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OPENSEQ.org
cIV_C_20_cI_J_20_human
Genes: A B A+B
Length: 261 174 426
Sequences: 2745 1614 1000
Seq/Len: 10.52 9.28 2.35
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 2.30
20 0.00 0.00 2.30
100 0.00 0.00 2.30
∞ 0.01 0.00 2.30
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 1.76 0.98 0.90
189_S 75_I 1.70 0.97 0.88
103_H 48_G 1.62 0.96 0.84
217_I 64_M 1.42 0.91 0.72
61_V 35_S 1.41 0.90 0.71
103_H 41_V 1.39 0.89 0.70
143_S 146_Y 1.39 0.89 0.69
114_G 48_G 1.38 0.89 0.68
50_N 72_A 1.37 0.88 0.67
189_S 73_M 1.36 0.88 0.66
212_S 159_T 1.33 0.86 0.64
114_G 139_P 1.32 0.86 0.63
125_N 9_S 1.28 0.83 0.59
150_S 156_T 1.27 0.83 0.59
125_N 11_G 1.27 0.83 0.58
103_H 139_P 1.27 0.82 0.58
195_S 11_G 1.27 0.82 0.58
162_A 145_L 1.24 0.80 0.55
127_L 164_V 1.24 0.80 0.55
114_G 41_V 1.22 0.79 0.53
104_S 139_P 1.22 0.79 0.53
65_S 110_D 1.20 0.77 0.51
25_L 74_A 1.18 0.75 0.48
112_L 64_M 1.16 0.73 0.46
143_S 170_I 1.15 0.73 0.46
153_E 41_V 1.14 0.72 0.45
229_S 11_G 1.13 0.71 0.43
103_H 81_A 1.12 0.70 0.42
103_H 8_L 1.11 0.69 0.42
123_P 157_G 1.11 0.69 0.42
144_I 29_G 1.11 0.69 0.41
167_I 162_V 1.09 0.67 0.40
167_I 28_G 1.08 0.66 0.38
178_A 157_G 1.07 0.65 0.37
213_T 64_M 1.06 0.64 0.37
165_I 75_I 1.06 0.64 0.36
62_T 64_M 1.05 0.63 0.35
46_G 19_F 1.05 0.62 0.35
114_G 81_A 1.04 0.62 0.34
7_A 170_I 1.03 0.61 0.34
212_S 135_I 1.03 0.61 0.33
8_Y 90_V 1.03 0.60 0.33
158_Q 97_A 1.02 0.60 0.33
189_S 152_L 1.02 0.60 0.32
212_S 27_Y 1.02 0.59 0.32
143_S 37_V 1.01 0.59 0.32
12_K 14_M 1.01 0.59 0.31
191_G 52_G 1.00 0.57 0.30
20_G 146_Y 0.99 0.56 0.29
2_T 144_A 0.99 0.56 0.29
191_G 18_G 0.98 0.55 0.29
195_S 17_V 0.98 0.54 0.28
8_Y 156_T 0.97 0.54 0.28
217_I 12_L 0.97 0.54 0.28
213_T 9_S 0.97 0.54 0.27
143_S 9_S 0.97 0.54 0.27
225_F 124_W 0.97 0.53 0.27
48_L 147_D 0.96 0.53 0.26
127_L 36_G 0.96 0.53 0.26
49_T 9_S 0.96 0.52 0.26
253_Y 159_T 0.95 0.52 0.26
21_A 153_V 0.95 0.52 0.26
65_S 8_L 0.95 0.51 0.25
151_L 161_F 0.95 0.51 0.25
67_Y 7_L 0.95 0.51 0.25
213_T 41_V 0.94 0.51 0.25
41_T 96_L 0.94 0.51 0.25
175_L 58_I 0.94 0.51 0.25
125_N 140_I 0.93 0.49 0.23
162_A 9_S 0.93 0.49 0.23
42_L 139_P 0.93 0.49 0.23
27_M 162_V 0.93 0.49 0.23
107_A 74_A 0.92 0.48 0.23
192_I 34_V 0.92 0.47 0.23
161_Q 69_Y 0.91 0.47 0.22
229_S 71_T 0.91 0.46 0.22
229_S 165_Y 0.91 0.46 0.22
23_S 36_G 0.90 0.45 0.21
