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OPENSEQ.org
cI_2_20_cI_5_20_tt
Genes: A B A+B
Length: 181 207 361
Sequences: 2565 1089 715
Seq/Len: 14.17 5.26 1.98
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 0.37
2 0.00 0.00 1.32
5 0.01 0.00 1.65
10 0.01 0.01 1.67
20 0.02 0.01 1.68
100 0.04 0.02 1.69
∞ 0.10 0.04 1.84
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
28_M 50_A 1.30 0.81 0.07
46_I 135_I 1.27 0.78 0.06
102_E 29_L 1.16 0.69 0.05
80_L 114_L 1.16 0.69 0.05
119_V 146_L 1.15 0.68 0.04
148_A 103_T 1.06 0.59 0.04
30_L 130_P 1.05 0.58 0.03
67_Y 151_P 1.03 0.55 0.03
73_V 13_K 1.00 0.52 0.03
65_S 73_E 0.95 0.47 0.02
109_G 48_F 0.95 0.46 0.02
139_E 119_Y 0.90 0.41 0.02
62_G 160_R 0.90 0.41 0.02
118_S 77_L 0.89 0.40 0.02
80_L 88_F 0.89 0.39 0.02
80_L 135_I 0.88 0.39 0.02
164_E 124_I 0.88 0.39 0.02
5_D 128_G 0.87 0.38 0.02
149_R 65_P 0.87 0.38 0.02
94_E 144_H 0.86 0.37 0.02
62_G 75_V 0.86 0.37 0.02
173_G 112_N 0.85 0.36 0.02
62_G 138_P 0.84 0.35 0.02
4_F 122_F 0.83 0.34 0.02
105_G 42_K 0.83 0.34 0.02
49_I 146_L 0.82 0.33 0.01
175_H 53_V 0.81 0.32 0.01
46_I 108_W 0.81 0.32 0.01
153_L 47_N 0.81 0.32 0.01
28_M 77_L 0.81 0.32 0.01
74_P 49_L 0.80 0.31 0.01
136_V 37_E 0.80 0.31 0.01
80_L 127_E 0.79 0.30 0.01
103_T 52_I 0.79 0.29 0.01
163_L 171_R 0.78 0.29 0.01
90_L 38_M 0.78 0.29 0.01
175_H 13_K 0.78 0.29 0.01
72_F 91_R 0.78 0.29 0.01
16_A 74_L 0.78 0.29 0.01
90_L 12_A 0.78 0.28 0.01
62_G 139_E 0.77 0.28 0.01
4_F 34_F 0.77 0.28 0.01
29_P 121_L 0.77 0.28 0.01
112_T 88_F 0.77 0.28 0.01
42_R 125_V 0.77 0.28 0.01
23_R 98_D 0.76 0.27 0.01
52_L 107_L 0.76 0.27 0.01
14_T 119_Y 0.76 0.27 0.01
123_E 153_G 0.75 0.26 0.01
106_I 73_E 0.75 0.26 0.01
9_D 105_T 0.75 0.26 0.01
30_L 170_F 0.75 0.26 0.01
137_N 119_Y 0.74 0.26 0.01
60_V 137_T 0.74 0.25 0.01
69_Y 140_D 0.74 0.25 0.01
158_R 135_I 0.74 0.25 0.01
143_E 160_R 0.73 0.25 0.01
54_G 9_E 0.73 0.25 0.01
95_E 16_P 0.73 0.25 0.01
66_F 151_P 0.73 0.25 0.01
62_G 156_P 0.73 0.25 0.01
115_G 23_G 0.73 0.24 0.01
158_R 109_G 0.72 0.24 0.01
153_L 7_L 0.72 0.24 0.01
136_V 35_K 0.72 0.24 0.01
62_G 141_L 0.72 0.24 0.01
37_E 175_T 0.72 0.24 0.01
24_R 146_L 0.72 0.24 0.01
61_M 152_L 0.72 0.24 0.01
60_V 108_W 0.72 0.23 0.01
126_G 174_L 0.72 0.23 0.01
152_A 9_E 0.71 0.23 0.01
23_R 161_E 0.71 0.23 0.01
154_L 128_G 0.71 0.23 0.01
28_M 157_T 0.70 0.23 0.01
125_L 49_L 0.70 0.23 0.01
13_E 35_K 0.70 0.22 0.01
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
4857 2.03 cI_2_2_cI_5_6_tt Δgene:(1, ∞) A:(1E-02, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.21 Done - Shared
4856 1.86 cI_2_2_cI_5_10_tt Δgene:(1, ∞) A:(1E-02, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.79 Done - Shared
4855 1.98 cI_2_4_cI_5_20_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
4854 1.88 cI_2_4_cI_5_10_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.70 Done - Shared
4844 1.86 cI_2_6_cI_5_10_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.67 Done - Shared
4843 1.98 cI_2_20_cI_5_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
4842 1.86 cI_2_10_cI_5_10_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.57 Done - Shared
4841 2.02 cI_2_6_cI_5_6_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.27 Done - Shared
4840 1.99 cI_2_4_cI_5_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
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