33 0.14
40_M 43_I 0.78 0.33 0.14
12_K 43_I 0.78 0.32 0.14
127_L 153_V 0.78 0.32 0.14
45_L 10_V 0.78 0.32 0.14
182_F 27_Y 0.78 0.32 0.14
212_S 89_L 0.78 0.32 0.14
225_F 11_G 0.78 0.32 0.14
136_V 58_I 0.78 0.32 0.14
248_V 151_W 0.77 0.32 0.14
162_A 146_Y 0.77 0.32 0.14
43_L 5_L 0.77 0.32 0.14
155_N 157_G 0.77 0.32 0.14
39_S 54_M 0.77 0.32 0.14
33_M 163_G 0.77 0.32 0.14
213_T 42_I 0.77 0.32 0.14
112_L 170_I 0.77 0.31 0.14
144_I 163_G 0.77 0.31 0.14
74_P 162_V 0.77 0.31 0.14
49_T 73_M 0.77 0.31 0.14
51_T 96_L 0.77 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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