May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
2qi9_A_C
Genes: A B A+B
Length: 326 249 530
Sequences: 6627 71358 4515
Seq/Len: 20.33 286.58 8.52
MirrorTree (Pazo et al. 2001) 0.23
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 0.36 0.10 5.78
2 0.37 0.11 6.92
5 0.37 0.14 7.18
10 0.37 0.19 7.40
20 0.38 0.23 7.85
100 0.39 0.34 8.83
∞ 0.43 0.36 9.18
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
219_I 44_A 2.41 1.00 1.00
213_M 99_H 1.16 0.96 0.76
270_T 88_T 1.01 0.91 0.61
223_Q 77_Y 0.99 0.90 0.59
219_I 49_M 0.97 0.88 0.56
220_S 139_A 0.93 0.85 0.51
223_Q 49_M 0.80 0.71 0.35
227_P 68_A 0.78 0.68 0.32
224_L 100_D 0.71 0.57 0.24
222_R 68_A 0.68 0.52 0.21
220_S 79_S 0.66 0.49 0.20
216_L 93_Y 0.65 0.48 0.18
256_I 210_K 0.65 0.47 0.18
308_V 140_V 0.60 0.40 0.14
216_L 124_T 0.56 0.33 0.11
102_I 93_Y 0.55 0.33 0.11
222_R 49_M 0.55 0.32 0.11
29_L 178_A 0.55 0.31 0.10
292_I 78_L 0.54 0.31 0.10
175_L 230_Y 0.54 0.31 0.10
89_G 37_A 0.54 0.31 0.10
100_G 230_Y 0.54 0.30 0.10
276_L 67_S 0.54 0.30 0.10
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 0.0595 seconds.