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OPENSEQ.org
cI_5_10_cI_9_4_tt
Genes: A B A+B
Length: 207 182 335
Sequences: 1025 870 510
Seq/Len: 4.95 4.78 1.52
MirrorTree (Pazo et al. 2001) 0.89
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 0.01
2 0.00 0.00 0.04
5 0.01 0.01 0.20
10 0.01 0.01 1.05
20 0.01 0.01 1.15
100 0.02 0.01 1.19
∞ 0.06 0.02 1.31
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
109_G 22_V 1.49 0.86 0.16
154_E 85_E 1.43 0.83 0.14
174_L 5_A 1.32 0.75 0.10
171_R 48_N 1.27 0.71 0.09
103_T 19_S 1.19 0.64 0.07
77_L 85_E 1.18 0.62 0.07
92_V 149_E 1.17 0.62 0.06
154_E 96_L 1.15 0.60 0.06
110_S 145_P 1.14 0.59 0.06
49_L 43_L 1.11 0.56 0.05
31_R 7_A 1.09 0.54 0.05
48_F 130_V 1.08 0.53 0.05
21_G 2_T 1.08 0.53 0.05
124_I 7_A 1.08 0.53 0.05
96_E 134_E 1.06 0.51 0.04
146_L 122_A 1.06 0.51 0.04
172_A 100_F 1.05 0.49 0.04
101_L 142_G 1.02 0.46 0.04
144_H 47_P 1.02 0.46 0.04
135_I 15_K 1.00 0.44 0.04
94_V 22_V 0.99 0.44 0.04
31_R 103_L 0.99 0.43 0.04
65_P 19_S 0.99 0.43 0.04
59_T 103_L 0.99 0.43 0.03
84_D 126_Y 0.99 0.43 0.03
129_H 146_Q 0.98 0.43 0.03
29_L 74_E 0.98 0.42 0.03
106_D 19_S 0.97 0.41 0.03
49_L 33_L 0.96 0.41 0.03
72_Y 117_Y 0.95 0.39 0.03
47_N 10_L 0.95 0.39 0.03
132_L 147_R 0.95 0.39 0.03
77_L 73_A 0.94 0.39 0.03
30_P 22_V 0.94 0.38 0.03
108_W 31_V 0.94 0.38 0.03
101_L 74_E 0.93 0.37 0.03
77_L 13_T 0.93 0.37 0.03
36_E 8_Q 0.92 0.37 0.03
38_M 107_A 0.92 0.37 0.03
172_A 123_D 0.92 0.37 0.03
12_A 82_S 0.92 0.36 0.03
109_G 151_K 0.92 0.36 0.03
77_L 9_S 0.91 0.36 0.03
90_V 71_E 0.91 0.35 0.03
96_E 74_E 0.89 0.34 0.02
84_D 138_V 0.89 0.34 0.02
127_E 107_A 0.89 0.34 0.02
168_A 48_N 0.89 0.34 0.02
39_A 11_G 0.89 0.33 0.02
161_E 74_E 0.89 0.33 0.02
91_R 17_L 0.88 0.32 0.02
35_K 8_Q 0.88 0.32 0.02
62_D 152_R 0.87 0.32 0.02
157_T 14_L 0.87 0.32 0.02
63_P 19_S 0.87 0.32 0.02
50_A 135_D 0.87 0.32 0.02
65_P 20_K 0.86 0.31 0.02
33_R 8_Q 0.86 0.31 0.02
88_F 112_A 0.86 0.31 0.02
85_G 116_G 0.86 0.31 0.02
119_Y 132_G 0.86 0.31 0.02
72_Y 150_A 0.86 0.30 0.02
86_S 7_A 0.86 0.30 0.02
94_V 62_A 0.85 0.30 0.02
34_F 2_T 0.85 0.30 0.02
10_A 103_L 0.85 0.30 0.02
9_E 96_L 0.85 0.30 0.02
33_R 150_A 0.85 0.30 0.02
128_G 84_G 0.85 0.30 0.02
85_G 45_R 0.85 0.30 0.02
94_V 74_E 0.85 0.30 0.02
64_R 25_P 0.84 0.30 0.02
129_H 38_H 0.84 0.29 0.02
30_P 15_K 0.84 0.29 0.02
38_M 28_D 0.84 0.29 0.02
102_P 30_P 0.84 0.29 0.02
172_A 118_D 0.84 0.29 0.02
