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OPENSEQ.org
AR
Genes: A B A+B
Length: 195 125 309
Sequences: 11908 88991 435
Seq/Len: 61.07 711.93 1.41
MirrorTree (Pazo et al. 2001) 0.29
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 0.04 0.11 0.16
2 0.05 0.13 0.23
5 0.06 0.16 0.45
10 0.08 0.19 0.80
20 0.10 0.23 1.36
100 0.19 0.31 3.78
∞ 0.26 0.34 6.31
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
174_V 7_V 1.41 0.80 0.04
160_H 7_V 1.30 0.72 0.03
28_N 68_L 1.17 0.60 0.02
172_T 102_H 1.09 0.51 0.02
92_I 54_V 1.06 0.49 0.02
130_D 50_V 1.03 0.45 0.01
166_Y 57_P 1.02 0.45 0.01
31_Y 8_A 0.99 0.41 0.01
23_C 68_L 0.97 0.40 0.01
150_T 69_K 0.93 0.36 0.01
137_V 79_V 0.91 0.34 0.01
103_A 56_M 0.90 0.32 0.01
97_D 86_F 0.89 0.32 0.01
176_V 6_L 0.89 0.32 0.01
138_I 18_I 0.88 0.31 0.01
160_H 50_V 0.88 0.31 0.01
101_F 107_F 0.86 0.29 0.01
112_A 102_H 0.85 0.29 0.01
46_S 29_V 0.84 0.28 0.01
63_S 37_D 0.84 0.28 0.01
98_G 51_L 0.83 0.27 0.01
86_D 27_F 0.83 0.27 0.01
17_Y 116_V 0.83 0.27 0.01
145_L 67_A 0.83 0.27 0.01
153_E 35_G 0.81 0.25 0.01
179_T 34_N 0.80 0.25 0.01
97_D 102_H 0.80 0.24 0.01
147_N 80_V 0.79 0.23 0.01
64_L 116_V 0.78 0.23 0.01
114_M 103_V 0.78 0.23 0.01
28_N 112_L 0.77 0.23 0.01
144_D 106_P 0.77 0.23 0.01
50_E 96_A 0.76 0.22 0.01
150_T 83_A 0.76 0.21 0.01
101_F 44_E 0.76 0.21 0.01
114_M 79_V 0.76 0.21 0.01
31_Y 13_T 0.75 0.21 0.01
100_V 54_V 0.75 0.21 0.01
190_E 9_D 0.74 0.21 0.01
178_D 89_F 0.74 0.21 0.01
149_V 68_L 0.74 0.20 0.01
172_T 66_E 0.73 0.20 0.01
32_I 13_T 0.73 0.20 0.01
66_E 38_A 0.72 0.19 0.01
74_F 32_V 0.72 0.19 0.01
66_E 31_A 0.72 0.19 0.01
159_N 83_A 0.72 0.19 0.01
163_I 7_V 0.71 0.19 0.01
120_L 60_S 0.71 0.19 0.01
165_E 73_A 0.71 0.18 0.01
158_L 47_P 0.71 0.18 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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