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OPENSEQ.org
XF
Genes: A B A+B
Length: 307 228 488
Sequences: 1803 87698 132
Seq/Len: 5.87 384.64 0.27
MirrorTree (Pazo et al. 2001) 0.19
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 0.03 0.10 0.01
2 0.03 0.11 0.01
5 0.03 0.15 0.07
10 0.03 0.20 0.12
20 0.03 0.25 0.25
100 0.03 0.36 0.80
∞ 0.08 0.38 1.46
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
105_Q 38_I 1.66 0.49 0.00
110_I 22_V 1.32 0.29 0.00
28_L 182_L 1.29 0.27 0.00
191_T 9_L 1.29 0.27 0.00
147_E 47_T 1.20 0.23 0.00
10_G 22_V 1.12 0.19 0.00
107_K 64_I 1.11 0.18 0.00
251_A 149_R 1.05 0.17 0.00
254_Y 102_V 1.04 0.16 0.00
179_A 106_I 1.02 0.15 0.00
63_N 64_I 1.01 0.15 0.00
7_L 185_R 1.01 0.15 0.00
122_I 47_T 1.00 0.15 0.00
247_I 101_T 0.99 0.14 0.00
179_A 5_E 0.99 0.14 0.00
182_G 144_L 0.98 0.14 0.00
109_V 213_V 0.98 0.14 0.00
43_V 149_R 0.97 0.14 0.00
100_A 38_I 0.96 0.13 0.00
159_T 30_I 0.95 0.13 0.00
230_S 39_M 0.94 0.13 0.00
179_A 149_R 0.93 0.12 0.00
147_E 60_S 0.92 0.12 0.00
133_E 53_L 0.91 0.12 0.00
31_I 26_I 0.90 0.12 0.00
97_F 30_I 0.90 0.12 0.00
210_A 9_L 0.89 0.11 0.00
251_A 4_L 0.88 0.11 0.00
172_N 10_T 0.88 0.11 0.00
251_A 9_L 0.87 0.11 0.00
7_L 165_I 0.86 0.11 0.00
28_L 122_N 0.86 0.11 0.00
62_M 101_T 0.86 0.11 0.00
131_P 30_I 0.85 0.10 0.00
208_P 158_F 0.85 0.10 0.00
98_G 124_Y 0.84 0.10 0.00
232_V 210_A 0.84 0.10 0.00
203_K 27_N 0.84 0.10 0.00
109_V 2_A 0.83 0.10 0.00
28_L 81_D 0.83 0.10 0.00
110_I 10_T 0.83 0.10 0.00
251_A 158_F 0.82 0.10 0.00
159_T 87_I 0.82 0.10 0.00
254_Y 127_V 0.82 0.10 0.00
64_Q 138_D 0.82 0.10 0.00
68_A 48_T 0.81 0.10 0.00
12_G 148_Q 0.81 0.09 0.00
12_G 196_T 0.81 0.09 0.00
120_E 13_Y 0.81 0.09 0.00
15_G 92_Q 0.80 0.09 0.00
134_T 198_I 0.80 0.09 0.00
239_Q 6_V 0.80 0.09 0.00
162_V 70_K 0.79 0.09 0.00
45_M 214_V 0.79 0.09 0.00
131_P 180_Q 0.79 0.09 0.00
172_N 129_E 0.79 0.09 0.00
252_V 44_S 0.78 0.09 0.00
260_Y 50_L 0.78 0.09 0.00
133_E 198_I 0.78 0.09 0.00
15_G 201_T 0.78 0.09 0.00
68_A 123_R 0.77 0.09 0.00
183_Y 26_I 0.77 0.09 0.00
22_I 198_I 0.77 0.09 0.00
110_I 199_M 0.77 0.09 0.00
69_V 47_T 0.77 0.09 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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