37_E 134_E 0.83 0.29 0.02
33_R 4_K 0.83 0.29 0.02
77_L 10_L 0.83 0.28 0.02
110_S 73_A 0.83 0.28 0.02
58_L 129_L 0.83 0.28 0.02
119_Y 5_A 0.83 0.28 0.02
34_F 31_V 0.83 0.28 0.02
96_E 15_K 0.82 0.28 0.02
65_P 16_Y 0.82 0.28 0.02
121_L 5_A 0.82 0.28 0.02
7_L 19_S 0.82 0.27 0.02
88_F 11_G 0.81 0.27 0.02
137_T 54_I 0.81 0.27 0.02
15_Y 17_L 0.81 0.27 0.02
59_T 19_S 0.81 0.26 0.02
23_G 122_A 0.81 0.26 0.02
110_S 143_T 0.81 0.26 0.02
172_A 128_D 0.80 0.26 0.02
72_Y 131_Y 0.80 0.26 0.02
107_L 62_A 0.80 0.26 0.02
92_V 17_L 0.79 0.25 0.02
86_S 19_S 0.79 0.25 0.02
129_H 102_G 0.79 0.25 0.02
47_N 9_S 0.78 0.25 0.02
97_E 15_K 0.78 0.24 0.01
78_P 134_E 0.78 0.24 0.01
39_A 2_T 0.78 0.24 0.01
132_L 102_G 0.77 0.24 0.01
8_E 142_G 0.77 0.24 0.01
110_S 28_D 0.77 0.24 0.01
8_E 4_K 0.77 0.24 0.01
122_F 149_E 0.77 0.23 0.01
178_D 116_G 0.77 0.23 0.01
34_F 130_V 0.77 0.23 0.01
163_R 89_K 0.77 0.23 0.01
5_R 82_S 0.77 0.23 0.01
169_E 135_D 0.76 0.23 0.01
118_V 33_L 0.76 0.23 0.01
141_L 57_S 0.76 0.23 0.01
47_N 13_T 0.76 0.23 0.01
49_L 130_V 0.76 0.23 0.01
58_L 131_Y 0.76 0.23 0.01
65_P 25_P 0.76 0.22 0.01
62_D 131_Y 0.76 0.22 0.01
11_R 14_L 0.75 0.22 0.01
95_P 147_R 0.75 0.22 0.01
108_W 25_P 0.75 0.22 0.01
33_R 73_A 0.75 0.22 0.01
9_E 33_L 0.74 0.22 0.01
34_F 119_F 0.74 0.22 0.01
90_V 22_V 0.74 0.21 0.01
34_F 33_L 0.74 0.21 0.01
72_Y 135_D 0.74 0.21 0.01
172_A 139_D 0.74 0.21 0.01
27_V 134_E 0.74 0.21 0.01
77_L 6_L 0.74 0.21 0.01
36_E 16_Y 0.74 0.21 0.01
32_E 142_G 0.74 0.21 0.01
130_P 2_T 0.74 0.21 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
4911 1.52 cI_5_10_cI_9_4_tt2 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.30 Done - Shared
4910 1.59 cI_5_6_cI_2_4_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.38 Done - Shared
4909 1.52 cI_5_10_cI_9_4_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.16 Done - Shared
4908 1.56 cI_5_6_cI_9_4_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.28 Done - Shared
4907 1.7 cI_5_10_cI_9_10_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.18 Done - Shared
4906 1.69 cI_5_6_cI_9_6_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.22 Done - Shared
4905 1.52 cI_5_4_cI_9_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.22 Done - Shared
4904 0.04 cI_5_40_cI_9_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) Killed - Shared
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