May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
1yti A vs B
Genes: A B A+B
Length: 520 192 649
Sequences: 3810 16237 1917
Seq/Len: 7.33 84.57 2.95
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 0.01 0.03 2.19
2 0.01 0.03 2.32
5 0.01 0.03 2.45
10 0.01 0.04 2.58
20 0.01 0.05 2.69
100 0.03 0.12 2.94
∞ 0.12 0.20 3.64
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
258_A 99_Q 3.93 1.00 1.00
379_P 21_R 2.46 1.00 1.00
488_L 103_I 2.24 1.00 0.99
254_K 99_Q 2.03 1.00 0.98
374_A 18_D 1.82 0.99 0.97
159_E 31_R 1.82 0.99 0.97
257_R 99_Q 1.59 0.97 0.92
363_L 129_A 1.41 0.93 0.86
363_L 174_L 1.33 0.90 0.81
255_A 58_G 1.31 0.89 0.80
489_D 107_K 1.12 0.77 0.64
260_E 62_E 1.03 0.68 0.53
260_E 58_G 0.99 0.63 0.48
409_H 68_E 0.97 0.60 0.45
379_P 17_A 0.92 0.54 0.39
379_P 27_V 0.81 0.41 0.26
426_L 129_A 0.80 0.40 0.26
408_R 21_R 0.78 0.37 0.23
245_F 128_V 0.78 0.37 0.23
450_G 129_A 0.76 0.35 0.21
160_A 34_I 0.73 0.33 0.19
387_L 173_I 0.73 0.32 0.19
312_L 65_C 0.72 0.31 0.18
258_A 59_V 0.71 0.30 0.17
388_T 129_A 0.71 0.30 0.17
321_I 53_L 0.71 0.29 0.17
456_F 72_R 0.70 0.29 0.17
245_F 93_Y 0.70 0.29 0.16
419_A 182_L 0.70 0.28 0.16
251_Q 120_A 0.69 0.28 0.16
404_V 20_L 0.69 0.28 0.16
432_V 31_R 0.69 0.28 0.16
450_G 27_V 0.68 0.27 0.15
267_S 14_W 0.68 0.27 0.15
456_F 47_K 0.67 0.26 0.14
247_A 120_A 0.67 0.26 0.14
360_S 18_D 0.67 0.26 0.14
493_Q 124_N 0.66 0.25 0.14
437_L 125_P 0.66 0.25 0.13
393_Y 176_T 0.65 0.24 0.13
416_A 152_M 0.65 0.24 0.13
131_Q 168_F 0.64 0.23 0.12
219_L 39_L 0.64 0.23 0.12
219_L 166_F 0.64 0.23 0.12
257_R 103_I 0.64 0.23 0.12
251_Q 47_K 0.64 0.23 0.12
48_D 2_D 0.64 0.23 0.12
377_C 89_I 0.63 0.22 0.12
390_V 183_E 0.62 0.22 0.11
203_R 118_M 0.62 0.21 0.11
21_P 13_T 0.62 0.21 0.11
181_L 51_L 0.61 0.21 0.10
127_F 20_L 0.61 0.20 0.10
376_I 53_L 0.61 0.20 0.10
210_A 28_V 0.61 0.20 0.10
205_K 151_G 0.60 0.20 0.10
262_F 175_T 0.60 0.20 0.10
499_T 16_L 0.60 0.20 0.10
129_L 82_I 0.60 0.20 0.10
376_I 43_L 0.60 0.20 0.10
244_A 45_T 0.60 0.20 0.10
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 0.7173 seconds.