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OPENSEQ.org
3PNL_AB
Genes: A B A+B
Length: 355 209 541
Sequences: 1272 1439 1265
Seq/Len: 3.58 6.89 2.34
MirrorTree (Pazo et al. 2001) 0.74
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 0.01 0.01 2.17
2 0.10 0.06 2.20
5 0.16 0.07 2.23
10 0.16 0.08 2.23
20 0.16 0.08 2.23
100 0.17 0.08 2.22
∞ 0.19 0.11 2.24
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 1.27 0.82 0.10
118_L 88_I 1.13 0.71 0.07
121_D 92_Q 1.11 0.69 0.06
83_D 73_S 1.09 0.67 0.06
113_E 119_R 1.09 0.67 0.06
121_D 88_I 1.06 0.64 0.05
117_E 119_R 1.02 0.59 0.05
75_E 71_L 0.96 0.52 0.04
152_T 79_S 0.95 0.51 0.04
145_G 180_Y 0.94 0.51 0.04
185_S 182_G 0.93 0.49 0.03
150_A 35_A 0.92 0.48 0.03
56_E 77_G 0.90 0.46 0.03
113_E 121_K 0.87 0.42 0.03
103_K 79_S 0.87 0.42 0.03
185_S 204_A 0.86 0.40 0.03
177_R 54_A 0.84 0.39 0.03
82_P 37_H 0.83 0.38 0.02
78_T 43_R 0.81 0.36 0.02
68_L 180_Y 0.81 0.35 0.02
130_V 82_L 0.80 0.34 0.02
210_M 41_M 0.80 0.34 0.02
56_E 76_G 0.80 0.34 0.02
47_L 41_M 0.80 0.34 0.02
118_L 69_M 0.79 0.33 0.02
145_G 179_S 0.78 0.32 0.02
78_T 71_L 0.78 0.32 0.02
59_H 79_S 0.78 0.32 0.02
59_H 180_Y 0.77 0.31 0.02
109_I 121_K 0.76 0.31 0.02
82_P 195_S 0.75 0.30 0.02
202_S 30_R 0.75 0.29 0.02
131_I 79_S 0.75 0.29 0.02
185_S 67_T 0.75 0.29 0.02
192_A 30_R 0.75 0.29 0.02
113_E 78_A 0.75 0.29 0.02
234_V 18_F 0.74 0.28 0.02
78_T 40_N 0.73 0.28 0.02
10_V 75_V 0.73 0.28 0.02
350_A 77_G 0.73 0.28 0.02
71_A 79_S 0.73 0.28 0.02
106_T 37_H 0.73 0.27 0.02
123_G 95_Q 0.73 0.27 0.02
224_R 60_I 0.72 0.27 0.02
125_K 163_S 0.72 0.27 0.01
279_A 167_S 0.71 0.25 0.01
117_E 89_R 0.70 0.25 0.01
322_L 109_F 0.70 0.25 0.01
295_V 198_F 0.70 0.24 0.01
103_K 180_Y 0.70 0.24 0.01
65_Q 94_T 0.69 0.24 0.01
170_D 13_R 0.69 0.24 0.01
24_S 116_V 0.69 0.24 0.01
151_N 35_A 0.69 0.24 0.01
290_S 81_P 0.68 0.23 0.01
216_I 79_S 0.68 0.23 0.01
11_L 203_L 0.68 0.23 0.01
209_E 92_Q 0.67 0.22 0.01
62_Y 91_A 0.67 0.22 0.01
149_V 45_F 0.67 0.22 0.01
152_T 180_Y 0.67 0.22 0.01
136_A 191_P 0.66 0.21 0.01
243_V 151_P 0.66 0.21 0.01
109_I 82_L 0.65 0.21 0.01
198_A 39_L 0.65 0.21 0.01
281_V 13_R 0.65 0.21 0.01
102_I 180_Y 0.65 0.21 0.01
142_Y 78_A 0.65 0.21 0.01
330_T 144_S 0.65 0.21 0.01
118_L 73_S 0.65 0.21 0.01
56_E 81_P 0.65 0.20 0.01
106_T 195_S 0.64 0.20 0.01
292_L 200_M 0.64 0.20 0.01
73_P 43_R 0.64 0.20 0.01
59_H 40_N 0.64 0.20 0.01
78_T 175_K 0.64 0.20 0.01
17_G 76_G 0.64 0.20 0.01
155_I 7_I 0.64 0.20 0.01
109_I 43_R 0.64 0.20 0.01
170_D 155_E 0.64 0.20 0.01
176_G 156_A 0.63 0.19 0.01
279_A 8_V 0.62 0.19 0.01
141_L 78_A 0.62 0.18 0.01
152_T 77_G 0.62 0.18 0.01
70_G 18_F 0.61 0.18 0.01
109_I 195_S 0.61 0.18 0.01
84_K 78_A 0.61 0.18 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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