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OPENSEQ.org
L4-vs-
Genes: A B A+B
Length: 201 179 357
Sequences: 3177 1685 1361
Seq/Len: 15.81 9.41 3.81
MirrorTree (Pazo et al. 2001) 0.67
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 0.11 0.00
2 0.08 0.11 0.00
5 0.08 0.11 2.14
10 0.09 0.11 2.49
20 0.09 0.11 2.64
100 0.09 0.11 3.01
∞ 0.09 0.11 3.58
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
13_T 57_S 1.10 0.81 0.06
169_V 17_K 0.96 0.67 0.04
137_K 138_R 0.96 0.67 0.04
27_L 9_Q 0.92 0.62 0.03
164_L 76_K 0.90 0.59 0.03
164_L 64_V 0.82 0.50 0.02
61_R 33_D 0.82 0.49 0.02
189_T 89_V 0.82 0.49 0.02
183_F 141_V 0.82 0.49 0.02
175_I 84_T 0.77 0.43 0.02
85_F 70_R 0.77 0.42 0.02
116_D 43_V 0.76 0.42 0.02
164_L 16_P 0.76 0.41 0.02
195_Q 149_K 0.76 0.41 0.02
37_A 93_P 0.75 0.40 0.02
79_R 49_T 0.74 0.39 0.02
92_H 43_V 0.73 0.38 0.02
64_G 104_I 0.73 0.38 0.02
26_A 20_S 0.71 0.36 0.02
187_V 78_R 0.70 0.34 0.01
113_V 128_A 0.70 0.34 0.01
108_I 83_S 0.70 0.34 0.01
10_S 109_R 0.70 0.34 0.01
24_N 141_V 0.70 0.34 0.01
108_I 101_M 0.70 0.34 0.01
44_R 152_A 0.69 0.34 0.01
98_K 143_R 0.69 0.33 0.01
57_K 137_K 0.68 0.32 0.01
102_R 16_P 0.68 0.32 0.01
92_H 37_S 0.67 0.31 0.01
70_S 80_V 0.67 0.30 0.01
73_I 73_V 0.67 0.30 0.01
187_V 154_Y 0.67 0.30 0.01
51_E 73_V 0.66 0.30 0.01
96_V 130_N 0.66 0.30 0.01
64_G 76_K 0.66 0.29 0.01
50_A 114_K 0.66 0.29 0.01
175_I 29_I 0.66 0.29 0.01
23_F 149_K 0.66 0.29 0.01
115_Q 105_V 0.66 0.29 0.01
83_V 154_Y 0.65 0.28 0.01
12_L 66_L 0.64 0.27 0.01
124_F 98_A 0.64 0.27 0.01
147_L 18_F 0.64 0.27 0.01
85_F 121_A 0.64 0.27 0.01
33_V 20_S 0.63 0.27 0.01
194_K 98_A 0.63 0.27 0.01
180_L 139_E 0.63 0.26 0.01
64_G 92_R 0.63 0.26 0.01
80_S 77_S 0.63 0.26 0.01
162_R 138_R 0.63 0.26 0.01
157_L 114_K 0.62 0.26 0.01
170_R 37_S 0.62 0.25 0.01
164_L 28_N 0.62 0.25 0.01
56_G 126_D 0.62 0.25 0.01
1_M 101_M 0.62 0.25 0.01
196_V 130_N 0.62 0.25 0.01
127_E 100_A 0.62 0.25 0.01
190_A 105_V 0.62 0.25 0.01
178_V 83_S 0.61 0.25 0.01
41_Q 119_R 0.61 0.25 0.01
116_D 22_L 0.61 0.25 0.01
83_V 138_R 0.61 0.24 0.01
197_E 18_F 0.61 0.24 0.01
77_I 36_K 0.61 0.24 0.01
31_V 131_K 0.61 0.24 0.01
43_T 27_V 0.61 0.24 0.01
189_T 47_L 0.60 0.24 0.01
104_A 152_A 0.60 0.24 0.01
136_Q 134_A 0.60 0.24 0.01
122_E 147_A 0.60 0.23 0.01
121_V 114_K 0.60 0.23 0.01
30_Q 84_T 0.60 0.23 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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