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OPENSEQ.org
1UJZ
Genes: A B A+B
Length: 87 128 210
Sequences: 211 134 103
Seq/Len: 2.43 1.05 0.49
MirrorTree (Pazo et al. 2001) 0.54
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 0.27 0.01 0.47
2 0.31 0.03 0.48
5 0.33 0.03 0.48
10 0.33 0.03 0.48
20 0.33 0.03 0.48
100 0.33 0.03 0.48
∞ 0.36 0.06 0.48
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
52_D 86_T 2.05 0.87 0.28
39_E 94_R 1.69 0.69 0.12
56_Y 72_N 1.65 0.67 0.10
42_V 86_T 1.55 0.60 0.08
83_G 15_V 1.52 0.57 0.07
64_S 125_I 1.52 0.57 0.07
23_E 71_N 1.44 0.51 0.06
31_D 75_R 1.37 0.45 0.04
38_L 95_S 1.31 0.41 0.04
38_L 83_Q 1.27 0.38 0.03
45_T 96_F 1.22 0.35 0.03
4_K 116_I 1.21 0.34 0.03
53_L 117_S 1.19 0.33 0.02
38_L 75_R 1.19 0.33 0.02
37_L 95_S 1.16 0.30 0.02
64_S 90_S 1.15 0.30 0.02
42_V 76_M 1.11 0.28 0.02
62_D 8_A 1.11 0.28 0.02
73_K 40_R 1.11 0.28 0.02
72_I 63_E 1.10 0.27 0.02
63_D 69_S 1.10 0.27 0.02
55_Y 106_Q 1.08 0.26 0.02
78_A 57_E 1.08 0.26 0.02
51_T 98_L 1.06 0.24 0.01
36_V 92_K 1.05 0.24 0.01
52_D 85_R 1.03 0.23 0.01
35_Y 95_S 1.01 0.22 0.01
5_N 42_K 1.01 0.22 0.01
68_I 72_N 1.01 0.22 0.01
42_V 83_Q 0.98 0.20 0.01
51_T 89_V 0.97 0.20 0.01
64_S 97_E 0.95 0.19 0.01
67_G 97_E 0.95 0.19 0.01
86_Q 15_V 0.95 0.19 0.01
55_Y 116_I 0.94 0.18 0.01
46_E 61_D 0.94 0.18 0.01
53_L 109_G 0.93 0.18 0.01
54_I 96_F 0.92 0.17 0.01
72_I 53_K 0.90 0.16 0.01
59_D 84_T 0.89 0.16 0.01
83_G 35_I 0.89 0.16 0.01
57_P 111_Y 0.88 0.16 0.01
38_L 88_D 0.86 0.15 0.01
10_Y 37_N 0.86 0.15 0.01
10_Y 110_V 0.85 0.15 0.01
69_V 11_K 0.85 0.14 0.01
49_D 77_K 0.85 0.14 0.01
81_K 123_R 0.85 0.14 0.01
74_E 21_N 0.84 0.14 0.01
12_E 40_R 0.84 0.14 0.01
67_G 89_V 0.84 0.14 0.01
81_K 102_K 0.83 0.14 0.01
28_A 80_K 0.82 0.13 0.01
14_E 39_L 0.81 0.13 0.01
78_A 14_P 0.81 0.13 0.01
79_N 15_V 0.81 0.13 0.01
64_S 113_M 0.81 0.13 0.01
79_N 13_K 0.81 0.13 0.01
86_Q 21_N 0.81 0.13 0.01
22_I 96_F 0.81 0.13 0.01
53_L 59_S 0.81 0.13 0.01
31_D 95_S 0.80 0.13 0.01
39_E 92_K 0.80 0.13 0.01
8_S 116_I 0.80 0.13 0.01
81_K 9_T 0.80 0.13 0.01
17_Q 118_V 0.80 0.13 0.01
9_D 24_G 0.79 0.13 0.01
53_L 66_K 0.79 0.13 0.01
78_A 43_E 0.79 0.12 0.01
54_I 79_G 0.79 0.12 0.01
62_D 48_D 0.79 0.12 0.01
55_Y 109_G 0.79 0.12 0.01
80_G 117_S 0.79 0.12 0.01
78_A 46_S 0.78 0.12 0.01
51_T 109_G 0.78 0.12 0.01
8_S 105_S 0.78 0.12 0.01
47_H 40_R 0.77 0.12 0.00
67_G 82_P 0.77 0.12 0.00
37_L 9_T 0.77 0.12 0.00
40_H 9_T 0.77 0.12 0.00
12_E 99_H 0.77 0.12 0.00
55_Y 84_T 0.76 0.12 0.00
80_G 59_S 0.76 0.12 0.00
85_K 63_E 0.76 0.11 0.00
19_L 88_D 0.76 0.11 0.00
82_P 121_P 0.75 0.11 0.00
72_I 78_V 0.75 0.11 0.00
81_K 61_D 0.75 0.11 0.00
74_E 58_V 0.75 0.11 0.00
60_N 41_D 0.74 0.11 0.00
86_Q 56_E 0.74 0.11 0.00
14_E 30_P 0.74 0.11 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)
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