May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
SO0547-amtB
Genes: A B A+B
Length: 230 408 582
Sequences: 781 3983 332
Seq/Len: 3.4 9.76 0.57
MirrorTree (Pazo et al. 2001) 0.24
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 0.03 0.02 0.02
2 0.04 0.04 0.18
5 0.04 0.04 0.22
10 0.04 0.05 0.22
20 0.04 0.05 0.23
100 0.06 0.06 0.28
∞ 0.15 0.13 0.52
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
25_V 335_M 1.32 0.46 0.00
67_A 328_V 1.19 0.36 0.00
43_T 377_I 1.17 0.35 0.00
193_V 54_A 1.15 0.33 0.00
191_Y 265_A 1.07 0.28 0.00
193_V 62_L 1.05 0.26 0.00
61_F 281_I 1.04 0.26 0.00
212_D 350_L 1.03 0.25 0.00
224_Y 354_A 0.98 0.22 0.00
56_S 179_L 0.97 0.22 0.00
86_Y 371_L 0.96 0.21 0.00
75_D 293_A 0.94 0.20 0.00
134_I 201_N 0.94 0.20 0.00
27_G 348_A 0.91 0.19 0.00
187_N 366_A 0.91 0.19 0.00
225_S 315_K 0.87 0.17 0.00
31_G 265_A 0.86 0.17 0.00
113_D 211_I 0.86 0.17 0.00
224_Y 198_P 0.85 0.16 0.00
159_F 347_T 0.84 0.16 0.00
123_W 245_T 0.84 0.15 0.00
50_Q 303_L 0.83 0.15 0.00
61_F 134_M 0.83 0.15 0.00
226_Y 351_T 0.83 0.15 0.00
227_S 129_V 0.83 0.15 0.00
29_I 10_L 0.83 0.15 0.00
228_F 293_A 0.82 0.15 0.00
193_V 371_L 0.82 0.15 0.00
86_Y 270_I 0.82 0.15 0.00
51_G 371_L 0.82 0.15 0.00
225_S 134_M 0.81 0.14 0.00
30_G 280_A 0.80 0.14 0.00
62_Y 120_E 0.80 0.14 0.00
29_I 364_S 0.79 0.14 0.00
218_A 362_S 0.79 0.14 0.00
120_T 123_K 0.78 0.13 0.00
157_A 346_I 0.78 0.13 0.00
55_Y 201_N 0.78 0.13 0.00
51_G 204_M 0.78 0.13 0.00
29_I 251_A 0.78 0.13 0.00
61_F 178_V 0.78 0.13 0.00
152_Y 359_W 0.78 0.13 0.00
90_I 151_F 0.77 0.13 0.00
204_I 204_M 0.77 0.13 0.00
107_D 114_V 0.77 0.13 0.00
223_G 244_N 0.77 0.13 0.00
140_V 298_L 0.77 0.13 0.00
223_G 188_Y 0.76 0.13 0.00
47_V 62_L 0.76 0.13 0.00
122_T 188_Y 0.76 0.12 0.00
223_G 18_S 0.75 0.12 0.00
100_Y 358_A 0.75 0.12 0.00
159_F 300_A 0.75 0.12 0.00
61_F 160_F 0.75 0.12 0.00
100_Y 285_P 0.75 0.12 0.00
138_E 301_G 0.75 0.12 0.00
193_V 58_V 0.74 0.12 0.00
212_D 253_S 0.74 0.12 0.00
125_W 352_G 0.74 0.12 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 0.0774 seconds.