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OPENSEQ.org
1RM6_B_C
Genes: A B A+B
Length: 324 161 436
Sequences: 3456 4844 2224
Seq/Len: 10.67 30.09 5.1
MirrorTree (Pazo et al. 2001) 0.84
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 4.01
2 0.01 0.02 4.54
5 0.02 0.03 4.56
10 0.03 0.04 4.58
20 0.10 0.06 4.59
100 0.13 0.10 4.60
∞ 0.22 0.19 4.67
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 2.75 1.00 1.00
30_L 67_Q 2.29 1.00 0.99
37_L 64_L 2.01 1.00 0.99
41_R 23_L 1.55 0.99 0.94
109_A 59_L 1.46 0.98 0.91
11_R 69_A 1.38 0.97 0.88
103_G 59_L 1.35 0.97 0.87
9_T 66_H 1.30 0.96 0.85
77_T 56_R 1.14 0.90 0.73
109_A 63_T 1.13 0.89 0.72
99_E 128_A 1.10 0.88 0.69
105_T 110_A 1.10 0.87 0.69
55_G 69_A 1.08 0.86 0.68
41_R 42_D 1.06 0.84 0.65
83_E 117_K 1.04 0.83 0.63
105_T 50_T 0.97 0.76 0.54
55_G 71_K 0.96 0.76 0.54
79_E 56_R 0.96 0.75 0.53
54_T 67_Q 0.93 0.72 0.50
35_D 45_E 0.91 0.70 0.47
34_T 62_S 0.82 0.58 0.36
106_H 59_L 0.79 0.55 0.33
109_A 67_Q 0.78 0.52 0.31
228_R 131_A 0.76 0.50 0.29
7_F 21_N 0.76 0.49 0.28
40_L 64_L 0.74 0.47 0.27
52_D 67_Q 0.74 0.47 0.26
193_E 73_V 0.70 0.41 0.22
202_E 124_D 0.69 0.40 0.21
41_R 45_E 0.69 0.39 0.21
108_A 57_P 0.68 0.38 0.20
34_T 44_G 0.66 0.36 0.19
317_V 153_A 0.65 0.34 0.17
258_G 67_Q 0.64 0.33 0.16
233_F 45_E 0.63 0.32 0.16
252_L 102_F 0.63 0.32 0.16
109_A 58_R 0.63 0.32 0.16
102_A 133_N 0.63 0.32 0.16
269_D 127_K 0.62 0.31 0.15
41_R 43_G 0.62 0.31 0.15
315_K 97_G 0.62 0.30 0.15
7_F 64_L 0.61 0.30 0.14
109_A 71_K 0.60 0.29 0.14
230_A 45_E 0.60 0.28 0.14
41_R 129_A 0.60 0.28 0.13
282_E 97_G 0.59 0.27 0.13
103_G 43_G 0.59 0.27 0.13
290_K 144_I 0.59 0.27 0.13
103_G 45_E 0.59 0.27 0.12
42_R 43_G 0.58 0.26 0.12
104_P 129_A 0.58 0.26 0.12
305_R 139_G 0.58 0.26 0.12
3_I 26_D 0.58 0.26 0.12
233_F 42_D 0.58 0.26 0.12
111_T 67_Q 0.58 0.26 0.12
50_L 66_H 0.58 0.26 0.12
106_H 44_G 0.58 0.26 0.12
162_D 132_G 0.57 0.25 0.12
79_E 117_K 0.57 0.25 0.11
212_V 54_D 0.57 0.25 0.11
4_L 23_L 0.57 0.25 0.11
224_K 45_E 0.57 0.24 0.11
103_G 26_D 0.56 0.24 0.11
263_P 91_A 0.56 0.24 0.11
231_V 107_M 0.56 0.23 0.10
89_T 152_A 0.56 0.23 0.10
34_T 38_K 0.55 0.23 0.10
36_L 59_L 0.55 0.23 0.10
232_D 57_P 0.54 0.22 0.10
115_N 38_K 0.54 0.21 0.09
72_I 94_E 0.53 0.21 0.09
317_V 79_L 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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