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OPENSEQ.org
du
Genes: A B A+B
Length: 158 153 311
Sequences: 734 5080 381
Seq/Len: 4.65 33.2 1.23
MirrorTree (Pazo et al. 2001) 0.57
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 0.00 0.01 0.67
2 0.00 0.01 0.68
5 0.00 0.01 0.68
10 0.00 0.02 0.69
20 0.00 0.02 0.70
100 0.00 0.05 0.79
∞ 0.00 0.14 1.23
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_T 1_P 1.31 0.68 0.01
78_P 144_P 1.19 0.57 0.00
73_T 72_T 1.17 0.55 0.00
62_Y 118_T 1.14 0.53 0.00
151_R 144_P 1.11 0.50 0.00
1_D 122_P 1.06 0.45 0.00
39_S 38_R 1.04 0.43 0.00
62_Y 109_M 1.01 0.40 0.00
154_R 95_T 1.01 0.40 0.00
8_R 40_L 1.00 0.39 0.00
36_K 66_K 0.99 0.38 0.00
35_A 95_T 0.98 0.37 0.00
29_A 97_I 0.98 0.37 0.00
10_L 10_L 0.96 0.35 0.00
156_L 9_P 0.95 0.34 0.00
88_N 10_L 0.94 0.33 0.00
1_D 62_E 0.93 0.33 0.00
101_N 123_L 0.92 0.32 0.00
130_Y 50_T 0.92 0.32 0.00
64_A 42_E 0.92 0.31 0.00
24_A 34_Q 0.92 0.31 0.00
21_E 126_P 0.91 0.30 0.00
24_A 78_V 0.90 0.30 0.00
41_A 72_T 0.89 0.29 0.00
142_R 139_Y 0.89 0.29 0.00
23_P 98_V 0.87 0.28 0.00
1_D 153_Y 0.87 0.27 0.00
98_V 63_L 0.85 0.26 0.00
55_E 1_P 0.84 0.25 0.00
8_R 36_F 0.84 0.25 0.00
55_E 151_N 0.83 0.25 0.00
58_A 153_Y 0.83 0.24 0.00
124_A 117_E 0.83 0.24 0.00
17_P 91_L 0.83 0.24 0.00
21_E 12_F 0.82 0.24 0.00
1_D 67_R 0.82 0.24 0.00
7_Y 104_A 0.82 0.24 0.00
19_L 87_A 0.81 0.23 0.00
104_R 97_I 0.81 0.23 0.00
124_A 10_L 0.81 0.23 0.00
113_P 40_L 0.80 0.22 0.00
85_S 122_P 0.80 0.22 0.00
56_D 146_A 0.80 0.22 0.00
69_A 106_F 0.80 0.22 0.00
23_P 36_F 0.79 0.22 0.00
85_S 105_A 0.78 0.21 0.00
4_A 86_D 0.78 0.21 0.00
142_R 89_R 0.78 0.21 0.00
105_L 93_R 0.78 0.21 0.00
46_K 82_R 0.77 0.21 0.00
86_N 131_G 0.77 0.21 0.00
36_K 52_V 0.77 0.21 0.00
54_V 49_Q 0.77 0.20 0.00
140_N 24_A 0.77 0.20 0.00
71_R 126_P 0.77 0.20 0.00
150_K 83_W 0.76 0.20 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
7836 1.23 du Δgene:(0, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.01 Done
7832 0.67 du Δgene:(0, 0) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done
7831 0 DUF Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed - Shared
7829 0.02 DUF Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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