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OPENSEQ.org
TrpS
Genes: A B A+B
Length: 239 389 554
Sequences: 2566 6227 1761
Seq/Len: 10.74 16.01 3.18
MirrorTree (Pazo et al. 2001) 0.69
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 0.08 0.03 2.57
2 0.08 0.03 2.67
5 0.08 0.03 2.70
10 0.08 0.04 2.79
20 0.08 0.04 2.80
100 0.08 0.06 2.85
∞ 0.09 0.18 3.11
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
90_N 270_K 2.71 1.00 1.00
43_V 170_L 2.66 1.00 1.00
85_L 273_Y 2.12 1.00 0.99
89_V 278_K 1.66 0.98 0.94
63_I 286_W 1.43 0.94 0.87
62_T 286_W 1.33 0.92 0.82
50_Q 168_E 1.33 0.91 0.82
64_K 286_W 1.31 0.91 0.81
89_V 273_Y 1.30 0.90 0.80
159_Y 178_Q 1.05 0.72 0.57
64_K 285_D 1.01 0.68 0.52
43_V 193_Y 0.88 0.52 0.36
18_T 56_Y 0.82 0.45 0.29
136_N 177_L 0.81 0.42 0.27
214_V 170_L 0.79 0.40 0.25
77_Y 179_T 0.77 0.38 0.23
44_A 81_A 0.77 0.38 0.23
39_F 289_V 0.76 0.37 0.23
134_A 177_L 0.71 0.32 0.18
133_V 335_S 0.71 0.31 0.18
50_Q 171_R 0.70 0.30 0.17
25_L 341_I 0.70 0.30 0.17
90_N 128_I 0.69 0.29 0.17
7_Y 378_V 0.68 0.29 0.16
90_N 209_K 0.68 0.28 0.15
64_K 196_I 0.68 0.28 0.15
43_V 274_L 0.68 0.28 0.15
100_D 359_K 0.67 0.27 0.15
47_P 239_P 0.67 0.27 0.15
159_Y 175_T 0.67 0.27 0.14
110_L 347_S 0.66 0.27 0.14
62_T 318_L 0.66 0.27 0.14
66_I 84_I 0.66 0.26 0.14
137_T 259_T 0.66 0.26 0.14
107_V 49_A 0.65 0.25 0.13
18_T 146_K 0.65 0.25 0.13
124_D 322_V 0.65 0.25 0.13
174_I 159_S 0.64 0.24 0.13
28_L 309_A 0.63 0.24 0.12
4_F 193_Y 0.63 0.23 0.12
28_L 366_N 0.63 0.23 0.12
124_D 123_G 0.62 0.23 0.12
33_V 238_Y 0.62 0.23 0.12
157_S 289_V 0.62 0.23 0.12
195_E 380_N 0.62 0.23 0.12
65_K 286_W 0.62 0.23 0.12
207_V 239_P 0.62 0.23 0.12
82_M 171_R 0.62 0.22 0.11
159_Y 177_L 0.62 0.22 0.11
175_K 325_E 0.62 0.22 0.11
196_Q 203_V 0.62 0.22 0.11
26_N 222_Y 0.61 0.22 0.11
126_A 363_V 0.61 0.22 0.11
79_L 321_A 0.61 0.21 0.11
100_D 68_R 0.61 0.21 0.11
25_L 279_T 0.61 0.21 0.11
155_Y 279_T 0.60 0.21 0.10
104_K 88_I 0.60 0.21 0.10
89_V 277_S 0.60 0.21 0.10
159_Y 119_A 0.60 0.20 0.10
39_F 206_E 0.59 0.20 0.10
5_I 176_N 0.59 0.20 0.10
123_V 215_K 0.59 0.20 0.10
68_E 210_K 0.59 0.20 0.10
74_S 94_A 0.59 0.20 0.10
158_R 275_H 0.59 0.20 0.10
182_K 238_Y 0.59 0.20 0.09
115_L 55_L 0.59 0.20 0.09
56_A 170_L 0.58 0.19 0.09
140_E 63_E 0.58 0.19 0.09
200_V 253_G 0.58 0.19 0.09
104_K 214_E 0.58 0.19 0.09
48_V 133_E 0.58 0.19 0.09
156_I 121_L 0.58 0.19 0.09
35_I 215_K 0.58 0.19 0.09
182_K 325_E 0.57 0.19 0.09
56_A 321_A 0.57 0.19 0.09
90_N 283_Q 0.57 0.19 0.09
191_I 286_W 0.57 0.18 0.09
194_H 253_G 0.57 0.18 0.09
217_M 367_L 0.57 0.18 0.09
161_V 125_E 0.57 0.18 0.09
57_L 284_D 0.57 0.18 0.09
207_V 190_P 0.57 0.18 0.08
152_F 196_I 0.57 0.18 0.08
36_G 144_R 0.57 0.18 0.08
153_V 148_L 0.57 0.18 0.08
43_V 166_I 0.56 0.18 0.08
54_S 128_I 0.56 0.18 0.08
137_T 87_A 0.56 0.18 0.08
43_V 184_I 0.56 0.18 0.08
192_S 335_S 0.56 0.18 0.08
85_L 124_M 0.56 0.18 0.08
35_I 174_I 0.56 0.17 0.08
112_I 247_L 0.56 0.17 0.08
208_I 323_T 0.56 0.17 0.08
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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