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OPENSEQ.org
FleNFleQ
Genes: A B A+B
Length: 280 490 736
Sequences: 12819 6701 373
Seq/Len: 45.78 13.68 0.51
MirrorTree (Pazo et al. 2001) 0.46
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.02 0.01
2 0.02 0.07 0.02
5 0.02 0.08 0.09
10 0.05 0.08 0.19
20 0.06 0.09 0.48
100 0.08 0.12 1.62
∞ 0.13 0.17 3.33
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
125_V 199_V 1.37 0.47 0.00
157_I 10_I 1.14 0.30 0.00
179_L 229_S 1.09 0.27 0.00
179_L 369_V 1.07 0.26 0.00
178_V 110_S 1.01 0.22 0.00
178_V 351_M 1.00 0.22 0.00
238_K 7_L 0.99 0.21 0.00
214_I 373_A 0.95 0.19 0.00
250_V 31_Q 0.94 0.19 0.00
150_V 312_I 0.92 0.18 0.00
148_L 362_V 0.92 0.18 0.00
237_S 289_N 0.92 0.18 0.00
32_A 280_V 0.92 0.18 0.00
80_L 199_V 0.90 0.17 0.00
223_A 294_I 0.90 0.17 0.00
12_V 36_S 0.90 0.17 0.00
148_L 289_N 0.89 0.17 0.00
241_L 378_Y 0.89 0.17 0.00
41_R 42_V 0.88 0.16 0.00
36_A 385_E 0.87 0.16 0.00
31_L 150_S 0.87 0.16 0.00
44_L 9_L 0.87 0.16 0.00
178_V 279_D 0.87 0.16 0.00
125_V 283_I 0.86 0.15 0.00
205_D 250_M 0.85 0.15 0.00
12_V 347_S 0.85 0.15 0.00
82_L 167_D 0.85 0.15 0.00
114_F 36_S 0.84 0.15 0.00
148_L 130_Q 0.84 0.15 0.00
110_L 74_A 0.84 0.14 0.00
214_I 382_G 0.83 0.14 0.00
148_L 274_K 0.82 0.14 0.00
12_V 56_L 0.81 0.14 0.00
44_L 73_L 0.81 0.13 0.00
232_E 242_L 0.81 0.13 0.00
247_A 204_G 0.81 0.13 0.00
235_P 187_L 0.80 0.13 0.00
12_V 166_T 0.80 0.13 0.00
32_A 269_R 0.80 0.13 0.00
76_L 314_M 0.80 0.13 0.00
196_L 83_L 0.80 0.13 0.00
80_L 373_A 0.80 0.13 0.00
117_I 475_M 0.80 0.13 0.00
80_L 275_T 0.79 0.13 0.00
29_V 440_N 0.79 0.13 0.00
44_L 118_L 0.79 0.13 0.00
150_V 182_V 0.78 0.12 0.00
45_L 104_S 0.78 0.12 0.00
157_I 24_L 0.78 0.12 0.00
48_D 100_R 0.78 0.12 0.00
77_R 187_L 0.77 0.12 0.00
57_L 282_I 0.77 0.12 0.00
95_G 105_L 0.77 0.12 0.00
150_V 282_I 0.77 0.12 0.00
147_L 75_S 0.76 0.12 0.00
38_L 328_L 0.76 0.12 0.00
148_L 73_L 0.76 0.12 0.00
250_V 39_W 0.76 0.12 0.00
89_I 304_Y 0.76 0.12 0.00
210_Y 340_R 0.76 0.12 0.00
15_V 171_L 0.75 0.11 0.00
125_V 35_N 0.74 0.11 0.00
210_Y 293_M 0.74 0.11 0.00
69_V 176_S 0.74 0.11 0.00
237_S 350_I 0.73 0.11 0.00
157_I 292_K 0.73 0.11 0.00
80_L 356_H 0.73 0.11 0.00
110_L 291_E 0.73 0.11 0.00
72_G 41_E 0.73 0.11 0.00
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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