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OPENSEQ.org
2Y69_AB
Genes: A B A+B
Length: 513 227 736
Sequences: 3012 4332 1930
Seq/Len: 5.87 19.08 2.62
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 2.28
5 0.01 0.01 2.43
10 0.01 0.01 2.57
20 0.01 0.01 2.61
100 0.01 0.02 2.66
∞ 0.04 0.07 2.79
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
228_I 175_I 3.27 1.00 1.00
368_D 198_E 3.12 1.00 1.00
368_D 173_D 2.14 1.00 0.99
368_D 171_K 2.13 1.00 0.99
433_S 6_Q 1.96 0.99 0.98
439_Y 205_S 1.81 0.99 0.96
352_L 35_S 1.74 0.98 0.95
446_Y 2_A 1.62 0.97 0.92
440_S 205_S 1.62 0.97 0.92
226_D 178_R 1.58 0.96 0.91
318_K 62_E 1.46 0.93 0.86
448_M 5_M 1.45 0.93 0.86
358_A 76_I 1.28 0.85 0.75
267_F 66_T 1.23 0.82 0.71
231_Q 160_L 1.21 0.81 0.69
294_V 180_N 1.21 0.81 0.69
310_I 70_A 1.19 0.79 0.67
368_D 197_S 1.15 0.76 0.63
368_D 162_S 1.14 0.75 0.61
339_W 205_S 1.14 0.75 0.61
373_V 198_E 1.12 0.73 0.60
371_Y 24_H 1.06 0.68 0.53
293_T 162_S 1.05 0.66 0.51
279_I 62_E 1.04 0.66 0.51
333_W 46_L 1.04 0.65 0.51
57_V 199_I 0.98 0.58 0.43
348_T 38_V 0.96 0.56 0.41
313_I 38_V 0.96 0.56 0.41
427_Q 14_S 0.96 0.56 0.41
306_S 81_L 0.95 0.54 0.39
323_L 42_I 0.94 0.54 0.39
371_Y 144_L 0.94 0.54 0.39
323_L 45_M 0.94 0.53 0.38
352_L 31_V 0.92 0.52 0.36
96_M 213_L 0.90 0.49 0.34
295_G 180_N 0.88 0.46 0.32
53_Y 152_M 0.88 0.46 0.31
267_F 62_E 0.87 0.45 0.31
315_T 69_P 0.87 0.45 0.30
491_L 168_L 0.86 0.44 0.29
50_D 203_N 0.82 0.40 0.25
422_M 146_M 0.82 0.40 0.25
312_A 62_E 0.81 0.38 0.24
50_D 205_S 0.81 0.38 0.24
320_F 66_T 0.81 0.38 0.24
349_V 35_S 0.81 0.38 0.23
199_P 104_W 0.80 0.37 0.23
373_V 171_K 0.80 0.36 0.23
283_G 219_F 0.79 0.36 0.22
429_F 73_L 0.79 0.36 0.22
410_K 165_V 0.79 0.36 0.22
138_A 33_L 0.78 0.35 0.21
418_V 100_M 0.77 0.34 0.20
171_K 110_Y 0.76 0.33 0.20
277_M 197_S 0.76 0.32 0.19
369_T 21_L 0.76 0.32 0.19
298_V 211_L 0.75 0.32 0.19
392_F 155_S 0.75 0.32 0.19
355_I 93_P 0.75 0.32 0.19
131_L 199_I 0.75 0.31 0.18
316_G 69_P 0.75 0.31 0.18
439_Y 195_Q 0.74 0.31 0.18
409_A 125_T 0.74 0.31 0.18
368_D 160_L 0.74 0.30 0.18
309_M 195_Q 0.74 0.30 0.17
324_A 87_M 0.74 0.30 0.17
323_L 41_I 0.73 0.30 0.17
261_S 101_G 0.73 0.30 0.17
42_Q 163_W 0.73 0.29 0.17
294_V 175_I 0.73 0.29 0.17
474_A 6_Q 0.73 0.29 0.17
159_G 28_L 0.72 0.29 0.16
462_T 32_F 0.72 0.28 0.16
302_A 85_Y 0.71 0.28 0.16
362_L 75_L 0.71 0.28 0.15
318_K 66_T 0.71 0.27 0.15
180_T 95_L 0.71 0.27 0.15
110_L 67_I 0.70 0.27 0.15
103_L 221_K 0.70 0.27 0.15
267_F 65_W 0.70 0.27 0.15
165_T 17_M 0.70 0.27 0.15
244_I 198_E 0.70 0.27 0.14
246_I 62_E 0.70 0.27 0.14
365_V 9_F 0.70 0.26 0.14
250_F 62_E 0.70 0.26 0.14
6_L 213_L 0.70 0.26 0.14
292_F 176_P 0.69 0.26 0.14
422_M 75_L 0.69 0.26 0.14
28_V 146_M 0.69 0.26 0.14
161_I 15_P 0.69 0.26 0.14
282_L 197_S 0.69 0.26 0.14
313_I 83_I 0.69 0.26 0.14
321_S 62_E 0.69 0.25 0.14
337_M 168_L 0.68 0.25 0.13
369_T 221_K 0.68 0.25 0.13
165_T 184_L 0.68 0.25 0.13
465_M 43_S 0.68 0.25 0.13
261_S 99_T 0.68 0.25 0.13
200_V 69_P 0.68 0.24 0.13
147_F 205_S 0.68 0.24 0.13
362_L 27_T 0.67 0.24 0.13
228_I 68_L 0.67 0.24 0.13
367_H 174_A 0.67 0.24 0.13
390_G 36_S 0.67 0.24 0.12
170_M 156_S 0.67 0.24 0.12
19_L 203_N 0.67 0.24 0.12
344_I 58_A 0.67 0.24 0.12
90_D 69_P 0.67 0.24 0.12
256_I 99_T 0.67 0.23 0.12
254_S 62_E 0.67 0.23 0.12
232_H 173_D 0.66 0.23 0.12
288_A 50_L 0.66 0.23 0.12
322_W 104_W 0.66 0.23 0.12
356_V 27_T 0.66 0.23 0.12
396_F 6_Q 0.66 0.23 0.12
311_I 80_S 0.66 0.23 0.12
95_R 178_R 0.65 0.22 0.11
156_S 69_P 0.65 0.22 0.11
379_V 211_L 0.65 0.22 0.11
342_G 34_I 0.65 0.22 0.11
195_L 188_R 0.65 0.22 0.11
389_M 152_M 0.65 0.22 0.11
75_G 80_S 0.65 0.22 0.11
173_P 76_I 0.65 0.22 0.11
446_Y 152_M 0.65 0.22 0.11
399_F 71_I 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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