May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
3PNL_AB
Genes: A B A+B
Length: 355 209 535
Sequences: 1023 1128 553
Seq/Len: 2.88 5.4 1.03
MirrorTree (Pazo et al. 2001) 0.69
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 0.94
2 0.08 0.04 0.96
5 0.11 0.04 0.98
10 0.11 0.04 0.98
20 0.11 0.05 0.98
100 0.12 0.05 0.98
∞ 0.15 0.09 0.99
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
78_T 78_A 1.52 0.79 0.03
121_D 88_I 1.42 0.72 0.02
78_T 71_L 1.28 0.60 0.02
123_G 95_Q 1.25 0.57 0.01
113_E 119_R 1.21 0.53 0.01
118_L 88_I 1.19 0.52 0.01
117_E 119_R 1.17 0.50 0.01
202_S 30_R 1.17 0.50 0.01
78_T 32_I 1.15 0.48 0.01
59_H 180_Y 1.14 0.47 0.01
150_A 35_A 1.11 0.45 0.01
82_P 37_H 1.07 0.41 0.01
56_E 37_H 1.06 0.40 0.01
113_E 121_K 1.06 0.40 0.01
56_E 77_G 1.05 0.39 0.01
106_T 180_Y 1.05 0.39 0.01
71_A 79_S 1.03 0.38 0.01
56_E 76_G 1.01 0.36 0.01
103_K 180_Y 1.01 0.35 0.01
78_T 43_R 1.00 0.35 0.01
56_E 81_P 0.99 0.34 0.01
82_P 129_M 0.96 0.32 0.01
290_S 81_P 0.96 0.31 0.01
81_T 81_P 0.95 0.30 0.01
75_E 71_L 0.92 0.28 0.01
289_L 111_D 0.92 0.28 0.01
59_H 79_S 0.91 0.28 0.01
103_K 40_N 0.91 0.27 0.01
11_L 68_G 0.91 0.27 0.01
350_A 77_G 0.89 0.26 0.01
82_P 195_S 0.89 0.26 0.01
59_H 40_N 0.89 0.26 0.01
103_K 79_S 0.88 0.25 0.01
170_D 103_E 0.88 0.25 0.01
296_Y 171_M 0.88 0.25 0.01
137_V 73_S 0.87 0.24 0.01
290_S 37_H 0.86 0.24 0.00
332_L 121_K 0.86 0.24 0.00
276_R 133_W 0.86 0.24 0.00
136_A 191_P 0.86 0.24 0.00
210_M 41_M 0.85 0.23 0.00
131_I 79_S 0.85 0.23 0.00
200_K 27_G 0.85 0.23 0.00
156_E 40_N 0.85 0.23 0.00
170_D 155_E 0.84 0.23 0.00
152_T 180_Y 0.84 0.23 0.00
56_E 195_S 0.84 0.23 0.00
34_V 200_M 0.83 0.22 0.00
75_E 43_R 0.83 0.22 0.00
117_E 126_D 0.83 0.22 0.00
110_L 140_L 0.83 0.22 0.00
70_G 18_F 0.83 0.22 0.00
78_T 195_S 0.83 0.22 0.00
49_S 40_N 0.82 0.21 0.00
112_F 120_G 0.82 0.21 0.00
174_E 146_Q 0.82 0.21 0.00
46_A 51_K 0.82 0.21 0.00
119_L 45_F 0.82 0.21 0.00
6_D 147_N 0.82 0.21 0.00
336_D 149_S 0.82 0.21 0.00
214_V 71_L 0.81 0.21 0.00
114_T 115_G 0.81 0.21 0.00
49_S 79_S 0.81 0.20 0.00
227_F 130_C 0.80 0.20 0.00
71_A 77_G 0.80 0.20 0.00
78_T 74_S 0.80 0.20 0.00
78_T 40_N 0.80 0.20 0.00
56_E 79_S 0.80 0.20 0.00
114_T 72_L 0.80 0.20 0.00
122_S 99_S 0.80 0.20 0.00
216_I 79_S 0.79 0.20 0.00
152_T 40_N 0.79 0.20 0.00
137_V 188_H 0.79 0.20 0.00
103_K 175_K 0.79 0.19 0.00
53_S 39_L 0.78 0.19 0.00
106_T 81_P 0.78 0.19 0.00
309_T 109_F 0.78 0.19 0.00
113_E 78_A 0.78 0.19 0.00
325_T 200_M 0.77 0.18 0.00
85_I 101_T 0.77 0.18 0.00
78_T 37_H 0.77 0.18 0.00
125_K 11_L 0.77 0.18 0.00
37_A 142_Q 0.77 0.18 0.00
152_T 79_S 0.77 0.18 0.00
189_A 191_P 0.77 0.18 0.00
18_L 41_M 0.77 0.18 0.00
33_Y 100_L 0.76 0.18 0.00
230_L 161_A 0.76 0.18 0.00
152_T 77_G 0.76 0.18 0.00
78_T 175_K 0.76 0.18 0.00
15_L 138_E 0.76 0.18 0.00
9_D 138_E 0.75 0.17 0.00
68_L 180_Y 0.75 0.17 0.00
350_A 84_G 0.75 0.17 0.00
121_D 92_Q 0.75 0.17 0.00
187_G 184_R 0.75 0.17 0.00
329_I 47_K 0.74 0.17 0.00
190_L 25_L 0.74 0.17 0.00
322_L 179_S 0.74 0.17 0.00
109_I 82_L 0.74 0.17 0.00
70_G 61_G 0.74 0.17 0.00
151_N 35_A 0.74 0.17 0.00
83_D 175_K 0.74 0.17 0.00
50_G 120_G 0.73 0.16 0.00
49_S 76_G 0.73 0.16 0.00
102_I 180_Y 0.73 0.16 0.00
305_Q 103_E 0.73 0.16 0.00
59_H 175_K 0.73 0.16 0.00
106_T 37_H 0.72 0.16 0.00
13_E 201_Q 0.72 0.16 0.00
78_T 79_S 0.72 0.16 0.00
327_F 26_T 0.72 0.16 0.00
198_A 92_Q 0.72 0.16 0.00
281_V 169_I 0.72 0.16 0.00
114_T 81_P 0.72 0.15 0.00
194_T 182_G 0.72 0.15 0.00
153_V 91_A 0.71 0.15 0.00
158_L 154_L 0.71 0.15 0.00
156_E 77_G 0.71 0.15 0.00
153_V 124_P 0.71 0.15 0.00
220_P 32_I 0.71 0.15 0.00
99_L 7_I 0.70 0.15 0.00
295_V 198_F 0.70 0.15 0.00
56_E 72_L 0.70 0.15 0.00
334_V 18_F 0.70 0.15 0.00
15_L 122_A 0.70 0.15 0.00
82_P 32_I 0.70 0.15 0.00
204_T 5_T 0.70 0.15 0.00
143_T 195_S 0.70 0.15 0.00
202_S 133_W 0.70 0.15 0.00
71_A 40_N 0.70 0.15 0.00
113_E 32_I 0.70 0.14 0.00
82_P 188_H 0.69 0.14 0.00
25_L 67_T 0.69 0.14 0.00
137_V 180_Y 0.69 0.14 0.00
69_S 161_A 0.69 0.14 0.00
145_G 175_K 0.69 0.14 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
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
Page generated in 0.2977 seconds.