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OPENSEQ.org
ATP6 - ATPF
Genes: A B A+B
Length: 271 156 421
Sequences: 3767 2355 1757
Seq/Len: 13.9 15.1 4.17
MirrorTree (Pazo et al. 2001) 0.64
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 0.08 0.14
2 0.00 0.08 3.90
5 0.00 0.08 4.11
10 0.00 0.08 4.11
20 0.00 0.08 4.11
100 0.00 0.08 4.15
∞ 0.00 0.09 4.20
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 3.01 1.00 1.00
77_T 33_I 1.99 1.00 0.99
149_V 10_Q 1.69 0.99 0.96
57_L 20_F 1.53 0.98 0.93
99_K 34_E 1.53 0.98 0.93
152_S 7_I 1.52 0.98 0.93
53_G 13_A 1.27 0.93 0.82
87_N 30_M 1.27 0.93 0.81
122_P 14_F 1.21 0.90 0.77
83_I 29_L 1.19 0.89 0.76
208_G 102_V 1.13 0.85 0.70
50_V 13_A 1.11 0.84 0.69
41_I 40_I 1.06 0.80 0.63
167_K 23_K 1.05 0.80 0.62
243_I 20_F 1.05 0.79 0.62
74_K 37_Q 1.05 0.79 0.62
106_L 26_W 1.05 0.79 0.61
255_I 139_S 0.99 0.73 0.55
111_W 10_Q 0.97 0.72 0.53
238_N 13_A 0.97 0.71 0.53
49_S 10_Q 0.97 0.71 0.52
239_V 13_A 0.91 0.64 0.45
83_I 30_M 0.89 0.62 0.43
152_S 11_A 0.88 0.60 0.41
107_T 17_F 0.87 0.59 0.40
87_N 37_Q 0.87 0.59 0.40
243_I 17_F 0.86 0.57 0.39
84_G 33_I 0.86 0.57 0.39
206_S 128_A 0.85 0.56 0.37
197_G 143_A 0.83 0.54 0.35
70_G 39_E 0.83 0.53 0.35
45_S 6_T 0.82 0.52 0.34
254_F 150_D 0.82 0.52 0.34
74_K 39_E 0.82 0.52 0.33
154_A 60_S 0.81 0.51 0.33
148_N 6_T 0.80 0.50 0.32
42_N 5_A 0.80 0.49 0.31
213_G 10_Q 0.79 0.48 0.31
56_F 21_C 0.79 0.48 0.30
36_A 68_A 0.79 0.48 0.30
85_F 109_I 0.78 0.47 0.29
68_T 32_A 0.77 0.45 0.28
237_L 13_A 0.77 0.45 0.28
145_A 131_G 0.77 0.45 0.27
84_G 39_E 0.76 0.44 0.27
239_V 16_L 0.76 0.44 0.27
64_A 32_A 0.76 0.43 0.26
82_V 154_A 0.75 0.42 0.26
71_V 135_I 0.74 0.41 0.25
74_K 33_I 0.74 0.41 0.24
201_L 133_E 0.73 0.40 0.23
241_W 25_V 0.73 0.39 0.23
112_V 16_L 0.72 0.38 0.22
147_V 7_I 0.72 0.38 0.22
154_A 78_Q 0.71 0.38 0.22
196_E 17_F 0.71 0.38 0.22
114_L 12_I 0.71 0.38 0.22
125_L 11_A 0.70 0.36 0.21
77_T 39_E 0.70 0.36 0.20
108_I 14_F 0.70 0.36 0.20
217_A 68_A 0.70 0.36 0.20
71_V 41_A 0.69 0.35 0.20
250_T 60_S 0.69 0.35 0.20
79_I 40_I 0.69 0.34 0.19
70_G 89_E 0.68 0.34 0.19
122_P 120_L 0.68 0.34 0.19
151_L 3_L 0.68 0.34 0.19
263_Y 120_L 0.68 0.33 0.18
104_L 20_F 0.67 0.33 0.18
110_V 106_Q 0.67 0.33 0.18
261_I 37_Q 0.67 0.33 0.18
63_V 29_L 0.66 0.32 0.17
201_L 108_E 0.66 0.32 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
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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