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OPENSEQ.org
3A8K-2
Genes: A B A+B
Length: 360 128 473
Sequences: 5269 3075 1245
Seq/Len: 14.64 24.02 2.63
MirrorTree (Pazo et al. 2001) 0.53
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 0.05 0.06 2.34
2 0.06 0.06 2.45
5 0.08 0.07 2.53
10 0.16 0.07 2.53
20 0.17 0.07 2.55
100 0.19 0.07 2.69
∞ 0.26 0.10 3.71
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
342_R 46_E 1.31 0.88 0.23
13_A 77_I 1.06 0.67 0.11
30_Q 24_Y 0.95 0.54 0.07
168_M 58_A 0.94 0.54 0.07
100_Y 39_M 0.93 0.52 0.07
341_N 48_G 0.89 0.48 0.06
141_M 65_A 0.88 0.47 0.06
61_E 98_G 0.87 0.45 0.06
171_F 66_A 0.86 0.44 0.05
6_E 86_D 0.85 0.43 0.05
332_G 78_V 0.84 0.41 0.05
171_F 39_M 0.82 0.39 0.04
66_L 65_A 0.80 0.37 0.04
54_L 60_A 0.79 0.36 0.04
83_S 43_D 0.79 0.35 0.04
3_P 41_F 0.77 0.34 0.04
356_N 66_A 0.76 0.33 0.04
238_D 97_A 0.76 0.33 0.04
230_M 105_K 0.76 0.32 0.04
121_W 63_V 0.76 0.32 0.04
235_Q 59_V 0.75 0.32 0.04
57_S 90_L 0.75 0.32 0.04
242_S 87_S 0.75 0.32 0.03
15_M 63_V 0.74 0.31 0.03
64_R 66_A 0.73 0.30 0.03
71_V 68_D 0.73 0.30 0.03
310_T 29_T 0.73 0.30 0.03
341_N 49_A 0.73 0.29 0.03
153_A 11_K 0.73 0.29 0.03
122_I 106_A 0.72 0.29 0.03
204_F 76_E 0.71 0.27 0.03
43_M 38_D 0.70 0.26 0.03
223_T 1_S 0.69 0.26 0.03
12_G 52_S 0.69 0.26 0.03
214_K 66_A 0.69 0.25 0.03
287_G 43_D 0.69 0.25 0.03
32_D 16_L 0.68 0.25 0.03
76_K 77_I 0.68 0.25 0.03
209_V 68_D 0.68 0.25 0.03
3_P 95_P 0.68 0.24 0.03
46_V 84_L 0.67 0.24 0.02
149_A 78_V 0.66 0.23 0.02
181_I 102_F 0.66 0.23 0.02
309_I 68_D 0.66 0.23 0.02
64_R 89_E 0.66 0.23 0.02
19_H 10_S 0.66 0.23 0.02
112_S 101_I 0.66 0.23 0.02
47_S 40_V 0.66 0.23 0.02
69_N 33_Q 0.66 0.23 0.02
277_K 26_V 0.65 0.22 0.02
89_S 78_V 0.64 0.22 0.02
132_E 46_E 0.63 0.21 0.02
83_S 105_K 0.63 0.21 0.02
74_L 63_V 0.63 0.21 0.02
109_V 15_W 0.62 0.20 0.02
79_K 67_S 0.62 0.20 0.02
70_D 90_L 0.62 0.20 0.02
63_L 83_A 0.62 0.20 0.02
13_A 94_E 0.62 0.20 0.02
54_L 80_V 0.61 0.19 0.02
23_M 28_I 0.61 0.19 0.02
205_W 91_V 0.61 0.19 0.02
133_I 96_Y 0.61 0.19 0.02
9_T 10_S 0.61 0.19 0.02
52_V 96_Y 0.61 0.19 0.02
70_D 84_L 0.60 0.19 0.02
19_H 76_E 0.60 0.19 0.02
46_V 67_S 0.60 0.19 0.02
98_V 78_V 0.60 0.19 0.02
288_V 33_Q 0.60 0.19 0.02
344_M 41_F 0.60 0.18 0.02
192_Y 101_I 0.60 0.18 0.02
340_R 40_V 0.60 0.18 0.02
55_R 16_L 0.60 0.18 0.02
216_C 49_A 0.60 0.18 0.02
282_V 74_S 0.60 0.18 0.02
322_I 123_A 0.60 0.18 0.02
335_A 78_V 0.60 0.18 0.02
264_R 6_E 0.59 0.18 0.02
124_Q 114_S 0.59 0.18 0.02
172_F 70_Y 0.59 0.18 0.02
109_V 67_S 0.59 0.18 0.02
151_A 18_K 0.59 0.18 0.02
31_I 31_H 0.59 0.18 0.02
1_Q 76_E 0.59 0.18 0.02
294_P 77_I 0.59 0.18 0.02
106_F 126_E 0.59 0.18 0.02
190_A 28_I 0.59 0.17 0.02
339_I 40_V 0.59 0.17 0.02
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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