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OPENSEQ.org
3RN9
Genes: A B A+B
Length: 260 77 311
Sequences: 15241 738 597
Seq/Len: 58.62 9.58 1.92
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 0.02 0.10 1.78
2 0.03 0.10 1.77
5 0.03 0.10 1.77
10 0.05 0.10 1.77
20 0.06 0.10 1.77
100 0.11 0.10 1.81
∞ 0.18 0.10 1.83
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
236_G 15_V 1.60 0.94 0.62
4_I 15_V 1.45 0.89 0.49
150_V 17_E 1.24 0.75 0.31
37_I 13_N 1.20 0.72 0.28
192_D 16_A 1.15 0.67 0.24
4_I 3_T 1.14 0.66 0.23
37_I 33_K 1.13 0.65 0.22
76_K 28_L 1.12 0.64 0.22
79_R 46_D 1.10 0.62 0.21
140_I 30_Q 1.07 0.59 0.19
150_V 14_I 1.07 0.59 0.18
237_K 15_V 1.04 0.55 0.17
72_Q 26_H 1.03 0.55 0.16
116_F 5_N 1.03 0.55 0.16
19_S 68_V 1.03 0.55 0.16
7_V 68_V 1.03 0.54 0.16
79_R 15_V 1.03 0.54 0.16
34_T 32_R 1.01 0.53 0.15
147_V 7_A 0.99 0.50 0.14
23_I 21_S 0.98 0.48 0.13
206_K 16_A 0.96 0.47 0.12
197_E 49_M 0.96 0.47 0.12
208_V 50_V 0.94 0.44 0.11
102_V 66_L 0.92 0.43 0.11
116_F 26_H 0.91 0.41 0.10
61_V 46_D 0.90 0.41 0.10
130_L 14_I 0.90 0.41 0.10
110_K 54_L 0.90 0.40 0.10
7_V 55_E 0.90 0.40 0.10
246_L 62_S 0.90 0.40 0.10
48_L 66_L 0.89 0.39 0.09
52_C 29_P 0.88 0.39 0.09
253_F 61_I 0.88 0.38 0.09
164_S 56_Q 0.88 0.38 0.09
17_T 18_R 0.87 0.37 0.09
22_A 62_S 0.87 0.37 0.09
236_G 2_N 0.87 0.37 0.09
50_M 39_I 0.87 0.37 0.09
223_Q 17_E 0.86 0.36 0.08
23_I 4_A 0.86 0.36 0.08
215_Q 6_I 0.85 0.35 0.08
156_I 39_I 0.85 0.35 0.08
180_L 34_D 0.85 0.35 0.08
79_R 8_K 0.85 0.35 0.08
221_S 15_V 0.85 0.35 0.08
199_V 32_R 0.85 0.35 0.08
61_V 31_L 0.84 0.34 0.08
39_F 17_E 0.84 0.34 0.07
121_S 12_Q 0.84 0.34 0.07
36_V 43_V 0.83 0.33 0.07
217_V 13_N 0.83 0.33 0.07
242_T 18_R 0.83 0.33 0.07
87_P 62_S 0.83 0.33 0.07
64_I 16_A 0.83 0.33 0.07
219_R 62_S 0.82 0.32 0.07
19_S 62_S 0.82 0.32 0.07
199_V 4_A 0.82 0.32 0.07
217_V 12_Q 0.82 0.32 0.07
227_V 35_I 0.81 0.31 0.07
3_R 55_E 0.81 0.31 0.07
35_V 37_E 0.81 0.31 0.07
130_L 60_D 0.81 0.31 0.07
227_V 52_V 0.81 0.31 0.07
147_V 9_E 0.81 0.31 0.07
180_L 57_K 0.80 0.30 0.07
199_V 23_A 0.80 0.30 0.06
89_S 71_P 0.80 0.30 0.06
179_L 3_T 0.80 0.30 0.06
121_S 8_K 0.80 0.30 0.06
229_L 21_S 0.79 0.29 0.06
60_F 8_K 0.79 0.29 0.06
65_Q 29_P 0.79 0.29 0.06
177_H 28_L 0.78 0.28 0.06
50_M 28_L 0.78 0.28 0.06
141_I 5_N 0.78 0.28 0.06
140_I 67_N 0.78 0.28 0.06
7_V 43_V 0.77 0.28 0.06
39_F 65_E 0.77 0.28 0.06
61_V 21_S 0.77 0.28 0.06
178_L 54_L 0.77 0.28 0.06
103_A 2_N 0.77 0.28 0.06
23_I 34_D 0.77 0.27 0.06
118_V 21_S 0.77 0.27 0.06
37_I 40_C 0.77 0.27 0.06
195_S 72_E 0.77 0.27 0.06
89_S 60_D 0.76 0.27 0.05
32_K 49_M 0.76 0.27 0.05
202_I 14_I 0.76 0.26 0.05
50_M 57_K 0.75 0.26 0.05
211_I 34_D 0.75 0.26 0.05
202_I 31_L 0.75 0.26 0.05
148_S 50_V 0.74 0.25 0.05
49_I 65_E 0.74 0.25 0.05
36_V 50_V 0.74 0.25 0.05
37_I 56_Q 0.74 0.25 0.05
148_S 17_E 0.73 0.24 0.05
138_E 52_V 0.73 0.24 0.05
187_R 63_I 0.73 0.24 0.05
194_L 16_A 0.73 0.24 0.05
27_L 15_V 0.73 0.24 0.05
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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