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OPENSEQ.org
AQP0CaM
Genes: A B A+B
Length: 263 149 374
Sequences: 3521 7032 64
Seq/Len: 13.39 47.19 0.17
MirrorTree (Pazo et al. 2001) 0.27
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 0.07 0.01
2 0.04 0.08 0.02
5 0.04 0.08 0.06
10 0.05 0.09 0.10
20 0.05 0.09 0.16
100 0.06 0.14 0.52
∞ 0.11 0.18 1.42
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
100_G 97_G 1.51 0.29 0.00
222_L 101_I 1.43 0.26 0.00
203_V 140_E 1.35 0.22 0.00
63_S 17_F 1.32 0.21 0.00
96_G 135_G 1.22 0.17 0.00
145_I 62_G 1.21 0.17 0.00
68_N 17_F 1.19 0.16 0.00
172_H 23_D 1.11 0.14 0.00
134_E 114_G 1.09 0.14 0.00
142_V 123_D 1.07 0.13 0.00
203_V 96_D 1.07 0.13 0.00
49_G 26_G 1.06 0.13 0.00
180_G 69_F 1.04 0.12 0.00
138_T 21_D 1.04 0.12 0.00
134_E 99_G 1.04 0.12 0.00
75_F 39_S 1.02 0.12 0.00
93_Q 99_G 1.02 0.12 0.00
179_T 38_R 1.01 0.12 0.00
184_N 17_F 1.00 0.11 0.00
20_T 28_I 1.00 0.11 0.00
138_T 19_L 1.00 0.11 0.00
121_L 60_G 0.99 0.11 0.00
96_G 94_D 0.99 0.11 0.00
213_G 37_M 0.98 0.11 0.00
222_L 26_G 0.98 0.11 0.00
144_C 102_S 0.96 0.10 0.00
212_G 70_L 0.96 0.10 0.00
208_P 66_F 0.96 0.10 0.00
77_V 52_M 0.95 0.10 0.00
210_I 147_T 0.95 0.10 0.00
94_L 91_R 0.95 0.10 0.00
70_A 94_D 0.93 0.10 0.00
219_Y 69_F 0.93 0.10 0.00
62_I 113_L 0.93 0.10 0.00
132_T 26_G 0.91 0.09 0.00
215_G 68_E 0.90 0.09 0.00
184_N 135_G 0.90 0.09 0.00
102_A 44_P 0.88 0.09 0.00
22_F 138_N 0.88 0.09 0.00
184_N 90_F 0.88 0.09 0.00
62_I 126_I 0.87 0.09 0.00
96_G 130_D 0.87 0.09 0.00
18_F 96_D 0.87 0.09 0.00
92_A 124_E 0.87 0.09 0.00
181_A 137_V 0.87 0.09 0.00
44_V 10_I 0.87 0.09 0.00
67_V 122_V 0.87 0.09 0.00
101_A 118_T 0.87 0.09 0.00
214_L 108_H 0.86 0.09 0.00
64_G 135_G 0.86 0.08 0.00
87_F 123_D 0.85 0.08 0.00
96_G 141_E 0.85 0.08 0.00
181_A 142_F 0.85 0.08 0.00
136_F 38_R 0.85 0.08 0.00
27_G 40_L 0.84 0.08 0.00
109_P 123_D 0.84 0.08 0.00
145_I 79_D 0.84 0.08 0.00
126_S 128_E 0.84 0.08 0.00
218_L 110_M 0.84 0.08 0.00
94_L 26_G 0.84 0.08 0.00
60_G 28_I 0.84 0.08 0.00
141_F 11_A 0.83 0.08 0.00
25_F 98_N 0.83 0.08 0.00
82_S 54_N 0.83 0.08 0.00
186_A 142_F 0.83 0.08 0.00
171_G 93_F 0.83 0.08 0.00
214_L 24_G 0.82 0.08 0.00
189_F 110_M 0.82 0.08 0.00
65_A 19_L 0.82 0.08 0.00
56_V 32_E 0.82 0.08 0.00
171_G 20_F 0.82 0.08 0.00
211_G 17_F 0.82 0.08 0.00
64_G 101_I 0.81 0.08 0.00
71_V 137_V 0.81 0.08 0.00
93_Q 17_F 0.81 0.08 0.00
69_P 142_F 0.81 0.07 0.00
96_G 64_I 0.81 0.07 0.00
64_G 99_G 0.80 0.07 0.00
215_G 135_G 0.80 0.07 0.00
126_S 85_E 0.80 0.07 0.00
138_T 83_E 0.80 0.07 0.00
190_A 90_F 0.80 0.07 0.00
190_A 86_I 0.79 0.07 0.00
192_A 140_E 0.79 0.07 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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