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OPENSEQ.org
1ACM-2
Genes: A B A+B
Length: 310 145 427
Sequences: 4521 692 547
Seq/Len: 14.58 4.77 1.28
MirrorTree (Pazo et al. 2001) 0.47
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 0.07 1.12
2 0.02 0.07 1.15
5 0.04 0.07 1.18
10 0.05 0.07 1.20
20 0.05 0.07 1.20
100 0.07 0.07 1.21
∞ 0.13 0.08 1.30
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_L 107_I 1.61 0.88 0.24
289_A 75_V 1.44 0.79 0.15
132_N 35_T 1.43 0.79 0.15
69_S 96_D 1.33 0.71 0.11
87_T 112_P 1.28 0.67 0.10
264_L 78_I 1.27 0.66 0.09
49_F 54_E 1.22 0.61 0.08
61_T 1_V 1.21 0.60 0.08
75_D 1_V 1.16 0.55 0.06
242_N 53_I 1.10 0.49 0.05
259_A 45_M 1.09 0.49 0.05
236_D 37_G 1.08 0.48 0.05
154_N 77_R 1.08 0.47 0.05
74_S 57_F 1.08 0.47 0.05
299_L 54_E 1.07 0.47 0.05
68_A 136_E 1.05 0.45 0.04
247_F 108_S 1.05 0.44 0.04
175_A 98_V 1.04 0.44 0.04
71_V 6_R 1.04 0.44 0.04
111_A 113_V 1.04 0.44 0.04
275_T 10_I 1.03 0.43 0.04
305_N 99_L 1.03 0.43 0.04
293_I 19_F 1.02 0.42 0.04
250_R 4_I 1.01 0.41 0.04
19_D 134_E 1.00 0.40 0.04
114_L 113_V 0.99 0.39 0.04
116_T 82_E 0.98 0.38 0.03
289_A 1_V 0.98 0.38 0.03
219_M 36_I 0.97 0.37 0.03
49_F 83_V 0.96 0.36 0.03
43_V 112_P 0.95 0.35 0.03
154_N 80_N 0.94 0.35 0.03
302_L 10_I 0.94 0.34 0.03
177_A 95_I 0.93 0.34 0.03
87_T 8_T 0.93 0.34 0.03
49_F 135_K 0.93 0.33 0.03
47_C 37_G 0.93 0.33 0.03
187_I 91_L 0.93 0.33 0.03
254_L 40_L 0.93 0.33 0.03
274_A 77_R 0.93 0.33 0.03
37_E 53_I 0.92 0.33 0.03
237_P 109_H 0.92 0.33 0.03
178_K 108_S 0.92 0.32 0.03
232_K 126_I 0.92 0.32 0.03
127_A 46_G 0.91 0.32 0.03
24_L 3_A 0.91 0.32 0.03
165_Y 78_I 0.91 0.32 0.03
49_F 110_A 0.90 0.31 0.03
230_V 108_S 0.90 0.31 0.03
39_L 83_V 0.90 0.31 0.03
97_T 70_A 0.89 0.30 0.02
293_I 68_L 0.88 0.29 0.02
20_L 122_R 0.88 0.29 0.02
263_V 34_I 0.88 0.29 0.02
95_I 134_E 0.88 0.29 0.02
227_M 3_A 0.88 0.29 0.02
263_V 53_I 0.88 0.29 0.02
125_L 82_E 0.87 0.29 0.02
23_V 75_V 0.87 0.28 0.02
20_L 24_L 0.86 0.28 0.02
139_L 55_N 0.86 0.27 0.02
23_V 58_L 0.86 0.27 0.02
65_R 112_P 0.85 0.27 0.02
125_L 85_G 0.85 0.27 0.02
303_V 108_S 0.85 0.27 0.02
76_S 96_D 0.85 0.27 0.02
186_F 40_L 0.84 0.26 0.02
87_T 34_I 0.84 0.26 0.02
297_Q 40_L 0.83 0.26 0.02
