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OPENSEQ.org
ScpA - ScpB
Genes: A B A+B
Length: 251 197 428
Sequences: 2291 2260 1819
Seq/Len: 9.13 11.47 4.25
MirrorTree (Pazo et al. 2001) 0.81
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 0.00 3.95
2 0.00 0.00 3.96
5 0.00 0.00 3.98
10 0.00 0.00 4.00
20 0.00 0.00 4.01
100 0.00 0.00 4.06
∞ 0.00 0.00 4.44
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
125_F 76_A 1.89 1.00 0.97
59_Y 68_M 1.59 0.99 0.93
107_Y 104_K 1.36 0.96 0.84
121_R 156_E 1.32 0.94 0.82
59_Y 156_E 1.28 0.93 0.79
57_S 57_G 1.27 0.93 0.78
117_R 160_L 1.22 0.91 0.74
218_L 148_Y 1.21 0.90 0.73
159_K 29_L 1.19 0.90 0.72
157_F 104_K 1.18 0.89 0.71
127_K 17_Y 1.15 0.87 0.69
234_E 101_V 1.14 0.87 0.68
64_A 149_G 1.14 0.86 0.67
57_S 121_E 1.14 0.86 0.67
60_L 113_E 1.12 0.85 0.65
54_D 168_P 1.11 0.84 0.64
105_R 163_L 1.03 0.78 0.56
126_T 70_S 1.01 0.75 0.53
4_Y 121_E 1.00 0.75 0.52
42_L 179_Q 0.99 0.74 0.51
157_F 86_P 0.97 0.72 0.48
132_L 20_G 0.95 0.70 0.46
110_A 168_P 0.95 0.69 0.45
25_L 23_G 0.94 0.68 0.45
58_E 165_E 0.93 0.67 0.43
59_Y 23_G 0.93 0.67 0.43
120_E 73_K 0.92 0.66 0.42
127_K 19_A 0.92 0.66 0.42
42_L 115_I 0.91 0.65 0.41
57_S 56_R 0.91 0.65 0.41
196_G 101_V 0.88 0.61 0.38
38_T 104_K 0.88 0.61 0.37
24_R 28_Q 0.88 0.61 0.37
58_E 91_S 0.87 0.59 0.36
160_V 99_A 0.87 0.59 0.36
64_A 160_L 0.86 0.59 0.35
57_S 135_E 0.86 0.58 0.35
61_V 64_A 0.86 0.58 0.35
25_L 129_A 0.86 0.58 0.34
124_S 59_E 0.85 0.57 0.34
190_H 101_V 0.85 0.57 0.34
124_S 73_K 0.85 0.57 0.34
51_L 111_E 0.84 0.56 0.33
242_I 29_L 0.82 0.53 0.31
192_L 19_A 0.82 0.53 0.31
121_R 61_I 0.82 0.53 0.30
197_T 133_L 0.82 0.52 0.30
59_Y 132_L 0.82 0.52 0.30
110_A 169_L 0.82 0.52 0.30
35_A 104_K 0.81 0.52 0.29
39_E 107_I 0.81 0.52 0.29
40_Q 113_E 0.81 0.51 0.29
141_Q 60_L 0.81 0.51 0.29
154_I 84_E 0.81 0.51 0.29
111_A 76_A 0.80 0.50 0.28
179_I 130_K 0.80 0.50 0.28
118_E 157_Q 0.80 0.50 0.28
26_E 57_G 0.80 0.50 0.28
108_K 43_I 0.80 0.50 0.28
215_V 160_L 0.79 0.49 0.27
111_A 47_V 0.78 0.47 0.26
80_E 77_P 0.77 0.46 0.25
218_L 68_M 0.77 0.46 0.25
4_Y 139_A 0.77 0.46 0.25
225_K 80_K 0.77 0.46 0.25
9_D 19_A 0.77 0.46 0.25
64_A 92_Q 0.77 0.46 0.25
108_K 13_E 0.77 0.46 0.25
48_M 69_L 0.77 0.46 0.25
162_K 97_V 0.76 0.45 0.24
208_E 163_L 0.76 0.45 0.24
67_L 121_E 0.76 0.45 0.24
42_L 173_A 0.76 0.44 0.24
53_L 81_K 0.76 0.44 0.24
195_R 33_L 0.76 0.44 0.24
41_Y 112_I 0.76 0.44 0.23
194_S 95_L 0.75 0.44 0.23
90_E 82_L 0.75 0.43 0.23
32_I 11_I 0.75 0.43 0.23
107_Y 115_I 0.75 0.43 0.23
208_E 133_L 0.75 0.43 0.23
