May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
beta flap (A, 50-660) (A, 100-200)
Genes: A B A+B
Length: 101 50 147
Sequences: 7718 851 298
Seq/Len: 76.42 17.02 2.03
MirrorTree (Pazo et al. 2001) 0.25
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 0.09 0.01
2 0.04 0.09 0.01
5 0.05 0.09 0.07
10 0.06 0.09 0.19
20 0.06 0.09 0.32
100 0.13 0.09 1.97
∞ 0.24 0.09 9.23
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
73_H 5_T 1.35 0.84 0.13
53_K 44_N 1.29 0.80 0.11
25_V 21_E 1.12 0.65 0.07
99_C 36_I 1.11 0.65 0.07
64_F 23_R 1.08 0.62 0.06
87_L 13_A 1.07 0.60 0.06
41_S 1_V 1.05 0.59 0.05
69_F 41_K 0.97 0.50 0.04
5_N 37_I 0.97 0.49 0.04
47_L 30_P 0.95 0.47 0.04
65_Y 4_L 0.95 0.47 0.04
87_L 20_R 0.94 0.46 0.04
77_Y 23_R 0.90 0.42 0.03
55_F 5_T 0.89 0.40 0.03
56_D 28_R 0.88 0.40 0.03
49_M 42_V 0.88 0.39 0.03
72_I 49_D 0.87 0.38 0.03
49_M 9_R 0.86 0.38 0.03
72_I 42_V 0.86 0.38 0.03
83_A 9_R 0.85 0.37 0.03
73_H 9_R 0.85 0.36 0.03
69_F 50_E 0.84 0.35 0.03
86_M 48_G 0.83 0.34 0.02
99_C 23_R 0.81 0.32 0.02
49_M 31_H 0.80 0.31 0.02
15_K 48_G 0.79 0.31 0.02
88_V 16_G 0.78 0.29 0.02
26_S 25_T 0.78 0.29 0.02
97_N 38_H 0.77 0.28 0.02
45_D 41_K 0.77 0.28 0.02
98_L 23_R 0.77 0.28 0.02
91_L 29_V 0.76 0.28 0.02
57_R 5_T 0.76 0.28 0.02
31_D 40_V 0.75 0.27 0.02
5_N 49_D 0.75 0.27 0.02
25_V 50_E 0.75 0.27 0.02
40_Q 37_I 0.75 0.27 0.02
55_F 21_E 0.75 0.27 0.02
57_R 44_N 0.74 0.26 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)
ID Seq/Len Name Options I_Prob Status
9986 2.03 beta flap (A, 50-660) (A, 100-200) Δgene:(1, 100) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.13 Done - Shared
9985 0.34 beta flap (A, 50-660) (A, 100-200) Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) Killed - Shared
9984 0.01 beta flap (A, 50-660) (A, 100-200) Δgene:(1, 20) A:(1E-60, 8) B:(1E-60, 8) msa: HHblits (2015_06) Killed - Shared
9983 0.15 beta flap (A, 50-660) (A, 100-200) Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
Page generated in 0.0242 seconds.