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OPENSEQ.org
cIV_C_40_cI_J_10_human
Genes: A B A+B
Length: 261 174 428
Sequences: 2457 2877 2054
Seq/Len: 9.41 16.53 4.8
MirrorTree (Pazo et al. 2001) 0.77
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 0.05
2 0.00 0.00 0.11
5 0.00 0.00 4.37
10 0.00 0.00 4.68
20 0.00 0.00 4.72
100 0.00 0.00 4.72
∞ 0.00 0.00 4.72
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
191_G 161_F 1.72 0.99 0.95
28_T 49_G 1.39 0.97 0.84
155_N 170_I 1.33 0.96 0.81
52_L 17_V 1.26 0.94 0.76
127_L 73_M 1.25 0.93 0.75
153_E 166_I 1.23 0.93 0.73
104_S 65_V 1.19 0.91 0.70
70_H 149_G 1.19 0.91 0.70
120_G 65_V 1.18 0.91 0.69
209_I 156_T 1.16 0.90 0.68
226_H 163_G 1.16 0.90 0.67
13_P 58_I 1.13 0.88 0.64
53_T 153_V 1.13 0.88 0.64
31_L 41_V 1.08 0.85 0.60
125_N 28_G 1.08 0.85 0.59
161_Q 55_V 1.07 0.84 0.58
55_Y 141_G 1.07 0.84 0.58
61_V 121_V 1.03 0.81 0.53
213_T 42_I 1.02 0.80 0.52
164_L 145_L 1.02 0.80 0.52
230_K 145_L 1.00 0.78 0.50
189_S 8_L 0.99 0.77 0.49
61_V 98_M 0.99 0.77 0.49
220_I 30_L 0.98 0.77 0.48
103_H 8_L 0.98 0.76 0.48
135_S 59_Y 0.98 0.76 0.47
20_G 65_V 0.96 0.74 0.45
10_M 26_I 0.96 0.73 0.45
179_S 35_S 0.94 0.72 0.43
107_A 38_V 0.94 0.72 0.43
135_S 78_Y 0.94 0.72 0.43
150_S 55_V 0.94 0.72 0.43
193_Y 156_T 0.93 0.70 0.41
189_S 108_E 0.92 0.70 0.41
103_H 64_M 0.92 0.69 0.40
184_S 17_V 0.91 0.68 0.40
27_M 136_R 0.91 0.68 0.39
43_L 20_S 0.91 0.68 0.39
96_G 28_G 0.90 0.67 0.38
101_F 24_S 0.90 0.67 0.38
101_F 171_A 0.90 0.67 0.38
124_L 159_T 0.90 0.66 0.38
46_G 155_V 0.89 0.66 0.37
142_V 57_L 0.89 0.65 0.37
103_H 48_G 0.89 0.65 0.36
103_H 41_V 0.88 0.64 0.35
226_H 51_M 0.87 0.64 0.35
8_Y 54_M 0.87 0.63 0.35
53_T 145_L 0.87 0.63 0.34
4_Q 70_T 0.87 0.63 0.34
4_Q 78_Y 0.86 0.62 0.34
42_L 16_F 0.86 0.62 0.34
162_A 105_W 0.86 0.62 0.33
19_T 49_G 0.85 0.61 0.33
127_L 71_T 0.84 0.59 0.31
162_A 145_L 0.84 0.59 0.31
21_A 61_G 0.84 0.59 0.31
139_A 81_A 0.84 0.59 0.31
85_L 64_M 0.84 0.58 0.31
174_T 65_V 0.83 0.58 0.30
8_Y 48_G 0.83 0.58 0.30
4_Q 141_G 0.83 0.58 0.30
8_Y 31_V 0.83 0.58 0.30
128_E 55_V 0.83 0.58 0.30
199_V 162_V 0.83 0.58 0.30
195_S 46_F 0.83 0.57 0.30
4_Q 146_Y 0.83 0.57 0.30
79_L 166_I 0.83 0.57 0.30
217_I 6_F 0.82 0.57 0.29
192_I 142_A 0.82 0.56 0.29
125_N 11_G 0.82 0.56 0.29
