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OPENSEQ.org
cI_2_4_cI_5_4_tt
Genes: A B A+B
Length: 181 207 360
Sequences: 2539 1052 715
Seq/Len: 14.03 5.08 1.99
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 0.37
2 0.00 0.00 1.33
5 0.01 0.01 1.65
10 0.01 0.01 1.66
20 0.02 0.01 1.68
100 0.04 0.01 1.70
∞ 0.10 0.03 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 1.27 0.79 0.05
46_I 135_I 1.20 0.73 0.04
80_L 114_L 1.18 0.71 0.04
139_E 119_Y 1.12 0.65 0.03
102_E 29_L 1.12 0.65 0.03
119_V 146_L 1.09 0.62 0.03
4_F 122_F 1.01 0.53 0.02
141_Y 180_G 0.99 0.52 0.02
109_G 48_F 0.99 0.51 0.02
80_L 135_I 0.98 0.50 0.02
118_S 94_V 0.97 0.49 0.02
73_V 12_A 0.95 0.46 0.02
30_L 130_P 0.95 0.46 0.02
3_F 92_V 0.94 0.46 0.02
141_Y 3_L 0.94 0.46 0.02
60_V 108_W 0.93 0.45 0.02
15_F 42_K 0.88 0.39 0.01
4_F 112_N 0.88 0.39 0.01
5_D 128_G 0.87 0.38 0.01
126_G 157_T 0.86 0.37 0.01
95_E 16_P 0.86 0.37 0.01
149_R 65_P 0.86 0.37 0.01
9_D 105_T 0.86 0.37 0.01
86_L 178_D 0.86 0.37 0.01
67_Y 151_P 0.86 0.37 0.01
90_L 38_M 0.86 0.36 0.01
101_T 65_P 0.85 0.36 0.01
106_I 73_E 0.84 0.35 0.01
72_F 111_A 0.84 0.35 0.01
106_I 122_F 0.84 0.35 0.01
4_F 88_F 0.84 0.34 0.01
9_D 13_K 0.83 0.34 0.01
115_G 23_G 0.83 0.34 0.01
68_S 89_F 0.83 0.34 0.01
137_N 103_T 0.83 0.33 0.01
141_Y 135_I 0.82 0.33 0.01
132_P 56_D 0.82 0.32 0.01
54_G 106_D 0.81 0.32 0.01
69_Y 140_D 0.81 0.32 0.01
28_M 157_T 0.81 0.32 0.01
62_G 75_V 0.81 0.31 0.01
144_C 10_A 0.80 0.31 0.01
46_I 108_W 0.80 0.31 0.01
137_N 107_L 0.80 0.31 0.01
153_L 105_T 0.79 0.30 0.01
58_T 50_A 0.79 0.30 0.01
16_A 118_V 0.78 0.29 0.01
24_R 146_L 0.78 0.29 0.01
146_T 25_L 0.78 0.29 0.01
15_F 73_E 0.77 0.28 0.01
21_E 91_R 0.77 0.28 0.01
118_S 77_L 0.76 0.27 0.01
74_P 49_L 0.76 0.27 0.01
23_R 98_D 0.76 0.27 0.01
27_I 191_G 0.76 0.27 0.01
62_G 87_R 0.76 0.27 0.01
73_V 37_E 0.75 0.26 0.01
131_A 36_E 0.75 0.26 0.01
125_L 49_L 0.74 0.26 0.01
162_R 124_I 0.74 0.26 0.01
161_K 47_N 0.74 0.26 0.01
94_E 144_H 0.74 0.26 0.01
102_E 188_S 0.74 0.25 0.01
164_E 128_G 0.74 0.25 0.01
29_P 121_L 0.74 0.25 0.01
141_Y 72_Y 0.74 0.25 0.01
103_T 52_I 0.73 0.25 0.01
49_I 106_D 0.73 0.25 0.01
69_Y 190_K 0.73 0.25 0.01
137_N 119_Y 0.73 0.25 0.01
112_T 7_L 0.73 0.24 0.01
5_D 27_V 0.73 0.24 0.01
137_N 149_D 0.73 0.24 0.01
62_G 137_T 0.72 0.24 0.01
172_C 32_E 0.72 0.24 0.01
80_L 127_E 0.72 0.24 0.01
38_E 129_H 0.72 0.24 0.01
62_G 139_E 0.72 0.24 0.01
6_D 107_L 0.72 0.24 0.01
123_E 150_Y 0.72 0.24 0.01
48_E 44_M 0.72 0.24 0.01
31_L 96_E 0.71 0.23 0.01
16_A 101_L 0.71 0.23 0.01
154_L 128_G 0.71 0.23 0.01
63_V 152_L 0.71 0.23 0.01
161_K 121_L 0.70 0.23 0.01
105_G 23_G 0.70 0.23 0.01
113_P 32_E 0.70 0.22 0.01
116_L 31_R 0.70 0.22 0.01
40_W 66_E 0.69 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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