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OPENSEQ.org
3ZVK_HHBlits
Genes: A B A+B
Length: 78 134 210
Sequences: 544 6854 386
Seq/Len: 6.97 51.15 1.84
MirrorTree (Pazo et al. 2001) 0.71
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 1.82
2 0.00 0.03 1.84
5 0.01 0.06 1.88
10 0.01 0.08 1.91
20 0.01 0.10 1.94
100 0.03 0.15 2.03
∞ 0.08 0.22 2.26
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
10_G 107_I 1.63 0.94 0.63
68_D 98_N 1.37 0.83 0.41
50_F 22_Y 1.32 0.80 0.37
26_K 25_L 1.21 0.71 0.27
58_S 57_N 1.17 0.68 0.25
7_F 114_V 1.12 0.63 0.21
24_S 119_K 1.12 0.62 0.21
58_S 41_L 1.10 0.61 0.20
30_V 101_L 1.08 0.58 0.18
17_L 109_E 1.06 0.56 0.17
6_I 65_L 1.01 0.51 0.14
72_Q 97_N 1.00 0.50 0.14
53_M 13_A 1.00 0.50 0.14
1_M 10_C 0.99 0.48 0.13
77_F 9_I 0.96 0.45 0.12
68_D 97_N 0.94 0.43 0.11
50_F 13_A 0.94 0.43 0.11
72_Q 49_S 0.93 0.43 0.11
19_K 10_C 0.93 0.42 0.11
3_K 93_L 0.92 0.41 0.10
23_F 40_V 0.92 0.41 0.10
17_L 36_I 0.91 0.40 0.10
41_P 5_L 0.90 0.39 0.09
69_L 97_N 0.89 0.38 0.09
70_P 61_L 0.89 0.38 0.09
62_F 131_N 0.88 0.37 0.09
31_I 10_C 0.87 0.36 0.08
63_P 15_N 0.87 0.36 0.08
6_I 35_A 0.87 0.36 0.08
57_S 61_L 0.87 0.36 0.08
71_P 101_L 0.86 0.35 0.08
57_S 73_F 0.85 0.34 0.07
30_V 63_I 0.84 0.33 0.07
49_V 42_A 0.84 0.33 0.07
41_P 117_N 0.83 0.32 0.07
27_E 62_D 0.83 0.32 0.07
6_I 116_N 0.82 0.32 0.07
30_V 127_L 0.82 0.31 0.07
46_W 70_I 0.82 0.31 0.07
75_K 49_S 0.81 0.31 0.07
39_L 124_I 0.80 0.30 0.06
9_N 42_A 0.80 0.29 0.06
36_G 105_H 0.80 0.29 0.06
75_K 105_H 0.80 0.29 0.06
58_S 53_K 0.79 0.29 0.06
69_L 98_N 0.78 0.28 0.06
46_W 73_F 0.78 0.27 0.06
25_V 124_I 0.78 0.27 0.06
49_V 108_A 0.77 0.27 0.05
32_P 90_Q 0.77 0.27 0.05
27_E 82_G 0.77 0.26 0.05
59_D 119_K 0.77 0.26 0.05
70_P 131_N 0.76 0.26 0.05
49_V 63_I 0.76 0.26 0.05
62_F 56_Q 0.76 0.26 0.05
72_Q 98_N 0.74 0.24 0.05
20_E 39_I 0.74 0.24 0.05
72_Q 64_F 0.74 0.24 0.05
9_N 77_C 0.74 0.24 0.05
44_N 131_N 0.74 0.24 0.05
21_F 82_G 0.74 0.24 0.05
67_K 89_E 0.74 0.24 0.05
46_W 14_I 0.74 0.24 0.05
4_A 61_L 0.73 0.24 0.04
26_K 80_Y 0.73 0.24 0.04
57_S 82_G 0.73 0.24 0.04
58_S 1_M 0.72 0.23 0.04
7_F 3_Y 0.72 0.23 0.04
52_E 29_A 0.72 0.23 0.04
58_S 52_K 0.72 0.23 0.04
30_V 76_K 0.72 0.23 0.04
49_V 13_A 0.72 0.23 0.04
15_V 3_Y 0.72 0.22 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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