May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
2w8b_A_H
Genes: A B A+B
Length: 409 118 514
Sequences: 968 10693 840
Seq/Len: 2.37 90.62 1.63
MirrorTree (Pazo et al. 2001) 0.78
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 0.08 0.02 1.51
2 0.08 0.02 1.54
5 0.08 0.03 1.58
10 0.08 0.04 1.59
20 0.08 0.06 1.59
100 0.08 0.13 1.63
∞ 0.08 0.21 1.72
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
314_Q 51_T 1.52 0.89 0.29
240_A 87_K 1.39 0.82 0.21
226_G 56_I 1.28 0.74 0.15
179_Q 89_K 1.25 0.72 0.14
235_S 39_K 1.20 0.67 0.12
402_F 52_P 1.16 0.62 0.10
381_N 75_V 1.15 0.62 0.10
182_M 56_I 1.12 0.59 0.09
75_I 23_Q 1.08 0.55 0.08
242_S 60_E 1.07 0.54 0.08
149_V 8_V 1.06 0.53 0.08
304_Q 101_S 1.06 0.53 0.07
345_G 29_A 1.05 0.51 0.07
372_S 8_V 1.04 0.51 0.07
60_G 8_V 1.04 0.51 0.07
251_V 20_D 1.02 0.49 0.07
267_S 68_M 1.02 0.49 0.07
174_V 17_I 1.02 0.49 0.07
241_L 105_R 1.01 0.48 0.06
293_V 76_S 1.01 0.48 0.06
270_T 66_V 1.00 0.46 0.06
248_N 60_E 1.00 0.46 0.06
149_V 13_D 1.00 0.46 0.06
133_E 13_D 0.99 0.46 0.06
145_R 19_S 0.98 0.45 0.06
267_S 100_Y 0.98 0.44 0.06
347_V 87_K 0.97 0.43 0.05
37_V 101_S 0.97 0.43 0.05
22_Q 41_T 0.97 0.43 0.05
267_S 20_D 0.96 0.43 0.05
7_D 109_V 0.96 0.42 0.05
384_S 28_H 0.95 0.41 0.05
337_I 43_E 0.95 0.41 0.05
218_V 71_Q 0.95 0.41 0.05
40_D 95_H 0.94 0.40 0.05
91_Y 85_Y 0.94 0.40 0.05
282_A 12_L 0.94 0.40 0.05
371_S 42_V 0.93 0.39 0.05
130_E 11_D 0.93 0.39 0.04
46_K 67_K 0.93 0.39 0.04
146_I 96_D 0.91 0.38 0.04
284_T 28_H 0.91 0.38 0.04
230_F 77_A 0.91 0.37 0.04
173_V 65_A 0.90 0.36 0.04
215_V 67_K 0.90 0.36 0.04
133_E 11_D 0.89 0.35 0.04
378_S 52_P 0.89 0.35 0.04
230_F 69_Y 0.89 0.35 0.04
201_G 61_R 0.88 0.35 0.04
89_G 80_I 0.88 0.35 0.04
393_L 65_A 0.88 0.35 0.04
260_R 78_D 0.88 0.34 0.04
246_S 60_E 0.88 0.34 0.04
156_Q 12_L 0.88 0.34 0.04
261_Q 42_V 0.88 0.34 0.04
160_E 8_V 0.88 0.34 0.04
73_L 82_I 0.87 0.33 0.04
305_R 60_E 0.86 0.33 0.04
153_N 101_S 0.86 0.32 0.04
362_A 43_E 0.86 0.32 0.03
106_T 77_A 0.85 0.32 0.03
80_V 9_Y 0.85 0.31 0.03
361_L 69_Y 0.84 0.31 0.03
151_Q 52_P 0.84 0.31 0.03
162_R 108_L 0.84 0.31 0.03
256_S 60_E 0.84 0.31 0.03
88_D 31_F 0.84 0.30 0.03
316_A 82_I 0.84 0.30 0.03
370_Y 66_V 0.84 0.30 0.03
