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OPENSEQ.org
cI_2_2_cI_5_10_tt
Genes: A B A+B
Length: 181 207 361
Sequences: 2502 1025 671
Seq/Len: 13.82 4.95 1.86
MirrorTree (Pazo et al. 2001) 0.81
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 0.34
2 0.00 0.00 1.23
5 0.01 0.01 1.55
10 0.01 0.01 1.57
20 0.02 0.01 1.58
100 0.04 0.02 1.60
∞ 0.09 0.06 1.73
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
46_I 135_I 1.72 0.96 0.79
28_M 50_A 1.32 0.80 0.46
139_E 119_Y 1.26 0.76 0.41
102_E 29_L 1.22 0.73 0.37
80_L 114_L 1.06 0.56 0.23
39_G 23_G 1.04 0.54 0.21
119_V 146_L 1.00 0.50 0.19
30_L 130_P 0.98 0.48 0.17
9_D 105_T 0.95 0.45 0.15
90_L 38_M 0.95 0.45 0.15
118_S 77_L 0.94 0.43 0.15
137_N 107_L 0.93 0.43 0.14
67_Y 151_P 0.93 0.43 0.14
4_F 112_N 0.92 0.41 0.14
73_V 12_A 0.88 0.38 0.12
109_G 48_F 0.87 0.36 0.11
154_L 128_G 0.86 0.36 0.11
5_D 128_G 0.86 0.35 0.11
74_P 49_L 0.86 0.35 0.10
46_I 107_L 0.85 0.34 0.10
25_A 171_R 0.85 0.34 0.10
158_R 135_I 0.85 0.34 0.10
95_E 16_P 0.85 0.34 0.10
16_A 101_L 0.85 0.34 0.10
49_I 106_D 0.85 0.34 0.10
77_K 11_R 0.85 0.34 0.10
106_I 73_E 0.84 0.33 0.10
69_Y 140_D 0.83 0.33 0.10
113_P 32_E 0.83 0.32 0.09
94_E 45_G 0.83 0.32 0.09
57_P 163_R 0.82 0.32 0.09
147_R 30_P 0.82 0.31 0.09
46_I 108_W 0.82 0.31 0.09
62_G 75_V 0.82 0.31 0.09
101_T 65_P 0.82 0.31 0.09
42_R 125_V 0.81 0.31 0.09
52_L 69_A 0.81 0.30 0.09
9_D 13_K 0.81 0.30 0.09
54_G 106_D 0.80 0.30 0.08
28_M 11_R 0.80 0.30 0.08
13_E 35_K 0.80 0.30 0.08
51_R 8_E 0.80 0.29 0.08
65_S 146_L 0.79 0.29 0.08
65_S 73_E 0.78 0.28 0.07
58_T 50_A 0.77 0.27 0.07
68_S 89_F 0.77 0.27 0.07
137_N 92_V 0.77 0.27 0.07
123_E 67_R 0.77 0.27 0.07
42_R 174_L 0.76 0.26 0.07
153_L 47_N 0.76 0.26 0.07
148_A 103_T 0.76 0.26 0.07
137_N 119_Y 0.76 0.26 0.07
172_C 180_G 0.76 0.26 0.07
125_L 146_L 0.76 0.26 0.07
89_K 73_E 0.76 0.26 0.07
115_G 23_G 0.76 0.26 0.07
26_A 131_D 0.75 0.26 0.07
72_F 91_R 0.75 0.25 0.06
150_L 119_Y 0.75 0.25 0.06
146_T 25_L 0.75 0.25 0.06
19_P 67_R 0.74 0.25 0.06
90_L 53_V 0.74 0.24 0.06
73_V 37_E 0.74 0.24 0.06
144_C 175_T 0.73 0.24 0.06
79_H 99_P 0.73 0.24 0.06
6_D 28_V 0.73 0.24 0.06
172_C 176_G 0.73 0.24 0.06
51_R 100_R 0.73 0.23 0.06
77_K 16_P 0.73 0.23 0.06
16_A 74_L 0.73 0.23 0.06
37_E 160_R 0.73 0.23 0.06
149_R 65_P 0.72 0.23 0.06
80_L 65_P 0.72 0.23 0.06
22_G 102_P 0.72 0.23 0.06
28_M 22_L 0.72 0.23 0.06
141_Y 180_G 0.72 0.23 0.05
4_F 122_F 0.72 0.23 0.05
132_P 56_D 0.71 0.22 0.05
107_G 35_K 0.71 0.22 0.05
29_P 121_L 0.71 0.22 0.05
173_G 112_N 0.71 0.22 0.05
90_L 11_R 0.71 0.22 0.05
46_I 34_F 0.71 0.22 0.05
103_T 37_E 0.71 0.22 0.05
82_V 136_L 0.71 0.22 0.05
60_V 108_W 0.71 0.22 0.05
162_R 124_I 0.70 0.22 0.05
16_A 8_E 0.70 0.22 0.05
15_F 73_E 0.70 0.21 0.05
123_E 57_Y 0.70 0.21 0.05
154_L 59_T 0.70 0.21 0.05
24_R 103_T 0.70 0.21 0.05
72_F 111_A 0.70 0.21 0.05
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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