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OPENSEQ.org
3ZVK_Jackhmmer
Genes: A B A+B
Length: 78 134 210
Sequences: 985 7137 466
Seq/Len: 12.63 53.26 2.22
MirrorTree (Pazo et al. 2001) 0.72
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 0.01 2.20
2 0.00 0.03 2.25
5 0.01 0.05 2.35
10 0.01 0.07 2.41
20 0.02 0.09 2.48
100 0.02 0.14 2.75
∞ 0.06 0.19 3.25
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 1.55 0.94 0.63
56_I 61_L 1.31 0.84 0.42
57_S 57_N 1.29 0.82 0.40
50_F 22_Y 1.27 0.81 0.38
71_P 97_N 1.24 0.79 0.35
68_D 97_N 1.22 0.78 0.34
15_V 82_G 1.17 0.73 0.30
68_D 98_N 1.13 0.69 0.27
17_L 36_I 1.09 0.66 0.24
34_G 117_N 1.06 0.63 0.22
73_K 89_E 1.06 0.62 0.21
15_V 3_Y 1.05 0.62 0.21
69_L 97_N 1.04 0.59 0.20
17_L 35_A 1.03 0.59 0.19
49_V 42_A 1.00 0.55 0.17
24_S 126_N 1.00 0.55 0.17
66_R 10_C 0.99 0.55 0.17
17_L 22_Y 0.95 0.50 0.14
52_E 60_K 0.95 0.49 0.14
25_V 104_S 0.93 0.48 0.14
30_V 101_L 0.93 0.47 0.13
53_M 61_L 0.91 0.46 0.12
21_F 108_A 0.91 0.45 0.12
39_L 42_A 0.90 0.44 0.12
50_F 13_A 0.90 0.44 0.12
53_M 13_A 0.89 0.43 0.12
59_D 91_K 0.88 0.41 0.11
20_E 39_I 0.86 0.39 0.10
3_K 93_L 0.85 0.38 0.10
62_F 131_N 0.85 0.38 0.10
26_K 25_L 0.83 0.37 0.09
33_L 101_L 0.83 0.36 0.09
49_V 66_S 0.83 0.36 0.09
75_K 49_S 0.82 0.36 0.09
37_I 35_A 0.81 0.34 0.08
23_F 93_L 0.81 0.34 0.08
17_L 109_E 0.81 0.34 0.08
21_F 46_Y 0.81 0.34 0.08
30_V 68_L 0.81 0.34 0.08
23_F 35_A 0.81 0.34 0.08
7_F 114_V 0.80 0.34 0.08
34_G 120_E 0.80 0.33 0.08
39_L 31_N 0.79 0.33 0.08
77_F 114_V 0.79 0.32 0.07
9_N 23_N 0.78 0.32 0.07
4_A 61_L 0.77 0.30 0.07
9_N 40_V 0.77 0.30 0.07
27_E 129_L 0.77 0.30 0.07
67_K 89_E 0.76 0.29 0.07
34_G 48_V 0.76 0.29 0.07
32_P 90_Q 0.75 0.29 0.06
47_K 64_F 0.75 0.28 0.06
53_M 60_K 0.75 0.28 0.06
62_F 40_V 0.75 0.28 0.06
23_F 10_C 0.74 0.28 0.06
41_P 14_I 0.74 0.28 0.06
30_V 46_Y 0.74 0.28 0.06
44_N 131_N 0.74 0.27 0.06
2_N 11_V 0.73 0.27 0.06
58_S 51_S 0.73 0.27 0.06
61_I 112_T 0.73 0.26 0.06
7_F 47_G 0.73 0.26 0.06
30_V 63_I 0.72 0.26 0.06
6_I 65_L 0.72 0.26 0.05
59_D 119_K 0.72 0.26 0.05
36_G 101_L 0.71 0.25 0.05
32_P 29_A 0.71 0.25 0.05
64_E 17_H 0.71 0.25 0.05
41_P 121_F 0.71 0.25 0.05
52_E 25_L 0.71 0.24 0.05
72_Q 97_N 0.71 0.24 0.05
68_D 85_R 0.70 0.24 0.05
41_P 117_N 0.70 0.24 0.05
49_V 60_K 0.70 0.23 0.05
72_Q 49_S 0.70 0.23 0.05
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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