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OPENSEQ.org
3KXE
Genes: A B A+B
Length: 88 96 178
Sequences: 1078 2853 662
Seq/Len: 12.25 29.72 3.72
MirrorTree (Pazo et al. 2001) 0.58
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 0.00 3.60
2 0.00 0.00 3.59
5 0.00 0.01 3.64
10 0.01 0.02 3.68
20 0.01 0.03 3.72
100 0.02 0.05 3.84
∞ 0.06 0.10 4.23
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
75_E 11_K 2.63 1.00 1.00
75_E 15_D 2.36 1.00 0.99
57_E 9_R 2.12 1.00 0.99
59_E 61_Y 2.10 1.00 0.99
58_G 83_R 1.94 1.00 0.98
55_L 61_Y 1.84 0.99 0.97
55_L 72_F 1.73 0.99 0.96
73_I 35_R 1.69 0.99 0.96
77_S 31_A 1.65 0.99 0.95
56_I 58_R 1.50 0.97 0.91
79_A 19_T 1.35 0.94 0.85
58_G 82_I 1.29 0.92 0.82
59_E 74_R 1.24 0.89 0.78
77_S 38_Q 1.12 0.82 0.68
16_A 19_T 1.11 0.81 0.66
64_I 7_S 1.10 0.81 0.66
66_D 8_R 1.10 0.81 0.66
73_I 31_A 1.07 0.78 0.62
65_E 11_K 1.03 0.74 0.57
54_A 83_R 1.01 0.72 0.55
7_S 91_A 0.95 0.66 0.48
54_A 89_M 0.95 0.66 0.48
77_S 30_A 0.95 0.65 0.48
79_A 15_D 0.94 0.64 0.46
52_R 57_L 0.93 0.63 0.46
72_F 14_L 0.92 0.62 0.44
67_F 18_W 0.91 0.61 0.43
76_R 19_T 0.91 0.61 0.43
73_I 38_Q 0.88 0.57 0.40
42_E 83_R 0.82 0.48 0.32
36_A 48_P 0.82 0.48 0.31
69_F 41_I 0.80 0.46 0.29
7_S 7_S 0.80 0.46 0.29
77_S 35_R 0.80 0.45 0.29
21_Q 25_W 0.78 0.44 0.27
16_A 79_V 0.78 0.43 0.27
7_S 57_L 0.77 0.42 0.26
69_F 6_L 0.77 0.42 0.26
70_D 77_V 0.77 0.41 0.26
73_I 34_A 0.75 0.40 0.24
22_V 90_N 0.75 0.40 0.24
52_R 60_G 0.75 0.39 0.24
62_G 83_R 0.75 0.39 0.24
34_I 24_R 0.74 0.38 0.23
7_S 18_W 0.73 0.37 0.22
59_E 82_I 0.73 0.37 0.22
14_F 72_F 0.72 0.36 0.21
70_D 22_E 0.72 0.36 0.21
76_R 15_D 0.72 0.36 0.21
8_V 70_V 0.72 0.36 0.21
67_F 11_K 0.72 0.36 0.21
55_L 66_S 0.72 0.36 0.21
8_V 58_R 0.72 0.36 0.21
61_S 8_R 0.71 0.35 0.20
38_L 44_I 0.71 0.35 0.20
17_F 51_G 0.71 0.35 0.20
65_E 9_R 0.71 0.35 0.20
54_A 37_L 0.71 0.34 0.20
80_S 18_W 0.70 0.34 0.19
61_S 9_R 0.70 0.34 0.19
69_F 38_Q 0.69 0.33 0.18
14_F 20_Y 0.69 0.33 0.18
76_R 18_W 0.69 0.33 0.18
77_S 27_V 0.69 0.32 0.18
8_V 32_D 0.69 0.32 0.18
34_I 64_C 0.69 0.32 0.18
52_R 56_N 0.67 0.30 0.17
19_D 54_D 0.67 0.30 0.17
55_L 58_R 0.67 0.30 0.17
72_F 15_D 0.67 0.30 0.16
29_S 56_N 0.66 0.29 0.16
58_G 13_D 0.66 0.29 0.16
5_N 25_W 0.66 0.29 0.16
44_N 37_L 0.66 0.29 0.15
44_N 87_Q 0.65 0.28 0.15
37_G 50_M 0.65 0.28 0.15
47_K 63_R 0.64 0.27 0.14
18_I 44_I 0.64 0.27 0.14
63_F 73_Y 0.64 0.27 0.14
23_A 31_A 0.64 0.27 0.14
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
1175 0.67 TT Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.91 Done - Shared
0718 3.72 3KXE Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 1.00 Done - Shared
0663 3.67 Caulobacter ParD-ParE Δgene:(1, 1) A:(1E-04, 4) B:(1E-04, 4) msa: Jackhmmer (2014_03) 1.00 Done - Shared
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