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OPENSEQ.org
3N39-2
Genes: A B A+B
Length: 313 128 439
Sequences: 1951 723 452
Seq/Len: 6.23 5.65 1.03
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 0.84
5 0.02 0.05 0.97
10 0.02 0.05 1.00
20 0.02 0.05 1.02
100 0.02 0.06 1.05
∞ 0.07 0.07 1.13
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
191_V 89_G 1.49 0.77 0.02
312_E 104_L 1.24 0.56 0.01
276_N 3_V 1.21 0.54 0.01
311_D 19_L 1.20 0.53 0.01
219_A 82_R 1.19 0.52 0.01
199_K 45_P 1.17 0.50 0.01
84_E 84_F 1.15 0.48 0.01
204_M 9_S 1.12 0.46 0.01
149_I 82_R 1.12 0.46 0.01
195_Y 119_V 1.08 0.42 0.01
133_Q 123_V 1.08 0.42 0.01
206_K 88_Y 1.08 0.42 0.01
149_I 123_V 1.08 0.42 0.01
33_V 75_G 1.08 0.42 0.01
35_L 75_G 1.07 0.41 0.01
180_D 4_Y 1.07 0.41 0.01
276_N 7_S 1.04 0.39 0.01
126_A 16_I 1.04 0.38 0.01
198_Y 84_F 1.03 0.38 0.01
221_D 73_L 1.03 0.37 0.01
265_E 104_L 1.02 0.36 0.01
312_E 40_Y 1.01 0.36 0.01
272_M 92_G 1.01 0.36 0.01
142_D 97_R 1.00 0.35 0.01
66_L 43_I 0.99 0.34 0.01
186_I 104_L 0.97 0.33 0.01
148_K 45_P 0.97 0.33 0.01
177_N 84_F 0.97 0.32 0.01
12_S 82_R 0.96 0.31 0.01
173_G 85_G 0.94 0.30 0.00
241_T 9_S 0.94 0.30 0.00
243_W 128_Q 0.94 0.30 0.00
52_L 9_S 0.94 0.29 0.00
120_A 41_I 0.94 0.29 0.00
59_G 11_N 0.93 0.29 0.00
184_L 75_G 0.93 0.29 0.00
263_G 108_E 0.92 0.28 0.00
41_A 116_I 0.92 0.28 0.00
307_V 101_V 0.92 0.28 0.00
181_L 9_S 0.91 0.28 0.00
237_L 89_G 0.91 0.28 0.00
93_F 12_T 0.90 0.27 0.00
187_R 75_G 0.90 0.27 0.00
275_V 6_S 0.90 0.26 0.00
51_Q 41_I 0.89 0.26 0.00
208_S 79_S 0.89 0.26 0.00
212_R 117_E 0.89 0.26 0.00
153_F 92_G 0.89 0.26 0.00
239_A 16_I 0.88 0.25 0.00
86_A 39_P 0.88 0.25 0.00
62_L 107_F 0.88 0.25 0.00
133_Q 88_Y 0.88 0.25 0.00
190_A 116_I 0.87 0.25 0.00
164_W 45_P 0.87 0.24 0.00
213_E 114_S 0.87 0.24 0.00
312_E 124_T 0.87 0.24 0.00
191_V 12_T 0.87 0.24 0.00
34_P 75_G 0.86 0.24 0.00
236_E 5_F 0.86 0.24 0.00
270_A 88_Y 0.86 0.24 0.00
119_Y 92_G 0.86 0.24 0.00
204_M 74_R 0.86 0.24 0.00
76_M 121_K 0.85 0.23 0.00
259_L 81_N 0.85 0.23 0.00
27_F 107_F 0.85 0.23 0.00
135_I 51_G 0.85 0.23 0.00
229_N 48_G 0.85 0.23 0.00
217_S 123_V 0.85 0.23 0.00
49_E 40_Y 0.85 0.23 0.00
200_Y 10_E 0.85 0.23 0.00
260_M 110_M 0.84 0.23 0.00
23_L 49_G 0.84 0.23 0.00
243_W 52_T 0.84 0.22 0.00
20_W 83_N 0.83 0.22 0.00
55_R 67_E 0.83 0.22 0.00
39_I 73_L 0.82 0.21 0.00
30_P 94_V 0.82 0.21 0.00
309_T 84_F 0.82 0.21 0.00
6_I 12_T 0.82 0.21 0.00
104_S 89_G 0.82 0.21 0.00
307_V 13_Q 0.82 0.21 0.00
115_V 18_R 0.82 0.21 0.00
200_Y 18_R 0.82 0.21 0.00
250_F 119_V 0.82 0.21 0.00
279_I 126_F 0.82 0.21 0.00
252_C 78_A 0.81 0.20 0.00
224_L 89_G 0.80 0.20 0.00
73_P 89_G 0.80 0.20 0.00
206_K 96_A 0.80 0.20 0.00
66_L 96_A 0.80 0.20 0.00
273_A 10_E 0.80 0.20 0.00
204_M 88_Y 0.80 0.20 0.00
50_Q 61_I 0.80 0.20 0.00
31_E 60_V 0.80 0.20 0.00
223_L 123_V 0.79 0.20 0.00
116_D 55_A 0.79 0.20 0.00
149_I 38_E 0.79 0.20 0.00
271_E 123_V 0.79 0.20 0.00
119_Y 10_E 0.79 0.19 0.00
243_W 51_G 0.79 0.19 0.00
249_A 37_D 0.79 0.19 0.00
81_T 45_P 0.79 0.19 0.00
252_C 46_S 0.79 0.19 0.00
6_I 75_G 0.79 0.19 0.00
68_N 104_L 0.79 0.19 0.00
229_N 52_T 0.78 0.19 0.00
284_S 38_E 0.78 0.19 0.00
14_D 95_I 0.78 0.19 0.00
239_A 103_W 0.78 0.19 0.00
270_A 114_S 0.78 0.19 0.00
168_Y 101_V 0.77 0.19 0.00
177_N 60_V 0.77 0.18 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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