May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
bola_4pug_grx_2wci
Genes: A B A+B
Length: 92 115 184
Sequences: 1797 2782 149
Seq/Len: 19.53 24.19 0.81
MirrorTree (Pazo et al. 2001) 0.68
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.02 0.64
2 0.01 0.02 0.72
5 0.01 0.02 0.76
10 0.01 0.02 0.78
20 0.01 0.02 0.81
100 0.01 0.03 1.14
∞ 0.03 0.05 3.75
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_L 86_I 1.32 0.56 0.00
22_I 7_K 1.31 0.55 0.00
84_V 90_M 1.30 0.54 0.00
27_Y 65_Y 1.26 0.52 0.00
50_V 6_E 1.23 0.48 0.00
58_N 12_I 1.23 0.48 0.00
74_L 50_V 1.16 0.42 0.00
82_S 54_Q 1.15 0.42 0.00
65_L 49_Y 1.12 0.39 0.00
74_L 12_I 1.11 0.39 0.00
59_L 76_V 1.11 0.38 0.00
20_L 101_K 1.08 0.35 0.00
64_R 38_Q 1.07 0.35 0.00
60_V 6_E 1.06 0.34 0.00
23_E 56_P 1.05 0.33 0.00
82_S 38_Q 1.02 0.31 0.00
65_L 29_S 1.00 0.29 0.00
41_D 19_L 0.99 0.29 0.00
60_V 51_D 0.99 0.29 0.00
59_L 17_I 0.98 0.28 0.00
58_N 97_Q 0.98 0.28 0.00
41_D 74_L 0.97 0.28 0.00
47_V 47_F 0.97 0.27 0.00
83_I 43_C 0.96 0.27 0.00
72_E 81_V 0.95 0.26 0.00
53_G 55_N 0.94 0.25 0.00
25_V 24_S 0.92 0.24 0.00
48_K 9_Q 0.92 0.24 0.00
25_V 60_A 0.91 0.24 0.00
75_D 27_L 0.88 0.22 0.00
22_I 10_R 0.87 0.21 0.00
33_A 51_D 0.87 0.21 0.00
58_N 103_T 0.86 0.21 0.00
44_H 69_P 0.86 0.20 0.00
75_D 25_P 0.86 0.20 0.00
64_R 67_N 0.85 0.20 0.00
28_Q 41_A 0.85 0.20 0.00
73_E 19_L 0.85 0.20 0.00
43_T 66_A 0.84 0.20 0.00
17_P 14_E 0.83 0.19 0.00
21_V 80_L 0.83 0.19 0.00
61_K 38_Q 0.83 0.19 0.00
22_I 58_I 0.83 0.19 0.00
23_E 20_Y 0.83 0.19 0.00
52_K 17_I 0.82 0.18 0.00
33_A 41_A 0.82 0.18 0.00
65_L 39_A 0.82 0.18 0.00
84_V 49_Y 0.81 0.18 0.00
70_L 89_E 0.81 0.18 0.00
76_T 88_I 0.81 0.18 0.00
26_S 87_V 0.81 0.18 0.00
69_L 18_L 0.81 0.18 0.00
20_L 36_A 0.81 0.18 0.00
21_V 62_L 0.81 0.18 0.00
64_R 88_I 0.80 0.17 0.00
65_L 97_Q 0.80 0.17 0.00
84_V 76_V 0.80 0.17 0.00
55_E 9_Q 0.79 0.17 0.00
18_V 65_Y 0.79 0.17 0.00
73_E 64_K 0.79 0.17 0.00
33_A 16_P 0.78 0.16 0.00
90_E 36_A 0.78 0.16 0.00
69_L 76_V 0.78 0.16 0.00
45_F 50_V 0.78 0.16 0.00
36_K 56_P 0.78 0.16 0.00
36_K 47_F 0.78 0.16 0.00
73_E 60_A 0.77 0.16 0.00
19_E 34_A 0.77 0.16 0.00
86_K 93_R 0.77 0.16 0.00
26_S 54_Q 0.76 0.15 0.00
57_M 18_L 0.75 0.15 0.00
87_T 51_D 0.74 0.14 0.00
65_L 38_Q 0.74 0.14 0.00
57_M 56_P 0.73 0.14 0.00
77_G 36_A 0.73 0.14 0.00
73_E 42_A 0.73 0.14 0.00
64_R 4_T 0.73 0.14 0.00
61_K 50_V 0.72 0.14 0.00
23_E 98_Q 0.72 0.14 0.00
61_K 18_L 0.72 0.14 0.00
49_I 61_E 0.72 0.14 0.00
60_V 58_I 0.72 0.14 0.00
49_I 9_Q 0.72 0.14 0.00
87_T 26_K 0.72 0.14 0.00
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
2046 0.81 bola_4pug_grx_2wci Δgene:(1, 2) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
2045 0.04 bola_4pug_grx_2wci Δgene:(1, 2) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) Killed - Shared
Page generated in 0.0754 seconds.