81_Y 53_L 0.81 0.56 0.28
8_Y 157_G 0.81 0.55 0.28
175_L 18_G 0.81 0.55 0.28
150_S 156_T 0.80 0.53 0.27
48_L 18_G 0.80 0.53 0.27
21_A 78_Y 0.80 0.53 0.27
4_Q 162_V 0.80 0.53 0.27
55_Y 14_M 0.80 0.53 0.27
167_I 97_A 0.80 0.53 0.27
48_L 110_D 0.79 0.53 0.26
50_N 140_I 0.79 0.52 0.26
52_L 103_V 0.79 0.52 0.26
160_I 81_A 0.79 0.52 0.26
184_S 59_Y 0.79 0.52 0.26
22_L 38_V 0.79 0.52 0.26
48_L 8_L 0.79 0.52 0.26
161_Q 74_A 0.79 0.52 0.26
47_L 151_W 0.78 0.51 0.25
124_L 52_G 0.78 0.51 0.25
119_T 146_Y 0.78 0.51 0.25
212_S 159_T 0.78 0.51 0.25
223_L 80_E 0.78 0.50 0.25
103_H 139_P 0.78 0.50 0.25
222_Q 143_G 0.78 0.50 0.25
135_S 157_G 0.78 0.50 0.24
184_S 164_V 0.77 0.50 0.24
189_S 46_F 0.77 0.50 0.24
40_M 89_L 0.77 0.49 0.24
18_L 36_G 0.77 0.49 0.24
78_G 54_M 0.77 0.49 0.24
123_P 49_G 0.77 0.49 0.24
142_V 78_Y 0.77 0.49 0.24
61_V 95_G 0.77 0.49 0.24
123_P 85_G 0.77 0.49 0.23
216_T 58_I 0.76 0.48 0.23
135_S 166_I 0.76 0.48 0.23
217_I 86_V 0.76 0.48 0.23
212_S 135_I 0.76 0.48 0.23
74_P 40_C 0.76 0.48 0.23
110_P 147_D 0.76 0.48 0.23
168_L 103_V 0.76 0.48 0.23
229_S 131_G 0.76 0.48 0.23
220_I 45_N 0.76 0.47 0.23
147_A 14_M 0.76 0.47 0.22
164_L 6_F 0.75 0.47 0.22
19_T 71_T 0.75 0.47 0.22
121_I 105_W 0.75 0.47 0.22
40_M 104_L 0.75 0.47 0.22
62_T 59_Y 0.75 0.47 0.22
192_I 18_G 0.75 0.47 0.22
233_F 167_V 0.75 0.46 0.22
80_R 153_V 0.75 0.46 0.22
143_S 146_Y 0.74 0.46 0.21
120_G 93_L 0.74 0.46 0.21
23_S 71_T 0.74 0.45 0.21
189_S 152_L 0.74 0.45 0.21
32_A 72_A 0.73 0.44 0.21
96_G 66_V 0.73 0.44 0.21
33_M 57_L 0.73 0.44 0.20
206_L 148_Y 0.73 0.44 0.20
27_M 128_E 0.73 0.43 0.20
8_Y 159_T 0.72 0.43 0.20
233_F 13_V 0.72 0.43 0.20
28_T 65_V 0.72 0.42 0.19
162_A 9_S 0.72 0.42 0.19
224_M 37_V 0.72 0.42 0.19
220_I 34_V 0.72 0.42 0.19
61_V 93_L 0.71 0.42 0.19
55_Y 135_I 0.71 0.42 0.19
184_S 32_L 0.71 0.41 0.19
216_T 42_I 0.71 0.41 0.19
4_Q 145_L 0.71 0.41 0.19
74_P 98_M 0.71 0.41 0.19
53_T 49_G 0.71 0.41 0.19
21_A 148_Y 0.71 0.41 0.18
189_S 75_I 0.71 0.41 0.18
51_T 65_V 0.71 0.41 0.18
216_T 37_V 0.71 0.41 0.18
81_Y 66_V 0.71 0.41 0.18
226_H 13_V 0.71 0.41 0.18
51_T 8_L 0.71 0.41 0.18
174_T 40_C 0.71 0.41 0.18
120_G 108_E 0.71 0.40 0.18
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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