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OPENSEQ.org
3mml_ab
Genes: A B A+B
Length: 289 210 485
Sequences: 2298 2183 1434
Seq/Len: 7.95 10.4 2.96
MirrorTree (Pazo et al. 2001) 0.75
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 0.00 0.00 2.78
2 0.00 0.00 2.86
5 0.00 0.00 2.86
10 0.01 0.01 2.88
20 0.02 0.02 2.87
100 0.03 0.03 2.87
∞ 0.10 0.10 2.88
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
265_E 11_D 2.98 1.00 1.00
230_G 50_L 1.97 0.99 0.98
241_N 149_E 1.74 0.99 0.96
254_T 125_F 1.73 0.99 0.95
22_G 41_D 1.52 0.96 0.90
229_E 45_A 1.46 0.95 0.88
25_H 32_R 1.25 0.86 0.75
229_E 48_T 1.06 0.71 0.57
229_E 129_A 1.01 0.66 0.50
28_V 188_F 0.99 0.64 0.48
240_P 147_R 0.94 0.57 0.42
230_G 44_P 0.90 0.53 0.37
228_S 146_R 0.88 0.50 0.35
235_A 113_I 0.88 0.50 0.35
254_T 45_A 0.88 0.50 0.34
228_S 125_F 0.87 0.49 0.34
226_L 45_A 0.87 0.48 0.33
206_D 153_S 0.85 0.47 0.32
211_R 152_T 0.85 0.46 0.31
24_A 52_K 0.85 0.46 0.30
28_V 196_A 0.84 0.44 0.29
217_L 187_M 0.83 0.44 0.29
206_D 138_G 0.83 0.43 0.28
229_E 15_L 0.82 0.43 0.28
62_F 125_F 0.82 0.43 0.28
26_M 196_A 0.81 0.41 0.26
252_P 165_F 0.80 0.40 0.25
227_P 47_R 0.80 0.39 0.25
29_T 129_A 0.80 0.39 0.25
232_T 13_A 0.79 0.38 0.24
257_Y 176_G 0.79 0.38 0.24
265_E 12_Q 0.78 0.38 0.24
232_T 9_Y 0.78 0.38 0.23
26_M 189_D 0.77 0.36 0.23
245_V 150_P 0.76 0.35 0.21
259_V 9_Y 0.76 0.35 0.21
229_E 162_A 0.75 0.34 0.21
265_E 53_L 0.74 0.34 0.20
229_E 87_V 0.74 0.33 0.20
236_I 39_V 0.74 0.33 0.20
229_E 7_H 0.74 0.33 0.19
193_I 142_L 0.74 0.33 0.19
230_G 52_K 0.73 0.32 0.19
232_T 50_L 0.71 0.30 0.17
144_L 14_L 0.71 0.30 0.17
252_P 136_V 0.71 0.30 0.17
132_S 42_I 0.71 0.30 0.17
41_L 98_L 0.71 0.29 0.17
207_R 131_G 0.70 0.29 0.17
183_P 47_R 0.70 0.29 0.17
227_P 45_A 0.70 0.29 0.16
28_V 195_P 0.69 0.28 0.16
132_S 191_N 0.69 0.28 0.16
258_P 177_W 0.69 0.28 0.15
230_G 15_L 0.69 0.28 0.15
248_G 67_G 0.69 0.27 0.15
233_R 52_K 0.68 0.27 0.15
253_V 126_C 0.68 0.27 0.15
247_L 126_C 0.68 0.27 0.15
225_Q 163_G 0.68 0.27 0.14
237_Q 134_Y 0.68 0.26 0.14
228_S 177_W 0.67 0.26 0.14
134_D 125_F 0.67 0.26 0.14
227_P 46_A 0.67 0.26 0.14
246_I 111_Q 0.67 0.25 0.14
249_P 195_P 0.66 0.25 0.14
3_T 135_L 0.66 0.25 0.14
31_S 190_V 0.66 0.25 0.14
276_P 162_A 0.66 0.25 0.13
26_M 126_C 0.66 0.25 0.13
261_G 123_V 0.66 0.25 0.13
180_V 8_N 0.66 0.25 0.13
184_R 46_A 0.65 0.24 0.13
24_A 43_V 0.65 0.24 0.13
250_D 131_G 0.65 0.24 0.13
105_L 53_L 0.65 0.24 0.13
28_V 198_L 0.65 0.24 0.13
242_G 146_R 0.65 0.24 0.12
128_L 196_A 0.65 0.24 0.12
28_V 126_C 0.64 0.23 0.12
248_G 168_V 0.64 0.23 0.12
242_G 134_Y 0.64 0.23 0.12
183_P 125_F 0.64 0.23 0.12
28_V 130_P 0.64 0.23 0.12
177_L 199_T 0.64 0.23 0.12
271_L 172_Q 0.64 0.23 0.12
227_P 165_F 0.64 0.23 0.12
232_T 52_K 0.63 0.22 0.11
103_I 53_L 0.63 0.22 0.11
208_V 161_L 0.63 0.22 0.11
13_A 166_S 0.63 0.22 0.11
252_P 128_F 0.63 0.22 0.11
229_E 134_Y 0.63 0.22 0.11
24_A 154_V 0.62 0.22 0.11
38_S 106_G 0.62 0.22 0.11
170_I 51_V 0.62 0.22 0.11
180_V 29_E 0.62 0.22 0.11
242_G 132_F 0.62 0.21 0.11
183_P 45_A 0.62 0.21 0.11
91_T 208_A 0.62 0.21 0.11
214_G 167_G 0.61 0.21 0.10
180_V 78_H 0.61 0.21 0.10
134_D 46_A 0.61 0.21 0.10
208_V 128_F 0.61 0.21 0.10
2_T 91_V 0.61 0.21 0.10
257_Y 177_W 0.61 0.21 0.10
255_G 128_F 0.61 0.21 0.10
34_A 61_P 0.61 0.20 0.10
177_L 20_S 0.61 0.20 0.10
267_D 11_D 0.61 0.20 0.10
65_R 113_I 0.61 0.20 0.10
242_G 177_W 0.61 0.20 0.10
182_G 128_F 0.61 0.20 0.10
137_S 198_L 0.60 0.20 0.10
225_Q 147_R 0.60 0.20 0.10
254_T 195_P 0.60 0.20 0.10
210_M 209_V 0.60 0.20 0.10
228_S 174_P 0.60 0.20 0.10
252_P 124_G 0.60 0.20 0.10
225_Q 46_A 0.60 0.20 0.09
38_S 29_E 0.59 0.19 0.09
60_G 128_F 0.59 0.19 0.09
184_R 9_Y 0.59 0.19 0.09
196_R 113_I 0.59 0.19 0.09
14_L 171_R 0.59 0.19 0.09
236_I 119_T 0.59 0.19 0.09
184_R 47_R 0.59 0.19 0.09
210_M 87_V 0.59 0.19 0.09
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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