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OPENSEQ.org
cI_5_20_cI_6_60_tt
Genes: A B A+B
Length: 207 181 346
Sequences: 1089 850 626
Seq/Len: 5.26 4.7 1.81
MirrorTree (Pazo et al. 2001) 0.90
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 1.53
2 0.00 0.01 1.55
5 0.00 0.01 1.55
10 0.01 0.01 1.57
20 0.01 0.01 1.57
100 0.02 0.02 1.56
∞ 0.04 0.04 1.61
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
111_A 62_R 1.37 0.83 0.20
146_L 85_S 1.34 0.81 0.18
71_V 71_S 1.27 0.76 0.15
89_F 103_K 1.23 0.73 0.13
124_I 31_G 1.23 0.73 0.13
109_G 56_A 1.23 0.72 0.13
53_V 103_K 1.21 0.71 0.12
23_G 21_F 1.18 0.68 0.11
161_E 152_M 1.18 0.68 0.11
75_V 110_A 1.13 0.64 0.10
32_E 20_L 1.13 0.63 0.10
37_E 103_K 1.13 0.63 0.10
124_I 135_V 1.12 0.62 0.09
138_P 125_Q 1.12 0.62 0.09
138_P 117_M 1.11 0.61 0.09
12_A 19_I 1.07 0.57 0.08
171_R 148_I 1.07 0.56 0.08
77_L 37_W 1.04 0.54 0.07
108_W 150_A 1.03 0.53 0.07
157_T 85_S 1.02 0.52 0.07
141_L 125_Q 1.01 0.50 0.06
138_P 114_S 1.01 0.50 0.06
52_I 106_I 1.01 0.50 0.06
111_A 32_R 1.00 0.50 0.06
10_A 77_V 0.99 0.48 0.06
72_Y 62_R 0.97 0.46 0.06
35_K 20_L 0.97 0.46 0.06
38_M 130_V 0.97 0.46 0.06
98_D 27_L 0.97 0.46 0.06
137_T 125_Q 0.97 0.46 0.05
42_K 18_G 0.97 0.46 0.05
2_R 48_I 0.96 0.45 0.05
29_L 156_K 0.96 0.45 0.05
142_E 156_K 0.95 0.44 0.05
141_L 127_V 0.95 0.43 0.05
122_F 104_W 0.94 0.43 0.05
141_L 114_S 0.92 0.41 0.05
88_F 67_V 0.92 0.40 0.04
158_L 144_P 0.91 0.40 0.04
67_R 95_V 0.91 0.40 0.04
166_I 31_G 0.91 0.39 0.04
99_P 25_E 0.91 0.39 0.04
141_L 117_M 0.91 0.39 0.04
88_F 60_L 0.90 0.39 0.04
54_G 137_V 0.90 0.38 0.04
72_Y 32_R 0.90 0.38 0.04
137_T 137_V 0.90 0.38 0.04
139_E 125_Q 0.89 0.38 0.04
150_Y 91_V 0.89 0.38 0.04
89_F 77_V 0.89 0.38 0.04
77_L 65_S 0.89 0.38 0.04
147_R 153_Q 0.88 0.37 0.04
138_P 144_P 0.88 0.36 0.04
85_G 58_N 0.88 0.36 0.04
36_E 151_V 0.88 0.36 0.04
140_D 119_N 0.88 0.36 0.04
104_V 26_K 0.87 0.36 0.04
37_E 21_F 0.87 0.35 0.04
139_E 118_F 0.86 0.35 0.04
126_F 76_D 0.86 0.35 0.04
126_F 38_P 0.86 0.34 0.04
36_E 106_I 0.86 0.34 0.04
88_F 106_I 0.86 0.34 0.04
150_Y 86_K 0.86 0.34 0.04
107_L 159_R 0.86 0.34 0.04
30_P 56_A 0.86 0.34 0.04
