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OPENSEQ.org
4XGQ
Genes: A B A+B
Length: 78 134 210
Sequences: 1015 9281 622
Seq/Len: 13.01 69.26 2.96
MirrorTree (Pazo et al. 2001) 0.76
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 0.00 0.04 2.93
2 0.01 0.05 2.93
5 0.01 0.08 3.03
10 0.02 0.09 3.07
20 0.02 0.11 3.12
100 0.04 0.15 3.35
∞ 0.08 0.20 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
57_S 57_N 1.32 0.90 0.31
56_I 61_L 1.31 0.90 0.31
53_M 60_K 1.26 0.87 0.27
71_P 97_N 1.23 0.85 0.25
50_F 22_Y 1.19 0.82 0.23
10_G 107_I 1.18 0.82 0.22
62_F 131_N 1.06 0.71 0.15
15_V 82_G 1.06 0.71 0.15
73_K 89_E 1.06 0.71 0.15
50_F 13_A 1.04 0.69 0.14
68_D 97_N 1.04 0.68 0.14
59_D 91_K 1.02 0.67 0.14
45_S 129_L 1.00 0.65 0.13
61_I 112_T 0.98 0.62 0.12
17_L 35_A 0.98 0.62 0.12
3_K 93_L 0.95 0.58 0.10
17_L 109_E 0.92 0.55 0.09
70_P 125_P 0.90 0.52 0.09
52_E 60_K 0.90 0.52 0.09
39_L 31_N 0.89 0.51 0.08
77_F 26_E 0.89 0.50 0.08
46_W 64_F 0.88 0.50 0.08
20_E 34_I 0.88 0.50 0.08
49_V 66_S 0.86 0.48 0.08
21_F 108_A 0.86 0.48 0.08
42_L 70_I 0.86 0.47 0.07
20_E 14_I 0.85 0.46 0.07
6_I 65_L 0.85 0.46 0.07
68_D 98_N 0.84 0.44 0.07
56_I 67_R 0.82 0.43 0.07
9_N 113_L 0.82 0.42 0.06
24_S 126_N 0.81 0.41 0.06
34_G 117_N 0.79 0.39 0.06
77_F 100_L 0.79 0.38 0.06
30_V 63_I 0.78 0.38 0.06
9_N 40_V 0.78 0.38 0.06
4_A 124_I 0.78 0.38 0.05
69_L 97_N 0.78 0.37 0.05
15_V 3_Y 0.77 0.37 0.05
57_S 14_I 0.77 0.37 0.05
49_V 42_A 0.77 0.36 0.05
41_P 14_I 0.76 0.35 0.05
39_L 42_A 0.76 0.35 0.05
34_G 120_E 0.76 0.35 0.05
63_P 91_K 0.75 0.34 0.05
10_G 79_F 0.74 0.34 0.05
64_E 17_H 0.74 0.33 0.04
22_R 95_I 0.73 0.32 0.04
20_E 87_E 0.73 0.32 0.04
26_K 129_L 0.73 0.32 0.04
25_V 104_S 0.72 0.32 0.04
36_G 101_L 0.72 0.31 0.04
67_K 89_E 0.72 0.31 0.04
20_E 107_I 0.72 0.31 0.04
49_V 60_K 0.72 0.31 0.04
15_V 109_E 0.72 0.31 0.04
53_M 13_A 0.71 0.30 0.04
70_P 97_N 0.71 0.30 0.04
50_F 70_I 0.71 0.30 0.04
77_F 14_I 0.71 0.30 0.04
27_E 14_I 0.71 0.30 0.04
37_I 35_A 0.70 0.29 0.04
63_P 126_N 0.70 0.29 0.04
61_I 15_N 0.70 0.29 0.04
72_Q 39_I 0.70 0.29 0.04
69_L 50_K 0.70 0.29 0.04
40_Q 73_F 0.70 0.28 0.04
9_N 74_S 0.69 0.28 0.04
30_V 101_L 0.69 0.28 0.04
41_P 57_N 0.69 0.28 0.04
4_A 129_L 0.69 0.28 0.04
23_F 47_G 0.69 0.28 0.04
17_L 22_Y 0.69 0.27 0.04
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
4848 2.96 4XGQ Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.31 Done - Shared
0727 1.84 3ZVK_HHBlits Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) 0.63 Done
0723 2.22 3ZVK_Jackhmmer Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.63 Done
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