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OPENSEQ.org
1a2k_pdbseq
Genes: A B A+B
Length: 124 196 286
Sequences: 916 10330 61
Seq/Len: 7.39 52.7 0.21
MirrorTree (Pazo et al. 2001) 0.28
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 0.05 0.05 0.02
2 0.05 0.05 0.02
5 0.05 0.07 0.06
10 0.05 0.08 0.11
20 0.05 0.11 0.19
100 0.05 0.20 0.72
∞ 0.07 0.27 1.39
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
80_S 24_L 1.56 0.37 0.00
80_S 100_D 1.41 0.28 0.00
80_S 7_V 1.36 0.26 0.00
65_I 161_L 1.36 0.26 0.00
78_I 26_G 1.33 0.24 0.00
55_S 111_V 1.32 0.24 0.00
96_F 152_K 1.21 0.20 0.00
80_S 147_N 1.20 0.19 0.00
29_I 81_I 1.16 0.18 0.00
79_I 157_L 1.15 0.17 0.00
111_C 59_T 1.15 0.17 0.00
53_L 126_A 1.14 0.17 0.00
12_I 9_V 1.13 0.17 0.00
27_G 8_L 1.11 0.16 0.00
84_G 118_D 1.09 0.15 0.00
20_D 112_L 1.08 0.15 0.00
92_P 19_F 1.08 0.15 0.00
96_F 53_K 1.08 0.15 0.00
36_L 80_I 1.04 0.14 0.00
116_F 154_F 1.03 0.14 0.00
80_S 63_E 1.01 0.13 0.00
38_W 53_K 1.01 0.13 0.00
73_T 100_D 1.00 0.13 0.00
109_W 20_V 0.99 0.12 0.00
104_N 71_G 0.98 0.12 0.00
6_Q 84_D 0.97 0.12 0.00
84_G 116_K 0.97 0.12 0.00
84_G 143_S 0.97 0.12 0.00
53_L 107_N 0.96 0.12 0.00
96_F 144_A 0.96 0.12 0.00
32_D 91_Y 0.96 0.12 0.00
84_G 10_G 0.96 0.12 0.00
84_G 15_G 0.96 0.12 0.00
84_G 16_K 0.96 0.12 0.00
66_T 83_F 0.95 0.11 0.00
69_D 118_D 0.94 0.11 0.00
96_F 146_S 0.94 0.11 0.00
40_G 115_N 0.94 0.11 0.00
23_R 112_L 0.94 0.11 0.00
12_I 151_E 0.93 0.11 0.00
84_G 58_D 0.93 0.11 0.00
114_D 73_Y 0.93 0.11 0.00
104_N 7_V 0.93 0.11 0.00
102_L 59_T 0.92 0.11 0.00
57_P 23_H 0.92 0.11 0.00
62_Q 23_H 0.92 0.11 0.00
76_S 39_E 0.91 0.10 0.00
78_I 81_I 0.90 0.10 0.00
65_I 47_T 0.89 0.10 0.00
7_I 96_N 0.88 0.10 0.00
45_G 118_D 0.88 0.10 0.00
65_I 147_N 0.87 0.10 0.00
89_D 112_L 0.87 0.10 0.00
80_S 152_K 0.87 0.10 0.00
104_N 145_K 0.87 0.10 0.00
30_Y 61_G 0.86 0.09 0.00
79_I 124_V 0.86 0.09 0.00
117_R 143_S 0.86 0.09 0.00
66_T 79_A 0.86 0.09 0.00
98_Q 113_C 0.86 0.09 0.00
115_M 45_F 0.85 0.09 0.00
102_L 19_F 0.85 0.09 0.00
111_C 49_R 0.85 0.09 0.00
55_S 107_N 0.85 0.09 0.00
77_C 78_C 0.85 0.09 0.00
105_I 25_T 0.84 0.09 0.00
86_L 55_N 0.84 0.09 0.00
72_P 54_F 0.83 0.09 0.00
36_L 139_Y 0.83 0.09 0.00
21_N 90_T 0.83 0.09 0.00
12_I 89_V 0.83 0.09 0.00
102_L 35_T 0.82 0.09 0.00
62_Q 7_V 0.82 0.09 0.00
109_W 65_F 0.82 0.09 0.00
36_L 17_T 0.82 0.09 0.00
11_F 118_D 0.81 0.09 0.00
16_Y 118_D 0.81 0.09 0.00
13_Q 43_L 0.81 0.08 0.00
46_K 13_G 0.81 0.08 0.00
80_S 57_W 0.81 0.08 0.00
100_F 84_D 0.81 0.08 0.00
113_N 91_Y 0.81 0.08 0.00
80_S 93_N 0.81 0.08 0.00
78_I 157_L 0.80 0.08 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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