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OPENSEQ.org
1LZW
Genes: A B A+B
Length: 194 90 272
Sequences: 24658 385 251
Seq/Len: 127.1 4.28 0.92
MirrorTree (Pazo et al. 2001) 0.64
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 0.01 0.00 0.89
2 0.01 0.00 0.88
5 0.03 0.00 0.88
10 0.06 0.00 0.88
20 0.09 0.00 0.88
100 0.17 0.00 0.88
∞ 0.23 0.00 0.91
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
185_D 35_S 2.00 0.95 0.72
138_I 43_M 1.59 0.80 0.39
64_L 37_H 1.54 0.77 0.35
143_E 21_N 1.38 0.66 0.24
22_Q 66_E 1.30 0.58 0.18
144_D 55_I 1.26 0.55 0.16
35_K 13_E 1.23 0.53 0.15
170_V 62_A 1.22 0.51 0.14
149_I 23_L 1.21 0.50 0.14
85_A 4_E 1.19 0.48 0.13
38_S 40_R 1.11 0.41 0.09
88_Y 6_L 1.11 0.41 0.09
23_K 5_Q 1.10 0.41 0.09
184_I 53_F 1.09 0.40 0.09
77_L 41_D 1.07 0.38 0.08
91_A 45_G 1.03 0.35 0.07
154_L 38_L 1.03 0.35 0.07
114_A 55_I 1.02 0.34 0.07
92_Q 5_Q 1.00 0.33 0.06
84_T 33_W 1.00 0.32 0.06
35_K 63_I 0.99 0.31 0.06
26_N 60_M 0.99 0.31 0.06
188_V 68_V 0.98 0.31 0.06
26_N 59_V 0.98 0.31 0.06
139_E 66_E 0.98 0.31 0.06
191_L 34_E 0.98 0.30 0.06
19_K 71_P 0.98 0.30 0.06
39_L 37_H 0.98 0.30 0.06
155_D 39_I 0.97 0.30 0.05
41_S 67_P 0.97 0.30 0.05
64_L 45_G 0.97 0.30 0.05
18_Q 23_L 0.97 0.30 0.05
85_A 8_A 0.96 0.29 0.05
137_T 62_A 0.95 0.29 0.05
49_V 15_L 0.95 0.28 0.05
63_A 89_P 0.94 0.28 0.05
82_V 44_R 0.94 0.28 0.05
133_I 22_E 0.94 0.28 0.05
161_E 87_K 0.93 0.27 0.04
136_R 28_E 0.92 0.26 0.04
30_V 56_S 0.91 0.26 0.04
130_L 21_N 0.91 0.26 0.04
36_V 19_L 0.91 0.26 0.04
103_A 23_L 0.91 0.26 0.04
91_A 56_S 0.91 0.25 0.04
144_D 9_L 0.90 0.25 0.04
35_K 5_Q 0.90 0.25 0.04
125_M 60_M 0.90 0.25 0.04
149_I 18_E 0.90 0.25 0.04
134_V 23_L 0.89 0.24 0.04
72_A 67_P 0.88 0.24 0.04
31_R 40_R 0.88 0.23 0.04
27_L 26_N 0.88 0.23 0.04
65_D 69_R 0.88 0.23 0.04
170_V 55_I 0.88 0.23 0.04
19_K 70_Q 0.87 0.23 0.04
36_V 16_D 0.86 0.22 0.03
133_I 10_M 0.85 0.22 0.03
182_E 12_G 0.85 0.21 0.03
127_S 55_I 0.85 0.21 0.03
26_N 45_G 0.84 0.21 0.03
19_K 69_R 0.84 0.21 0.03
154_L 64_E 0.82 0.20 0.03
154_L 44_R 0.82 0.20 0.03
84_T 86_Q 0.82 0.20 0.03
143_E 38_L 0.82 0.20 0.03
22_Q 64_E 0.82 0.20 0.03
43_Y 10_M 0.82 0.20 0.03
110_E 9_L 0.82 0.20 0.03
140_S 9_L 0.81 0.20 0.03
63_A 20_L 0.81 0.19 0.03
146_R 14_T 0.81 0.19 0.03
50_P 15_L 0.80 0.19 0.03
185_D 56_S 0.80 0.18 0.03
26_N 35_S 0.80 0.18 0.03
92_Q 42_S 0.80 0.18 0.03
157_L 46_D 0.80 0.18 0.02
91_A 17_S 0.80 0.18 0.02
11_Q 33_W 0.79 0.18 0.02
49_V 45_G 0.79 0.18 0.02
150_T 42_S 0.79 0.18 0.02
26_N 41_D 0.79 0.18 0.02
191_L 67_P 0.78 0.18 0.02
43_Y 35_S 0.78 0.18 0.02
89_L 50_V 0.78 0.18 0.02
77_L 21_N 0.78 0.18 0.02
165_I 63_I 0.78 0.18 0.02
66_S 59_V 0.78 0.18 0.02
82_V 46_D 0.78 0.17 0.02
59_K 56_S 0.78 0.17 0.02
127_S 17_S 0.77 0.17 0.02
91_A 59_V 0.77 0.17 0.02
102_D 68_V 0.77 0.17 0.02
160_E 35_S 0.77 0.17 0.02
125_M 55_I 0.77 0.17 0.02
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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