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OPENSEQ.org
L1-vs-S7
Genes: A B A+B
Length: 234 179 381
Sequences: 3196 1685 1310
Seq/Len: 13.66 9.41 3.44
MirrorTree (Pazo et al. 2001) 0.80
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 0.11 0.00
2 0.09 0.11 0.00
5 0.09 0.11 0.16
10 0.09 0.11 1.74
20 0.09 0.11 1.96
100 0.09 0.11 2.32
∞ 0.10 0.11 3.17
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
129_Q 76_K 1.13 0.81 0.07
198_K 17_K 0.94 0.62 0.04
5_T 16_P 0.90 0.57 0.03
35_T 43_V 0.89 0.56 0.03
58_N 77_S 0.87 0.53 0.03
27_I 66_L 0.83 0.48 0.03
99_D 11_K 0.82 0.46 0.02
182_A 50_L 0.81 0.45 0.02
141_K 90_E 0.81 0.45 0.02
196_L 129_E 0.80 0.44 0.02
196_L 121_A 0.80 0.43 0.02
89_A 93_P 0.79 0.42 0.02
147_P 135_V 0.78 0.41 0.02
166_D 20_S 0.78 0.41 0.02
155_N 9_Q 0.77 0.40 0.02
160_Q 149_K 0.76 0.39 0.02
210_K 139_E 0.76 0.39 0.02
218_M 83_S 0.75 0.38 0.02
149_V 128_A 0.75 0.38 0.02
59_V 141_V 0.74 0.36 0.02
167_K 100_A 0.73 0.36 0.02
175_I 27_V 0.72 0.35 0.02
58_N 70_R 0.72 0.34 0.02
104_I 149_K 0.71 0.33 0.02
120_A 70_R 0.71 0.33 0.02
98_E 12_I 0.71 0.33 0.02
64_V 76_K 0.71 0.33 0.02
185_L 46_A 0.71 0.33 0.02
122_R 143_R 0.70 0.32 0.02
214_I 133_T 0.70 0.32 0.02
59_V 87_V 0.70 0.32 0.01
127_L 76_K 0.68 0.30 0.01
17_A 122_N 0.68 0.30 0.01
204_A 83_S 0.68 0.29 0.01
207_V 13_L 0.68 0.29 0.01
78_F 48_E 0.67 0.29 0.01
223_A 47_L 0.67 0.29 0.01
165_N 20_S 0.67 0.29 0.01
169_G 26_F 0.67 0.28 0.01
15_V 143_R 0.67 0.28 0.01
99_D 12_I 0.66 0.28 0.01
81_G 124_L 0.66 0.28 0.01
7_R 100_A 0.65 0.27 0.01
113_V 131_K 0.65 0.27 0.01
73_V 5_R 0.65 0.27 0.01
185_L 97_N 0.65 0.27 0.01
170_I 4_R 0.65 0.26 0.01
123_V 106_E 0.64 0.26 0.01
54_K 29_I 0.64 0.26 0.01
227_A 58_E 0.64 0.26 0.01
158_A 149_K 0.64 0.25 0.01
160_Q 77_S 0.64 0.25 0.01
58_N 131_K 0.64 0.25 0.01
164_R 102_R 0.64 0.25 0.01
126_Q 135_V 0.64 0.25 0.01
5_T 154_Y 0.64 0.25 0.01
215_S 94_V 0.64 0.25 0.01
113_V 60_E 0.63 0.25 0.01
208_Y 93_P 0.63 0.25 0.01
130_V 115_S 0.63 0.25 0.01
149_V 38_T 0.63 0.24 0.01
211_K 138_R 0.63 0.24 0.01
12_R 125_S 0.63 0.24 0.01
189_L 29_I 0.63 0.24 0.01
27_I 87_V 0.62 0.24 0.01
151_E 133_T 0.62 0.23 0.01
183_D 52_Q 0.61 0.23 0.01
212_V 49_T 0.61 0.23 0.01
68_G 81_G 0.61 0.23 0.01
28_A 128_A 0.61 0.23 0.01
153_V 87_V 0.61 0.22 0.01
185_L 156_W 0.61 0.22 0.01
196_L 124_L 0.61 0.22 0.01
195_A 31_M 0.60 0.22 0.01
216_T 152_A 0.60 0.22 0.01
47_N 23_L 0.60 0.22 0.01
79_T 80_V 0.60 0.22 0.01
27_I 14_P 0.60 0.22 0.01
163_Y 110_K 0.60 0.22 0.01
160_Q 152_A 0.59 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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