207_Y 50_E 0.75 0.43 0.23
156_A 99_A 0.75 0.43 0.23
37_I 145_A 0.74 0.42 0.23
121_R 23_G 0.74 0.42 0.22
185_M 119_K 0.74 0.42 0.22
26_E 168_P 0.74 0.42 0.22
114_L 158_F 0.74 0.41 0.22
121_R 76_A 0.73 0.41 0.21
180_P 124_L 0.73 0.41 0.21
183_A 39_E 0.73 0.41 0.21
238_S 57_G 0.73 0.41 0.21
135_Y 139_A 0.73 0.41 0.21
85_D 64_A 0.73 0.41 0.21
56_A 64_A 0.73 0.40 0.21
64_A 143_G 0.73 0.40 0.21
240_I 67_Y 0.72 0.40 0.21
147_S 60_L 0.72 0.40 0.21
30_Y 150_T 0.72 0.39 0.20
214_V 84_E 0.72 0.39 0.20
126_T 17_Y 0.72 0.39 0.20
19_L 109_R 0.72 0.39 0.20
15_L 23_G 0.72 0.39 0.20
129_P 20_G 0.72 0.39 0.20
38_T 125_H 0.72 0.39 0.20
191_S 45_A 0.72 0.39 0.20
150_V 158_F 0.72 0.39 0.20
137_K 26_K 0.71 0.38 0.19
116_E 46_D 0.71 0.38 0.19
199_I 43_I 0.71 0.38 0.19
179_I 123_I 0.71 0.38 0.19
100_K 57_G 0.71 0.38 0.19
125_F 71_T 0.71 0.37 0.19
62_M 143_G 0.71 0.37 0.19
107_Y 107_I 0.71 0.37 0.19
38_T 97_V 0.70 0.37 0.19
171_E 79_L 0.70 0.37 0.19
29_I 152_P 0.70 0.37 0.18
179_I 15_L 0.70 0.36 0.18
178_D 120_S 0.69 0.36 0.18
34_V 121_E 0.69 0.36 0.18
123_K 15_L 0.69 0.36 0.18
154_I 158_F 0.69 0.36 0.18
199_I 133_L 0.69 0.35 0.17
216_T 58_I 0.69 0.35 0.17
13_G 96_E 0.69 0.35 0.17
185_M 92_Q 0.69 0.35 0.17
245_S 131_A 0.69 0.35 0.17
214_V 53_G 0.69 0.35 0.17
207_Y 52_R 0.69 0.35 0.17
27_I 186_F 0.69 0.35 0.17
76_P 109_R 0.68 0.34 0.17
216_T 158_F 0.68 0.34 0.17
43_L 24_L 0.68 0.34 0.17
242_I 119_K 0.68 0.34 0.17
74_L 118_V 0.68 0.34 0.17
126_T 23_G 0.68 0.34 0.17
95_E 145_A 0.68 0.34 0.17
214_V 120_S 0.68 0.34 0.17
22_I 134_C 0.68 0.34 0.16
132_L 99_A 0.67 0.33 0.16
69_I 69_L 0.67 0.33 0.16
61_V 56_R 0.67 0.33 0.16
82_L 27_K 0.67 0.33 0.16
52_E 74_D 0.67 0.33 0.16
15_L 113_E 0.67 0.33 0.16
47_T 45_A 0.67 0.33 0.16
167_N 24_L 0.67 0.33 0.16
59_Y 121_E 0.67 0.33 0.16
50_V 7_N 0.67 0.33 0.16
139_V 124_L 0.67 0.33 0.16
161_L 149_G 0.67 0.33 0.16
111_A 105_Q 0.67 0.33 0.16
143_E 64_A 0.67 0.32 0.16
78_Q 12_V 0.67 0.32 0.16
8_I 94_S 0.67 0.32 0.15
79_E 103_Y 0.66 0.32 0.15
246_E 97_V 0.66 0.32 0.15
25_L 145_A 0.66 0.32 0.15
161_L 58_I 0.66 0.32 0.15
225_K 137_G 0.66 0.32 0.15
11_F 82_L 0.66 0.32 0.15
194_S 49_D 0.66 0.32 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
5361 4.81 Gremlin ScpAB Complex Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.96 Done - Shared
2871 4.25 ScpA - ScpB Δgene:(1, 100) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.97 Done - Shared
2537 4.17 ScpAB Δgene:(1, 10) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.98 Done - Shared
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