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OPENSEQ.org
Gremlin ScpAB Complex
Genes: A B A+B
Length: 251 197 416
Sequences: 2308 2312 2002
Seq/Len: 9.2 11.74 4.81
MirrorTree (Pazo et al. 2001) 0.85
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 0.02 0.02 3.95
2 0.02 0.02 3.98
5 0.02 0.02 3.99
10 0.02 0.02 4.02
20 0.02 0.02 4.03
100 0.02 0.02 4.06
∞ 0.02 0.02 4.47
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 1.76 1.00 0.96
121_R 156_E 1.66 0.99 0.94
59_Y 68_M 1.54 0.99 0.91
107_Y 104_K 1.46 0.98 0.88
64_A 149_G 1.21 0.92 0.73
57_S 121_E 1.20 0.92 0.72
157_F 104_K 1.19 0.91 0.71
57_S 57_G 1.16 0.90 0.69
218_L 148_Y 1.11 0.87 0.64
110_A 168_P 1.11 0.87 0.63
54_D 168_P 1.08 0.85 0.61
180_P 124_L 1.08 0.85 0.60
117_R 160_L 1.06 0.84 0.58
59_Y 156_E 1.05 0.83 0.57
150_V 158_F 1.05 0.82 0.56
105_R 163_L 1.02 0.80 0.53
126_T 70_S 1.02 0.80 0.53
57_S 56_R 1.01 0.79 0.53
42_L 115_I 1.00 0.78 0.51
218_L 68_M 0.97 0.76 0.48
25_L 129_A 0.97 0.76 0.48
188_I 151_T 0.97 0.75 0.47
58_E 91_S 0.96 0.74 0.47
91_E 64_A 0.96 0.74 0.47
118_E 157_Q 0.95 0.73 0.45
156_A 99_A 0.94 0.72 0.45
159_K 29_L 0.94 0.72 0.44
107_Y 107_I 0.93 0.71 0.43
160_V 99_A 0.93 0.70 0.42
60_L 113_E 0.88 0.64 0.36
26_E 57_G 0.87 0.63 0.36
26_E 168_P 0.87 0.63 0.35
127_K 17_Y 0.86 0.62 0.35
242_I 97_V 0.85 0.61 0.33
40_Q 113_E 0.85 0.61 0.33
186_N 12_V 0.85 0.60 0.33
59_Y 23_G 0.85 0.60 0.33
116_E 46_D 0.83 0.58 0.31
42_L 173_A 0.83 0.58 0.31
59_Y 121_E 0.83 0.58 0.31
34_V 129_A 0.83 0.58 0.31
161_L 136_V 0.83 0.57 0.31
234_E 101_V 0.83 0.57 0.31
124_S 59_E 0.83 0.57 0.31
62_M 143_G 0.82 0.57 0.30
111_A 160_L 0.82 0.57 0.30
81_E 21_D 0.82 0.56 0.29
120_E 73_K 0.81 0.56 0.29
179_I 107_I 0.81 0.55 0.29
185_M 119_K 0.81 0.55 0.29
4_Y 121_E 0.81 0.54 0.28
59_Y 132_L 0.81 0.54 0.28
19_L 109_R 0.81 0.54 0.28
100_K 57_G 0.80 0.54 0.28
199_I 73_K 0.79 0.53 0.27
25_L 23_G 0.79 0.53 0.27
24_R 56_R 0.79 0.52 0.27
13_G 96_E 0.79 0.52 0.27
157_F 84_E 0.79 0.52 0.26
191_S 16_L 0.79 0.52 0.26
8_I 94_S 0.78 0.51 0.26
9_D 19_A 0.78 0.51 0.26
113_D 133_L 0.78 0.51 0.26
196_G 133_L 0.78 0.51 0.26
56_A 64_A 0.78 0.50 0.25
154_I 158_F 0.77 0.50 0.25
222_E 150_T 0.76 0.48 0.24
149_T 172_N 0.76 0.48 0.23
71_S 44_M 0.76 0.48 0.23
