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OPENSEQ.org
3PNL_AB
Genes: A B A+B
Length: 355 209 539
Sequences: 1023 1128 952
Seq/Len: 2.88 5.4 1.77
MirrorTree (Pazo et al. 2001) 0.76
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 0.01 1.63
2 0.08 0.04 1.65
5 0.11 0.04 1.67
10 0.11 0.04 1.68
20 0.11 0.05 1.68
100 0.12 0.05 1.68
∞ 0.15 0.09 1.69
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
106_T 180_Y 1.30 0.78 0.04
113_E 119_R 1.20 0.69 0.03
78_T 43_R 1.15 0.64 0.02
118_L 88_I 1.06 0.55 0.02
117_E 119_R 1.05 0.54 0.02
121_D 88_I 1.04 0.54 0.02
56_E 77_G 1.02 0.51 0.02
75_E 71_L 0.99 0.48 0.01
150_A 35_A 0.97 0.45 0.01
202_S 30_R 0.96 0.44 0.01
103_K 79_S 0.96 0.44 0.01
59_H 79_S 0.95 0.43 0.01
59_H 180_Y 0.95 0.43 0.01
83_D 73_S 0.94 0.42 0.01
152_T 79_S 0.92 0.41 0.01
113_E 121_K 0.91 0.40 0.01
131_I 79_S 0.91 0.39 0.01
78_T 78_A 0.90 0.38 0.01
56_E 76_G 0.88 0.36 0.01
82_P 37_H 0.88 0.36 0.01
350_A 77_G 0.87 0.35 0.01
82_P 195_S 0.86 0.34 0.01
210_M 41_M 0.85 0.33 0.01
68_L 180_Y 0.85 0.33 0.01
209_E 92_Q 0.85 0.33 0.01
71_A 79_S 0.84 0.32 0.01
121_D 92_Q 0.84 0.32 0.01
145_G 180_Y 0.83 0.32 0.01
210_M 91_A 0.83 0.32 0.01
48_L 106_Y 0.83 0.31 0.01
151_N 35_A 0.83 0.31 0.01
109_I 82_L 0.82 0.31 0.01
78_T 71_L 0.82 0.31 0.01
103_K 180_Y 0.81 0.29 0.01
78_T 40_N 0.81 0.29 0.01
170_D 155_E 0.80 0.28 0.01
352_N 82_L 0.80 0.28 0.01
84_K 78_A 0.79 0.28 0.01
206_A 9_N 0.79 0.28 0.01
152_T 180_Y 0.79 0.27 0.01
156_E 179_S 0.77 0.26 0.01
47_L 41_M 0.77 0.26 0.01
71_A 77_G 0.77 0.26 0.01
123_G 95_Q 0.77 0.26 0.01
327_F 26_T 0.77 0.26 0.01
137_V 44_G 0.76 0.25 0.01
56_E 81_P 0.76 0.25 0.01
17_G 76_G 0.75 0.25 0.01
216_I 79_S 0.75 0.25 0.01
48_L 152_V 0.75 0.24 0.01
67_M 68_G 0.75 0.24 0.01
336_D 149_S 0.74 0.24 0.01
192_A 30_R 0.74 0.24 0.01
78_T 195_S 0.73 0.23 0.01
43_G 166_Q 0.73 0.23 0.01
118_L 69_M 0.73 0.23 0.01
106_T 37_H 0.73 0.23 0.01
113_E 78_A 0.73 0.23 0.01
330_T 144_S 0.72 0.22 0.01
301_T 167_S 0.72 0.22 0.01
15_L 122_A 0.71 0.21 0.01
152_T 77_G 0.71 0.21 0.01
136_A 191_P 0.71 0.21 0.01
111_N 112_G 0.71 0.21 0.01
290_S 81_P 0.71 0.21 0.01
145_G 179_S 0.70 0.21 0.01
322_L 109_F 0.70 0.21 0.01
164_E 27_G 0.70 0.20 0.01
62_Y 174_R 0.70 0.20 0.01
117_E 89_R 0.69 0.20 0.01
113_E 32_I 0.69 0.20 0.01
142_Y 78_A 0.69 0.20 0.01
181_N 61_G 0.69 0.20 0.01
125_K 106_Y 0.69 0.20 0.01
155_I 79_S 0.69 0.20 0.01
156_E 79_S 0.69 0.20 0.01
25_L 67_T 0.69 0.20 0.01
65_Q 94_T 0.69 0.20 0.01
130_V 82_L 0.69 0.20 0.01
82_P 81_P 0.69 0.20 0.01
59_H 40_N 0.69 0.20 0.01
198_A 39_L 0.69 0.20 0.01
284_L 35_A 0.69 0.20 0.01
56_E 79_S 0.68 0.19 0.01
214_V 40_N 0.68 0.19 0.01
78_T 119_R 0.68 0.19 0.01
185_S 182_G 0.68 0.19 0.01
276_R 133_W 0.68 0.19 0.01
81_T 81_P 0.68 0.19 0.01
114_T 72_L 0.68 0.19 0.01
102_I 180_Y 0.68 0.19 0.01
174_E 146_Q 0.68 0.19 0.01
33_Y 100_L 0.67 0.19 0.01
181_N 142_Q 0.67 0.19 0.01
189_A 191_P 0.67 0.19 0.01
35_T 82_L 0.67 0.19 0.01
348_T 198_F 0.67 0.19 0.01
123_G 108_M 0.67 0.18 0.01
234_V 18_F 0.67 0.18 0.01
111_N 81_P 0.67 0.18 0.01
273_S 162_E 0.66 0.18 0.01
81_T 40_N 0.66 0.18 0.01
10_V 75_V 0.66 0.18 0.01
72_C 199_M 0.66 0.18 0.01
75_E 40_N 0.65 0.17 0.01
279_A 8_V 0.65 0.17 0.01
110_L 165_A 0.65 0.17 0.01
227_F 94_T 0.65 0.17 0.01
149_V 45_F 0.65 0.17 0.01
137_V 195_S 0.65 0.17 0.01
59_H 179_S 0.65 0.17 0.01
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
0132 2.34 3PNL_AB Δgene:(0, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.10 Done
0131 1.77 3PNL_AB Δgene:(0, ∞) A:(1E-20, 8) B:(1E-20, 8) (2013_03) 0.04 Done - Shared
0130 1.03 3PNL_AB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) (2013_03) 0.03 Done - Shared
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