May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
1jwh
Genes: A B A+B
Length: 337 215 507
Sequences: 20490 448 80
Seq/Len: 60.8 2.08 0.16
MirrorTree (Pazo et al. 2001) 0.17
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 0.06 0.02 0.01
2 0.09 0.02 0.01
5 0.11 0.03 0.03
10 0.14 0.03 0.06
20 0.18 0.03 0.14
100 0.28 0.04 0.47
∞ 0.33 0.06 0.71
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
50_Y 174_Y 1.49 0.27 0.00
121_F 158_Y 1.38 0.23 0.00
200_P 144_Y 1.19 0.16 0.00
323_Y 139_K 1.18 0.16 0.00
305_L 90_T 1.16 0.15 0.00
111_L 23_C 1.15 0.15 0.00
226_I 101_Y 1.13 0.14 0.00
219_G 106_F 1.08 0.13 0.00
42_V 87_Y 1.05 0.12 0.00
47_R 162_G 1.04 0.12 0.00
155_R 123_G 1.04 0.12 0.00
96_T 101_Y 1.02 0.11 0.00
121_F 97_M 1.00 0.11 0.00
50_Y 28_D 1.00 0.11 0.00
78_I 21_F 0.99 0.11 0.00
143_A 87_Y 0.98 0.10 0.00
250_G 46_Y 0.97 0.10 0.00
94_I 99_E 0.96 0.10 0.00
300_F 108_Y 0.96 0.10 0.00
195_R 183_F 0.96 0.10 0.00
91_G 66_P 0.94 0.10 0.00
209_Y 191_K 0.94 0.10 0.00
246_A 21_F 0.94 0.10 0.00
171_L 99_E 0.94 0.10 0.00
327_V 187_L 0.94 0.10 0.00
70_L 72_I 0.93 0.10 0.00
155_R 81_G 0.93 0.10 0.00
316_R 143_V 0.93 0.09 0.00
53_V 86_R 0.93 0.09 0.00
45_L 166_M 0.92 0.09 0.00
164_I 87_Y 0.92 0.09 0.00
96_T 25_V 0.91 0.09 0.00
305_L 82_L 0.91 0.09 0.00
328_V 164_P 0.90 0.09 0.00
84_I 167_L 0.90 0.09 0.00
176_W 89_L 0.90 0.09 0.00
92_P 18_G 0.89 0.09 0.00
57_I 118_P 0.89 0.09 0.00
81_E 53_I 0.89 0.09 0.00
176_W 35_N 0.89 0.09 0.00
247_K 158_Y 0.89 0.09 0.00
179_A 169_M 0.89 0.09 0.00
218_L 28_D 0.88 0.09 0.00
299_D 162_G 0.88 0.09 0.00
121_F 82_L 0.88 0.09 0.00
48_G 144_Y 0.88 0.09 0.00
219_G 163_F 0.88 0.09 0.00
56_A 99_E 0.88 0.09 0.00
156_D 109_C 0.87 0.08 0.00
156_D 114_C 0.87 0.08 0.00
156_D 121_P 0.87 0.08 0.00
156_D 137_C 0.87 0.08 0.00
156_D 156_G 0.87 0.08 0.00
156_D 160_G 0.87 0.08 0.00
214_D 109_C 0.87 0.08 0.00
214_D 114_C 0.87 0.08 0.00
214_D 121_P 0.87 0.08 0.00
214_D 137_C 0.87 0.08 0.00
214_D 156_G 0.87 0.08 0.00
214_D 160_G 0.87 0.08 0.00
312_R 109_C 0.87 0.08 0.00
312_R 114_C 0.87 0.08 0.00
312_R 121_P 0.87 0.08 0.00
312_R 137_C 0.87 0.08 0.00
312_R 156_G 0.87 0.08 0.00
312_R 160_G 0.87 0.08 0.00
165_D 113_Y 0.87 0.08 0.00
42_V 92_R 0.86 0.08 0.00
112_V 183_F 0.86 0.08 0.00
114_E 105_D 0.86 0.08 0.00
210_D 87_Y 0.86 0.08 0.00
171_L 90_T 0.86 0.08 0.00
186_Q 72_I 0.86 0.08 0.00
284_F 162_G 0.86 0.08 0.00
172_R 131_A 0.86 0.08 0.00
162_V 99_E 0.86 0.08 0.00
114_E 122_I 0.85 0.08 0.00
81_E 189_G 0.85 0.08 0.00
318_A 12_W 0.85 0.08 0.00
300_F 162_G 0.85 0.08 0.00
223_A 171_H 0.84 0.08 0.00
203_L 89_L 0.84 0.08 0.00
134_R 15_G 0.84 0.08 0.00
50_Y 98_L 0.84 0.08 0.00
81_E 120_L 0.84 0.08 0.00
242_L 83_I 0.84 0.08 0.00
137_M 168_F 0.84 0.08 0.00
237_D 50_L 0.83 0.08 0.00
240_D 46_Y 0.83 0.08 0.00
175_D 144_Y 0.83 0.08 0.00
231_P 22_F 0.82 0.08 0.00
112_V 96_Q 0.82 0.08 0.00
202_L 92_R 0.82 0.07 0.00
216_W 83_I 0.82 0.07 0.00
213_L 139_K 0.82 0.07 0.00
300_F 183_F 0.82 0.07 0.00
216_W 84_H 0.81 0.07 0.00
216_W 93_G 0.81 0.07 0.00
148_H 111_R 0.81 0.07 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)
Page generated in 0.0697 seconds.