214_V 84_E 0.76 0.47 0.23
199_I 43_I 0.75 0.47 0.23
238_S 77_P 0.75 0.46 0.23
162_K 97_V 0.75 0.46 0.22
58_E 165_E 0.75 0.46 0.22
110_A 169_L 0.75 0.46 0.22
165_K 101_V 0.74 0.46 0.22
11_F 96_E 0.74 0.46 0.22
50_V 27_K 0.74 0.45 0.22
238_S 57_G 0.74 0.45 0.21
126_T 17_Y 0.73 0.44 0.21
38_T 104_K 0.73 0.44 0.21
150_V 129_A 0.73 0.44 0.21
132_L 20_G 0.73 0.44 0.21
124_S 73_K 0.73 0.43 0.21
30_Y 150_T 0.72 0.43 0.20
225_K 80_K 0.72 0.43 0.20
20_H 122_R 0.72 0.42 0.20
33_P 123_I 0.72 0.42 0.20
114_L 158_F 0.72 0.42 0.20
230_L 112_I 0.71 0.41 0.19
54_D 114_E 0.71 0.41 0.19
23_N 158_F 0.71 0.41 0.19
79_E 153_T 0.71 0.41 0.19
223_L 126_S 0.71 0.41 0.19
179_I 86_P 0.70 0.40 0.18
125_F 71_T 0.70 0.40 0.18
37_I 95_L 0.70 0.40 0.18
78_Q 12_V 0.70 0.40 0.18
212_H 139_A 0.70 0.40 0.18
153_M 102_S 0.70 0.40 0.18
196_G 45_A 0.70 0.40 0.18
231_I 49_D 0.70 0.39 0.18
22_I 130_K 0.69 0.39 0.18
37_I 145_A 0.69 0.39 0.18
28_D 59_E 0.69 0.38 0.17
222_E 155_L 0.69 0.38 0.17
164_K 124_L 0.69 0.38 0.17
110_A 8_W 0.69 0.38 0.17
31_D 29_L 0.69 0.38 0.17
108_K 13_E 0.69 0.38 0.17
12_E 92_Q 0.69 0.38 0.17
111_A 76_A 0.69 0.38 0.17
116_E 44_M 0.69 0.38 0.17
116_E 65_D 0.68 0.37 0.17
13_G 166_L 0.68 0.37 0.17
34_V 69_L 0.68 0.37 0.17
162_K 21_D 0.68 0.37 0.17
38_T 125_H 0.68 0.36 0.16
114_L 136_V 0.68 0.36 0.16
182_E 17_Y 0.68 0.36 0.16
65_T 104_K 0.68 0.36 0.16
58_E 124_L 0.68 0.36 0.16
220_V 21_D 0.67 0.36 0.16
244_G 40_L 0.67 0.36 0.16
57_S 10_A 0.67 0.36 0.16
240_I 61_I 0.67 0.36 0.16
24_R 28_Q 0.67 0.36 0.16
66_L 116_R 0.67 0.35 0.16
54_D 172_N 0.67 0.35 0.16
242_I 48_A 0.67 0.35 0.16
45_V 38_P 0.67 0.35 0.15
57_S 61_I 0.67 0.35 0.15
136_A 29_L 0.66 0.35 0.15
220_V 61_I 0.66 0.35 0.15
242_I 29_L 0.66 0.35 0.15
6_V 121_E 0.66 0.35 0.15
3_E 60_L 0.66 0.35 0.15
109_D 101_V 0.66 0.35 0.15
26_E 139_A 0.66 0.34 0.15
151_Y 171_E 0.66 0.34 0.15
225_K 71_T 0.66 0.34 0.15
149_T 161_K 0.66 0.34 0.15
111_A 99_A 0.66 0.34 0.15
33_P 111_E 0.66 0.34 0.15
7_K 24_L 0.66 0.34 0.15
227_Q 24_L 0.66 0.34 0.15
60_L 36_E 0.66 0.34 0.15
227_Q 97_V 0.65 0.34 0.14
128_P 133_L 0.65 0.34 0.14
64_A 177_V 0.65 0.33 0.14
224_M 128_V 0.65 0.33 0.14
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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