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OPENSEQ.org
83
Genes: A B A+B
Length: 401 202 559
Sequences: 3696 9108 207
Seq/Len: 9.22 45.09 0.37
MirrorTree (Pazo et al. 2001) 0.32
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 0.05 0.04 0.02
2 0.05 0.05 0.05
5 0.06 0.06 0.09
10 0.06 0.08 0.16
20 0.06 0.10 0.34
100 0.08 0.18 0.99
∞ 0.14 0.25 1.83
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
230_Y 100_H 1.14 0.24 0.00
94_K 9_V 1.10 0.22 0.00
341_T 50_N 1.08 0.21 0.00
242_Y 112_I 1.07 0.21 0.00
387_G 120_D 1.07 0.21 0.00
387_G 146_A 1.02 0.19 0.00
230_Y 85_F 1.01 0.18 0.00
381_V 151_N 1.00 0.18 0.00
116_D 78_A 1.00 0.18 0.00
69_Y 36_A 0.99 0.17 0.00
263_P 96_V 0.99 0.17 0.00
187_V 103_L 0.98 0.17 0.00
157_V 148_S 0.96 0.16 0.00
97_L 19_T 0.96 0.16 0.00
206_P 75_Y 0.95 0.16 0.00
104_V 51_R 0.94 0.15 0.00
369_V 38_L 0.94 0.15 0.00
346_V 36_A 0.92 0.15 0.00
77_G 59_W 0.92 0.15 0.00
52_A 26_L 0.91 0.14 0.00
274_K 93_Y 0.91 0.14 0.00
77_G 54_I 0.90 0.14 0.00
119_R 8_L 0.90 0.14 0.00
55_G 80_C 0.89 0.14 0.00
268_S 82_I 0.89 0.14 0.00
125_S 114_L 0.88 0.13 0.00
170_D 87_V 0.87 0.13 0.00
64_K 21_F 0.87 0.13 0.00
276_W 95_N 0.87 0.13 0.00
93_G 130_S 0.86 0.13 0.00
46_P 10_L 0.86 0.13 0.00
172_D 70_L 0.86 0.13 0.00
340_V 19_T 0.86 0.13 0.00
394_L 95_N 0.85 0.12 0.00
107_G 75_Y 0.85 0.12 0.00
159_S 19_T 0.85 0.12 0.00
17_V 8_L 0.85 0.12 0.00
95_V 95_N 0.84 0.12 0.00
251_Q 15_G 0.84 0.12 0.00
339_A 101_R 0.84 0.12 0.00
275_S 21_F 0.84 0.12 0.00
279_F 54_I 0.83 0.12 0.00
185_G 146_A 0.83 0.12 0.00
75_D 92_T 0.83 0.12 0.00
288_C 48_H 0.83 0.12 0.00
236_S 41_E 0.83 0.12 0.00
12_T 82_I 0.83 0.12 0.00
101_V 140_Q 0.82 0.12 0.00
169_A 115_C 0.82 0.12 0.00
165_V 132_V 0.82 0.11 0.00
241_V 138_N 0.82 0.11 0.00
293_G 114_L 0.81 0.11 0.00
151_D 22_V 0.81 0.11 0.00
225_A 119_V 0.81 0.11 0.00
62_L 9_V 0.81 0.11 0.00
390_H 124_R 0.81 0.11 0.00
120_V 86_D 0.81 0.11 0.00
380_V 151_N 0.81 0.11 0.00
213_S 146_A 0.80 0.11 0.00
60_V 111_P 0.80 0.11 0.00
346_V 11_V 0.80 0.11 0.00
226_F 160_A 0.80 0.11 0.00
126_F 58_V 0.80 0.11 0.00
160_G 64_Q 0.80 0.11 0.00
320_L 102_D 0.80 0.11 0.00
394_L 114_L 0.79 0.11 0.00
333_G 12_G 0.79 0.11 0.00
182_G 54_I 0.79 0.11 0.00
16_L 159_L 0.79 0.11 0.00
180_E 152_F 0.79 0.11 0.00
244_F 82_I 0.78 0.10 0.00
296_Y 56_F 0.78 0.10 0.00
70_S 96_V 0.78 0.10 0.00
265_N 163_L 0.78 0.10 0.00
65_S 151_N 0.78 0.10 0.00
208_C 36_A 0.78 0.10 0.00
52_A 8_L 0.78 0.10 0.00
74_N 121_I 0.77 0.10 0.00
49_V 107_C 0.77 0.10 0.00
333_G 120_D 0.77 0.10 0.00
330_V 136_K 0.77 0.10 0.00
384_V 114_L 0.77 0.10 0.00
170_D 36_A 0.77 0.10 0.00
154_V 114_L 0.76 0.10 0.00
112_A 53_P 0.76 0.10 0.00
101_V 163_L 0.76 0.10 0.00
18_L 83_I 0.76 0.10 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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