119_Y 37_W 0.85 0.34 0.04
156_P 118_F 0.85 0.34 0.04
12_A 27_L 0.85 0.34 0.03
166_I 27_L 0.85 0.34 0.03
138_P 119_N 0.85 0.34 0.03
8_E 24_L 0.85 0.34 0.03
110_S 100_P 0.85 0.34 0.03
74_L 37_W 0.84 0.33 0.03
138_P 127_V 0.84 0.32 0.03
156_P 48_I 0.83 0.32 0.03
107_L 29_A 0.83 0.32 0.03
70_V 81_A 0.83 0.32 0.03
65_P 152_M 0.83 0.32 0.03
92_V 90_P 0.82 0.31 0.03
104_V 13_E 0.82 0.31 0.03
59_T 58_N 0.82 0.31 0.03
56_D 83_R 0.82 0.31 0.03
165_I 118_F 0.82 0.31 0.03
165_I 110_A 0.81 0.30 0.03
137_T 117_M 0.81 0.30 0.03
64_R 160_G 0.81 0.30 0.03
156_P 114_S 0.81 0.29 0.03
141_L 143_R 0.80 0.29 0.03
187_G 135_V 0.80 0.29 0.03
163_R 103_K 0.80 0.29 0.03
87_R 84_L 0.80 0.29 0.03
77_L 145_E 0.79 0.28 0.03
152_L 31_G 0.79 0.28 0.03
141_L 144_P 0.79 0.28 0.03
121_L 107_S 0.79 0.28 0.03
140_D 91_V 0.79 0.28 0.03
2_R 65_S 0.79 0.28 0.03
56_D 69_R 0.79 0.28 0.03
26_W 156_K 0.78 0.28 0.03
108_W 78_M 0.78 0.28 0.03
135_I 33_S 0.78 0.28 0.03
49_L 56_A 0.78 0.28 0.03
104_V 62_R 0.78 0.27 0.03
174_L 54_T 0.78 0.27 0.03
121_L 12_Q 0.78 0.27 0.03
50_A 100_P 0.78 0.27 0.03
151_P 93_R 0.78 0.27 0.03
34_F 62_R 0.78 0.27 0.03
73_E 28_V 0.78 0.27 0.03
109_G 85_S 0.78 0.27 0.03
139_E 117_M 0.78 0.27 0.03
77_L 38_P 0.77 0.27 0.03
48_F 21_F 0.77 0.27 0.03
149_D 141_P 0.77 0.27 0.03
7_L 36_L 0.77 0.27 0.03
47_N 56_A 0.77 0.27 0.03
135_I 124_V 0.77 0.26 0.03
19_D 20_L 0.77 0.26 0.03
131_D 75_A 0.77 0.26 0.02
54_G 147_L 0.76 0.26 0.02
52_I 13_E 0.76 0.26 0.02
17_I 152_M 0.76 0.26 0.02
49_L 62_R 0.76 0.26 0.02
65_P 26_K 0.76 0.26 0.02
94_V 63_F 0.76 0.26 0.02
135_I 130_V 0.76 0.25 0.02
15_Y 52_A 0.75 0.25 0.02
180_G 94_R 0.75 0.25 0.02
88_F 148_I 0.75 0.25 0.02
27_V 24_L 0.75 0.25 0.02
98_D 156_K 0.75 0.25 0.02
134_K 126_N 0.75 0.25 0.02
120_D 147_L 0.75 0.25 0.02
109_G 70_A 0.75 0.25 0.02
57_Y 55_D 0.75 0.25 0.02
34_F 151_V 0.75 0.25 0.02
139_E 114_S 0.75 0.25 0.02
169_E 10_D 0.75 0.24 0.02
107_L 52_A 0.74 0.24 0.02
138_P 143_R 0.74 0.24 0.02
90_V 130_V 0.74 0.24 0.02
2_R 77_V 0.74 0.24 0.02
167_P 68_F 0.74 0.24 0.02
156_P 119_N 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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