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OPENSEQ.org
L1-vs-L4
Genes: A B A+B
Length: 234 201 426
Sequences: 3196 3177 1637
Seq/Len: 13.66 15.81 3.84
MirrorTree (Pazo et al. 2001) 0.79
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 0.09 0.08 0.00
2 0.09 0.08 0.00
5 0.09 0.08 0.01
10 0.09 0.09 0.23
20 0.09 0.09 1.37
100 0.09 0.09 2.14
∞ 0.10 0.09 3.76
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
35_T 189_T 1.06 0.78 0.03
224_V 191_D 0.78 0.45 0.01
50_I 79_R 0.77 0.43 0.01
122_R 180_L 0.76 0.41 0.01
20_Q 61_R 0.75 0.40 0.01
59_V 32_V 0.74 0.39 0.01
210_K 139_K 0.70 0.34 0.01
229_L 187_V 0.69 0.34 0.01
130_V 61_R 0.69 0.33 0.01
224_V 36_A 0.67 0.31 0.01
222_V 142_A 0.67 0.31 0.01
171_I 124_F 0.65 0.28 0.01
147_P 154_D 0.65 0.28 0.01
203_Q 30_Q 0.64 0.28 0.01
185_L 135_A 0.64 0.28 0.01
181_D 186_V 0.64 0.27 0.01
15_V 193_V 0.63 0.27 0.01
207_V 193_V 0.63 0.27 0.01
73_V 101_Y 0.63 0.27 0.01
53_R 51_E 0.62 0.26 0.01
55_S 104_A 0.62 0.26 0.01
59_V 39_A 0.62 0.26 0.01
98_E 142_A 0.62 0.26 0.01
105_K 61_R 0.62 0.25 0.01
213_S 169_V 0.62 0.25 0.01
224_V 119_I 0.62 0.25 0.01
104_I 57_K 0.61 0.25 0.01
7_R 18_T 0.61 0.24 0.01
129_Q 86_A 0.60 0.24 0.01
42_V 169_V 0.60 0.23 0.01
149_V 82_G 0.60 0.23 0.01
11_I 120_V 0.59 0.22 0.01
142_V 175_I 0.59 0.22 0.01
46_V 194_K 0.59 0.22 0.01
182_A 166_K 0.58 0.22 0.01
153_V 153_L 0.58 0.22 0.01
25_E 73_I 0.58 0.22 0.01
28_A 191_D 0.58 0.21 0.01
164_R 94_Q 0.58 0.21 0.01
193_L 193_V 0.58 0.21 0.01
189_L 164_L 0.58 0.21 0.01
142_V 98_K 0.58 0.21 0.01
99_D 167_V 0.57 0.21 0.01
105_K 75_S 0.57 0.21 0.01
185_L 192_A 0.57 0.21 0.01
78_F 124_F 0.57 0.21 0.01
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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