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pred_1GPW_l_u_FpdbFfas_1GPW_r_u_DpdbDfastable_PRtxt

Genes: A B A+B
Length: 200 79 269
Sequences: 15281 1396 1892
Seq/Len: 76.41 17.67 7.03
MirrorTree (Pazo et al. 2001) 0.37
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 0.09 1.44
2 0.03 0.09 5.43
5 0.03 0.09 6.49
10 0.04 0.09 6.68
20 0.05 0.09 6.78
100 0.12 0.10 7.27
0.20 0.11 8.32
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
136_Y 3_A 3.02 1.00 1.00
187_R 74_D 1.99 1.00 0.99
22_R 74_D 1.85 1.00 0.98
124_N 2_L 1.35 0.98 0.88
183_S 75_I 1.12 0.93 0.73
183_S 40_S 1.11 0.93 0.72
14_M 71_E 1.09 0.92 0.70
121_M 2_L 0.98 0.85 0.58
184_K 40_S 0.96 0.84 0.56
158_Y 2_L 0.95 0.83 0.55
125_E 3_A 0.90 0.78 0.48
184_K 41_E 0.88 0.76 0.46
14_M 67_E 0.78 0.62 0.33
137_Y 70_A 0.77 0.60 0.31
21_K 71_E 0.76 0.58 0.30
83_V 7_I 0.75 0.58 0.29
183_S 35_L 0.74 0.56 0.28
53_H 17_V 0.73 0.55 0.27
91_F 73_I 0.71 0.51 0.24
94_S 22_N 0.70 0.50 0.23
130_D 60_K 0.69 0.48 0.22
113_L 2_L 0.69 0.48 0.22
120_H 70_A 0.69 0.48 0.22
22_R 72_Q 0.68 0.47 0.21
21_K 55_S 0.67 0.46 0.21
163_F 2_L 0.67 0.46 0.20
56_E 12_V 0.65 0.43 0.19
5_I 75_I 0.65 0.42 0.18
174_G 35_L 0.65 0.41 0.18
174_G 29_S 0.64 0.41 0.18
18_R 28_D 0.64 0.40 0.17
140_V 78_T 0.64 0.40 0.17
23_A 77_F 0.63 0.40 0.17
9_G 18_V 0.63 0.40 0.17
11_G 32_P 0.62 0.38 0.16
10_P 66_V 0.61 0.36 0.15
59_R 41_E 0.61 0.36 0.15
87_M 65_L 0.59 0.34 0.14
97_A 77_F 0.59 0.34 0.14
152_V 77_F 0.59 0.33 0.13
145_A 35_L 0.59 0.33 0.13
18_R 50_L 0.58 0.32 0.13
80_V 66_V 0.58 0.32 0.13
115_S 73_I 0.58 0.32 0.12
88_Q 43_G 0.58 0.32 0.12
132_F 67_E 0.57 0.31 0.12
188_K 41_E 0.57 0.31 0.12
189_L 75_I 0.57 0.31 0.12
154_G 41_E 0.57 0.30 0.12
60_R 3_A 0.56 0.30 0.12
87_M 40_S 0.56 0.29 0.11
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)

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