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OPENSEQ.org
3PNLA
Genes: A B A+B
Length: 357 211 543
Sequences: 1718 2044 814
Seq/Len: 4.81 9.69 1.5
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 0.01 0.02 2.86
2 0.07 0.05 2.88
5 0.09 0.05 2.91
10 0.10 0.05 2.91
20 0.10 0.05 2.91
100 0.11 0.06 2.92
∞ 0.14 0.09 2.93
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
115_E 24_S 1.36 0.78 0.03
187_S 184_G 1.35 0.77 0.03
19_G 78_G 1.18 0.62 0.02
187_S 177_K 1.16 0.61 0.02
342_A 52_E 1.16 0.60 0.02
245_V 165_S 1.14 0.58 0.02
123_D 114_G 1.14 0.58 0.02
147_G 182_Y 1.11 0.56 0.02
336_V 46_G 1.11 0.56 0.02
119_E 121_R 1.11 0.55 0.02
195_C 17_G 1.11 0.55 0.02
105_K 81_S 1.10 0.55 0.02
301_L 15_R 1.09 0.53 0.01
160_L 13_L 1.09 0.53 0.01
50_L 157_E 1.08 0.52 0.01
104_I 43_M 1.07 0.52 0.01
115_E 121_R 1.06 0.51 0.01
147_G 80_A 1.06 0.50 0.01
173_A 180_A 1.05 0.49 0.01
158_E 166_A 1.04 0.49 0.01
49_L 22_T 1.04 0.48 0.01
324_L 107_L 1.02 0.46 0.01
154_T 81_S 1.01 0.45 0.01
189_G 65_I 1.01 0.45 0.01
61_H 42_N 1.01 0.45 0.01
112_L 121_R 1.00 0.45 0.01
49_L 43_M 0.98 0.42 0.01
322_T 180_A 0.98 0.42 0.01
199_A 77_V 0.98 0.42 0.01
153_N 77_V 0.97 0.41 0.01
320_Y 176_R 0.97 0.41 0.01
147_G 39_H 0.97 0.41 0.01
195_C 78_G 0.97 0.41 0.01
220_G 122_G 0.97 0.41 0.01
332_T 119_I 0.96 0.41 0.01
83_T 159_A 0.96 0.40 0.01
145_T 128_D 0.95 0.39 0.01
78_I 148_Q 0.95 0.39 0.01
241_D 109_Q 0.94 0.38 0.01
100_V 93_A 0.93 0.37 0.01
105_K 189_G 0.92 0.36 0.01
116_T 110_M 0.92 0.36 0.01
162_G 114_G 0.91 0.35 0.01
90_C 54_L 0.91 0.35 0.01
320_Y 30_L 0.91 0.35 0.01
108_T 182_Y 0.91 0.35 0.01
108_T 39_H 0.90 0.34 0.01
172_D 15_R 0.89 0.34 0.01
139_V 129_K 0.89 0.33 0.01
75_P 45_R 0.89 0.33 0.01
85_D 75_S 0.89 0.33 0.01
112_L 47_F 0.88 0.33 0.01
39_A 155_A 0.88 0.32 0.01
185_G 161_S 0.88 0.32 0.01
122_H 199_M 0.88 0.32 0.01
281_A 173_M 0.88 0.32 0.01
332_T 139_V 0.88 0.32 0.01
172_D 55_P 0.88 0.32 0.01
280_I 64_F 0.87 0.32 0.01
205_F 66_L 0.87 0.31 0.01
185_G 46_G 0.87 0.31 0.01
113_N 83_P 0.86 0.31 0.01
340_T 50_V 0.86 0.31 0.01
151_V 184_G 0.86 0.31 0.01
222_P 46_G 0.86 0.31 0.01
120_L 184_G 0.86 0.30 0.01
49_L 104_L 0.85 0.30 0.01
187_S 206_A 0.84 0.29 0.01
179_R 140_E 0.84 0.29 0.01
220_G 28_T 0.84 0.29 0.01
222_P 187_S 0.84 0.29 0.01
282_L 202_M 0.83 0.28 0.01
50_L 108_Y 0.83 0.28 0.01
80_T 121_R 0.83 0.28 0.01
119_E 120_S 0.83 0.28 0.01
283_V 15_R 0.83 0.28 0.01
116_T 118_V 0.82 0.28 0.01
133_I 81_S 0.82 0.28 0.01
61_H 181_S 0.82 0.27 0.01
285_N 39_H 0.82 0.27 0.01
160_L 157_E 0.82 0.27 0.01
158_E 42_N 0.82 0.27 0.01
235_T 51_V 0.81 0.27 0.01
112_L 83_P 0.81 0.27 0.01
304_R 13_L 0.81 0.27 0.01
83_T 137_P 0.81 0.27 0.01
332_T 23_E 0.81 0.26 0.01
121_L 166_A 0.80 0.26 0.01
51_S 166_A 0.80 0.26 0.01
352_A 190_H 0.80 0.26 0.01
70_L 182_Y 0.80 0.26 0.01
62_C 134_V 0.80 0.26 0.01
173_A 109_Q 0.80 0.26 0.01
187_S 96_T 0.80 0.26 0.01
284_N 134_V 0.80 0.26 0.01
352_A 131_M 0.80 0.25 0.01
83_T 89_F 0.80 0.25 0.01
