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OPENSEQ.org
Clp_AP
Genes: A B A+B
Length: 758 207 920
Sequences: 3960 6472 96
Seq/Len: 5.22 31.27 0.1
MirrorTree (Pazo et al. 2001) 0.06
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 0.08 0.01
2 0.01 0.09 0.01
5 0.01 0.09 0.03
10 0.01 0.09 0.05
20 0.01 0.09 0.10
100 0.03 0.12 0.51
∞ 0.14 0.22 2.04
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
717_A 189_S 1.54 0.21 0.00
553_V 65_E 1.51 0.20 0.00
527_R 199_V 1.20 0.12 0.00
644_L 166_L 1.20 0.12 0.00
184_G 75_L 1.18 0.12 0.00
710_D 148_D 1.18 0.12 0.00
174_T 130_N 1.18 0.12 0.00
224_A 161_G 1.17 0.12 0.00
467_I 43_I 1.17 0.12 0.00
350_S 183_E 1.13 0.11 0.00
712_L 40_E 1.10 0.10 0.00
430_V 134_M 1.10 0.10 0.00
372_R 108_Q 1.10 0.10 0.00
178_Q 189_S 1.10 0.10 0.00
91_A 49_V 1.09 0.10 0.00
471_T 142_Y 1.09 0.10 0.00
717_A 199_V 1.08 0.10 0.00
378_V 75_L 1.08 0.10 0.00
601_L 199_V 1.06 0.10 0.00
505_T 166_L 1.05 0.09 0.00
457_K 121_A 1.04 0.09 0.00
407_A 43_I 1.04 0.09 0.00
245_I 199_V 1.03 0.09 0.00
699_M 202_I 1.02 0.09 0.00
247_S 156_I 1.01 0.09 0.00
524_Y 149_I 1.01 0.09 0.00
432_R 43_I 1.00 0.09 0.00
675_Q 57_I 1.00 0.09 0.00
429_V 160_K 0.99 0.08 0.00
680_L 198_L 0.99 0.08 0.00
646_N 192_E 0.98 0.08 0.00
64_Q 199_V 0.98 0.08 0.00
252_S 127_C 0.98 0.08 0.00
548_L 104_I 0.97 0.08 0.00
234_G 172_G 0.97 0.08 0.00
524_Y 119_A 0.96 0.08 0.00
505_T 49_V 0.96 0.08 0.00
607_A 57_I 0.96 0.08 0.00
658_I 53_M 0.96 0.08 0.00
486_K 199_V 0.96 0.08 0.00
443_Q 199_V 0.94 0.08 0.00
524_Y 86_A 0.94 0.08 0.00
307_I 129_P 0.94 0.08 0.00
175_N 57_I 0.94 0.08 0.00
658_I 160_K 0.94 0.08 0.00
426_I 195_E 0.94 0.08 0.00
213_V 199_V 0.93 0.08 0.00
402_I 49_V 0.93 0.07 0.00
129_V 127_C 0.93 0.07 0.00
525_M 113_G 0.93 0.07 0.00
134_V 75_L 0.93 0.07 0.00
354_T 86_A 0.92 0.07 0.00
407_A 105_C 0.92 0.07 0.00
512_L 65_E 0.92 0.07 0.00
479_A 115_F 0.92 0.07 0.00
440_S 71_K 0.91 0.07 0.00
633_K 152_H 0.91 0.07 0.00
346_I 160_K 0.91 0.07 0.00
712_L 189_S 0.91 0.07 0.00
597_R 131_S 0.91 0.07 0.00
677_G 89_S 0.90 0.07 0.00
138_I 143_Q 0.90 0.07 0.00
647_I 71_K 0.90 0.07 0.00
103_V 148_D 0.90 0.07 0.00
281_I 49_V 0.89 0.07 0.00
374_T 48_Q 0.89 0.07 0.00
672_Q 43_I 0.89 0.07 0.00
235_D 173_Q 0.89 0.07 0.00
699_M 167_M 0.88 0.07 0.00
59_E 57_I 0.88 0.07 0.00
290_I 132_R 0.88 0.07 0.00
213_V 202_I 0.88 0.07 0.00
373_Y 149_I 0.88 0.07 0.00
317_R 49_V 0.88 0.07 0.00
566_I 192_E 0.88 0.07 0.00
431_A 113_G 0.88 0.07 0.00
529_T 131_S 0.88 0.07 0.00
595_D 173_Q 0.88 0.07 0.00
582_D 131_S 0.88 0.07 0.00
524_Y 183_E 0.87 0.07 0.00
609_V 114_A 0.87 0.07 0.00
185_I 43_I 0.87 0.07 0.00
211_L 27_G 0.87 0.07 0.00
603_M 90_I 0.87 0.07 0.00
479_A 113_G 0.86 0.07 0.00
683_S 155_E 0.86 0.07 0.00
426_I 71_K 0.86 0.07 0.00
680_L 203_L 0.86 0.07 0.00
287_I 181_D 0.86 0.07 0.00
717_A 171_T 0.86 0.07 0.00
282_L 49_V 0.86 0.07 0.00
442_S 94_M 0.86 0.07 0.00
330_I 94_M 0.86 0.07 0.00
658_I 177_Q 0.86 0.07 0.00
343_K 85_T 0.85 0.07 0.00
490_S 144_G 0.85 0.07 0.00
471_T 166_L 0.85 0.07 0.00
330_I 124_K 0.85 0.07 0.00
201_V 178_I 0.85 0.07 0.00
719_E 199_V 0.85 0.07 0.00
489_G 72_D 0.85 0.07 0.00
452_L 102_S 0.85 0.07 0.00
471_T 118_T 0.85 0.06 0.00
165_G 117_L 0.85 0.06 0.00
525_M 164_N 0.84 0.06 0.00
436_I 144_G 0.84 0.06 0.00
516_L 169_L 0.84 0.06 0.00
411_L 198_L 0.84 0.06 0.00
129_V 169_L 0.84 0.06 0.00
576_I 187_F 0.84 0.06 0.00
373_Y 193_A 0.84 0.06 0.00
721_L 155_E 0.84 0.06 0.00
390_N 40_E 0.84 0.06 0.00
423_V 199_V 0.84 0.06 0.00
129_V 136_H 0.84 0.06 0.00
346_I 87_G 0.84 0.06 0.00
686_A 198_L 0.83 0.06 0.00
461_F 129_P 0.83 0.06 0.00
580_V 131_S 0.83 0.06 0.00
244_T 57_I 0.83 0.06 0.00
447_D 166_L 0.83 0.06 0.00
353_E 71_K 0.83 0.06 0.00
559_A 95_Q 0.83 0.06 0.00
492_L 47_G 0.83 0.06 0.00
245_I 145_Q 0.83 0.06 0.00
489_G 192_E 0.83 0.06 0.00
408_R 155_E 0.83 0.06 0.00
344_I 57_I 0.82 0.06 0.00
467_I 64_L 0.82 0.06 0.00
525_M 33_I 0.82 0.06 0.00
365_Y 105_C 0.82 0.06 0.00
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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