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OPENSEQ.org
bcNrdFI
Genes: A B A+B
Length: 322 119 433
Sequences: 1963 713 435
Seq/Len: 6.1 5.99 1
MirrorTree (Pazo et al. 2001) 0.83
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 0.02 0.05 0.20
2 0.02 0.05 0.82
5 0.02 0.05 0.94
10 0.02 0.05 0.96
20 0.02 0.05 0.99
100 0.02 0.06 1.02
∞ 0.07 0.07 1.11
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
280_N 3_V 1.34 0.64 0.00
197_I 79_G 1.31 0.62 0.00
82_A 74_W 1.18 0.50 0.00
205_L 41_Y 1.17 0.49 0.00
53_R 59_N 1.14 0.46 0.00
31_I 65_G 1.10 0.43 0.00
225_T 72_R 1.09 0.42 0.00
186_E 4_A 1.08 0.41 0.00
155_V 113_V 1.07 0.40 0.00
204_I 74_W 1.05 0.38 0.00
154_M 41_Y 1.04 0.38 0.00
179_G 75_G 1.04 0.37 0.00
255_R 33_D 1.03 0.36 0.00
131_G 113_V 1.03 0.36 0.00
183_A 74_W 1.03 0.36 0.00
131_G 78_F 1.02 0.36 0.00
33_V 65_G 1.02 0.35 0.00
201_F 109_F 1.02 0.35 0.00
155_V 72_R 1.01 0.35 0.00
212_E 78_F 1.01 0.35 0.00
124_P 16_I 1.00 0.34 0.00
316_D 114_R 1.00 0.34 0.00
210_F 9_T 1.00 0.34 0.00
150_L 41_Y 0.99 0.34 0.00
280_N 7_S 0.99 0.33 0.00
276_E 82_A 0.99 0.33 0.00
271_E 94_V 0.98 0.33 0.00
315_D 19_L 0.98 0.32 0.00
190_L 65_G 0.97 0.32 0.00
10_E 72_R 0.96 0.31 0.00
235_I 5_Y 0.95 0.30 0.00
269_G 98_E 0.93 0.28 0.00
316_D 28_E 0.93 0.28 0.00
175_L 69_S 0.92 0.28 0.00
193_R 65_G 0.92 0.28 0.00
192_I 94_V 0.91 0.27 0.00
113_I 18_K 0.91 0.27 0.00
243_I 79_G 0.91 0.27 0.00
57_G 11_N 0.91 0.27 0.00
141_L 87_T 0.90 0.26 0.00
28_E 82_A 0.90 0.26 0.00
117_F 82_A 0.89 0.26 0.00
311_E 13_K 0.89 0.26 0.00
25_F 97_F 0.89 0.26 0.00
130_A 3_V 0.89 0.26 0.00
21_N 45_F 0.89 0.26 0.00
187_I 9_T 0.89 0.25 0.00
313_L 74_W 0.88 0.25 0.00
311_E 91_V 0.88 0.25 0.00
32_A 65_G 0.88 0.25 0.00
206_A 10_G 0.87 0.24 0.00
155_V 34_E 0.87 0.24 0.00
60_L 97_F 0.87 0.24 0.00
91_A 12_V 0.86 0.24 0.00
315_D 56_L 0.86 0.24 0.00
316_D 94_V 0.86 0.23 0.00
115_D 79_G 0.85 0.23 0.00
117_F 10_G 0.85 0.23 0.00
241_E 36_F 0.85 0.23 0.00
4_V 65_G 0.84 0.22 0.00
74_L 111_E 0.84 0.22 0.00
159_F 82_A 0.83 0.22 0.00
42_Q 36_F 0.83 0.22 0.00
229_L 113_V 0.83 0.22 0.00
98_K 82_A 0.83 0.22 0.00
226_Q 86_S 0.83 0.22 0.00
118_D 37_I 0.83 0.22 0.00
210_F 95_S 0.83 0.21 0.00
4_V 12_V 0.83 0.21 0.00
278_E 78_F 0.82 0.21 0.00
245_T 16_I 0.82 0.21 0.00
84_S 35_D 0.82 0.21 0.00
247_I 9_T 0.82 0.21 0.00
48_Q 64_K 0.81 0.20 0.00
266_M 100_S 0.81 0.20 0.00
206_A 45_F 0.81 0.20 0.00
205_L 74_W 0.81 0.20 0.00
217_E 78_F 0.81 0.20 0.00
196_S 106_V 0.81 0.20 0.00
48_Q 53_L 0.81 0.20 0.00
205_L 43_T 0.81 0.20 0.00
265_L 71_N 0.81 0.20 0.00
311_E 1_M 0.81 0.20 0.00
102_H 63_L 0.80 0.20 0.00
192_I 5_Y 0.80 0.20 0.00
154_M 43_T 0.80 0.20 0.00
277_E 10_G 0.80 0.20 0.00
170_F 41_Y 0.80 0.20 0.00
18_W 73_N 0.80 0.20 0.00
55_L 74_W 0.80 0.20 0.00
279_I 6_D 0.80 0.20 0.00
161_E 93_I 0.80 0.20 0.00
210_F 78_F 0.80 0.20 0.00
179_G 49_P 0.79 0.19 0.00
79_N 41_Y 0.79 0.19 0.00
256_F 109_F 0.79 0.19 0.00
9_K 78_F 0.79 0.19 0.00
71_P 79_G 0.79 0.19 0.00
142_K 78_F 0.79 0.19 0.00
247_I 28_E 0.79 0.19 0.00
138_R 18_K 0.79 0.19 0.00
243_I 102_T 0.79 0.19 0.00
218_Q 107_E 0.79 0.19 0.00
174_Y 91_V 0.79 0.19 0.00
88_F 74_W 0.79 0.19 0.00
111_E 76_D 0.79 0.19 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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