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OPENSEQ.org
2Y69_A_B
Genes: A B A+B
Length: 514 227 737
Sequences: 3001 4332 1938
Seq/Len: 5.84 19.08 2.63
MirrorTree (Pazo et al. 2001) 0.87
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 0.01 0.01 2.20
2 0.01 0.01 2.27
5 0.01 0.01 2.42
10 0.01 0.01 2.56
20 0.01 0.01 2.62
100 0.01 0.02 2.65
∞ 0.04 0.07 2.80
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
229_I 175_I 3.21 1.00 1.00
369_D 198_E 3.07 1.00 1.00
369_D 171_K 2.14 1.00 0.99
369_D 173_D 2.14 1.00 0.99
434_S 6_Q 2.00 0.99 0.98
440_Y 205_S 1.77 0.98 0.95
353_L 35_S 1.74 0.98 0.95
227_D 178_R 1.64 0.97 0.93
441_S 205_S 1.60 0.96 0.92
449_M 5_M 1.49 0.94 0.88
319_K 62_E 1.48 0.94 0.87
447_Y 2_A 1.46 0.93 0.86
359_A 76_I 1.25 0.84 0.73
268_F 66_T 1.24 0.83 0.71
232_Q 160_L 1.22 0.81 0.70
295_V 180_N 1.21 0.81 0.69
311_I 70_A 1.17 0.78 0.65
369_D 162_S 1.14 0.75 0.62
374_V 198_E 1.13 0.74 0.61
369_D 197_S 1.11 0.72 0.59
294_T 162_S 1.08 0.69 0.55
280_I 62_E 1.07 0.68 0.54
334_W 46_L 1.07 0.68 0.54
340_W 205_S 1.05 0.66 0.52
372_Y 24_H 1.05 0.66 0.52
58_V 199_I 1.03 0.65 0.50
349_T 38_V 0.99 0.60 0.45
314_I 38_V 0.97 0.57 0.42
307_S 81_L 0.93 0.53 0.37
428_Q 14_S 0.92 0.51 0.36
492_L 168_L 0.92 0.51 0.36
372_Y 144_L 0.92 0.51 0.36
353_L 31_V 0.91 0.50 0.35
324_L 45_M 0.91 0.50 0.35
296_G 180_N 0.90 0.48 0.33
423_M 146_M 0.89 0.47 0.32
139_A 33_L 0.88 0.47 0.32
324_L 42_I 0.88 0.47 0.32
268_F 62_E 0.88 0.46 0.31
316_T 69_P 0.88 0.46 0.31
430_F 73_L 0.85 0.43 0.28
97_M 213_L 0.85 0.43 0.28
54_Y 152_M 0.85 0.42 0.28
350_V 35_S 0.84 0.42 0.27
313_A 62_E 0.83 0.40 0.26
51_D 203_N 0.82 0.40 0.26
317_G 69_P 0.82 0.39 0.25
200_P 104_W 0.82 0.39 0.25
410_A 125_T 0.80 0.37 0.23
321_F 66_T 0.80 0.37 0.23
475_A 6_Q 0.80 0.37 0.23
374_V 171_K 0.79 0.35 0.22
229_I 68_L 0.79 0.35 0.22
370_T 21_L 0.78 0.35 0.21
20_L 203_N 0.77 0.34 0.21
325_A 87_M 0.77 0.34 0.20
172_K 110_Y 0.76 0.33 0.20
278_M 197_S 0.76 0.33 0.20
104_L 221_K 0.76 0.33 0.19
440_Y 195_Q 0.76 0.32 0.19
284_G 219_F 0.76 0.32 0.19
295_V 175_I 0.75 0.32 0.19
411_K 165_V 0.75 0.32 0.18
132_L 199_I 0.74 0.31 0.18
247_I 62_E 0.74 0.30 0.17
319_K 66_T 0.73 0.30 0.17
111_L 67_I 0.73 0.30 0.17
251_F 62_E 0.73 0.30 0.17
393_F 155_S 0.73 0.30 0.17
166_T 17_M 0.73 0.30 0.17
366_V 9_F 0.73 0.29 0.17
356_I 93_P 0.73 0.29 0.17
29_V 146_M 0.72 0.29 0.16
64_V 150_I 0.72 0.29 0.16
303_A 85_Y 0.72 0.28 0.16
419_V 100_M 0.72 0.28 0.16
369_D 160_L 0.72 0.28 0.16
51_D 205_S 0.71 0.28 0.16
160_G 28_L 0.71 0.28 0.15
268_F 65_W 0.71 0.28 0.15
416_I 144_L 0.71 0.28 0.15
162_I 15_P 0.71 0.27 0.15
400_F 71_I 0.70 0.27 0.15
155_V 143_V 0.70 0.27 0.15
262_S 99_T 0.70 0.27 0.15
7_L 213_L 0.70 0.27 0.15
289_A 50_L 0.70 0.27 0.15
230_L 168_L 0.70 0.27 0.15
201_V 69_P 0.70 0.27 0.14
314_I 83_I 0.69 0.26 0.14
283_L 197_S 0.69 0.26 0.14
467_L 75_L 0.69 0.26 0.14
170_N 199_I 0.69 0.26 0.14
423_M 75_L 0.69 0.26 0.14
455_S 217_K 0.69 0.26 0.14
368_H 174_A 0.69 0.26 0.14
363_L 75_L 0.69 0.26 0.14
166_T 184_L 0.69 0.25 0.14
323_W 104_W 0.69 0.25 0.14
310_M 195_Q 0.69 0.25 0.14
463_T 32_F 0.68 0.25 0.14
327_L 64_I 0.68 0.25 0.13
363_L 27_T 0.68 0.25 0.13
346_F 39_L 0.68 0.25 0.13
174_P 76_I 0.68 0.25 0.13
233_H 173_D 0.68 0.25 0.13
322_S 62_E 0.68 0.25 0.13
111_L 71_I 0.68 0.25 0.13
245_I 198_E 0.68 0.25 0.13
181_T 95_L 0.68 0.24 0.13
155_V 152_M 0.68 0.24 0.13
408_T 211_L 0.68 0.24 0.13
354_T 219_F 0.67 0.24 0.13
91_D 69_P 0.67 0.24 0.12
441_S 213_L 0.67 0.24 0.12
391_G 36_S 0.67 0.23 0.12
388_A 82_R 0.67 0.23 0.12
345_I 58_A 0.66 0.23 0.12
366_V 164_A 0.66 0.23 0.12
293_F 176_P 0.66 0.23 0.12
157_S 69_P 0.66 0.23 0.12
138_H 154_V 0.66 0.23 0.12
43_Q 163_W 0.65 0.22 0.11
255_S 62_E 0.65 0.22 0.11
380_V 211_L 0.65 0.22 0.11
177_S 165_V 0.65 0.22 0.11
324_L 41_I 0.65 0.22 0.11
59_T 219_F 0.65 0.22 0.11
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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