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OPENSEQ.org
ScpAB
Genes: A B A+B
Length: 251 197 428
Sequences: 2136 2265 1784
Seq/Len: 8.51 11.5 4.17
MirrorTree (Pazo et al. 2001) 0.80
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 3.93
2 0.00 0.00 3.94
5 0.00 0.00 3.98
10 0.00 0.00 3.98
20 0.00 0.00 4.00
100 0.00 0.00 4.02
∞ 0.00 0.00 4.27
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 1.95 1.00 0.98
59_Y 68_M 1.58 0.98 0.93
107_Y 104_K 1.40 0.96 0.86
121_R 156_E 1.36 0.95 0.84
59_Y 156_E 1.33 0.95 0.83
57_S 57_G 1.27 0.93 0.79
157_F 104_K 1.26 0.92 0.78
127_K 17_Y 1.23 0.91 0.76
117_R 160_L 1.23 0.91 0.76
64_A 149_G 1.22 0.91 0.75
218_L 148_Y 1.15 0.86 0.69
159_K 29_L 1.13 0.85 0.67
57_S 121_E 1.13 0.85 0.67
54_D 168_P 1.12 0.84 0.65
157_F 86_P 1.11 0.84 0.65
110_A 168_P 1.10 0.83 0.63
105_R 163_L 1.08 0.82 0.62
60_L 113_E 1.07 0.81 0.61
124_S 59_E 1.06 0.80 0.59
4_Y 121_E 1.05 0.79 0.58
234_E 101_V 1.05 0.79 0.58
196_G 101_V 0.99 0.74 0.52
25_L 23_G 0.99 0.74 0.52
120_E 73_K 0.99 0.73 0.51
141_Q 60_L 0.98 0.72 0.49
126_T 70_S 0.97 0.71 0.49
42_L 179_Q 0.96 0.70 0.47
42_L 115_I 0.93 0.66 0.44
132_L 20_G 0.92 0.66 0.43
38_T 104_K 0.92 0.65 0.43
25_L 129_A 0.91 0.63 0.41
190_H 101_V 0.90 0.62 0.40
110_A 169_L 0.89 0.61 0.39
58_E 91_S 0.89 0.61 0.38
59_Y 132_L 0.88 0.60 0.37
51_L 111_E 0.87 0.59 0.36
197_T 133_L 0.87 0.58 0.36
124_S 73_K 0.86 0.58 0.36
218_L 68_M 0.86 0.58 0.36
57_S 135_E 0.86 0.58 0.36
242_I 29_L 0.86 0.57 0.35
57_S 56_R 0.86 0.57 0.35
160_V 99_A 0.86 0.57 0.35
111_A 160_L 0.85 0.56 0.34
59_Y 23_G 0.85 0.56 0.34
58_E 165_E 0.85 0.56 0.34
61_V 64_A 0.84 0.55 0.34
39_E 107_I 0.84 0.55 0.34
24_R 28_Q 0.83 0.54 0.32
179_I 130_K 0.83 0.54 0.32
37_I 145_A 0.83 0.54 0.32
111_A 76_A 0.83 0.54 0.32
227_Q 51_Y 0.83 0.54 0.32
56_A 64_A 0.83 0.53 0.32
240_I 67_Y 0.82 0.52 0.31
154_I 84_E 0.82 0.52 0.30
85_D 64_A 0.82 0.52 0.30
214_V 53_G 0.81 0.51 0.30
48_M 69_L 0.81 0.51 0.30
40_Q 113_E 0.81 0.51 0.30
32_I 11_I 0.81 0.50 0.29
4_Y 139_A 0.80 0.50 0.29
147_S 60_L 0.80 0.50 0.29
156_A 99_A 0.80 0.50 0.29
95_E 145_A 0.80 0.49 0.28
153_M 117_G 0.80 0.49 0.28
69_I 69_L 0.79 0.48 0.27
15_L 23_G 0.79 0.47 0.27
192_L 19_A 0.78 0.47 0.27
32_I 140_D 0.78 0.47 0.27
29_I 152_P 0.78 0.46 0.26
121_R 23_G 0.78 0.46 0.26
225_K 80_K 0.78 0.46 0.26
26_E 168_P 0.78 0.46 0.26
34_V 69_L 0.77 0.46 0.26
118_E 157_Q 0.77 0.45 0.25