43_L 146_Y 0.90 0.45 0.21
150_S 79_P 0.90 0.45 0.21
18_L 76_E 0.89 0.45 0.21
216_T 58_I 0.89 0.44 0.20
121_I 171_A 0.89 0.44 0.20
195_S 41_V 0.88 0.43 0.20
212_S 133_G 0.88 0.43 0.20
187_T 56_F 0.88 0.43 0.20
49_T 43_I 0.88 0.43 0.20
27_M 51_M 0.88 0.43 0.19
228_T 20_S 0.88 0.43 0.19
229_S 30_L 0.88 0.43 0.19
38_H 27_Y 0.87 0.43 0.19
48_L 93_L 0.87 0.42 0.19
121_I 101_G 0.86 0.42 0.18
41_T 14_M 0.86 0.42 0.18
189_S 48_G 0.86 0.41 0.18
155_N 157_G 0.86 0.41 0.18
38_H 28_G 0.86 0.41 0.18
225_F 11_G 0.86 0.41 0.18
23_S 55_V 0.86 0.41 0.18
125_N 172_R 0.85 0.40 0.18
31_L 89_L 0.85 0.40 0.18
8_Y 46_F 0.85 0.40 0.17
18_L 36_G 0.85 0.40 0.17
22_L 55_V 0.85 0.40 0.17
182_F 27_Y 0.85 0.40 0.17
178_A 150_R 0.85 0.40 0.17
136_V 58_I 0.85 0.39 0.17
112_L 170_I 0.84 0.39 0.17
88_T 70_T 0.84 0.39 0.17
73_P 107_K 0.84 0.38 0.16
23_S 95_G 0.83 0.38 0.16
152_M 44_L 0.83 0.38 0.16
213_T 17_V 0.83 0.38 0.16
49_T 73_M 0.83 0.38 0.16
153_E 8_L 0.83 0.38 0.16
160_I 37_V 0.83 0.38 0.16
171_L 123_S 0.83 0.37 0.16
230_K 163_G 0.82 0.37 0.16
103_H 156_T 0.82 0.37 0.15
61_V 111_G 0.82 0.37 0.15
123_P 110_D 0.82 0.37 0.15
248_V 151_W 0.82 0.37 0.15
23_S 70_T 0.82 0.36 0.15
219_F 33_I 0.81 0.36 0.15
178_A 31_V 0.81 0.36 0.15
150_S 51_M 0.81 0.35 0.15
23_S 85_G 0.81 0.35 0.15
27_M 72_A 0.81 0.35 0.14
39_S 137_E 0.81 0.35 0.14
135_S 164_V 0.81 0.35 0.14
154_N 150_R 0.81 0.35 0.14
53_T 153_V 0.81 0.35 0.14
55_Y 135_I 0.81 0.35 0.14
153_E 64_M 0.80 0.34 0.14
56_Q 167_V 0.80 0.34 0.14
50_N 54_M 0.80 0.34 0.14
73_P 138_D 0.80 0.34 0.14
212_S 89_L 0.80 0.34 0.14
184_S 122_G 0.79 0.34 0.14
35_F 49_G 0.79 0.33 0.13
191_G 82_W 0.79 0.33 0.13
54_M 52_G 0.79 0.33 0.13
12_K 133_G 0.79 0.33 0.13
92_L 4_A 0.78 0.33 0.13
49_T 103_V 0.78 0.33 0.13
74_P 33_I 0.78 0.33 0.13
192_I 18_G 0.78 0.33 0.13
62_T 27_Y 0.78 0.33 0.13
103_H 170_I 0.78 0.33 0.13
191_G 159_T 0.78 0.33 0.13
43_L 44_L 0.78 0.32 0.13
162_A 162_V 0.78 0.32 0.13
56_Q 60_L 0.78 0.32 0.12
155_N 163_G 0.78 0.32 0.12
25_L 64_M 0.77 0.32 0.12
144_I 163_G 0.77 0.32 0.12
73_P 52_G 0.77 0.32 0.12
27_M 136_R 0.77 0.32 0.12
156_R 37_V 0.77 0.32 0.12
128_E 20_S 0.77 0.31 0.12
184_S 172_R 0.77 0.31 0.12
213_T 42_I 0.77 0.31 0.12
104_S 56_F 0.77 0.31 0.12
91_V 72_A 0.77 0.31 0.12
153_E 96_L 0.76 0.31 0.12
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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