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OPENSEQ.org
1IBR_l_u_A_1IBR_r_u_A
Genes: A B A+B
Length: 440 184 601
Sequences: 2381 11315 178
Seq/Len: 5.41 61.49 0.3
MirrorTree (Pazo et al. 2001) 0.16
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 0.05 0.01
2 0.05 0.06 0.04
5 0.06 0.07 0.07
10 0.06 0.09 0.14
20 0.06 0.12 0.29
100 0.08 0.22 1.04
∞ 0.15 0.28 1.86
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
91_V 87_V 1.47 0.40 0.00
406_V 85_F 1.32 0.30 0.00
97_H 11_V 1.18 0.23 0.00
16_L 74_Y 1.13 0.21 0.00
364_V 11_V 1.12 0.21 0.00
348_A 9_V 1.11 0.20 0.00
129_L 92_T 1.09 0.19 0.00
138_T 92_T 1.08 0.19 0.00
280_I 115_C 1.05 0.18 0.00
260_L 24_R 1.05 0.17 0.00
8_E 151_N 1.03 0.17 0.00
124_N 152_F 1.03 0.17 0.00
128_E 123_D 1.03 0.17 0.00
371_I 114_L 1.02 0.16 0.00
391_G 150_Y 1.01 0.16 0.00
113_V 56_F 1.01 0.16 0.00
170_S 135_R 1.01 0.16 0.00
91_V 92_T 1.00 0.16 0.00
88_R 133_F 1.00 0.16 0.00
58_G 21_F 1.00 0.16 0.00
436_C 86_D 0.99 0.15 0.00
287_C 142_Y 0.97 0.14 0.00
78_Q 16_T 0.97 0.14 0.00
61_I 152_F 0.97 0.14 0.00
84_D 77_Q 0.96 0.14 0.00
171_N 70_L 0.96 0.14 0.00
127_P 80_C 0.96 0.14 0.00
157_I 82_I 0.96 0.14 0.00
390_F 78_A 0.96 0.14 0.00
282_F 116_G 0.96 0.14 0.00
87_A 8_L 0.96 0.14 0.00
186_P 147_K 0.95 0.14 0.00
59_L 69_G 0.94 0.14 0.00
395_E 85_F 0.94 0.14 0.00
116_I 82_I 0.94 0.14 0.00
343_N 92_T 0.93 0.13 0.00
116_I 102_D 0.93 0.13 0.00
91_V 8_L 0.93 0.13 0.00
138_T 144_I 0.92 0.13 0.00
63_N 82_I 0.91 0.13 0.00
269_K 9_V 0.90 0.12 0.00
356_A 19_T 0.90 0.12 0.00
86_N 139_L 0.90 0.12 0.00
283_W 87_V 0.90 0.12 0.00
194_A 82_I 0.90 0.12 0.00
133_L 92_T 0.89 0.12 0.00
389_A 112_I 0.89 0.12 0.00
306_P 116_G 0.89 0.12 0.00
91_V 114_L 0.89 0.12 0.00
370_F 56_F 0.88 0.12 0.00
10_T 144_I 0.88 0.12 0.00
337_D 151_N 0.88 0.12 0.00
203_E 151_N 0.88 0.12 0.00
12_S 11_V 0.87 0.12 0.00
287_C 92_T 0.87 0.12 0.00
351_C 49_T 0.87 0.12 0.00
425_R 19_T 0.87 0.12 0.00
196_N 135_R 0.87 0.12 0.00
265_I 45_L 0.86 0.11 0.00
150_T 96_V 0.86 0.11 0.00
7_L 17_G 0.86 0.11 0.00
417_M 83_I 0.86 0.11 0.00
126_W 120_D 0.86 0.11 0.00
18_L 161_R 0.86 0.11 0.00
283_W 51_R 0.85 0.11 0.00
363_I 147_K 0.85 0.11 0.00
390_F 148_S 0.85 0.11 0.00
17_E 92_T 0.85 0.11 0.00
425_R 54_I 0.85 0.11 0.00
244_I 141_Y 0.85 0.11 0.00
421_S 114_L 0.85 0.11 0.00
7_L 118_K 0.85 0.11 0.00
169_K 115_C 0.85 0.11 0.00
413_L 147_K 0.85 0.11 0.00
3_L 88_T 0.85 0.11 0.00
219_M 132_V 0.85 0.11 0.00
419_D 19_T 0.85 0.11 0.00
145_H 82_I 0.84 0.11 0.00
57_A 83_I 0.84 0.11 0.00
348_A 88_T 0.84 0.11 0.00
21_A 12_G 0.84 0.11 0.00
126_W 118_K 0.84 0.11 0.00
221_V 54_I 0.84 0.11 0.00
369_P 82_I 0.83 0.11 0.00
5_T 93_Y 0.83 0.11 0.00
93_N 103_L 0.83 0.11 0.00
51_Q 67_Y 0.83 0.11 0.00
154_I 102_D 0.83 0.10 0.00
287_C 113_V 0.83 0.10 0.00
11_V 93_Y 0.82 0.10 0.00
126_W 17_G 0.82 0.10 0.00
46_N 114_L 0.82 0.10 0.00
352_L 12_G 0.82 0.10 0.00
226_T 88_T 0.82 0.10 0.00
43_V 115_C 0.82 0.10 0.00
92_K 147_K 0.82 0.10 0.00
188_N 121_I 0.82 0.10 0.00
43_V 28_G 0.81 0.10 0.00
332_K 85_F 0.81 0.10 0.00
279_G 13_D 0.81 0.10 0.00
26_E 36_A 0.81 0.10 0.00
272_I 114_L 0.81 0.10 0.00
25_L 19_T 0.81 0.10 0.00
95_V 69_G 0.81 0.10 0.00
274_E 85_F 0.81 0.10 0.00
88_R 89_S 0.81 0.10 0.00
255_Y 30_F 0.81 0.10 0.00
210_D 8_L 0.80 0.10 0.00
393_I 116_G 0.80 0.10 0.00
288_D 63_G 0.80 0.10 0.00
19_E 116_G 0.80 0.10 0.00
95_V 123_D 0.80 0.10 0.00
65_L 140_Q 0.80 0.10 0.00
377_N 10_L 0.80 0.10 0.00
85_A 28_G 0.80 0.10 0.00
139_N 8_L 0.79 0.10 0.00
21_A 83_I 0.79 0.10 0.00
424_V 153_E 0.79 0.10 0.00
195_T 66_K 0.79 0.10 0.00
201_S 92_T 0.79 0.10 0.00
197_A 111_P 0.79 0.10 0.00
302_E 19_T 0.79 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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