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OPENSEQ.org
cI_5_10_cI_6_10_tt
Genes: A B A+B
Length: 207 181 351
Sequences: 1025 1433 638
Seq/Len: 4.95 7.92 1.82
MirrorTree (Pazo et al. 2001) 0.87
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 0.01 1.46
2 0.00 0.01 1.55
5 0.01 0.02 1.56
10 0.01 0.02 1.56
20 0.01 0.02 1.57
100 0.02 0.04 1.58
∞ 0.06 0.09 1.64
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
52_I 151_V 1.46 0.88 0.25
109_G 56_A 1.36 0.82 0.19
32_E 20_L 1.30 0.78 0.16
89_F 103_K 1.24 0.74 0.14
134_K 126_N 1.24 0.74 0.14
75_V 110_A 1.23 0.73 0.14
85_G 58_N 1.22 0.72 0.13
109_G 61_A 1.22 0.72 0.13
161_E 152_M 1.18 0.68 0.11
146_L 85_S 1.17 0.68 0.11
138_P 117_M 1.09 0.60 0.09
19_D 156_K 1.09 0.59 0.09
22_L 22_T 1.08 0.58 0.08
15_Y 135_V 1.08 0.58 0.08
151_P 93_R 1.03 0.53 0.07
23_G 21_F 1.01 0.50 0.07
138_P 125_Q 1.00 0.50 0.06
72_Y 32_R 0.99 0.48 0.06
111_A 62_R 0.99 0.48 0.06
53_V 103_K 0.99 0.48 0.06
99_P 25_E 0.98 0.48 0.06
103_T 150_A 0.97 0.47 0.06
77_L 37_W 0.97 0.47 0.06
15_Y 156_K 0.97 0.46 0.06
138_P 144_P 0.96 0.45 0.06
35_K 20_L 0.95 0.45 0.05
165_I 75_A 0.94 0.43 0.05
122_F 104_W 0.93 0.42 0.05
163_R 19_I 0.93 0.42 0.05
110_S 100_P 0.92 0.41 0.05
152_L 31_G 0.92 0.41 0.05
118_V 147_L 0.91 0.40 0.05
141_L 117_M 0.91 0.39 0.04
150_Y 91_V 0.90 0.38 0.04
139_E 118_F 0.90 0.38 0.04
111_A 32_R 0.89 0.38 0.04
45_G 159_R 0.89 0.38 0.04
139_E 144_P 0.88 0.37 0.04
159_F 114_S 0.88 0.37 0.04
124_I 135_V 0.88 0.36 0.04
143_G 101_D 0.87 0.36 0.04
6_V 24_L 0.87 0.36 0.04
138_P 114_S 0.87 0.36 0.04
106_D 135_V 0.87 0.36 0.04
107_L 159_R 0.87 0.35 0.04
156_P 123_I 0.87 0.35 0.04
92_V 122_A 0.86 0.35 0.04
90_V 143_R 0.86 0.34 0.04
108_W 60_L 0.85 0.34 0.04
59_T 159_R 0.85 0.34 0.04
34_F 28_V 0.85 0.34 0.04
144_H 161_Q 0.85 0.34 0.04
12_A 33_S 0.85 0.34 0.04
164_Y 27_L 0.85 0.34 0.04
37_E 103_K 0.85 0.33 0.04
77_L 38_P 0.85 0.33 0.04
140_D 118_F 0.84 0.33 0.04
139_E 117_M 0.84 0.33 0.03
119_Y 21_F 0.84 0.33 0.03
72_Y 106_I 0.84 0.33 0.03
35_K 135_V 0.84 0.33 0.03
38_M 130_V 0.84 0.33 0.03
45_G 54_T 0.84 0.33 0.03
92_V 16_R 0.84 0.33 0.03
141_L 125_Q 0.83 0.32 0.03
92_V 100_P 0.83 0.32 0.03
106_D 20_L 0.83 0.32 0.03
23_G 71_S 0.83 0.32 0.03
45_G 58_N 0.83 0.32 0.03
156_P 88_M 0.83 0.32 0.03
169_E 77_V 0.82 0.31 0.03
132_L 50_M 0.82 0.31 0.03
38_M 36_L 0.82 0.31 0.03
29_L 159_R 0.82 0.31 0.03
137_T 137_V 0.82 0.31 0.03
