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OPENSEQ.org
Fo_ab
Genes: A B A+B
Length: 271 156 407
Sequences: 1124 3481 1023
Seq/Len: 4.15 22.31 2.51
MirrorTree (Pazo et al. 2001) 0.70
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.04 0.19 0.09
2 0.04 0.19 2.37
5 0.04 0.19 2.40
10 0.04 0.19 2.41
20 0.04 0.19 2.41
100 0.04 0.19 2.44
∞ 0.04 0.19 2.48
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
74_K 34_E 2.35 1.00 0.99
52_L 13_A 1.67 0.97 0.93
77_T 33_I 1.61 0.96 0.91
152_S 7_I 1.50 0.94 0.87
83_I 30_M 1.50 0.94 0.87
238_N 13_A 1.38 0.90 0.80
125_L 11_A 1.36 0.89 0.79
99_K 34_E 1.31 0.86 0.75
239_V 16_L 1.23 0.81 0.68
239_V 13_A 1.19 0.78 0.64
122_P 44_L 1.17 0.76 0.62
243_I 17_F 1.15 0.74 0.60
247_L 44_L 1.10 0.70 0.55
74_K 37_Q 1.07 0.67 0.51
154_A 60_S 1.06 0.66 0.50
160_L 118_E 1.06 0.66 0.50
176_K 33_I 1.02 0.61 0.45
197_G 143_A 0.99 0.58 0.41
108_I 146_S 0.98 0.57 0.40
205_V 122_K 0.97 0.56 0.39
114_L 12_I 0.96 0.55 0.38
199_S 152_L 0.95 0.54 0.37
52_L 19_L 0.95 0.54 0.37
91_K 20_F 0.94 0.52 0.35
111_W 14_F 0.93 0.51 0.35
225_I 13_A 0.92 0.50 0.34
71_V 156_L 0.92 0.50 0.34
233_S 60_S 0.91 0.49 0.33
171_I 92_A 0.91 0.49 0.32
156_G 14_F 0.91 0.48 0.32
267_A 11_A 0.90 0.48 0.32
80_E 40_I 0.90 0.47 0.31
112_V 56_L 0.89 0.47 0.30
198_V 73_Q 0.89 0.46 0.30
61_R 20_F 0.89 0.46 0.30
83_I 33_I 0.88 0.46 0.29
263_Y 6_T 0.88 0.45 0.29
167_K 23_K 0.88 0.45 0.29
248_I 17_F 0.88 0.45 0.29
206_S 128_A 0.87 0.44 0.28
184_N 98_R 0.87 0.43 0.28
83_I 65_L 0.87 0.43 0.28
80_E 36_R 0.87 0.43 0.28
236_I 66_K 0.86 0.43 0.27
79_I 27_P 0.86 0.43 0.27
209_L 21_C 0.86 0.42 0.27
176_K 34_E 0.85 0.42 0.26
45_S 6_T 0.85 0.42 0.26
145_A 7_I 0.85 0.42 0.26
57_L 66_K 0.85 0.42 0.26
206_S 14_F 0.85 0.42 0.26
50_V 16_L 0.85 0.41 0.26
113_F 154_A 0.85 0.41 0.26
236_I 100_K 0.84 0.41 0.26
106_L 26_W 0.84 0.41 0.25
258_V 128_A 0.84 0.41 0.25
97_K 101_I 0.84 0.40 0.25
232_W 96_Q 0.84 0.40 0.25
197_G 117_R 0.84 0.40 0.25
50_V 20_F 0.84 0.40 0.25
46_M 151_K 0.84 0.40 0.25
177_E 27_P 0.83 0.40 0.24
69_S 58_K 0.83 0.40 0.24
75_F 15_V 0.83 0.40 0.24
77_T 37_Q 0.83 0.39 0.24
20_Q 2_N 0.82 0.38 0.23
70_G 32_A 0.82 0.38 0.23
105_A 138_R 0.82 0.38 0.23
215_M 97_E 0.82 0.38 0.23
215_M 128_A 0.82 0.38 0.23
119_D 25_V 0.81 0.37 0.22
75_F 99_T 0.81 0.37 0.22
233_S 154_A 0.80 0.36 0.21
47_F 31_A 0.80 0.36 0.21
119_D 116_A 0.80 0.36 0.21
201_L 53_D 0.80 0.36 0.21
244_F 134_K 0.80 0.35 0.21
83_I 86_I 0.79 0.35 0.20
65_K 58_K 0.79 0.35 0.20
235_W 87_L 0.79 0.35 0.20
68_T 32_A 0.79 0.34 0.20
67_A 42_D 0.78 0.34 0.20
184_N 33_I 0.78 0.34 0.20
213_G 9_G 0.78 0.34 0.20
172_G 143_A 0.77 0.33 0.19
243_I 20_F 0.77 0.33 0.19
84_G 119_E 0.77 0.33 0.19
81_L 102_V 0.77 0.32 0.18
206_S 152_L 0.77 0.32 0.18
167_K 16_L 0.76 0.32 0.18
108_I 87_L 0.76 0.32 0.18
254_F 57_A 0.76 0.32 0.18
163_F 49_R 0.76 0.31 0.17
64_A 32_A 0.76 0.31 0.17
114_L 75_I 0.75 0.31 0.17
156_G 16_L 0.75 0.31 0.17
164_Y 44_L 0.75 0.31 0.17
238_N 38_K 0.75 0.31 0.17
197_G 135_I 0.75 0.30 0.17
104_L 46_S 0.74 0.30 0.17
263_Y 32_A 0.74 0.30 0.17
17_N 2_N 0.74 0.30 0.16
150_T 21_C 0.74 0.30 0.16
221_I 20_F 0.74 0.30 0.16
257_M 109_I 0.74 0.30 0.16
107_T 73_Q 0.74 0.29 0.16
7_T 65_L 0.74 0.29 0.16
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
8013 2.51 Fo_ab Δgene:(1, 5) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.99 Done - Shared
0233 4.17 ATP6 - ATPF Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 1.00 Done - Shared
0069 2.6 ATP6 - ATPF Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) (2013_03) 1.00 Done - Shared
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