May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
pred_1A2K_l_u_ApdbAfas_1A2K_r_u_ApdbAfastable_PRtxt
Genes: A B A+B
Length: 202 125 290
Sequences: 9108 919 51
Seq/Len: 45.09 7.35 0.18
MirrorTree (Pazo et al. 2001) 0.22
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 0.04 0.05 0.02
2 0.05 0.05 0.02
5 0.06 0.05 0.06
10 0.08 0.05 0.09
20 0.10 0.05 0.16
100 0.18 0.05 0.59
∞ 0.25 0.07 1.30
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
128_A 55_L 1.51 0.30 0.00
102_D 82_S 1.47 0.28 0.00
28_G 80_I 1.45 0.28 0.00
82_I 38_L 1.38 0.24 0.00
26_L 82_S 1.36 0.23 0.00
9_V 82_S 1.30 0.21 0.00
149_N 82_S 1.24 0.19 0.00
75_Y 116_D 1.23 0.19 0.00
21_F 94_P 1.22 0.18 0.00
65_E 82_S 1.21 0.18 0.00
73_G 106_N 1.20 0.17 0.00
21_F 95_I 1.15 0.16 0.00
47_F 117_M 1.12 0.15 0.00
154_K 82_S 1.11 0.15 0.00
120_D 86_G 1.09 0.14 0.00
19_T 77_D 1.08 0.14 0.00
109_N 55_L 1.07 0.14 0.00
61_T 104_L 1.05 0.13 0.00
114_L 25_R 1.05 0.13 0.00
65_E 92_E 1.02 0.12 0.00
106_V 92_E 1.01 0.12 0.00
102_D 75_T 1.01 0.12 0.00
20_T 112_V 1.01 0.12 0.00
117_N 42_G 0.99 0.12 0.00
32_K 92_E 0.98 0.11 0.00
146_A 104_L 0.98 0.11 0.00
118_K 86_G 0.97 0.11 0.00
154_K 98_F 0.96 0.11 0.00
113_V 57_S 0.96 0.11 0.00
11_V 14_I 0.96 0.11 0.00
145_S 86_G 0.96 0.11 0.00
85_F 53_E 0.95 0.11 0.00
12_G 86_G 0.95 0.10 0.00
17_G 86_G 0.95 0.10 0.00
18_K 86_G 0.95 0.10 0.00
86_D 58_L 0.95 0.10 0.00
120_D 47_G 0.94 0.10 0.00
24_R 111_W 0.94 0.10 0.00
96_V 31_I 0.94 0.10 0.00
154_K 28_L 0.94 0.10 0.00
115_C 100_Q 0.94 0.10 0.00
120_D 13_F 0.94 0.10 0.00
120_D 18_Y 0.94 0.10 0.00
60_D 86_G 0.93 0.10 0.00
80_C 38_L 0.93 0.10 0.00
146_A 98_F 0.93 0.10 0.00
25_H 64_Q 0.93 0.10 0.00
10_L 29_G 0.92 0.10 0.00
92_T 23_N 0.92 0.10 0.00
61_T 113_C 0.92 0.10 0.00
149_N 67_I 0.91 0.10 0.00
54_I 93_D 0.91 0.10 0.00
120_D 71_D 0.90 0.09 0.00
83_I 31_I 0.90 0.09 0.00
75_Y 100_Q 0.90 0.09 0.00
57_N 88_L 0.90 0.09 0.00
93_Y 28_L 0.89 0.09 0.00
67_Y 42_G 0.89 0.09 0.00
63_G 32_Y 0.89 0.09 0.00
55_K 98_F 0.88 0.09 0.00
141_Y 38_L 0.88 0.09 0.00
159_L 49_A 0.87 0.09 0.00
92_T 31_I 0.87 0.09 0.00
93_Y 34_D 0.87 0.09 0.00
56_F 74_P 0.86 0.09 0.00
115_C 119_R 0.86 0.09 0.00
92_T 103_L 0.86 0.09 0.00
126_V 67_I 0.86 0.09 0.00
145_S 119_R 0.86 0.09 0.00
103_L 57_S 0.85 0.09 0.00
114_L 112_V 0.85 0.08 0.00
96_V 20_L 0.83 0.08 0.00
46_V 12_S 0.83 0.08 0.00
115_C 92_E 0.83 0.08 0.00
45_L 15_Q 0.83 0.08 0.00
19_T 38_L 0.83 0.08 0.00
146_A 86_G 0.82 0.08 0.00
146_A 47_G 0.82 0.08 0.00
119_V 14_I 0.81 0.08 0.00
86_D 56_S 0.81 0.08 0.00
19_T 102_F 0.81 0.08 0.00
120_D 102_F 0.81 0.08 0.00
9_V 110_A 0.81 0.08 0.00
95_N 82_S 0.81 0.08 0.00
114_L 22_D 0.81 0.08 0.00
120_D 32_Y 0.81 0.08 0.00
121_I 70_Q 0.81 0.08 0.00
63_G 102_F 0.80 0.08 0.00
6_F 64_Q 0.80 0.08 0.00
148_S 98_F 0.80 0.08 0.00
150_Y 121_A 0.80 0.08 0.00
145_S 47_G 0.80 0.07 0.00
12_G 47_G 0.79 0.07 0.00
17_G 47_G 0.79 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 0.429 seconds.