16_I 41_T 0.83 0.30 0.03
351_S 29_A 0.83 0.30 0.03
214_A 97_E 0.83 0.29 0.03
293_V 16_D 0.83 0.29 0.03
34_G 46_A 0.82 0.29 0.03
49_P 107_V 0.81 0.28 0.03
223_R 56_I 0.81 0.28 0.03
382_L 52_P 0.81 0.28 0.03
109_A 83_V 0.81 0.28 0.03
149_V 14_K 0.81 0.28 0.03
328_V 83_V 0.81 0.28 0.03
274_W 45_H 0.80 0.27 0.03
31_E 106_A 0.80 0.27 0.03
93_V 97_E 0.80 0.27 0.03
269_N 17_I 0.80 0.27 0.03
371_S 99_A 0.80 0.27 0.03
389_F 52_P 0.80 0.27 0.03
217_Q 83_V 0.80 0.27 0.03
78_V 56_I 0.80 0.27 0.03
166_Y 100_Y 0.79 0.27 0.03
386_D 89_K 0.79 0.27 0.03
12_S 78_D 0.79 0.26 0.03
353_T 91_A 0.79 0.26 0.03
244_T 64_N 0.79 0.26 0.03
193_L 96_D 0.79 0.26 0.03
220_S 92_V 0.79 0.26 0.03
174_V 69_Y 0.78 0.26 0.03
361_L 45_H 0.78 0.26 0.03
170_N 8_V 0.78 0.26 0.03
108_L 77_A 0.78 0.26 0.03
8_S 40_V 0.78 0.26 0.03
150_V 97_E 0.78 0.26 0.03
319_S 103_N 0.78 0.25 0.02
307_T 38_Y 0.77 0.25 0.02
227_A 19_S 0.77 0.25 0.02
4_I 41_T 0.77 0.25 0.02
71_S 43_E 0.77 0.25 0.02
84_T 23_Q 0.77 0.24 0.02
237_L 6_N 0.77 0.24 0.02
13_G 109_V 0.77 0.24 0.02
200_S 101_S 0.76 0.24 0.02
16_I 26_D 0.76 0.24 0.02
94_A 27_A 0.76 0.24 0.02
248_N 73_K 0.76 0.24 0.02
149_V 56_I 0.76 0.24 0.02
368_V 61_R 0.76 0.24 0.02
16_I 12_L 0.76 0.24 0.02
345_G 99_A 0.76 0.23 0.02
181_L 109_V 0.76 0.23 0.02
270_T 53_E 0.75 0.23 0.02
20_P 42_V 0.75 0.23 0.02
193_L 68_M 0.75 0.23 0.02
404_A 33_R 0.75 0.23 0.02
18_V 96_D 0.75 0.23 0.02
323_K 45_H 0.75 0.23 0.02
354_F 107_V 0.74 0.23 0.02
281_L 19_S 0.74 0.22 0.02
40_D 7_I 0.74 0.22 0.02
230_F 8_V 0.74 0.22 0.02
73_L 61_R 0.74 0.22 0.02
94_A 100_Y 0.74 0.22 0.02
406_S 69_Y 0.74 0.22 0.02
351_S 35_N 0.74 0.22 0.02
399_Q 40_V 0.74 0.22 0.02
6_I 87_K 0.74 0.22 0.02
59_P 87_K 0.74 0.22 0.02
209_T 92_V 0.73 0.22 0.02
298_I 35_N 0.73 0.22 0.02
224_H 63_A 0.73 0.22 0.02
340_Q 102_K 0.73 0.22 0.02
227_A 101_S 0.73 0.22 0.02
230_F 11_D 0.73 0.22 0.02
10_V 78_D 0.73 0.22 0.02
341_D 95_H 0.73 0.21 0.02
328_V 51_T 0.73 0.21 0.02
3_R 83_V 0.72 0.21 0.02
264_D 96_D 0.72 0.21 0.02
404_A 51_T 0.72 0.21 0.02
206_V 101_S 0.72 0.21 0.02
394_P 67_K 0.72 0.21 0.02
329_S 75_V 0.72 0.21 0.02
368_V 24_M 0.72 0.21 0.02
80_V 15_Y 0.72 0.21 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 0.5839 seconds.