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OPENSEQ.org
Barnase Barstar
Genes: A B A+B
Length: 110 90 196
Sequences: 375 303 151
Seq/Len: 3.41 3.37 0.77
MirrorTree (Pazo et al. 2001) 0.77
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 0.00 0.00 0.73
2 0.00 0.00 0.76
5 0.00 0.00 0.76
10 0.00 0.01 0.76
20 0.00 0.01 0.76
100 0.00 0.01 0.77
∞ 0.01 0.02 0.81
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
90_Y 39_W 1.50 0.70 0.00
88_I 50_L 1.44 0.64 0.00
50_S 54_W 1.42 0.63 0.00
47_P 78_A 1.35 0.58 0.00
59_R 39_W 1.31 0.54 0.00
46_A 31_Y 1.30 0.53 0.00
107_T 61_K 1.27 0.50 0.00
105_T 75_F 1.26 0.50 0.00
46_A 18_H 1.23 0.47 0.00
15_Q 71_V 1.22 0.47 0.00
61_G 48_Y 1.17 0.42 0.00
29_E 1_M 1.16 0.41 0.00
61_G 70_S 1.16 0.41 0.00
60_E 36_D 1.15 0.41 0.00
37_A 48_Y 1.15 0.40 0.00
23_N 31_Y 1.13 0.39 0.00
93_D 39_W 1.09 0.35 0.00
71_W 49_P 1.08 0.35 0.00
89_L 76_R 1.08 0.34 0.00
83_R 52_L 1.07 0.34 0.00
36_V 83_A 1.06 0.33 0.00
48_G 43_T 1.04 0.32 0.00
50_S 17_L 1.03 0.31 0.00
108_K 86_T 1.02 0.30 0.00
82_F 39_W 1.01 0.29 0.00
80_S 54_W 1.00 0.28 0.00
104_Q 78_A 0.99 0.28 0.00
23_N 18_H 0.98 0.28 0.00
86_D 44_G 0.98 0.27 0.00
7_F 11_I 0.98 0.27 0.00
37_A 46_V 0.97 0.27 0.00
92_S 9_E 0.97 0.26 0.00
85_S 28_P 0.97 0.26 0.00
19_K 80_A 0.96 0.26 0.00
89_L 46_V 0.96 0.26 0.00
71_W 39_W 0.95 0.25 0.00
48_G 59_Q 0.94 0.25 0.00
88_I 5_V 0.93 0.24 0.00
82_F 56_Q 0.92 0.23 0.00
68_G 26_A 0.92 0.23 0.00
7_F 54_W 0.92 0.23 0.00
26_T 74_V 0.91 0.23 0.00
23_N 8_G 0.91 0.23 0.00
5_N 78_A 0.91 0.23 0.00
24_Y 60_S 0.91 0.23 0.00
31_Q 23_K 0.91 0.23 0.00
99_T 37_A 0.91 0.22 0.00
14_L 56_Q 0.90 0.22 0.00
8_D 47_E 0.90 0.22 0.00
104_Q 24_E 0.90 0.22 0.00
54_D 44_G 0.90 0.22 0.00
49_K 53_E 0.90 0.22 0.00
59_R 74_V 0.89 0.22 0.00
19_K 29_E 0.89 0.21 0.00
71_W 13_S 0.89 0.21 0.00
90_Y 19_Q 0.89 0.21 0.00
59_R 77_E 0.89 0.21 0.00
24_Y 23_K 0.87 0.20 0.00
29_E 74_V 0.86 0.20 0.00
105_T 60_S 0.86 0.20 0.00
24_Y 25_L 0.86 0.20 0.00
22_D 2_K 0.85 0.20 0.00
97_Y 18_H 0.85 0.19 0.00
32_A 1_M 0.85 0.19 0.00
69_R 39_W 0.85 0.19 0.00
37_A 49_P 0.84 0.19 0.00
80_S 6_I 0.84 0.19 0.00
98_A 11_I 0.84 0.19 0.00
22_D 56_Q 0.84 0.19 0.00
14_L 20_T 0.84 0.19 0.00
94_W 40_A 0.84 0.19 0.00
70_T 56_Q 0.83 0.18 0.00
55_I 73_Q 0.83 0.18 0.00
97_Y 3_K 0.82 0.18 0.00
60_E 35_L 0.82 0.18 0.00
24_Y 65_E 0.81 0.17 0.00
43_A 18_H 0.81 0.17 0.00
77_N 4_A 0.81 0.17 0.00
14_L 14_I 0.80 0.17 0.00
50_S 18_H 0.80 0.17 0.00
23_N 68_A 0.80 0.17 0.00
84_N 14_I 0.80 0.17 0.00
51_I 86_T 0.80 0.17 0.00
50_S 31_Y 0.79 0.16 0.00
105_T 10_Q 0.79 0.16 0.00
108_K 1_M 0.79 0.16 0.00
38_S 27_L 0.79 0.16 0.00
13_Y 27_L 0.78 0.16 0.00
90_Y 43_T 0.78 0.16 0.00
19_K 75_F 0.78 0.16 0.00
59_R 36_D 0.78 0.16 0.00
109_I 22_K 0.78 0.16 0.00
110_R 62_Q 0.77 0.15 0.00
92_S 71_V 0.77 0.15 0.00
108_K 72_L 0.77 0.15 0.00
85_S 16_D 0.77 0.15 0.00
46_A 17_L 0.77 0.15 0.00
98_A 86_T 0.77 0.15 0.00
37_A 47_E 0.76 0.15 0.00
71_W 77_E 0.76 0.15 0.00
85_S 77_E 0.76 0.15 0.00
62_K 71_V 0.76 0.15 0.00
85_S 39_W 0.76 0.15 0.00
61_G 55_R 0.76 0.15 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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