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OPENSEQ.org
T0993s1_T0993s2auto
Genes: A B A+B
Length: 269 102 344
Sequences: 75042 399 275
Seq/Len: 278.97 3.91 0.8
MirrorTree (Pazo et al. 2001) 0.40
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 0.10 0.00 0.07
2 0.10 0.00 0.07
5 0.14 0.00 0.72
10 0.18 0.00 0.73
20 0.23 0.00 0.74
100 0.34 0.00 0.74
∞ 0.37 0.00 0.75
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
88_S 62_L 1.93 0.91 0.44
67_F 66_L 1.65 0.80 0.25
218_L 52_V 1.54 0.73 0.19
223_I 47_I 1.35 0.58 0.11
9_V 64_L 1.35 0.58 0.11
153_A 55_V 1.34 0.58 0.10
223_I 91_K 1.33 0.57 0.10
36_I 67_I 1.30 0.55 0.09
100_M 21_L 1.30 0.54 0.09
100_M 95_L 1.26 0.51 0.08
153_A 57_T 1.23 0.48 0.07
9_V 54_R 1.22 0.47 0.07
199_V 99_V 1.21 0.46 0.07
215_A 82_V 1.17 0.43 0.06
30_T 52_V 1.14 0.41 0.05
183_L 60_L 1.12 0.39 0.05
241_R 64_L 1.12 0.39 0.05
179_T 90_A 1.11 0.38 0.05
104_D 99_V 1.11 0.38 0.05
59_A 51_R 1.09 0.36 0.04
65_I 84_D 1.09 0.36 0.04
189_E 93_Y 1.08 0.36 0.04
214_H 95_L 1.08 0.36 0.04
225_A 94_N 1.08 0.35 0.04
102_V 60_L 1.07 0.35 0.04
179_T 65_H 1.04 0.33 0.04
78_S 50_S 1.04 0.32 0.04
75_M 57_T 1.03 0.32 0.04
50_L 57_T 1.02 0.31 0.03
228_S 97_A 1.01 0.30 0.03
123_S 68_D 1.00 0.29 0.03
215_A 99_V 1.00 0.29 0.03
11_M 21_L 0.99 0.28 0.03
101_N 52_V 0.98 0.28 0.03
228_S 16_G 0.97 0.27 0.03
117_P 95_L 0.97 0.27 0.03
127_M 95_L 0.97 0.27 0.03
112_E 56_D 0.96 0.26 0.03
241_R 74_G 0.96 0.26 0.03
78_S 43_G 0.96 0.26 0.03
70_E 38_E 0.93 0.25 0.02
27_I 85_K 0.93 0.25 0.02
217_I 54_R 0.93 0.24 0.02
31_V 55_V 0.93 0.24 0.02
239_R 62_L 0.92 0.24 0.02
127_M 61_A 0.92 0.24 0.02
229_A 30_L 0.92 0.24 0.02
108_Y 77_V 0.92 0.24 0.02
168_F 99_V 0.91 0.23 0.02
188_S 30_L 0.90 0.23 0.02
97_F 34_W 0.90 0.23 0.02
28_S 57_T 0.90 0.22 0.02
127_M 45_T 0.90 0.22 0.02
214_H 48_D 0.89 0.22 0.02
31_V 30_L 0.89 0.22 0.02
183_L 47_I 0.89 0.22 0.02
121_L 74_G 0.89 0.22 0.02
224_V 99_V 0.89 0.22 0.02
120_L 32_P 0.89 0.22 0.02
45_I 27_Q 0.88 0.22 0.02
192_S 98_D 0.88 0.22 0.02
48_T 19_L 0.88 0.22 0.02
153_A 82_V 0.88 0.21 0.02
224_V 60_L 0.88 0.21 0.02
223_I 77_V 0.88 0.21 0.02
100_M 36_M 0.88 0.21 0.02
100_M 33_L 0.87 0.21 0.02
192_S 85_K 0.86 0.20 0.02
124_T 10_L 0.86 0.20 0.02
232_L 36_M 0.86 0.20 0.02
193_A 83_N 0.85 0.20 0.02
221_K 57_T 0.85 0.20 0.02
102_V 47_I 0.84 0.19 0.02
219_A 86_V 0.84 0.19 0.02
110_L 26_D 0.84 0.19 0.01
222_K 96_P 0.84 0.19 0.01
14_V 62_L 0.84 0.19 0.01
139_K 47_I 0.84 0.19 0.01
6_A 63_L 0.84 0.19 0.01
198_C 93_Y 0.84 0.19 0.01
30_T 93_Y 0.84 0.19 0.01
244_L 89_L 0.83 0.19 0.01
173_V 62_L 0.82 0.18 0.01
27_I 89_L 0.82 0.18 0.01
97_F 79_L 0.82 0.18 0.01
117_P 36_M 0.82 0.18 0.01
14_V 67_I 0.81 0.18 0.01
229_A 47_I 0.81 0.18 0.01
248_A 12_W 0.81 0.17 0.01
196_V 6_Q 0.81 0.17 0.01
182_V 34_W 0.81 0.17 0.01
218_L 41_V 0.81 0.17 0.01
100_M 54_R 0.81 0.17 0.01
36_I 52_V 0.80 0.17 0.01
130_E 94_N 0.80 0.17 0.01
26_N 47_I 0.80 0.17 0.01
121_L 29_V 0.80 0.17 0.01
66_L 57_T 0.80 0.17 0.01
72_I 27_Q 0.80 0.17 0.01
179_T 34_W 0.79 0.17 0.01
199_V 24_E 0.79 0.17 0.01
67_F 27_Q 0.79 0.17 0.01
13_D 74_G 0.79 0.17 0.01
235_N 81_G 0.79 0.17 0.01
232_L 38_E 0.79 0.16 0.01
189_E 85_K 0.79 0.16 0.01
28_S 56_D 0.78 0.16 0.01
237_D 34_W 0.78 0.16 0.01
130_E 55_V 0.78 0.16 0.01
126_M 83_N 0.78 0.16 0.01
106_V 62_L 0.77 0.16 0.01
52_R 27_Q 0.77 0.16 0.01
218_L 49_L 0.77 0.16 0.01
173_V 65_H 0.77 0.16 0.01
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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