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OPENSEQ.org
cIV_B_40_cI_J_10_human
Genes: A B A+B
Length: 227 174 392
Sequences: 4037 2877 2099
Seq/Len: 17.78 16.53 5.35
MirrorTree (Pazo et al. 2001) 0.82
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 0.02
5 0.00 0.00 0.31
10 0.00 0.00 5.22
20 0.00 0.00 5.23
100 0.01 0.00 5.23
∞ 0.01 0.00 5.23
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
172_T 59_Y 1.50 0.99 0.85
160_L 161_F 1.39 0.97 0.78
68_L 64_M 1.36 0.97 0.76
11_D 32_L 1.27 0.95 0.70
183_T 56_F 1.27 0.95 0.69
72_I 167_V 1.26 0.95 0.69
175_I 71_T 1.25 0.95 0.68
137_D 170_I 1.25 0.95 0.67
156_S 66_V 1.22 0.94 0.65
30_I 155_V 1.19 0.93 0.62
167_T 73_M 1.19 0.93 0.62
15_P 164_V 1.13 0.90 0.56
123_L 94_V 1.13 0.90 0.56
27_A 77_E 1.12 0.90 0.55
146_I 60_L 1.11 0.89 0.53
221_M 162_V 1.06 0.86 0.48
9_L 52_G 1.05 0.85 0.47
184_F 55_V 1.03 0.84 0.45
28_L 161_F 1.03 0.83 0.45
63_T 52_G 1.03 0.83 0.45
146_I 65_V 1.02 0.83 0.44
18_E 70_T 0.98 0.79 0.39
68_L 57_L 0.97 0.78 0.39
46_L 157_G 0.97 0.78 0.38
53_T 24_S 0.96 0.77 0.37
147_E 153_V 0.96 0.77 0.37
155_T 147_D 0.95 0.76 0.36
81_L 40_C 0.94 0.75 0.35
11_D 43_I 0.94 0.75 0.35
72_I 103_V 0.94 0.75 0.35
129_E 96_L 0.94 0.75 0.35
52_N 128_E 0.94 0.75 0.35
49_K 123_S 0.94 0.74 0.35
193_Y 105_W 0.93 0.73 0.34
7_V 110_D 0.92 0.73 0.33
220_E 28_G 0.92 0.72 0.33
155_T 156_T 0.91 0.72 0.32
216_L 10_V 0.91 0.71 0.32
143_V 83_G 0.91 0.71 0.32
52_N 12_L 0.91 0.71 0.32
76_I 35_S 0.90 0.70 0.31
90_V 168_I 0.90 0.70 0.31
29_M 27_Y 0.89 0.69 0.30
193_Y 99_E 0.89 0.69 0.30
19_E 35_S 0.89 0.68 0.29
186_A 58_I 0.88 0.68 0.29
130_P 105_W 0.88 0.68 0.29
157_Q 51_M 0.88 0.67 0.29
216_L 60_L 0.88 0.67 0.29
160_L 154_V 0.88 0.67 0.28
165_V 10_V 0.87 0.67 0.28
73_L 8_L 0.87 0.66 0.28
90_V 65_V 0.87 0.66 0.28
146_I 40_C 0.86 0.66 0.28
68_L 145_L 0.86 0.65 0.27
11_D 29_G 0.86 0.65 0.27
96_T 146_Y 0.86 0.65 0.27
125_P 65_V 0.85 0.64 0.26
53_T 53_L 0.85 0.64 0.26
154_I 138_D 0.85 0.64 0.26
26_H 61_G 0.84 0.63 0.26
175_I 59_Y 0.84 0.63 0.26
142_V 167_V 0.84 0.63 0.25
131_G 141_G 0.84 0.63 0.25
7_V 104_L 0.84 0.62 0.25
96_T 141_G 0.84 0.62 0.25
142_V 161_F 0.84 0.62 0.25
123_L 142_A 0.83 0.61 0.24
28_L 77_E 0.83 0.61 0.24
187_T 81_A 0.83 0.61 0.24
68_L 30_L 0.83 0.61 0.24
21_I 71_T 0.83 0.61 0.24
