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OPENSEQ.org
1fft_A_C
Genes: A B A+B
Length: 663 204 831
Sequences: 2537 4395 1975
Seq/Len: 3.83 21.54 2.38
MirrorTree (Pazo et al. 2001) 0.88
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 0.04 1.25
2 0.01 0.04 1.42
5 0.01 0.04 2.04
10 0.01 0.04 2.21
20 0.02 0.04 2.28
100 0.02 0.05 2.32
∞ 0.09 0.09 2.48
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
248_V 42_I 1.66 0.97 0.82
252_L 137_S 1.37 0.88 0.62
255_L 141_A 1.32 0.86 0.57
632_E 167_R 1.19 0.77 0.45
245_I 38_I 1.15 0.73 0.41
252_L 46_T 1.07 0.65 0.33
273_M 26_I 1.00 0.58 0.27
432_C 35_S 1.00 0.57 0.26
402_A 140_F 0.97 0.55 0.24
422_N 36_D 0.97 0.55 0.24
465_F 36_D 0.97 0.54 0.23
479_M 197_V 0.96 0.53 0.23
100_D 119_E 0.95 0.52 0.22
577_P 204_M 0.94 0.51 0.21
303_A 74_F 0.94 0.50 0.21
65_A 133_S 0.93 0.49 0.20
261_T 130_P 0.92 0.49 0.20
278_L 46_T 0.92 0.48 0.20
241_A 34_M 0.92 0.48 0.20
99_Y 81_I 0.92 0.48 0.19
252_L 141_A 0.91 0.48 0.19
517_Y 48_A 0.90 0.46 0.18
100_D 36_D 0.90 0.46 0.18
208_F 73_T 0.88 0.43 0.17
626_I 159_V 0.88 0.43 0.17
259_L 130_P 0.87 0.42 0.16
432_C 157_M 0.87 0.42 0.16
467_A 120_F 0.87 0.42 0.16
378_H 31_I 0.86 0.41 0.16
551_N 200_L 0.86 0.41 0.15
61_Y 76_L 0.86 0.41 0.15
472_Y 116_E 0.85 0.41 0.15
252_L 43_L 0.85 0.41 0.15
413_S 148_L 0.85 0.41 0.15
137_A 109_G 0.84 0.40 0.15
336_F 108_F 0.84 0.39 0.14
291_I 31_I 0.83 0.38 0.14
622_I 155_I 0.83 0.38 0.14
240_I 35_S 0.83 0.38 0.14
210_V 27_F 0.82 0.37 0.13
393_V 93_N 0.82 0.37 0.13
204_T 145_T 0.82 0.37 0.13
496_M 192_I 0.82 0.37 0.13
309_R 202_G 0.81 0.36 0.13
214_K 24_T 0.81 0.36 0.12
468_F 120_F 0.81 0.35 0.12
245_I 92_K 0.80 0.35 0.12
141_L 161_M 0.80 0.35 0.12
247_T 39_L 0.80 0.34 0.12
49_L 170_T 0.80 0.34 0.12
275_Y 140_F 0.80 0.34 0.12
513_V 162_V 0.79 0.34 0.12
130_Q 200_L 0.79 0.34 0.12
30_A 151_T 0.79 0.34 0.12
497_I 117_I 0.79 0.34 0.11
304_T 155_I 0.79 0.33 0.11
240_I 85_M 0.78 0.33 0.11
51_S 74_F 0.78 0.33 0.11
242_S 38_I 0.78 0.33 0.11
630_F 162_V 0.78 0.33 0.11
191_I 101_W 0.78 0.32 0.11
301_I 82_T 0.77 0.32 0.11
221_T 46_T 0.77 0.32 0.11
278_L 42_I 0.77 0.32 0.11
423_V 46_T 0.77 0.32 0.10
327_S 31_I 0.77 0.32 0.10
501_G 119_E 0.77 0.32 0.10
466_V 161_M 0.77 0.32 0.10
198_G 153_G 0.77 0.32 0.10
359_T 150_V 0.77 0.32 0.10
494_M 87_A 0.77 0.31 0.10
336_F 195_F 0.77 0.31 0.10
39_G 125_V 0.77 0.31 0.10
318_W 87_A 0.76 0.31 0.10
544_S 104_L 0.76 0.31 0.10
557_H 104_L 0.76 0.31 0.10
388_I 94_N 0.76 0.31 0.10
144_L 194_V 0.76 0.30 0.10
198_G 119_E 0.76 0.30 0.10
483_L 29_F 0.76 0.30 0.10
152_G 182_L 0.75 0.30 0.10
517_Y 140_F 0.75 0.30 0.10
131_I 75_L 0.75 0.30 0.10
365_N 176_R 0.75 0.29 0.10
274_M 50_L 0.75 0.29 0.10
536_G 195_F 0.75 0.29 0.10
340_A 73_T 0.75 0.29 0.09
347_F 80_S 0.74 0.29 0.09
302_A 143_V 0.74 0.29 0.09
476_F 90_M 0.74 0.29 0.09
26_L 88_I 0.74 0.28 0.09
247_T 120_F 0.74 0.28 0.09
520_I 157_M 0.73 0.28 0.09
326_L 34_M 0.73 0.28 0.09
259_L 151_T 0.73 0.28 0.09
492_H 148_L 0.73 0.28 0.09
502_A 113_I 0.73 0.27 0.09
440_W 195_F 0.72 0.27 0.09
105_A 77_L 0.72 0.27 0.08
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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