281_A 22_T 0.79 0.25 0.01
111_I 197_S 0.79 0.25 0.01
99_G 81_S 0.79 0.25 0.01
84_P 83_P 0.79 0.25 0.01
283_V 27_L 0.79 0.25 0.01
174_C 131_M 0.79 0.25 0.01
220_G 118_V 0.79 0.24 0.01
100_V 87_T 0.79 0.24 0.01
338_D 109_Q 0.78 0.24 0.01
12_V 83_P 0.78 0.24 0.01
121_L 137_P 0.78 0.24 0.01
194_A 74_L 0.78 0.24 0.01
331_I 52_E 0.78 0.24 0.01
158_E 134_V 0.78 0.24 0.01
240_F 116_D 0.78 0.24 0.01
191_A 134_V 0.78 0.24 0.01
310_L 131_M 0.78 0.24 0.01
274_Q 198_V 0.78 0.24 0.01
311_T 148_Q 0.78 0.24 0.01
27_L 158_A 0.77 0.23 0.01
244_L 137_P 0.77 0.23 0.01
177_L 12_W 0.77 0.23 0.01
320_Y 83_P 0.77 0.23 0.01
281_A 204_M 0.77 0.23 0.01
216_V 47_F 0.77 0.23 0.01
64_Y 20_F 0.77 0.23 0.01
105_K 30_L 0.77 0.23 0.01
86_K 20_F 0.76 0.23 0.01
151_V 42_N 0.76 0.23 0.01
323_S 74_L 0.76 0.23 0.01
197_V 24_S 0.76 0.23 0.01
306_Q 140_E 0.76 0.23 0.01
270_K 122_G 0.76 0.23 0.01
294_L 208_A 0.76 0.23 0.01
246_N 141_S 0.76 0.23 0.01
131_V 157_E 0.76 0.22 0.01
307_Q 105_E 0.76 0.22 0.01
68_G 134_V 0.75 0.22 0.01
222_P 26_Y 0.75 0.22 0.01
111_I 45_R 0.75 0.22 0.01
192_L 85_F 0.75 0.22 0.01
4_K 92_A 0.75 0.22 0.01
240_F 96_T 0.75 0.22 0.01
22_K 193_P 0.74 0.21 0.01
281_A 17_G 0.74 0.21 0.01
316_L 83_P 0.74 0.21 0.01
343_L 171_I 0.74 0.21 0.01
152_A 20_F 0.74 0.21 0.01
103_I 202_M 0.73 0.21 0.01
275_S 186_R 0.73 0.21 0.01
108_T 80_A 0.73 0.21 0.01
174_C 173_M 0.73 0.21 0.01
125_G 166_A 0.73 0.21 0.01
146_A 72_T 0.73 0.21 0.01
134_D 107_L 0.73 0.21 0.01
272_P 19_I 0.73 0.20 0.01
103_I 22_T 0.73 0.20 0.01
188_I 96_T 0.73 0.20 0.01
225_D 165_S 0.73 0.20 0.01
24_H 116_D 0.73 0.20 0.01
104_I 94_Q 0.73 0.20 0.01
116_T 196_T 0.73 0.20 0.01
333_L 172_T 0.72 0.20 0.01
80_T 42_N 0.72 0.20 0.01
138_A 180_A 0.72 0.20 0.01
144_Y 123_K 0.72 0.20 0.01
55_S 156_L 0.72 0.20 0.00
35_Y 42_N 0.72 0.20 0.00
34_V 27_L 0.72 0.20 0.00
312_I 204_M 0.72 0.20 0.00
199_A 83_P 0.72 0.20 0.00
12_V 77_V 0.72 0.20 0.00
141_D 25_E 0.72 0.20 0.00
201_G 186_R 0.72 0.20 0.00
166_E 156_L 0.72 0.20 0.00
267_Q 69_T 0.72 0.20 0.00
174_C 47_F 0.72 0.20 0.00
295_Y 77_V 0.72 0.20 0.00
156_L 50_V 0.72 0.20 0.00
23_A 20_F 0.72 0.20 0.00
194_A 122_G 0.71 0.20 0.00
214_F 33_E 0.71 0.20 0.00
292_S 85_F 0.71 0.20 0.00
326_M 30_L 0.71 0.20 0.00
77_E 93_A 0.71 0.20 0.00
100_V 4_L 0.71 0.19 0.00
321_C 34_I 0.71 0.19 0.00
152_A 87_T 0.71 0.19 0.00
80_T 44_N 0.71 0.19 0.00
306_Q 161_S 0.71 0.19 0.00
25_P 114_G 0.71 0.19 0.00
323_S 181_S 0.71 0.19 0.00
183_N 106_E 0.71 0.19 0.00
331_I 209_A 0.71 0.19 0.00
22_K 34_I 0.71 0.19 0.00
301_L 96_T 0.71 0.19 0.00
307_Q 163_A 0.71 0.19 0.00
133_I 134_V 0.71 0.19 0.00
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
7278 1.5 3PNLA Δgene:(0, 0) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.03 Done - Shared
7269 3.06 3PNLA Δgene:(0, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.11 Done - Shared
7244 1.6 3PNLA Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.07 Done - Shared
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