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OPENSEQ.org
1mr6_BC
Genes: A B A+B
Length: 323 157 432
Sequences: 3395 4822 2213
Seq/Len: 10.51 30.71 5.12
MirrorTree (Pazo et al. 2001) 0.85
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 0.01 0.01 4.05
2 0.01 0.02 4.56
5 0.02 0.03 4.60
10 0.03 0.04 4.61
20 0.04 0.06 4.61
100 0.07 0.10 4.63
∞ 0.17 0.19 4.69
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_A 56_R 2.74 1.00 1.00
30_L 67_Q 2.26 1.00 0.99
37_L 64_L 1.98 1.00 0.99
41_R 23_L 1.50 0.99 0.93
109_A 59_L 1.46 0.98 0.91
11_R 69_A 1.39 0.97 0.89
103_G 59_L 1.35 0.97 0.87
9_T 66_H 1.25 0.94 0.82
77_T 56_R 1.16 0.91 0.75
109_A 63_T 1.14 0.90 0.73
105_T 110_A 1.07 0.86 0.66
55_G 69_A 1.06 0.85 0.66
99_E 128_A 1.06 0.84 0.65
83_E 117_K 1.03 0.82 0.62
41_R 42_D 1.03 0.82 0.61
79_E 56_R 0.98 0.78 0.56
105_T 50_T 0.96 0.76 0.54
54_T 67_Q 0.93 0.73 0.50
35_D 45_E 0.91 0.70 0.47
55_G 71_K 0.91 0.70 0.47
34_T 62_S 0.81 0.57 0.35
106_H 59_L 0.80 0.55 0.33
109_A 67_Q 0.77 0.51 0.29
7_F 21_N 0.74 0.47 0.27
40_L 64_L 0.73 0.45 0.25
52_D 67_Q 0.72 0.45 0.25
228_R 131_A 0.72 0.44 0.24
41_R 45_E 0.69 0.40 0.21
252_L 102_F 0.69 0.39 0.21
317_V 153_A 0.67 0.38 0.20
108_A 57_P 0.67 0.37 0.19
34_T 44_G 0.67 0.37 0.19
193_E 73_V 0.66 0.36 0.19
233_F 45_E 0.64 0.34 0.17
41_R 43_G 0.64 0.33 0.17
212_V 54_D 0.64 0.33 0.16
109_A 71_K 0.63 0.32 0.16
258_G 67_Q 0.63 0.32 0.15
102_A 133_N 0.62 0.31 0.15
109_A 58_R 0.62 0.31 0.15
41_R 129_A 0.61 0.30 0.15
50_L 66_H 0.61 0.30 0.14
7_F 64_L 0.61 0.30 0.14
315_K 97_G 0.61 0.29 0.14
202_E 124_D 0.61 0.29 0.14
42_R 43_G 0.60 0.29 0.14
233_F 42_D 0.60 0.28 0.14
230_A 45_E 0.60 0.28 0.13
103_G 45_E 0.60 0.28 0.13
111_T 67_Q 0.60 0.28 0.13
103_G 43_G 0.59 0.27 0.13
305_R 139_G 0.59 0.27 0.13
263_P 91_A 0.59 0.27 0.13
290_K 144_I 0.59 0.27 0.13
104_P 129_A 0.58 0.27 0.12
224_K 45_E 0.58 0.26 0.12
106_H 44_G 0.57 0.26 0.12
4_L 23_L 0.57 0.25 0.12
3_I 26_D 0.57 0.25 0.11
282_E 97_G 0.57 0.24 0.11
162_D 132_G 0.57 0.24 0.11
232_D 57_P 0.56 0.24 0.11
103_G 26_D 0.56 0.23 0.10
308_V 97_G 0.55 0.23 0.10
115_N 38_K 0.55 0.23 0.10
79_E 117_K 0.55 0.23 0.10
269_D 127_K 0.54 0.22 0.09
231_V 107_M 0.53 0.21 0.09
40_L 50_T 0.53 0.21 0.09
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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