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OPENSEQ.org
MATs-fish
Genes: A B A+B
Length: 395 334 665
Sequences: 2411 26119 185
Seq/Len: 6.1 78.2 0.28
MirrorTree (Pazo et al. 2001) 0.32
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 0.07 0.12 0.01
2 0.07 0.14 0.02
5 0.07 0.17 0.04
10 0.07 0.19 0.11
20 0.07 0.21 0.25
100 0.08 0.26 0.92
∞ 0.09 0.31 2.99
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
157_A 148_R 1.36 0.32 0.00
330_I 310_P 1.26 0.26 0.00
298_A 312_R 1.21 0.23 0.00
316_V 86_Q 1.15 0.21 0.00
87_V 236_E 1.13 0.20 0.00
34_C 86_Q 1.12 0.20 0.00
242_Y 298_S 1.11 0.19 0.00
259_A 223_H 1.11 0.19 0.00
222_L 89_V 1.08 0.18 0.00
110_L 44_V 1.08 0.18 0.00
147_E 114_V 1.08 0.18 0.00
141_Y 62_R 1.06 0.17 0.00
241_I 144_N 1.06 0.17 0.00
316_V 30_R 1.06 0.17 0.00
71_I 80_H 1.05 0.17 0.00
52_A 265_I 1.04 0.17 0.00
141_Y 265_I 1.03 0.16 0.00
318_V 140_F 1.03 0.16 0.00
311_C 48_F 1.01 0.15 0.00
185_T 223_H 1.00 0.15 0.00
157_A 202_D 1.00 0.15 0.00
103_T 114_V 0.98 0.14 0.00
223_K 33_V 0.96 0.14 0.00
150_M 149_E 0.96 0.14 0.00
300_W 55_A 0.95 0.13 0.00
332_I 261_M 0.94 0.13 0.00
33_I 134_I 0.94 0.13 0.00
310_L 92_H 0.93 0.13 0.00
318_V 233_Q 0.92 0.13 0.00
349_V 31_V 0.92 0.13 0.00
318_V 296_D 0.92 0.12 0.00
288_T 268_A 0.92 0.12 0.00
47_Q 119_N 0.91 0.12 0.00
203_I 254_E 0.91 0.12 0.00
326_H 30_R 0.89 0.12 0.00
52_A 312_R 0.89 0.12 0.00
288_T 250_W 0.89 0.12 0.00
243_H 179_V 0.88 0.12 0.00
37_I 120_L 0.88 0.12 0.00
319_S 129_A 0.88 0.11 0.00
345_L 131_L 0.87 0.11 0.00
52_A 56_V 0.87 0.11 0.00
110_L 297_C 0.87 0.11 0.00
349_V 87_P 0.86 0.11 0.00
34_C 36_A 0.86 0.11 0.00
349_V 65_P 0.84 0.10 0.00
141_Y 196_A 0.84 0.10 0.00
152_L 81_I 0.84 0.10 0.00
65_I 235_A 0.84 0.10 0.00
365_D 213_M 0.84 0.10 0.00
157_A 78_V 0.84 0.10 0.00
149_C 115_D 0.84 0.10 0.00
391_K 125_A 0.84 0.10 0.00
236_L 60_F 0.84 0.10 0.00
141_Y 230_V 0.83 0.10 0.00
376_A 120_L 0.83 0.10 0.00
364_L 62_R 0.83 0.10 0.00
390_P 29_R 0.83 0.10 0.00
203_I 81_I 0.83 0.10 0.00
213_V 78_V 0.83 0.10 0.00
65_I 179_V 0.83 0.10 0.00
312_R 298_S 0.83 0.10 0.00
215_L 90_I 0.82 0.10 0.00
257_G 75_S 0.82 0.10 0.00
222_L 126_A 0.82 0.10 0.00
174_P 150_E 0.82 0.10 0.00
129_D 39_L 0.81 0.10 0.00
394_K 316_K 0.81 0.10 0.00
72_T 260_E 0.81 0.10 0.00
52_A 166_G 0.81 0.10 0.00
316_V 295_L 0.81 0.10 0.00
40_A 58_C 0.81 0.10 0.00
313_R 48_F 0.80 0.10 0.00
259_A 232_R 0.80 0.10 0.00
298_A 162_T 0.80 0.10 0.00
34_C 172_E 0.80 0.10 0.00
143_T 319_L 0.80 0.10 0.00
305_L 86_Q 0.80 0.09 0.00
110_L 92_H 0.80 0.09 0.00
157_A 70_V 0.80 0.09 0.00
212_E 126_A 0.80 0.09 0.00
393_L 29_R 0.80 0.09 0.00
103_T 88_H 0.79 0.09 0.00
157_A 114_V 0.79 0.09 0.00
202_T 213_M 0.79 0.09 0.00
392_K 125_A 0.78 0.09 0.00
213_V 177_A 0.78 0.09 0.00
144_D 90_I 0.78 0.09 0.00
349_V 287_A 0.78 0.09 0.00
185_T 303_L 0.78 0.09 0.00
83_V 201_F 0.78 0.09 0.00
65_I 134_I 0.78 0.09 0.00
41_V 217_Q 0.77 0.09 0.00
66_L 317_E 0.77 0.09 0.00
160_L 141_D 0.77 0.09 0.00
143_T 296_D 0.77 0.09 0.00
213_V 257_T 0.77 0.09 0.00
130_I 187_G 0.76 0.09 0.00
205_I 126_A 0.76 0.09 0.00
88_K 33_V 0.76 0.09 0.00
220_D 296_D 0.76 0.09 0.00
330_I 267_D 0.76 0.09 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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