May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
YidC-sol Skp
Genes: A B A+B
Length: 321 161 451
Sequences: 1608 1586 516
Seq/Len: 5.01 9.85 1.14
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 0.07 0.16 0.00
2 0.07 0.16 0.00
5 0.07 0.17 0.00
10 0.07 0.17 0.01
20 0.07 0.17 0.01
100 0.07 0.17 0.05
∞ 0.07 0.17 1.07
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
156_V 146_S 1.37 0.71 0.01
63_Y 25_A 1.31 0.66 0.01
293_M 105_R 1.31 0.66 0.01
143_L 71_L 1.23 0.59 0.01
36_L 120_I 1.22 0.58 0.01
107_Y 79_D 1.20 0.56 0.01
151_N 155_D 1.20 0.56 0.01
34_G 157_L 1.19 0.55 0.01
308_W 18_A 1.16 0.52 0.00
194_F 94_F 1.16 0.52 0.00
289_I 23_K 1.14 0.50 0.00
64_P 27_V 1.12 0.48 0.00
37_I 129_N 1.11 0.47 0.00
253_A 105_R 1.09 0.46 0.00
155_N 32_L 1.06 0.42 0.00
165_E 124_V 1.05 0.42 0.00
109_V 10_L 1.05 0.42 0.00
137_F 144_Y 1.03 0.40 0.00
207_E 63_D 1.03 0.40 0.00
42_D 137_V 1.03 0.40 0.00
47_T 126_S 1.02 0.39 0.00
309_L 136_V 1.02 0.39 0.00
34_G 79_D 1.02 0.39 0.00
229_V 63_D 1.01 0.38 0.00
39_V 99_Q 1.01 0.38 0.00
120_Q 56_E 1.01 0.38 0.00
193_T 47_E 1.00 0.37 0.00
284_W 155_D 0.99 0.36 0.00
255_L 86_D 0.98 0.35 0.00
45_D 77_G 0.97 0.34 0.00
210_K 123_A 0.96 0.34 0.00
215_A 136_V 0.94 0.32 0.00
311_F 156_V 0.94 0.32 0.00
303_T 52_G 0.93 0.31 0.00
73_F 46_L 0.93 0.31 0.00
124_Q 99_Q 0.92 0.30 0.00
212_D 137_V 0.92 0.30 0.00
32_G 78_S 0.92 0.30 0.00
241_I 111_E 0.91 0.30 0.00
133_A 137_V 0.91 0.30 0.00
264_Y 152_I 0.91 0.30 0.00
47_T 28_N 0.91 0.29 0.00
53_G 144_Y 0.91 0.29 0.00
295_A 123_A 0.91 0.29 0.00
226_G 120_I 0.91 0.29 0.00
133_A 40_T 0.91 0.29 0.00
118_E 78_S 0.90 0.29 0.00
170_G 23_K 0.90 0.28 0.00
147_D 25_A 0.90 0.28 0.00
48_I 35_Q 0.90 0.28 0.00
78_T 28_N 0.89 0.28 0.00
295_A 62_T 0.89 0.28 0.00
293_M 30_G 0.89 0.28 0.00
143_L 48_N 0.89 0.28 0.00
212_D 90_Q 0.89 0.28 0.00
47_T 133_I 0.89 0.28 0.00
305_D 28_N 0.89 0.28 0.00
115_V 136_V 0.88 0.27 0.00
235_Y 153_T 0.88 0.27 0.00
124_Q 136_V 0.88 0.27 0.00
241_I 10_L 0.88 0.27 0.00
320_L 74_M 0.88 0.27 0.00
69_S 132_D 0.88 0.27 0.00
49_N 90_Q 0.88 0.27 0.00
230_A 120_I 0.87 0.27 0.00
37_I 99_Q 0.87 0.26 0.00
93_R 127_V 0.87 0.26 0.00
68_N 67_K 0.87 0.26 0.00
281_S 144_Y 0.87 0.26 0.00
295_A 124_V 0.86 0.26 0.00
34_G 32_L 0.86 0.26 0.00
141_F 36_V 0.86 0.26 0.00
319_L 136_V 0.86 0.26 0.00
150_V 44_N 0.86 0.25 0.00