82_R 56_F 0.83 0.60 0.24
153_M 30_L 0.82 0.60 0.24
27_A 139_P 0.82 0.60 0.24
94_S 27_Y 0.82 0.60 0.23
160_L 26_I 0.82 0.60 0.23
49_K 11_G 0.82 0.60 0.23
191_V 33_I 0.82 0.59 0.23
76_I 59_Y 0.81 0.59 0.23
144_L 132_S 0.81 0.59 0.23
210_V 71_T 0.81 0.58 0.23
8_G 145_L 0.81 0.58 0.23
23_F 52_G 0.81 0.58 0.23
47_S 57_L 0.81 0.58 0.22
182_T 142_A 0.81 0.58 0.22
140_N 24_S 0.81 0.58 0.22
193_Y 157_G 0.81 0.58 0.22
217_K 8_L 0.80 0.57 0.22
153_M 37_V 0.80 0.57 0.22
164_A 63_M 0.80 0.57 0.21
57_D 16_F 0.80 0.57 0.21
107_T 106_V 0.80 0.56 0.21
63_T 14_M 0.80 0.56 0.21
30_I 48_G 0.80 0.56 0.21
36_F 107_K 0.80 0.56 0.21
92_D 16_F 0.79 0.56 0.21
156_S 153_V 0.79 0.56 0.21
187_T 76_E 0.79 0.56 0.21
97_I 47_G 0.79 0.56 0.21
27_A 93_L 0.79 0.56 0.21
189_P 145_L 0.79 0.56 0.21
83_I 161_F 0.79 0.56 0.21
82_R 32_L 0.79 0.55 0.21
164_A 48_G 0.79 0.55 0.21
189_P 162_V 0.79 0.55 0.20
94_S 146_Y 0.79 0.55 0.20
116_L 172_R 0.79 0.55 0.20
11_D 79_P 0.79 0.55 0.20
95_L 131_G 0.79 0.55 0.20
30_I 165_Y 0.79 0.55 0.20
82_R 26_I 0.78 0.55 0.20
153_M 57_L 0.78 0.55 0.20
175_I 149_G 0.78 0.54 0.20
192_Y 13_V 0.78 0.54 0.20
4_A 53_L 0.78 0.54 0.20
51_T 75_I 0.78 0.54 0.20
95_L 138_D 0.78 0.54 0.20
167_T 65_V 0.78 0.54 0.20
225_F 84_S 0.78 0.53 0.20
218_I 105_W 0.78 0.53 0.20
210_V 30_L 0.78 0.53 0.20
22_T 32_L 0.78 0.53 0.20
149_P 157_G 0.77 0.53 0.19
35_C 39_G 0.77 0.53 0.19
155_T 49_G 0.77 0.52 0.19
112_D 73_M 0.77 0.52 0.19
32_F 60_L 0.76 0.52 0.19
53_T 64_M 0.76 0.52 0.18
168_L 164_V 0.76 0.51 0.18
215_P 60_L 0.76 0.51 0.18
78_L 154_V 0.76 0.51 0.18
83_I 61_G 0.76 0.51 0.18
91_N 143_G 0.76 0.51 0.18
56_S 52_G 0.76 0.51 0.18
191_V 57_L 0.76 0.51 0.18
5_A 171_A 0.76 0.51 0.18
13_T 169_E 0.76 0.50 0.18
164_A 126_I 0.76 0.50 0.18
167_T 62_G 0.75 0.50 0.18
221_M 96_L 0.75 0.50 0.18
131_G 59_Y 0.75 0.50 0.18
189_P 152_L 0.75 0.50 0.18
183_T 31_V 0.75 0.50 0.17
192_Y 162_V 0.75 0.50 0.17
82_R 61_G 0.75 0.50 0.17
116_L 46_F 0.75 0.50 0.17
160_L 66_V 0.75 0.49 0.17
160_L 166_I 0.75 0.49 0.17
27_A 141_G 0.75 0.49 0.17
39_L 50_Y 0.75 0.49 0.17
160_L 18_G 0.74 0.49 0.17
41_A 161_F 0.74 0.49 0.17
137_D 56_F 0.74 0.49 0.17
144_L 94_V 0.74 0.49 0.17
185_T 63_M 0.74 0.48 0.17
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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