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OPENSEQ.org
BxQ
Genes: A B A+B
Length: 362 89 441
Sequences: 1858 1330 1344
Seq/Len: 5.13 14.94 3.05
MirrorTree (Pazo et al. 2001) 0.72
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.13
2 0.00 0.00 2.39
5 0.01 0.00 2.46
10 0.01 0.01 2.58
20 0.02 0.01 2.68
100 0.03 0.02 2.98
∞ 0.07 0.05 3.25
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
144_S 41_T 1.18 0.82 0.09
132_L 41_T 1.07 0.72 0.06
30_Q 45_N 1.03 0.69 0.06
272_A 58_V 0.98 0.63 0.05
342_L 68_W 0.98 0.62 0.05
125_K 35_I 0.95 0.59 0.04
245_L 43_Q 0.94 0.58 0.04
137_S 43_Q 0.92 0.56 0.04
314_P 33_L 0.92 0.56 0.04
320_L 23_P 0.90 0.54 0.04
213_Q 43_Q 0.90 0.53 0.04
35_I 47_M 0.89 0.52 0.04
195_V 6_L 0.86 0.48 0.03
110_F 45_N 0.86 0.48 0.03
96_L 29_L 0.86 0.48 0.03
114_F 69_M 0.86 0.48 0.03
100_I 82_N 0.86 0.48 0.03
216_K 43_Q 0.85 0.47 0.03
95_V 69_M 0.85 0.47 0.03
293_D 38_F 0.85 0.47 0.03
218_L 40_A 0.85 0.47 0.03
273_V 79_N 0.84 0.46 0.03
260_G 60_V 0.84 0.46 0.03
42_V 12_Q 0.84 0.45 0.03
345_V 49_L 0.84 0.45 0.03
126_I 40_A 0.83 0.45 0.03
28_K 45_N 0.83 0.44 0.03
341_V 7_V 0.83 0.44 0.03
7_E 6_L 0.82 0.43 0.03
218_L 80_I 0.82 0.43 0.03
216_K 11_V 0.82 0.43 0.03
113_I 43_Q 0.82 0.43 0.03
85_F 30_I 0.81 0.42 0.03
152_G 30_I 0.80 0.41 0.03
85_F 26_L 0.80 0.41 0.03
204_V 56_I 0.80 0.41 0.03
284_A 53_P 0.80 0.41 0.03
242_I 45_N 0.80 0.40 0.03
199_F 36_S 0.79 0.40 0.03
116_T 69_M 0.79 0.40 0.03
349_N 57_L 0.79 0.40 0.03
38_L 36_S 0.79 0.39 0.02
112_F 36_S 0.79 0.39 0.02
213_Q 56_I 0.77 0.37 0.02
70_E 88_I 0.77 0.37 0.02
308_V 70_T 0.76 0.36 0.02
100_I 12_Q 0.76 0.36 0.02
217_G 45_N 0.76 0.36 0.02
211_R 56_I 0.75 0.35 0.02
73_L 30_I 0.75 0.35 0.02
125_K 67_P 0.75 0.34 0.02
165_F 24_M 0.74 0.34 0.02
60_Y 14_F 0.74 0.34 0.02
262_D 68_W 0.74 0.34 0.02
347_N 67_P 0.74 0.34 0.02
46_L 28_G 0.74 0.33 0.02
351_K 54_K 0.73 0.33 0.02
126_I 41_T 0.73 0.33 0.02
245_L 25_L 0.73 0.33 0.02
124_G 86_T 0.73 0.33 0.02
80_M 64_F 0.73 0.33 0.02
264_V 76_F 0.72 0.32 0.02
343_G 66_M 0.72 0.31 0.02
103_V 78_E 0.72 0.31 0.02
109_Q 45_N 0.72 0.31 0.02
308_V 80_I 0.72 0.31 0.02
151_V 38_F 0.71 0.31 0.02
337_A 13_T 0.71 0.31 0.02
38_L 18_L 0.71 0.31 0.02
88_L 22_L 0.71 0.31 0.02
148_I 2_D 0.71 0.30 0.02
288_V 75_D 0.71 0.30 0.02
229_Y 44_I 0.71 0.30 0.02
126_I 22_L 0.70 0.29 0.02
244_R 77_T 0.70 0.29 0.02
135_L 61_I 0.70 0.29 0.02
208_F 35_I 0.70 0.29 0.02
320_L 54_K 0.70 0.29 0.02
348_T 51_F 0.69 0.29 0.02
289_A 53_P 0.69 0.29 0.02
299_I 44_I 0.69 0.29 0.02
94_I 17_T 0.69 0.29 0.02
199_F 28_G 0.69 0.28 0.02
184_L 21_S 0.69 0.28 0.02
105_G 28_G 0.68 0.28 0.02
334_M 29_L 0.68 0.28 0.02
342_L 51_F 0.68 0.27 0.02
327_N 43_Q 0.68 0.27 0.02
337_A 40_A 0.68 0.27 0.02
45_T 72_T 0.68 0.27 0.02
18_E 29_L 0.68 0.27 0.02
8_K 35_I 0.68 0.27 0.02
210_V 47_M 0.68 0.27 0.02
343_G 41_T 0.68 0.27 0.02
65_S 60_V 0.67 0.27 0.02
34_A 41_T 0.67 0.26 0.01
297_L 87_F 0.67 0.26 0.01
27_P 88_I 0.67 0.26 0.01
307_N 73_M 0.67 0.26 0.01
68_G 31_A 0.67 0.26 0.01
254_M 48_T 0.66 0.26 0.01
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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