104_R 36_V 0.86 0.25 0.00
207_E 136_V 0.85 0.25 0.00
229_V 46_L 0.85 0.24 0.00
278_A 147_S 0.85 0.24 0.00
47_T 64_L 0.84 0.24 0.00
39_V 77_G 0.84 0.24 0.00
125_V 101_F 0.84 0.24 0.00
43_V 67_K 0.84 0.24 0.00
67_L 161_K 0.84 0.24 0.00
107_Y 55_S 0.84 0.24 0.00
51_R 89_A 0.84 0.24 0.00
42_D 27_V 0.84 0.24 0.00
55_V 89_A 0.84 0.24 0.00
137_F 81_T 0.84 0.24 0.00
263_G 50_F 0.83 0.24 0.00
204_E 158_K 0.83 0.24 0.00
293_M 157_L 0.83 0.23 0.00
159_A 135_L 0.83 0.23 0.00
311_F 146_S 0.83 0.23 0.00
79_S 34_Q 0.83 0.23 0.00
319_L 128_A 0.82 0.23 0.00
230_A 125_K 0.82 0.23 0.00
39_V 118_T 0.82 0.23 0.00
280_N 75_K 0.82 0.23 0.00
194_F 52_G 0.82 0.23 0.00
228_W 111_E 0.82 0.23 0.00
170_G 54_A 0.81 0.22 0.00
237_A 65_Q 0.81 0.22 0.00
245_D 156_V 0.81 0.22 0.00
109_V 44_N 0.81 0.22 0.00
218_E 132_D 0.80 0.22 0.00
73_F 155_D 0.80 0.21 0.00
244_N 137_V 0.80 0.21 0.00
241_I 135_L 0.80 0.21 0.00
160_G 129_N 0.80 0.21 0.00
74_Q 84_E 0.80 0.21 0.00
311_F 28_N 0.79 0.21 0.00
73_F 74_M 0.79 0.21 0.00
208_K 134_D 0.79 0.21 0.00
50_T 157_L 0.79 0.21 0.00
265_K 25_A 0.79 0.21 0.00
293_M 107_R 0.79 0.21 0.00
106_L 73_S 0.79 0.20 0.00
239_A 95_A 0.79 0.20 0.00
102_G 120_I 0.79 0.20 0.00
244_N 19_Q 0.79 0.20 0.00
62_A 152_I 0.78 0.20 0.00
153_N 12_L 0.78 0.20 0.00
218_E 93_T 0.78 0.20 0.00
237_A 161_K 0.78 0.20 0.00
73_F 145_N 0.78 0.20 0.00
162_K 126_S 0.78 0.20 0.00
178_L 129_N 0.78 0.20 0.00
150_V 107_R 0.78 0.20 0.00
35_K 157_L 0.78 0.20 0.00
306_Y 108_R 0.78 0.20 0.00
277_G 132_D 0.78 0.20 0.00
230_A 128_A 0.78 0.20 0.00
254_N 153_T 0.78 0.20 0.00
99_P 64_L 0.78 0.20 0.00
200_S 39_K 0.78 0.20 0.00
304_V 30_G 0.77 0.20 0.00
209_Y 113_R 0.77 0.20 0.00
138_T 20_A 0.77 0.20 0.00
76_L 28_N 0.77 0.20 0.00
247_T 63_D 0.77 0.20 0.00
156_V 123_A 0.77 0.20 0.00
46_L 67_K 0.77 0.20 0.00
70_T 131_Q 0.77 0.19 0.00
71_Q 32_L 0.77 0.19 0.00
284_W 105_R 0.77 0.19 0.00
64_P 58_Q 0.77 0.19 0.00
276_T 136_V 0.77 0.19 0.00
148_Y 65_Q 0.77 0.19 0.00
204_E 157_L 0.77 0.19 0.00
221_N 147_S 0.76 0.19 0.00
37_I 55_S 0.76 0.19 0.00
120_Q 149_V 0.76 0.19 0.00
163_P 135_L 0.76 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
11210 0.01 YidC-sol Skp Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
11200 1.14 YidC-sol Skp Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.01 Done
Page generated in 0.2609 seconds.