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OPENSEQ.org
cI_D_E
Genes: A B A+B
Length: 485 147 594
Sequences: 1691 3696 1407
Seq/Len: 3.49 25.14 2.37
MirrorTree (Pazo et al. 2001) 0.76
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 0.04
2 0.00 0.00 0.04
5 0.00 0.00 0.05
10 0.00 0.00 0.51
20 0.01 0.00 1.94
100 0.01 0.01 2.09
∞ 0.02 0.01 2.23
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
336_S 69_Y 1.28 0.84 0.12
134_L 19_F 1.23 0.79 0.10
280_S 80_V 1.20 0.77 0.09
120_A 16_F 1.16 0.74 0.08
419_A 77_I 1.11 0.69 0.07
381_L 95_S 1.10 0.68 0.07
311_V 34_G 1.08 0.67 0.07
388_M 52_S 1.08 0.67 0.07
178_Y 88_W 1.01 0.59 0.05
144_G 102_E 1.01 0.58 0.05
207_F 22_V 1.00 0.57 0.05
379_M 38_G 0.97 0.54 0.05
133_E 51_E 0.96 0.53 0.04
406_H 38_G 0.95 0.52 0.04
421_G 52_S 0.94 0.50 0.04
377_T 17_A 0.91 0.47 0.04
87_T 29_L 0.91 0.47 0.04
383_L 98_V 0.90 0.46 0.04
339_G 103_A 0.89 0.45 0.04
469_V 101_V 0.89 0.44 0.03
127_S 68_F 0.88 0.43 0.03
23_V 101_V 0.87 0.43 0.03
418_S 76_V 0.87 0.43 0.03
331_A 25_G 0.87 0.42 0.03
213_G 42_R 0.87 0.42 0.03
238_V 69_Y 0.86 0.42 0.03
384_A 115_V 0.86 0.41 0.03
113_A 68_F 0.86 0.41 0.03
422_L 69_Y 0.85 0.40 0.03
149_Q 12_H 0.85 0.40 0.03
156_S 102_E 0.85 0.40 0.03
308_Y 30_M 0.85 0.40 0.03
312_A 121_G 0.84 0.40 0.03
44_G 36_F 0.84 0.39 0.03
411_V 42_R 0.84 0.39 0.03
127_S 19_F 0.82 0.37 0.03
401_V 121_G 0.82 0.37 0.03
372_L 30_M 0.82 0.37 0.03
144_G 86_F 0.82 0.37 0.03
416_V 40_R 0.82 0.37 0.03
188_A 28_C 0.82 0.37 0.03
306_L 80_V 0.81 0.36 0.03
394_G 102_E 0.81 0.36 0.03
215_G 61_R 0.81 0.36 0.03
312_A 28_C 0.81 0.36 0.03
127_S 23_A 0.81 0.35 0.03
206_G 25_G 0.81 0.35 0.03
344_V 112_A 0.81 0.35 0.03
216_F 73_M 0.80 0.35 0.03
131_G 66_A 0.80 0.35 0.03
378_V 107_I 0.80 0.35 0.03
240_T 18_I 0.80 0.35 0.03
199_N 94_E 0.80 0.34 0.02
308_Y 84_Y 0.80 0.34 0.02
325_A 76_V 0.79 0.34 0.02
298_L 29_L 0.79 0.34 0.02
221_V 88_W 0.79 0.33 0.02
169_F 73_M 0.79 0.33 0.02
388_M 121_G 0.79 0.33 0.02
204_L 20_L 0.78 0.32 0.02
252_G 112_A 0.78 0.32 0.02
110_L 99_G 0.78 0.32 0.02
424_Y 61_R 0.78 0.32 0.02
342_G 103_A 0.77 0.32 0.02
141_G 52_S 0.77 0.32 0.02
175_A 73_M 0.77 0.31 0.02
253_V 19_F 0.77 0.31 0.02
390_L 56_S 0.77 0.31 0.02
199_N 28_C 0.77 0.31 0.02
459_I 25_G 0.77 0.31 0.02
396_F 35_W 0.76 0.31 0.02
172_F 76_V 0.76 0.30 0.02
282_I 20_L 0.76 0.30 0.02
401_V 107_I 0.76 0.30 0.02
421_G 73_M 0.76 0.30 0.02
172_F 10_I 0.75 0.30 0.02
131_G 15_A 0.75 0.30 0.02
418_S 92_I 0.75 0.30 0.02
410_L 21_I 0.75 0.29 0.02
290_S 50_F 0.75 0.29 0.02
231_Y 46_K 0.75 0.29 0.02
334_L 100_F 0.75 0.29 0.02
156_S 33_G 0.75 0.29 0.02
246_S 114_L 0.74 0.29 0.02
376_M 90_T 0.74 0.29 0.02
79_L 24_I 0.74 0.28 0.02
147_F 15_A 0.74 0.28 0.02
382_S 81_E 0.74 0.28 0.02
42_V 66_A 0.74 0.28 0.02
101_N 115_V 0.74 0.28 0.02
421_G 49_P 0.74 0.28 0.02
18_G 109_V 0.73 0.28 0.02
160_T 103_A 0.73 0.28 0.02
422_L 91_S 0.73 0.28 0.02
230_V 71_V 0.73 0.28 0.02
105_F 64_L 0.73 0.28 0.02
216_F 103_A 0.73 0.27 0.02
423_Y 60_A 0.73 0.27 0.02
232_Q 9_V 0.73 0.27 0.02
429_A 104_A 0.72 0.27 0.02
58_A 105_I 0.72 0.27 0.02
163_S 87_A 0.72 0.27 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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