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OPENSEQ.org
cI_5_10_cI_6_40_tt
Genes: A B A+B
Length: 207 181 347
Sequences: 1025 1163 637
Seq/Len: 4.95 6.43 1.84
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 1.47
2 0.00 0.01 1.57
5 0.01 0.01 1.57
10 0.01 0.02 1.58
20 0.01 0.02 1.58
100 0.02 0.03 1.60
∞ 0.06 0.08 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 1.43 0.87 0.20
109_G 56_A 1.40 0.85 0.18
32_E 20_L 1.37 0.83 0.17
161_E 152_M 1.22 0.72 0.11
111_A 62_R 1.20 0.71 0.10
85_G 58_N 1.20 0.71 0.10
75_V 110_A 1.20 0.70 0.10
134_K 126_N 1.14 0.64 0.08
23_G 21_F 1.09 0.59 0.07
89_F 103_K 1.08 0.58 0.07
109_G 61_A 1.07 0.58 0.07
124_I 135_V 1.07 0.57 0.07
138_P 117_M 1.05 0.56 0.06
22_L 22_T 1.04 0.55 0.06
146_L 85_S 1.04 0.54 0.06
138_P 125_Q 1.02 0.52 0.06
15_Y 135_V 1.01 0.51 0.06
36_E 151_V 1.01 0.51 0.06
151_P 93_R 1.01 0.51 0.06
77_L 37_W 1.00 0.50 0.05
103_T 150_A 1.00 0.50 0.05
163_R 19_I 1.00 0.49 0.05
152_L 31_G 0.99 0.49 0.05
19_D 156_K 0.99 0.49 0.05
53_V 103_K 0.99 0.49 0.05
122_F 104_W 0.98 0.48 0.05
138_P 144_P 0.98 0.48 0.05
110_S 100_P 0.97 0.47 0.05
29_L 56_A 0.96 0.45 0.04
35_K 20_L 0.95 0.44 0.04
107_L 159_R 0.94 0.44 0.04
139_E 118_F 0.94 0.43 0.04
37_E 103_K 0.93 0.42 0.04
169_E 31_G 0.92 0.41 0.04
106_D 135_V 0.92 0.41 0.04
171_R 18_G 0.91 0.40 0.04
141_L 117_M 0.91 0.40 0.04
99_P 25_E 0.91 0.40 0.04
165_I 75_A 0.91 0.40 0.04
143_G 101_D 0.90 0.39 0.04
59_T 159_R 0.90 0.39 0.04
156_P 123_I 0.90 0.39 0.04
118_V 147_L 0.90 0.39 0.04
156_P 118_F 0.90 0.39 0.04
90_V 143_R 0.90 0.39 0.04
72_Y 106_I 0.89 0.38 0.04
45_G 54_T 0.88 0.37 0.03
150_Y 91_V 0.88 0.37 0.03
164_Y 27_L 0.88 0.37 0.03
38_M 36_L 0.87 0.36 0.03
43_A 16_R 0.87 0.36 0.03
15_Y 156_K 0.87 0.36 0.03
85_G 123_I 0.86 0.35 0.03
126_F 38_P 0.86 0.35 0.03
17_I 152_M 0.86 0.35 0.03
124_I 154_L 0.86 0.35 0.03
166_I 48_I 0.86 0.35 0.03
34_F 17_E 0.86 0.35 0.03
45_G 159_R 0.85 0.34 0.03
35_K 135_V 0.85 0.34 0.03
12_A 33_S 0.85 0.34 0.03
6_V 24_L 0.85 0.34 0.03
124_I 30_W 0.85 0.34 0.03
71_V 71_S 0.84 0.33 0.03
168_A 18_G 0.84 0.33 0.03
138_P 113_S 0.84 0.33 0.03
77_L 38_P 0.84 0.33 0.03
64_R 85_S 0.84 0.33 0.03
92_V 100_P 0.84 0.33 0.03
157_T 85_S 0.84 0.33 0.03
68_F 158_V 0.83 0.33 0.03
140_D 118_F 0.83 0.33 0.03
159_F 117_M 0.83 0.32 0.03
139_E 144_P 0.83 0.32 0.03
15_Y 106_I 0.83 0.32 0.03
144_H 161_Q 0.83 0.32 0.03
128_G 97_E 0.83 0.32 0.03
29_L 159_R 0.83 0.32 0.03
92_V 122_A 0.83 0.32 0.03
23_G 71_S 0.82 0.31 0.03
141_L 125_Q 0.82 0.31 0.03
51_D 107_S 0.82 0.31 0.03
127_E 17_E 0.82 0.31 0.03
109_G 100_P 0.82 0.31 0.03
137_T 125_Q 0.81 0.30 0.03
102_P 29_A 0.81 0.30 0.03
151_P 43_L 0.81 0.30 0.03
87_R 44_A 0.81 0.30 0.03
147_R 161_Q 0.81 0.30 0.03
139_E 117_M 0.80 0.29 0.02
38_M 130_V 0.80 0.29 0.02
113_F 122_A 0.79 0.28 0.02
45_G 58_N 0.79 0.28 0.02
108_W 60_L 0.79 0.28 0.02
156_P 113_S 0.79 0.28 0.02
121_L 161_Q 0.79 0.28 0.02
61_P 27_L 0.79 0.28 0.02
150_Y 86_K 0.79 0.28 0.02
94_V 63_F 0.79 0.28 0.02
30_P 56_A 0.79 0.28 0.02
129_H 54_T 0.79 0.28 0.02
140_D 86_K 0.78 0.28 0.02
34_F 28_V 0.78 0.28 0.02
149_D 146_A 0.78 0.28 0.02
91_R 56_A 0.78 0.28 0.02
27_V 24_L 0.78 0.27 0.02
74_L 37_W 0.78 0.27 0.02
138_P 119_N 0.78 0.27 0.02
134_K 83_R 0.77 0.27 0.02
67_R 95_V 0.77 0.27 0.02
132_L 50_M 0.77 0.27 0.02
172_A 31_G 0.77 0.27 0.02
103_T 99_M 0.77 0.27 0.02
69_A 104_W 0.77 0.26 0.02
124_I 31_G 0.77 0.26 0.02
15_Y 21_F 0.77 0.26 0.02
27_V 135_V 0.77 0.26 0.02
67_R 44_A 0.76 0.26 0.02
169_E 77_V 0.76 0.26 0.02
72_Y 62_R 0.76 0.26 0.02
98_D 156_K 0.76 0.26 0.02
142_E 80_V 0.76 0.26 0.02
57_Y 44_A 0.76 0.26 0.02
59_T 58_N 0.76 0.26 0.02
111_A 32_R 0.76 0.25 0.02
9_E 16_R 0.75 0.25 0.02
11_R 100_P 0.75 0.25 0.02
121_L 23_T 0.75 0.25 0.02
108_W 152_M 0.75 0.25 0.02
57_Y 79_I 0.75 0.25 0.02
153_G 44_A 0.75 0.25 0.02
92_V 28_V 0.75 0.25 0.02
69_A 68_F 0.74 0.24 0.02
119_Y 21_F 0.74 0.24 0.02
159_F 114_S 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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