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OPENSEQ.org
MlaF-MlaB
Genes: A B A+B
Length: 269 97 343
Sequences: 75042 397 269
Seq/Len: 278.97 4.09 0.78
MirrorTree (Pazo et al. 2001) 0.44
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 0.73
10 0.18 0.00 0.75
20 0.23 0.00 0.75
100 0.34 0.00 0.75
∞ 0.37 0.00 0.77
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 57_L 1.93 0.91 0.43
67_F 61_L 1.63 0.79 0.23
218_L 47_V 1.53 0.72 0.18
100_M 16_L 1.52 0.71 0.17
223_I 42_I 1.41 0.62 0.12
9_V 59_L 1.40 0.62 0.12
153_A 52_T 1.37 0.59 0.11
153_A 50_V 1.35 0.58 0.10
36_I 62_I 1.28 0.52 0.08
223_I 86_K 1.23 0.47 0.07
179_T 60_H 1.22 0.47 0.07
9_V 49_R 1.22 0.47 0.07
183_L 55_L 1.20 0.44 0.06
214_H 90_L 1.19 0.44 0.06
30_T 47_V 1.18 0.43 0.06
215_A 77_V 1.17 0.42 0.06
100_M 90_L 1.16 0.41 0.05
199_V 94_V 1.15 0.41 0.05
228_S 92_A 1.14 0.40 0.05
225_A 89_N 1.14 0.40 0.05
104_D 94_V 1.13 0.39 0.05
241_R 59_L 1.13 0.39 0.05
75_M 52_T 1.12 0.38 0.05
59_A 46_R 1.12 0.38 0.05
50_L 52_T 1.12 0.38 0.05
179_T 85_A 1.11 0.38 0.04
102_V 55_L 1.10 0.37 0.04
215_A 94_V 1.09 0.36 0.04
11_M 16_L 1.08 0.35 0.04
123_S 63_D 1.07 0.34 0.04
189_E 88_Y 1.06 0.34 0.04
127_M 90_L 1.06 0.33 0.04
26_N 42_I 1.05 0.33 0.04
112_E 51_D 1.05 0.33 0.04
127_M 56_A 1.04 0.32 0.03
117_P 90_L 1.01 0.30 0.03
11_M 5_L 1.01 0.29 0.03
223_I 72_V 0.99 0.28 0.03
108_Y 72_V 0.99 0.28 0.03
27_I 80_K 0.99 0.28 0.03
239_R 57_L 0.98 0.28 0.03
67_F 22_Q 0.97 0.27 0.03
127_M 40_T 0.97 0.27 0.03
121_L 24_V 0.96 0.26 0.02
222_K 91_P 0.95 0.26 0.02
28_S 52_T 0.94 0.25 0.02
45_I 22_Q 0.94 0.24 0.02
241_R 69_G 0.93 0.24 0.02
168_F 94_V 0.93 0.24 0.02
224_V 94_V 0.93 0.24 0.02
121_L 69_G 0.93 0.24 0.02
65_I 79_D 0.92 0.24 0.02
70_E 33_E 0.92 0.24 0.02
198_C 88_Y 0.92 0.23 0.02
153_A 77_V 0.92 0.23 0.02
179_T 29_W 0.91 0.23 0.02
100_M 31_M 0.91 0.23 0.02
228_S 11_G 0.90 0.23 0.02
208_V 61_L 0.90 0.23 0.02
102_V 42_I 0.90 0.22 0.02
192_S 80_K 0.89 0.22 0.02
66_L 52_T 0.89 0.22 0.02
208_V 22_Q 0.89 0.22 0.02
101_N 47_V 0.89 0.22 0.02
214_H 43_D 0.89 0.22 0.02
183_L 42_I 0.89 0.22 0.02
48_T 14_L 0.88 0.21 0.02
221_K 52_T 0.88 0.21 0.02
196_V 1_M 0.88 0.21 0.02
229_A 25_L 0.88 0.21 0.02
217_I 49_R 0.88 0.21 0.02
14_V 62_I 0.87 0.21 0.02
219_A 81_V 0.87 0.20 0.02
196_V 60_H 0.86 0.20 0.02
97_F 29_W 0.85 0.20 0.01
215_A 85_A 0.85 0.20 0.01
120_L 47_V 0.85 0.19 0.01
28_S 51_D 0.85 0.19 0.01
127_M 5_L 0.84 0.19 0.01
199_V 19_E 0.84 0.19 0.01
33_R 70_N 0.84 0.19 0.01
120_L 27_P 0.84 0.19 0.01
189_E 80_K 0.84 0.19 0.01
126_M 40_T 0.84 0.19 0.01
74_A 8_M 0.83 0.19 0.01
237_D 29_W 0.83 0.18 0.01
102_V 93_D 0.83 0.18 0.01
14_V 57_L 0.83 0.18 0.01
8_L 25_L 0.83 0.18 0.01
179_T 76_G 0.83 0.18 0.01
244_L 84_L 0.83 0.18 0.01
173_V 60_H 0.83 0.18 0.01
78_S 38_G 0.82 0.18 0.01
11_M 94_V 0.82 0.18 0.01
162_E 22_Q 0.82 0.18 0.01
38_A 68_Q 0.82 0.18 0.01
78_S 45_S 0.82 0.18 0.01
209_L 81_V 0.82 0.18 0.01
182_V 29_W 0.82 0.18 0.01
224_V 55_L 0.82 0.18 0.01
232_L 31_M 0.81 0.18 0.01
126_M 78_N 0.81 0.17 0.01
205_V 56_A 0.81 0.17 0.01
193_A 78_N 0.81 0.17 0.01
120_L 50_V 0.80 0.17 0.01
173_V 16_L 0.80 0.17 0.01
88_S 52_T 0.80 0.17 0.01
173_V 57_L 0.80 0.17 0.01
114_T 50_V 0.80 0.17 0.01
52_R 22_Q 0.80 0.17 0.01
24_F 57_L 0.79 0.17 0.01
65_I 16_L 0.79 0.17 0.01
237_D 7_W 0.79 0.17 0.01
229_A 42_I 0.79 0.17 0.01
235_N 76_G 0.79 0.16 0.01
110_L 21_D 0.79 0.16 0.01
88_S 22_Q 0.79 0.16 0.01
175_Q 81_V 0.79 0.16 0.01
192_S 93_D 0.79 0.16 0.01
13_D 69_G 0.79 0.16 0.01
27_I 84_L 0.78 0.16 0.01
188_S 44_L 0.78 0.16 0.01
74_A 84_L 0.78 0.16 0.01
88_S 78_N 0.78 0.16 0.01
194_L 51_D 0.78 0.16 0.01
121_L 89_N 0.77 0.16 0.01
234_A 62_I 0.77 0.15 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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