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OPENSEQ.org
cI_5_20_cI_6_20_tt
Genes: A B A+B
Length: 207 181 349
Sequences: 1089 1141 662
Seq/Len: 5.26 6.3 1.9
MirrorTree (Pazo et al. 2001) 0.88
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 1.56
2 0.00 0.01 1.63
5 0.00 0.01 1.64
10 0.01 0.02 1.64
20 0.01 0.02 1.64
100 0.02 0.03 1.65
∞ 0.04 0.08 1.71
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
146_L 85_S 1.46 0.89 0.28
111_A 62_R 1.45 0.88 0.28
52_I 151_V 1.35 0.83 0.21
109_G 56_A 1.33 0.81 0.20
53_V 103_K 1.32 0.81 0.20
32_E 20_L 1.32 0.81 0.20
71_V 71_S 1.25 0.76 0.16
124_I 135_V 1.22 0.73 0.15
89_F 103_K 1.19 0.70 0.14
12_A 19_I 1.16 0.67 0.12
161_E 152_M 1.15 0.67 0.12
134_K 126_N 1.14 0.65 0.11
138_P 125_Q 1.12 0.63 0.11
98_D 27_L 1.09 0.60 0.10
126_F 38_P 1.07 0.59 0.09
138_P 114_S 1.07 0.58 0.09
138_P 117_M 1.06 0.58 0.09
150_Y 91_V 1.05 0.56 0.09
37_E 103_K 1.04 0.55 0.08
75_V 110_A 1.04 0.55 0.08
156_P 118_F 1.02 0.53 0.08
23_G 21_F 1.02 0.53 0.08
124_I 31_G 1.01 0.52 0.07
72_Y 32_R 1.01 0.52 0.07
72_Y 62_R 1.00 0.51 0.07
77_L 37_W 0.99 0.50 0.07
85_G 58_N 0.98 0.49 0.07
157_T 85_S 0.98 0.49 0.07
151_P 43_L 0.98 0.48 0.07
108_W 150_A 0.97 0.48 0.06
141_L 117_M 0.97 0.48 0.06
137_T 125_Q 0.97 0.48 0.06
122_F 104_W 0.97 0.47 0.06
10_A 77_V 0.96 0.46 0.06
90_V 130_V 0.95 0.45 0.06
171_R 148_I 0.95 0.45 0.06
77_L 65_S 0.94 0.45 0.06
139_E 118_F 0.94 0.45 0.06
138_P 144_P 0.94 0.44 0.06
29_L 156_K 0.93 0.43 0.05
151_P 93_R 0.91 0.41 0.05
49_L 56_A 0.91 0.41 0.05
42_K 18_G 0.91 0.41 0.05
99_P 25_E 0.90 0.40 0.05
141_L 125_Q 0.90 0.40 0.05
111_A 32_R 0.90 0.40 0.05
102_P 20_L 0.90 0.40 0.05
89_F 77_V 0.90 0.40 0.05
12_A 27_L 0.89 0.39 0.05
49_L 62_R 0.89 0.39 0.05
40_H 131_V 0.89 0.38 0.05
34_F 151_V 0.89 0.38 0.05
2_R 48_I 0.88 0.38 0.04
92_V 16_R 0.87 0.37 0.04
138_P 119_N 0.87 0.36 0.04
150_Y 86_K 0.86 0.36 0.04
158_L 144_P 0.86 0.36 0.04
88_F 106_I 0.86 0.36 0.04
52_I 106_I 0.85 0.35 0.04
138_P 127_V 0.85 0.35 0.04
163_R 103_K 0.84 0.34 0.04
50_A 100_P 0.84 0.34 0.04
137_T 137_V 0.84 0.34 0.04
15_Y 21_F 0.83 0.33 0.04
11_R 77_V 0.83 0.33 0.04
51_D 107_S 0.83 0.33 0.04
149_D 141_P 0.83 0.33 0.04
166_I 31_G 0.83 0.33 0.04
35_K 20_L 0.83 0.33 0.04
142_E 156_K 0.83 0.33 0.04
141_L 127_V 0.83 0.33 0.04
165_I 110_A 0.82 0.32 0.04
107_L 159_R 0.82 0.32 0.04
38_M 130_V 0.82 0.31 0.04
128_G 16_R 0.81 0.31 0.03
187_G 135_V 0.81 0.31 0.03
109_G 61_A 0.81 0.31 0.03
7_L 36_L 0.81 0.31 0.03
57_Y 104_W 0.81 0.30 0.03
30_P 56_A 0.81 0.30 0.03
15_Y 150_A 0.81 0.30 0.03
106_D 135_V 0.81 0.30 0.03
110_S 100_P 0.80 0.30 0.03
150_Y 114_S 0.80 0.30 0.03
135_I 33_S 0.80 0.30 0.03
2_R 65_S 0.80 0.30 0.03
141_L 114_S 0.80 0.30 0.03
147_R 153_Q 0.80 0.30 0.03
87_R 84_L 0.80 0.30 0.03
64_R 160_G 0.80 0.30 0.03
139_E 125_Q 0.79 0.29 0.03
65_P 26_K 0.79 0.29 0.03
59_T 58_N 0.79 0.29 0.03
88_F 56_A 0.79 0.29 0.03
152_L 31_G 0.79 0.29 0.03
166_I 27_L 0.79 0.29 0.03
174_L 54_T 0.79 0.29 0.03
150_Y 150_A 0.78 0.28 0.03
34_F 28_V 0.78 0.28 0.03
150_Y 125_Q 0.78 0.28 0.03
91_R 122_A 0.78 0.28 0.03
67_R 95_V 0.78 0.28 0.03
77_L 38_P 0.78 0.28 0.03
34_F 62_R 0.77 0.28 0.03
141_L 144_P 0.77 0.28 0.03
187_G 27_L 0.77 0.28 0.03
97_E 56_A 0.77 0.28 0.03
104_V 62_R 0.77 0.27 0.03
90_V 23_T 0.77 0.27 0.03
48_F 21_F 0.77 0.27 0.03
74_L 37_W 0.77 0.27 0.03
173_A 14_L 0.77 0.27 0.03
36_E 151_V 0.77 0.27 0.03
45_G 12_Q 0.77 0.27 0.03
105_T 106_I 0.77 0.27 0.03
30_P 53_S 0.77 0.27 0.03
156_P 83_R 0.76 0.27 0.03
37_E 21_F 0.76 0.27 0.03
92_V 122_A 0.76 0.27 0.03
140_D 118_F 0.76 0.26 0.03
140_D 86_K 0.76 0.26 0.03
138_P 118_F 0.76 0.26 0.03
69_A 104_W 0.76 0.26 0.03
88_F 67_V 0.76 0.26 0.03
36_E 20_L 0.75 0.26 0.03
121_L 161_Q 0.75 0.25 0.03
13_K 16_R 0.75 0.25 0.03
2_R 77_V 0.75 0.25 0.03
180_G 94_R 0.75 0.25 0.03
167_P 97_E 0.75 0.25 0.03
49_L 94_R 0.75 0.25 0.03
175_T 118_F 0.74 0.25 0.03
12_A 135_V 0.74 0.25 0.03
103_T 63_F 0.74 0.25 0.03
13_K 33_S 0.74 0.25 0.03
110_S 53_S 0.74 0.25 0.03
126_F 98_Q 0.74 0.24 0.03
176_G 70_A 0.74 0.24 0.03
94_V 63_F 0.74 0.24 0.03
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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