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OPENSEQ.org
1UJZ
Genes: A B A+B
Length: 85 128 210
Sequences: 211 134 103
Seq/Len: 2.48 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
50_D 86_T 2.05 0.87 0.28
37_E 94_R 1.68 0.68 0.11
54_Y 72_N 1.65 0.67 0.10
40_V 86_T 1.56 0.60 0.08
81_G 15_V 1.51 0.56 0.07
21_E 71_N 1.43 0.50 0.06
62_S 125_I 1.41 0.49 0.05
29_D 75_R 1.38 0.46 0.05
36_L 95_S 1.30 0.41 0.04
36_L 83_Q 1.26 0.37 0.03
43_T 96_F 1.22 0.35 0.03
51_L 117_S 1.21 0.34 0.03
2_K 116_I 1.20 0.33 0.03
36_L 75_R 1.19 0.32 0.02
40_V 76_M 1.18 0.32 0.02
35_L 95_S 1.15 0.30 0.02
62_S 90_S 1.15 0.30 0.02
10_E 40_R 1.13 0.28 0.02
76_A 57_E 1.12 0.28 0.02
60_D 8_A 1.10 0.27 0.02
61_D 69_S 1.10 0.27 0.02
53_Y 106_Q 1.08 0.26 0.02
49_T 98_L 1.05 0.24 0.01
50_D 85_R 1.04 0.23 0.01
34_V 92_K 1.03 0.23 0.01
70_I 63_E 1.03 0.23 0.01
40_V 83_Q 1.02 0.23 0.01
3_N 42_K 1.01 0.22 0.01
33_Y 95_S 1.00 0.21 0.01
66_I 72_N 1.00 0.21 0.01
49_T 89_V 0.97 0.20 0.01
70_I 53_K 0.96 0.20 0.01
65_G 97_E 0.95 0.19 0.01
62_S 97_E 0.95 0.19 0.01
53_Y 116_I 0.95 0.19 0.01
84_Q 15_V 0.94 0.18 0.01
51_L 109_G 0.93 0.18 0.01
52_I 96_F 0.91 0.17 0.01
57_D 84_T 0.89 0.16 0.01
55_P 111_Y 0.87 0.15 0.01
8_Y 37_N 0.86 0.15 0.01
36_L 88_D 0.86 0.15 0.01
8_Y 110_V 0.85 0.14 0.01
67_V 11_K 0.85 0.14 0.01
72_E 21_N 0.85 0.14 0.01
79_K 123_R 0.85 0.14 0.01
65_G 89_V 0.84 0.14 0.01
60_D 48_D 0.84 0.14 0.01
47_D 77_K 0.84 0.14 0.01
76_A 14_P 0.83 0.14 0.01
62_S 113_M 0.82 0.14 0.01
81_G 35_I 0.82 0.14 0.01
79_K 102_K 0.82 0.14 0.01
71_K 40_R 0.82 0.14 0.01
26_A 80_K 0.82 0.13 0.01
83_K 63_E 0.81 0.13 0.01
70_I 78_V 0.81 0.13 0.01
28_T 35_I 0.81 0.13 0.01
20_I 96_F 0.81 0.13 0.01
29_D 95_S 0.81 0.13 0.01
51_L 59_S 0.81 0.13 0.01
78_G 59_S 0.81 0.13 0.01
44_E 61_D 0.80 0.13 0.01
77_N 13_K 0.80 0.13 0.01
77_N 15_V 0.80 0.13 0.01
84_Q 21_N 0.80 0.13 0.01
70_I 38_K 0.80 0.13 0.01
79_K 9_T 0.80 0.13 0.01
6_S 105_S 0.79 0.12 0.01
51_L 66_K 0.79 0.12 0.01
52_I 79_G 0.79 0.12 0.01
53_Y 109_G 0.79 0.12 0.01
37_E 92_K 0.79 0.12 0.01
80_P 41_D 0.79 0.12 0.01
76_A 43_E 0.78 0.12 0.01
6_S 116_I 0.78 0.12 0.01
53_Y 84_T 0.78 0.12 0.01
7_D 24_G 0.78 0.12 0.01
49_T 109_G 0.78 0.12 0.01
12_E 39_L 0.77 0.12 0.01
35_L 9_T 0.77 0.12 0.01
65_G 82_P 0.77 0.12 0.00
81_G 61_D 0.77 0.12 0.00
38_H 9_T 0.77 0.12 0.00
68_K 59_S 0.76 0.12 0.00
10_E 99_H 0.75 0.11 0.00
15_Q 118_V 0.75 0.11 0.00
58_N 41_D 0.75 0.11 0.00
17_L 88_D 0.75 0.11 0.00
75_A 15_V 0.75 0.11 0.00
72_E 58_V 0.75 0.11 0.00
16_L 96_F 0.75 0.11 0.00
80_P 121_P 0.75 0.11 0.00
76_A 46_S 0.74 0.11 0.00
55_P 125_I 0.74 0.11 0.00
6_S 59_S 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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