165_K 101_V 0.77 0.45 0.25
116_E 46_D 0.77 0.45 0.25
42_L 173_A 0.76 0.44 0.25
67_L 121_E 0.76 0.44 0.24
35_A 104_K 0.76 0.44 0.24
246_E 44_M 0.76 0.44 0.24
19_L 109_R 0.76 0.44 0.24
158_Q 67_Y 0.76 0.43 0.24
71_S 134_C 0.76 0.43 0.24
194_S 95_L 0.75 0.43 0.23
30_Y 150_T 0.75 0.43 0.23
242_I 119_K 0.75 0.43 0.23
111_A 105_Q 0.75 0.43 0.23
127_K 19_A 0.75 0.42 0.23
26_E 57_G 0.75 0.42 0.23
30_Y 100_I 0.75 0.42 0.23
64_A 143_G 0.74 0.42 0.23
125_F 71_T 0.74 0.42 0.23
215_V 160_L 0.74 0.41 0.22
162_K 97_V 0.74 0.41 0.22
179_I 15_L 0.74 0.41 0.22
24_R 17_Y 0.74 0.41 0.22
121_R 61_I 0.74 0.41 0.22
22_I 134_C 0.73 0.41 0.22
214_V 84_E 0.73 0.41 0.22
8_I 94_S 0.73 0.40 0.22
53_L 81_K 0.73 0.40 0.21
64_A 92_Q 0.73 0.39 0.21
56_A 47_V 0.72 0.39 0.21
28_D 59_E 0.72 0.39 0.21
135_Y 130_K 0.72 0.39 0.21
185_M 119_K 0.72 0.39 0.21
60_L 36_E 0.72 0.39 0.21
41_Y 112_I 0.72 0.39 0.20
98_I 109_R 0.72 0.38 0.20
62_M 143_G 0.72 0.38 0.20
126_T 17_Y 0.72 0.38 0.20
108_K 43_I 0.72 0.38 0.20
225_K 136_V 0.71 0.38 0.20
9_D 19_A 0.71 0.37 0.20
108_K 13_E 0.71 0.37 0.19
25_L 145_A 0.71 0.37 0.19
123_K 73_K 0.71 0.37 0.19
199_I 43_I 0.71 0.37 0.19
216_T 58_I 0.70 0.36 0.19
111_A 47_V 0.70 0.36 0.19
64_A 160_L 0.70 0.36 0.19
52_E 74_D 0.70 0.36 0.18
128_P 133_L 0.70 0.36 0.18
82_L 27_K 0.70 0.36 0.18
108_K 148_Y 0.69 0.35 0.18
181_I 109_R 0.69 0.35 0.18
130_S 69_L 0.69 0.35 0.18
34_V 171_E 0.69 0.35 0.18
150_V 166_L 0.69 0.35 0.18
161_L 149_G 0.69 0.35 0.18
8_I 8_W 0.69 0.34 0.17
149_T 161_K 0.69 0.34 0.17
167_N 62_E 0.69 0.34 0.17
224_M 62_E 0.69 0.34 0.17
59_Y 121_E 0.68 0.34 0.17
41_Y 142_P 0.68 0.34 0.17
100_K 57_G 0.68 0.34 0.17
207_Y 52_R 0.68 0.34 0.17
50_V 7_N 0.68 0.33 0.17
167_N 24_L 0.68 0.33 0.17
197_T 45_A 0.67 0.33 0.16
90_E 82_L 0.67 0.33 0.16
160_V 53_G 0.67 0.33 0.16
4_Y 109_R 0.67 0.33 0.16
166_I 65_D 0.67 0.33 0.16
133_S 100_I 0.67 0.33 0.16
76_P 99_A 0.67 0.32 0.16
15_L 113_E 0.67 0.32 0.16
41_Y 23_G 0.67 0.32 0.16
11_F 82_L 0.67 0.32 0.16
188_I 151_T 0.67 0.32 0.16
178_D 120_S 0.67 0.32 0.16
183_A 39_E 0.67 0.32 0.16
121_R 76_A 0.67 0.32 0.16
179_I 107_I 0.67 0.32 0.16
214_V 120_S 0.66 0.32 0.16
143_E 64_A 0.66 0.32 0.15
114_L 113_E 0.66 0.31 0.15
31_D 29_L 0.66 0.31 0.15
62_M 175_E 0.66 0.31 0.15
52_E 22_E 0.66 0.31 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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