May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
3R9J-3
Genes: A B A+B
Length: 257 70 306
Sequences: 15475 723 584
Seq/Len: 60.21 10.33 1.91
MirrorTree (Pazo et al. 2001) 0.76
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 0.02 0.10 1.79
2 0.03 0.10 1.79
5 0.03 0.10 1.79
10 0.05 0.10 1.79
20 0.06 0.10 1.79
100 0.11 0.10 1.81
∞ 0.18 0.10 1.85
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
235_G 14_V 1.50 0.91 0.39
3_I 14_V 1.46 0.89 0.36
149_V 16_E 1.21 0.72 0.19
191_D 15_A 1.19 0.71 0.18
149_V 13_I 1.12 0.64 0.14
236_K 14_V 1.09 0.61 0.13
36_I 12_N 1.09 0.60 0.13
78_R 14_V 1.08 0.59 0.12
22_I 20_S 1.06 0.58 0.12
78_R 7_K 1.05 0.57 0.11
60_V 30_L 1.05 0.57 0.11
36_I 32_K 1.04 0.56 0.11
3_I 2_T 1.04 0.55 0.11
60_V 45_D 1.04 0.55 0.11
18_S 67_V 1.03 0.55 0.11
71_Q 25_H 1.03 0.55 0.11
78_R 45_D 1.03 0.55 0.10
205_K 15_A 1.01 0.52 0.10
33_T 31_R 1.00 0.51 0.09
198_V 31_R 0.99 0.49 0.09
115_F 4_N 0.98 0.48 0.09
22_I 3_A 0.97 0.47 0.08
16_T 17_R 0.94 0.45 0.08
86_P 61_S 0.94 0.45 0.08
75_K 27_L 0.93 0.44 0.07
6_V 54_E 0.93 0.43 0.07
101_V 65_L 0.93 0.43 0.07
220_S 14_V 0.92 0.42 0.07
120_S 11_Q 0.91 0.41 0.07
163_S 55_Q 0.91 0.41 0.07
26_L 14_V 0.91 0.41 0.07
109_K 53_L 0.90 0.40 0.06
6_V 67_V 0.90 0.40 0.06
245_L 61_S 0.89 0.39 0.06
196_E 48_M 0.88 0.38 0.06
139_I 29_Q 0.88 0.38 0.06
47_L 65_L 0.88 0.38 0.06
120_S 7_K 0.88 0.37 0.06
216_V 12_N 0.87 0.37 0.06
235_G 12_N 0.87 0.37 0.06
115_F 25_H 0.87 0.36 0.06
146_V 6_A 0.86 0.36 0.06
75_K 67_V 0.86 0.36 0.05
99_E 55_Q 0.86 0.36 0.05
216_V 30_L 0.85 0.35 0.05
6_V 42_V 0.85 0.35 0.05
252_F 60_I 0.85 0.34 0.05
129_L 13_I 0.85 0.34 0.05
129_L 59_D 0.84 0.34 0.05
139_I 66_N 0.84 0.34 0.05
21_A 61_S 0.84 0.34 0.05
60_V 31_R 0.84 0.34 0.05
34_V 36_E 0.84 0.34 0.05
38_F 16_E 0.83 0.33 0.05
178_L 2_T 0.83 0.33 0.05
49_M 27_L 0.83 0.33 0.05
198_V 22_A 0.82 0.32 0.05
19_S 69_L 0.81 0.32 0.04
35_V 49_V 0.81 0.31 0.04
22_I 33_D 0.81 0.31 0.04
48_I 64_E 0.81 0.31 0.04
35_V 42_V 0.81 0.31 0.04
222_Q 16_E 0.81 0.30 0.04
88_S 59_D 0.81 0.30 0.04
140_I 39_C 0.80 0.30 0.04
51_C 28_P 0.80 0.30 0.04
63_I 15_A 0.80 0.30 0.04
140_I 42_V 0.80 0.30 0.04
206_L 66_N 0.80 0.30 0.04
198_V 3_A 0.80 0.30 0.04
147_S 16_E 0.79 0.29 0.04
201_I 30_L 0.79 0.29 0.04
226_V 34_I 0.78 0.28 0.04
49_M 38_I 0.78 0.28 0.04
213_D 25_H 0.78 0.28 0.04
117_V 20_S 0.78 0.28 0.04
161_S 39_C 0.78 0.28 0.04
88_S 70_P 0.78 0.28 0.04
146_V 8_E 0.78 0.28 0.04
234_A 14_V 0.78 0.28 0.04
241_T 17_R 0.78 0.28 0.04
2_R 54_E 0.77 0.28 0.04
218_R 61_S 0.77 0.28 0.04
212_E 44_I 0.77 0.28 0.04
216_V 11_Q 0.77 0.27 0.04
36_I 55_Q 0.77 0.27 0.04
40_I 61_S 0.77 0.27 0.04
64_Q 28_P 0.77 0.27 0.04
73_L 53_L 0.77 0.27 0.04
60_V 20_S 0.76 0.27 0.04
120_S 22_A 0.76 0.27 0.04
141_T 31_R 0.76 0.27 0.04
59_F 7_K 0.76 0.26 0.04
91_R 39_C 0.76 0.26 0.03
207_V 49_V 0.75 0.26 0.03
75_K 51_V 0.75 0.26 0.03
2_R 40_K 0.75 0.26 0.03
201_I 13_I 0.75 0.26 0.03
23_A 69_L 0.75 0.26 0.03
86_P 33_D 0.74 0.25 0.03
18_S 61_S 0.74 0.25 0.03
137_E 51_V 0.74 0.24 0.03
213_D 17_R 0.73 0.24 0.03
47_L 3_A 0.73 0.24 0.03
200_E 60_I 0.73 0.24 0.03
219_A 12_N 0.73 0.24 0.03
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 0.0474 seconds.