May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
Zi
Genes: A B A+B
Length: 311 261 554
Sequences: 4241 8643 1063
Seq/Len: 13.64 33.11 1.92
MirrorTree (Pazo et al. 2001) 0.86
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 0.05 0.02 1.76
2 0.05 0.02 1.78
5 0.05 0.02 1.81
10 0.05 0.04 1.81
20 0.05 0.04 1.86
100 0.06 0.07 2.16
∞ 0.12 0.17 4.04
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
70_M 224_A 1.58 0.93 0.58
271_T 49_L 1.49 0.90 0.49
74_I 232_A 1.44 0.88 0.46
36_Y 94_M 1.25 0.76 0.30
60_T 244_A 1.15 0.67 0.22
299_L 250_D 1.11 0.63 0.19
63_V 232_A 1.04 0.56 0.15
49_A 231_Y 1.03 0.55 0.15
36_Y 227_I 1.02 0.54 0.15
62_R 52_R 0.95 0.45 0.11
275_A 49_L 0.93 0.44 0.10
285_D 41_L 0.93 0.43 0.10
64_A 222_R 0.93 0.43 0.10
251_A 49_L 0.93 0.43 0.10
271_T 96_P 0.92 0.42 0.10
33_Y 94_M 0.85 0.35 0.07
150_E 41_L 0.85 0.35 0.07
274_F 224_A 0.85 0.35 0.07
234_H 39_L 0.83 0.33 0.07
60_T 221_S 0.83 0.33 0.07
76_L 117_G 0.82 0.32 0.06
81_L 66_C 0.81 0.31 0.06
77_Q 246_K 0.81 0.31 0.06
105_V 234_V 0.80 0.30 0.06
27_F 229_A 0.79 0.29 0.06
295_R 135_G 0.79 0.29 0.06
104_N 229_A 0.79 0.29 0.06
252_N 11_S 0.79 0.29 0.06
193_L 44_P 0.77 0.28 0.05
271_T 194_Y 0.77 0.28 0.05
203_R 122_P 0.76 0.27 0.05
105_V 33_D 0.76 0.27 0.05
51_T 54_I 0.75 0.26 0.05
283_I 184_N 0.74 0.25 0.05
194_T 126_E 0.74 0.24 0.04
291_M 112_I 0.74 0.24 0.04
44_S 194_Y 0.74 0.24 0.04
175_V 39_L 0.73 0.24 0.04
288_P 219_M 0.72 0.23 0.04
49_A 234_V 0.71 0.23 0.04
73_A 167_A 0.71 0.22 0.04
291_M 140_I 0.71 0.22 0.04
80_G 220_E 0.71 0.22 0.04
214_A 234_V 0.70 0.22 0.04
10_K 154_N 0.70 0.22 0.04
103_A 232_A 0.70 0.21 0.04
17_K 227_I 0.69 0.21 0.04
116_V 234_V 0.69 0.21 0.04
65_E 52_R 0.69 0.21 0.04
229_A 123_P 0.69 0.21 0.04
101_I 139_T 0.69 0.21 0.03
274_F 227_I 0.68 0.20 0.03
291_M 92_D 0.68 0.20 0.03
286_K 227_I 0.68 0.20 0.03
74_I 231_Y 0.68 0.20 0.03
76_L 198_A 0.68 0.20 0.03
6_R 104_A 0.68 0.20 0.03
61_P 234_V 0.68 0.20 0.03
289_E 62_R 0.68 0.20 0.03
210_Q 23_V 0.67 0.20 0.03
122_D 181_M 0.67 0.20 0.03
94_E 86_E 0.67 0.20 0.03
223_P 49_L 0.67 0.20 0.03
228_V 105_E 0.67 0.20 0.03
35_K 249_E 0.67 0.19 0.03
10_K 207_K 0.67 0.19 0.03
62_R 50_L 0.66 0.19 0.03
68_S 46_G 0.66 0.19 0.03
194_T 229_A 0.66 0.19 0.03
62_R 78_G 0.66 0.19 0.03
193_L 193_L 0.66 0.19 0.03
286_K 224_A 0.65 0.18 0.03
269_V 99_N 0.65 0.18 0.03
137_N 52_R 0.65 0.18 0.03
39_L 202_L 0.65 0.18 0.03
181_I 169_D 0.65 0.18 0.03
76_L 177_G 0.65 0.18 0.03
65_E 78_G 0.65 0.18 0.03
109_E 124_L 0.65 0.18 0.03
158_A 15_V 0.64 0.18 0.03
74_I 7_M 0.64 0.18 0.03
8_S 172_S 0.64 0.18 0.03
253_A 93_V 0.64 0.18 0.03
33_Y 227_I 0.64 0.18 0.03
274_F 231_Y 0.64 0.18 0.03
83_V 241_E 0.64 0.18 0.03
60_T 234_V 0.64 0.18 0.03
269_V 80_Y 0.64 0.18 0.03
77_Q 234_V 0.64 0.17 0.03
164_K 82_L 0.64 0.17 0.03
110_E 227_I 0.64 0.17 0.03
244_I 199_P 0.64 0.17 0.03
175_V 54_I 0.63 0.17 0.03
276_D 43_V 0.63 0.17 0.03
76_L 168_T 0.63 0.17 0.03
252_N 255_L 0.63 0.17 0.03
42_L 229_A 0.63 0.17 0.03
177_D 121_V 0.63 0.17 0.03
228_V 22_M 0.63 0.17 0.03
11_L 24_L 0.63 0.17 0.03
63_V 222_R 0.63 0.17 0.03
144_A 224_A 0.63 0.17 0.03
11_L 82_L 0.62 0.17 0.03
289_E 90_K 0.62 0.16 0.03
44_S 127_L 0.62 0.16 0.03
63_V 104_A 0.62 0.16 0.03
272_A 249_E 0.62 0.16 0.02
276_D 94_M 0.62 0.16 0.02
144_A 215_L 0.62 0.16 0.02
10_K 8_T 0.61 0.16 0.02
306_V 244_A 0.61 0.16 0.02
253_A 229_A 0.61 0.16 0.02
228_V 167_A 0.61 0.16 0.02
67_A 47_A 0.61 0.16 0.02
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 0.0533 seconds.