179_F 63_V 0.83 0.26 0.02
104_M 118_A 0.83 0.25 0.02
147_Q 95_I 0.83 0.25 0.02
89_A 18_G 0.83 0.25 0.02
263_V 47_R 0.83 0.25 0.02
304_L 34_I 0.82 0.25 0.02
108_Q 109_H 0.82 0.25 0.02
291_N 83_V 0.82 0.25 0.02
191_A 108_S 0.82 0.24 0.02
133_Q 78_I 0.82 0.24 0.02
169_V 2_E 0.81 0.24 0.02
122_V 97_N 0.81 0.24 0.02
117_E 116_S 0.81 0.24 0.02
92_I 72_Q 0.81 0.24 0.02
160_V 104_S 0.81 0.24 0.02
124_V 23_S 0.81 0.24 0.02
70_V 134_E 0.81 0.24 0.02
238_S 135_K 0.81 0.24 0.02
263_V 116_S 0.81 0.23 0.02
144_T 16_Q 0.80 0.23 0.02
217_E 5_K 0.80 0.23 0.02
190_D 82_E 0.80 0.23 0.02
213_S 45_M 0.80 0.23 0.02
261_M 5_K 0.80 0.23 0.02
101_A 81_Y 0.80 0.23 0.02
214_S 95_I 0.80 0.23 0.02
214_S 53_I 0.79 0.23 0.02
293_I 2_E 0.79 0.23 0.02
92_I 51_I 0.79 0.22 0.02
99_V 75_V 0.79 0.22 0.02
61_T 98_V 0.79 0.22 0.02
10_I 108_S 0.79 0.22 0.02
16_S 37_G 0.79 0.22 0.02
116_T 80_N 0.79 0.22 0.02
133_Q 37_G 0.79 0.22 0.02
24_L 54_E 0.78 0.22 0.01
287_Q 80_N 0.78 0.22 0.01
277_V 53_I 0.78 0.22 0.01
250_R 100_V 0.78 0.22 0.01
136_T 74_T 0.78 0.22 0.01
95_I 80_N 0.78 0.21 0.01
259_A 43_G 0.78 0.21 0.01
7_K 120_R 0.78 0.21 0.01
75_D 18_G 0.77 0.21 0.01
289_A 111_E 0.77 0.21 0.01
185_Y 127_A 0.77 0.21 0.01
264_L 104_S 0.77 0.21 0.01
116_T 110_A 0.77 0.21 0.01
294_F 66_L 0.77 0.21 0.01
264_L 110_A 0.77 0.21 0.01
116_T 100_V 0.77 0.21 0.01
49_F 24_L 0.77 0.21 0.01
261_M 45_M 0.77 0.21 0.01
215_I 55_N 0.77 0.21 0.01
111_A 117_F 0.77 0.21 0.01
136_T 36_I 0.77 0.21 0.01
87_T 111_E 0.77 0.21 0.01
186_F 37_G 0.77 0.21 0.01
155_L 10_I 0.76 0.20 0.01
42_K 88_R 0.75 0.20 0.01
263_V 60_E 0.75 0.20 0.01
190_D 68_L 0.75 0.20 0.01
235_L 21_L 0.75 0.20 0.01
282_H 81_Y 0.75 0.20 0.01
93_S 110_A 0.74 0.19 0.01
131_S 35_T 0.74 0.19 0.01
297_Q 35_T 0.74 0.19 0.01
236_D 40_L 0.74 0.19 0.01
221_E 44_E 0.74 0.19 0.01
87_T 84_V 0.74 0.19 0.01
295_A 122_R 0.74 0.19 0.01
56_R 98_V 0.73 0.19 0.01
65_R 68_L 0.73 0.19 0.01
179_F 14_P 0.73 0.19 0.01
250_R 93_E 0.73 0.19 0.01
166_G 30_T 0.73 0.19 0.01
217_E 114_S 0.73 0.19 0.01
111_A 78_I 0.73 0.19 0.01
11_S 3_A 0.73 0.19 0.01
10_I 71_P 0.73 0.19 0.01
82_G 81_Y 0.73 0.19 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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