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OPENSEQ.org
MurDGm
Genes: A B A+B
Length: 358 451 778
Sequences: 9093 3405 1906
Seq/Len: 25.4 7.55 2.45
MirrorTree (Pazo et al. 2001) 0.65
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 0.06 0.49
2 0.09 0.08 2.19
5 0.10 0.09 2.33
10 0.10 0.09 2.34
20 0.11 0.09 2.36
100 0.12 0.09 2.45
∞ 0.20 0.09 2.97
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
333_S 99_V 0.96 0.54 0.00
301_A 185_V 0.89 0.46 0.00
249_M 197_H 0.83 0.39 0.00
7_F 351_L 0.82 0.38 0.00
41_G 377_V 0.81 0.36 0.00
104_F 336_A 0.79 0.34 0.00
76_V 381_S 0.75 0.30 0.00
345_Y 331_S 0.74 0.29 0.00
299_G 76_M 0.73 0.29 0.00
104_F 92_A 0.73 0.28 0.00
267_L 190_M 0.72 0.28 0.00
207_I 187_T 0.72 0.27 0.00
339_K 187_T 0.72 0.27 0.00
259_G 133_V 0.71 0.27 0.00
146_T 18_A 0.70 0.25 0.00
122_V 72_D 0.70 0.25 0.00
254_V 306_N 0.70 0.25 0.00
209_Q 201_E 0.69 0.25 0.00
277_I 32_G 0.68 0.24 0.00
108_P 425_N 0.68 0.23 0.00
345_Y 431_Y 0.68 0.23 0.00
206_F 418_V 0.67 0.23 0.00
253_D 124_T 0.67 0.23 0.00
279_L 175_G 0.67 0.23 0.00
307_S 325_F 0.67 0.23 0.00
166_M 74_C 0.67 0.23 0.00
61_T 210_I 0.66 0.22 0.00
274_H 250_D 0.66 0.22 0.00
219_V 94_E 0.66 0.22 0.00
161_A 357_D 0.66 0.22 0.00
70_W 326_Y 0.66 0.22 0.00
161_A 362_F 0.66 0.22 0.00
164_K 192_T 0.66 0.22 0.00
281_R 428_W 0.66 0.22 0.00
198_A 102_E 0.65 0.21 0.00
157_K 115_I 0.64 0.21 0.00
273_L 326_Y 0.64 0.21 0.00
118_V 189_L 0.64 0.20 0.00
101_K 362_F 0.64 0.20 0.00
122_V 244_S 0.64 0.20 0.00
298_K 286_T 0.64 0.20 0.00
309_L 309_G 0.64 0.20 0.00
61_T 133_V 0.63 0.20 0.00
314_L 165_V 0.63 0.20 0.00
323_S 215_S 0.62 0.19 0.00
155_K 268_S 0.62 0.19 0.00
352_M 326_Y 0.62 0.19 0.00
136_A 422_S 0.62 0.19 0.00
318_I 114_L 0.62 0.19 0.00
180_I 216_S 0.62 0.19 0.00
240_Y 283_A 0.62 0.19 0.00
262_N 196_Y 0.62 0.19 0.00
79_V 147_I 0.61 0.18 0.00
54_I 7_F 0.61 0.18 0.00
282_E 79_N 0.61 0.18 0.00
97_A 283_A 0.61 0.18 0.00
159_I 78_K 0.60 0.18 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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