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OPENSEQ.org
ATP6 - ATPF
Genes: A B A+B
Length: 271 156 410
Sequences: 1300 1931 1065
Seq/Len: 4.8 12.38 2.6
MirrorTree (Pazo et al. 2001) 0.73
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 0.12
2 0.00 0.09 2.44
5 0.00 0.09 2.48
10 0.00 0.09 2.49
20 0.00 0.09 2.49
100 0.00 0.09 2.49
∞ 0.01 0.10 2.50
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 3.17 1.00 1.00
149_V 10_Q 1.78 0.98 0.96
77_T 33_I 1.68 0.98 0.94
53_G 13_A 1.51 0.95 0.89
243_I 17_F 1.31 0.87 0.77
243_I 20_F 1.30 0.86 0.76
49_S 10_Q 1.29 0.86 0.76
255_I 139_S 1.28 0.85 0.75
206_S 152_L 1.28 0.85 0.75
208_G 102_V 1.27 0.85 0.74
125_L 11_A 1.25 0.84 0.73
155_L 11_A 1.20 0.80 0.68
50_V 13_A 1.19 0.79 0.67
152_S 7_I 1.16 0.77 0.64
148_N 4_N 1.14 0.75 0.62
111_W 10_Q 1.13 0.74 0.61
60_F 25_V 1.11 0.72 0.59
74_K 37_Q 1.08 0.69 0.55
139_L 33_I 1.08 0.69 0.55
263_Y 21_C 1.04 0.65 0.51
84_G 39_E 1.03 0.64 0.49
254_F 123_Q 1.03 0.64 0.49
67_A 32_A 1.01 0.61 0.47
115_M 86_I 0.98 0.58 0.43
196_E 17_F 0.98 0.58 0.43
70_G 32_A 0.97 0.57 0.42
57_L 20_F 0.97 0.57 0.42
164_Y 32_A 0.96 0.56 0.41
99_K 34_E 0.96 0.56 0.41
45_S 6_T 0.95 0.55 0.39
239_V 8_L 0.95 0.54 0.39
41_I 5_A 0.95 0.54 0.39
64_A 135_I 0.94 0.53 0.38
199_S 17_F 0.93 0.52 0.36
120_L 40_I 0.92 0.51 0.36
204_P 68_A 0.92 0.51 0.36
244_F 132_A 0.92 0.50 0.35
196_E 50_A 0.91 0.50 0.35
165_S 66_K 0.91 0.50 0.35
9_Q 29_L 0.91 0.49 0.34
106_L 26_W 0.91 0.49 0.34
198_V 23_K 0.90 0.48 0.34
64_A 24_Y 0.90 0.48 0.33
83_I 30_M 0.89 0.47 0.32
64_A 29_L 0.89 0.47 0.32
147_V 34_E 0.88 0.46 0.31
255_I 82_R 0.88 0.46 0.31
167_K 127_L 0.86 0.44 0.29
190_P 56_L 0.86 0.44 0.29
91_K 60_S 0.85 0.43 0.28
165_S 114_K 0.84 0.42 0.27
205_V 11_A 0.84 0.41 0.27
41_I 137_E 0.84 0.41 0.27
196_E 21_C 0.83 0.41 0.26
239_V 16_L 0.83 0.40 0.26
240_P 16_L 0.83 0.40 0.26
119_D 117_R 0.83 0.40 0.25
152_S 34_E 0.82 0.40 0.25
190_P 136_I 0.82 0.39 0.25
60_F 21_C 0.81 0.38 0.24
58_V 88_D 0.81 0.38 0.24
178_L 140_V 0.81 0.38 0.24
244_F 32_A 0.81 0.38 0.23
199_S 113_R 0.80 0.37 0.23
145_A 132_A 0.80 0.37 0.23
166_I 8_L 0.80 0.36 0.22
217_A 145_N 0.79 0.36 0.22
107_T 53_D 0.79 0.35 0.22
60_F 26_W 0.79 0.35 0.21
222_F 44_L 0.79 0.35 0.21
225_I 10_Q 0.78 0.35 0.21
149_V 7_I 0.78 0.34 0.21
82_V 20_F 0.77 0.34 0.20
67_A 20_F 0.77 0.34 0.20
191_V 146_S 0.77 0.34 0.20
147_V 114_K 0.77 0.34 0.20
74_K 75_I 0.77 0.34 0.20
86_V 31_A 0.77 0.34 0.20
97_K 103_A 0.77 0.33 0.20
257_M 135_I 0.77 0.33 0.20
269_E 85_Q 0.77 0.33 0.20
229_L 24_Y 0.76 0.32 0.19
91_K 20_F 0.76 0.32 0.19
198_V 142_E 0.76 0.32 0.19
228_L 135_I 0.76 0.32 0.19
49_S 6_T 0.75 0.32 0.19
112_V 107_A 0.75 0.32 0.18
191_V 140_V 0.75 0.31 0.18
200_L 8_L 0.75 0.31 0.18
69_S 32_A 0.75 0.31 0.18
81_L 48_E 0.75 0.31 0.18
160_L 102_V 0.75 0.31 0.18
250_T 128_A 0.75 0.31 0.18
64_A 46_S 0.75 0.31 0.18
154_A 82_R 0.74 0.31 0.18
201_L 130_A 0.74 0.31 0.18
105_A 139_S 0.74 0.31 0.18
238_N 13_A 0.74 0.31 0.18
104_L 153_V 0.74 0.30 0.17
91_K 16_L 0.74 0.30 0.17
241_W 6_T 0.74 0.30 0.17
73_G 125_A 0.73 0.30 0.17
48_F 31_A 0.73 0.30 0.17
268_S 127_L 0.73 0.30 0.17
195_L 77_E 0.73 0.29 0.17
112_V 65_L 0.73 0.29 0.17
43_I 65_L 0.73 0.29 0.17
81_L 37_Q 0.73 0.29 0.16
258_V 14_F 0.73 0.29 0.16
232_W 68_A 0.72 0.29 0.16
182_P 17_F 0.72 0.29 0.16
255_I 59_A 0.72 0.28 0.16
51_V 44_L 0.72 0.28 0.16
87_N 30_M 0.72 0.28 0.16
163_F 143_A 0.72 0.28 0.16
18_N 21_C 0.72 0.28 0.16
238_N 119_E 0.71 0.28 0.15
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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