169_E 31_G 0.82 0.31 0.03
36_E 151_V 0.82 0.31 0.03
156_P 146_A 0.82 0.31 0.03
71_V 71_S 0.82 0.31 0.03
138_P 119_N 0.82 0.31 0.03
35_K 17_E 0.82 0.31 0.03
121_L 161_Q 0.81 0.30 0.03
52_I 106_I 0.81 0.30 0.03
37_E 21_F 0.81 0.30 0.03
126_F 38_P 0.81 0.30 0.03
137_T 125_Q 0.81 0.30 0.03
109_G 100_P 0.81 0.30 0.03
156_P 118_F 0.79 0.29 0.03
75_V 113_S 0.79 0.28 0.03
17_I 152_M 0.79 0.28 0.03
153_G 44_A 0.79 0.28 0.03
51_D 107_S 0.79 0.28 0.03
91_R 56_A 0.78 0.28 0.03
52_I 123_I 0.78 0.28 0.03
15_Y 67_V 0.78 0.28 0.03
142_E 80_V 0.78 0.28 0.03
159_F 117_M 0.78 0.28 0.03
138_P 113_S 0.78 0.28 0.03
147_R 161_Q 0.78 0.28 0.03
108_W 152_M 0.78 0.27 0.03
57_Y 53_S 0.78 0.27 0.03
75_V 58_N 0.78 0.27 0.03
124_I 30_W 0.78 0.27 0.03
57_Y 79_I 0.78 0.27 0.03
61_P 27_L 0.78 0.27 0.03
157_T 85_S 0.78 0.27 0.03
68_F 158_V 0.78 0.27 0.03
129_H 152_M 0.78 0.27 0.03
171_R 18_G 0.77 0.27 0.03
168_A 18_G 0.77 0.27 0.03
156_P 113_S 0.77 0.27 0.03
64_R 85_S 0.77 0.27 0.03
67_R 95_V 0.77 0.26 0.03
172_A 31_G 0.77 0.26 0.03
103_T 138_P 0.77 0.26 0.03
15_Y 106_I 0.77 0.26 0.03
108_W 150_A 0.76 0.26 0.03
138_P 91_V 0.76 0.26 0.02
10_A 70_A 0.76 0.26 0.02
134_K 83_R 0.76 0.26 0.02
41_Y 70_A 0.76 0.26 0.02
73_E 159_R 0.76 0.25 0.02
98_D 27_L 0.75 0.25 0.02
149_D 148_I 0.75 0.25 0.02
150_Y 57_R 0.75 0.25 0.02
131_D 75_A 0.75 0.25 0.02
85_G 118_F 0.74 0.24 0.02
113_F 119_N 0.74 0.24 0.02
59_T 58_N 0.74 0.24 0.02
124_I 31_G 0.74 0.24 0.02
121_L 23_T 0.74 0.24 0.02
141_L 144_P 0.74 0.24 0.02
140_D 52_A 0.74 0.24 0.02
27_V 24_L 0.74 0.24 0.02
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
4920 1.81 cI_5_20_cI_6_60_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.25 Done - Shared
4919 1.84 cI_5_10_cI_6_40_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.20 Done - Shared
4918 1.94 cI_5_20_cI_6_40_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.33 Done - Shared
4917 0.03 cI_5_40_cI_6_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) Killed - Shared
4916 1.9 cI_5_20_cI_6_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.28 Done - Shared
4914 1.82 cI_5_10_cI_6_10_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.25 Done - Shared
4913 1.97 cI_5_6_cI_6_6_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
4912 1.86 cI_5_4_cI_6_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.08 Done - Shared
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