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OPENSEQ.org
ATP6 - ATPF (A, 70-271)
Genes: A B A+B
Length: 202 156 357
Sequences: 3511 1931 1440
Seq/Len: 17.38 12.38 4.03
MirrorTree (Pazo et al. 2001) 0.61
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 0.00 0.09 0.15
2 0.00 0.09 3.81
5 0.00 0.09 3.90
10 0.00 0.09 3.90
20 0.00 0.09 3.91
100 0.00 0.09 3.93
∞ 0.01 0.10 4.02
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
5_K 34_E 2.73 1.00 1.00
8_T 33_I 2.02 1.00 0.99
80_V 10_Q 1.69 0.99 0.96
30_K 34_E 1.41 0.96 0.89
86_L 11_A 1.26 0.92 0.80
139_G 102_V 1.21 0.90 0.77
37_L 26_W 1.19 0.88 0.75
186_I 139_S 1.16 0.87 0.73
83_S 7_I 1.12 0.84 0.69
18_N 30_M 1.08 0.81 0.65
56_L 11_A 1.06 0.79 0.62
137_S 152_L 1.04 0.78 0.61
70_L 33_I 1.02 0.76 0.58
38_T 21_C 0.98 0.72 0.54
194_Y 8_L 0.97 0.70 0.52
14_I 30_M 0.97 0.70 0.52
42_W 10_Q 0.95 0.68 0.50
79_N 4_N 0.94 0.67 0.48
5_K 37_Q 0.91 0.63 0.45
83_S 11_A 0.90 0.61 0.43
10_I 29_L 0.89 0.61 0.42
9_A 154_A 0.89 0.61 0.42
82_L 7_I 0.89 0.60 0.41
163_W 128_A 0.88 0.58 0.40
152_I 94_A 0.87 0.57 0.39
143_F 141_D 0.87 0.57 0.39
14_I 29_L 0.86 0.56 0.38
4_G 37_Q 0.85 0.55 0.37
136_V 8_L 0.84 0.54 0.36
6_F 93_E 0.84 0.53 0.35
84_M 17_F 0.83 0.53 0.34
18_N 37_Q 0.83 0.52 0.34
127_E 25_V 0.82 0.51 0.33
109_L 140_V 0.82 0.51 0.33
53_P 14_F 0.82 0.51 0.33
127_E 17_F 0.81 0.50 0.32
185_F 150_D 0.81 0.49 0.31
146_M 46_S 0.80 0.48 0.30
45_L 52_K 0.79 0.47 0.29
43_V 16_L 0.79 0.47 0.29
174_I 17_F 0.78 0.46 0.28
39_I 14_F 0.78 0.45 0.28
15_G 39_E 0.78 0.45 0.28
46_M 24_Y 0.77 0.45 0.28
149_G 79_A 0.77 0.45 0.28
22_K 20_F 0.76 0.43 0.27
148_A 128_A 0.76 0.43 0.27
39_I 16_L 0.76 0.43 0.26
79_N 6_T 0.76 0.42 0.26
191_T 25_V 0.75 0.41 0.25
48_L 38_K 0.75 0.41 0.25
44_F 154_A 0.74 0.41 0.24
194_Y 42_D 0.74 0.41 0.24
22_K 60_S 0.74 0.41 0.24
16_F 109_I 0.74 0.41 0.24
17_V 31_A 0.73 0.40 0.24
153_F 44_L 0.72 0.38 0.23
8_T 39_E 0.72 0.38 0.22
158_G 3_L 0.72 0.38 0.22
162_W 93_E 0.72 0.38 0.22
75_S 116_A 0.72 0.38 0.22
118_A 56_L 0.72 0.38 0.22
76_A 132_A 0.72 0.38 0.22
24_M 16_L 0.72 0.37 0.22
34_P 131_G 0.71 0.37 0.21
122_V 144_A 0.71 0.37 0.21
137_S 128_A 0.71 0.37 0.21
43_V 107_A 0.71 0.37 0.21
153_F 156_L 0.70 0.35 0.20
170_V 16_L 0.70 0.35 0.20
178_L 152_L 0.70 0.35 0.20
202_H 138_R 0.70 0.35 0.20
167_I 74_V 0.70 0.35 0.20
121_P 56_L 0.70 0.35 0.20
189_V 155_E 0.69 0.35 0.20
168_L 13_A 0.69 0.35 0.20
192_I 37_Q 0.69 0.35 0.20
170_V 13_A 0.69 0.34 0.19
102_I 16_L 0.69 0.34 0.19
127_E 50_A 0.69 0.34 0.19
174_I 94_A 0.68 0.33 0.19
42_W 21_C 0.68 0.33 0.19
79_N 1_M 0.68 0.33 0.18
15_G 33_I 0.68 0.33 0.18
48_L 53_D 0.68 0.33 0.18
85_A 22_M 0.68 0.32 0.18
186_I 106_Q 0.68 0.32 0.18
174_I 20_F 0.68 0.32 0.18
169_N 13_A 0.67 0.32 0.18
82_L 49_R 0.67 0.32 0.18
182_L 120_L 0.67 0.32 0.18
35_L 120_L 0.67 0.32 0.18
35_L 14_F 0.67 0.32 0.18
119_F 21_C 0.67 0.32 0.18
51_L 40_I 0.67 0.32 0.18
93_L 44_L 0.67 0.32 0.17
148_A 5_A 0.66 0.31 0.17
17_V 63_D 0.66 0.31 0.17
130_S 111_A 0.66 0.31 0.17
83_S 34_E 0.66 0.30 0.17
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
9395 6.85 test Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done
0070 4.03 ATP6 - ATPF (A, 70-271) Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) (2013_03) 1.00 Done - Shared
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