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OPENSEQ.org
L4-vs-L5
Genes: A B A+B
Length: 201 179 380
Sequences: 3177 2042 1804
Seq/Len: 15.81 11.41 4.75
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 0.08 0.09 0.00
2 0.08 0.09 0.01
5 0.08 0.09 0.02
10 0.09 0.09 0.43
20 0.09 0.09 4.45
100 0.09 0.09 4.57
∞ 0.09 0.09 4.75
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
11_A 18_T 0.77 0.49 0.00
24_N 93_G 0.77 0.48 0.00
115_Q 74_V 0.73 0.44 0.00
129_P 87_C 0.73 0.44 0.00
189_T 38_M 0.71 0.41 0.00
175_I 166_G 0.71 0.41 0.00
26_A 147_D 0.71 0.41 0.00
155_E 149_V 0.71 0.41 0.00
110_S 57_L 0.69 0.38 0.00
194_K 30_R 0.69 0.38 0.00
199_M 136_I 0.67 0.35 0.00
34_A 46_D 0.67 0.35 0.00
169_V 34_I 0.66 0.34 0.00
177_P 57_L 0.66 0.34 0.00
168_D 46_D 0.66 0.33 0.00
197_E 118_S 0.65 0.33 0.00
50_A 2_A 0.65 0.33 0.00
57_K 69_K 0.65 0.33 0.00
65_T 93_G 0.65 0.33 0.00
86_A 83_Y 0.64 0.32 0.00
97_N 137_I 0.63 0.31 0.00
41_Q 153_D 0.62 0.30 0.00
156_N 66_L 0.62 0.29 0.00
67_R 65_P 0.61 0.28 0.00
133_L 50_L 0.60 0.27 0.00
65_T 173_F 0.59 0.26 0.00
28_V 52_N 0.58 0.25 0.00
101_Y 143_Y 0.58 0.25 0.00
49_R 84_P 0.58 0.25 0.00
106_K 161_K 0.58 0.24 0.00
65_T 118_S 0.57 0.24 0.00
57_K 52_N 0.57 0.24 0.00
110_S 53_A 0.57 0.23 0.00
177_P 49_L 0.56 0.23 0.00
188_M 110_R 0.56 0.23 0.00
11_A 10_D 0.56 0.23 0.00
101_Y 133_R 0.56 0.23 0.00
78_W 106_I 0.56 0.23 0.00
178_V 152_L 0.56 0.23 0.00
92_H 174_D 0.56 0.22 0.00
187_V 120_K 0.55 0.22 0.00
11_A 19_E 0.55 0.22 0.00
99_K 74_V 0.55 0.22 0.00
79_R 100_F 0.55 0.21 0.00
40_R 174_D 0.54 0.21 0.00
84_T 178_R 0.54 0.21 0.00
98_K 64_K 0.54 0.21 0.00
194_K 71_R 0.54 0.21 0.00
1_M 136_I 0.54 0.21 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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