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OPENSEQ.org
PcrA_FL vs beta 2nd half
Genes: A B A+B
Length: 739 593 1181
Sequences: 3698 1403 1067
Seq/Len: 5 2.37 0.9
MirrorTree (Pazo et al. 2001) 0.20
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 0.09 0.09 0.00
2 0.09 0.09 0.00
5 0.09 0.09 0.01
10 0.09 0.09 0.03
20 0.09 0.09 0.04
100 0.10 0.09 0.11
∞ 0.16 0.09 0.80
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
220_I 287_I 1.18 0.47 0.00
125_I 54_E 1.17 0.46 0.00
148_I 13_V 1.16 0.45 0.00
430_I 8_V 1.05 0.36 0.00
331_G 232_I 1.01 0.33 0.00
205_R 430_V 1.00 0.32 0.00
482_E 232_I 0.97 0.30 0.00
336_V 232_I 0.93 0.27 0.00
558_D 10_Y 0.93 0.27 0.00
557_K 184_D 0.93 0.26 0.00
173_V 300_E 0.92 0.26 0.00
130_K 353_I 0.92 0.26 0.00
642_I 5_R 0.91 0.25 0.00
335_F 6_N 0.90 0.24 0.00
95_M 346_Y 0.90 0.24 0.00
462_D 232_I 0.87 0.22 0.00
99_I 335_I 0.86 0.22 0.00
377_N 83_E 0.85 0.22 0.00
239_L 127_R 0.85 0.21 0.00
246_L 10_Y 0.84 0.21 0.00
512_I 495_I 0.83 0.20 0.00
315_N 177_M 0.82 0.20 0.00
484_T 55_A 0.82 0.20 0.00
459_N 87_A 0.82 0.19 0.00
382_G 217_G 0.82 0.19 0.00
236_V 418_Y 0.82 0.19 0.00
471_L 141_I 0.81 0.19 0.00
262_A 184_D 0.80 0.19 0.00
217_F 287_I 0.80 0.18 0.00
211_E 425_P 0.80 0.18 0.00
556_G 368_I 0.80 0.18 0.00
290_K 232_I 0.80 0.18 0.00
220_I 51_M 0.79 0.18 0.00
641_E 153_L 0.79 0.18 0.00
22_T 90_V 0.79 0.18 0.00
562_L 51_M 0.79 0.18 0.00
434_A 184_D 0.79 0.18 0.00
358_Y 256_A 0.78 0.18 0.00
557_K 418_Y 0.78 0.18 0.00
575_V 21_A 0.78 0.17 0.00
58_N 57_F 0.78 0.17 0.00
196_I 25_C 0.78 0.17 0.00
613_E 93_R 0.78 0.17 0.00
436_I 171_Y 0.77 0.17 0.00
204_D 92_V 0.76 0.17 0.00
380_I 313_I 0.76 0.17 0.00
131_E 353_I 0.76 0.17 0.00
176_V 302_P 0.76 0.16 0.00
108_G 269_A 0.76 0.16 0.00
492_E 22_A 0.75 0.16 0.00
206_V 24_A 0.75 0.16 0.00
617_Y 79_P 0.75 0.16 0.00
638_F 81_I 0.75 0.16 0.00
215_R 232_I 0.75 0.16 0.00
515_F 371_V 0.75 0.16 0.00
340_I 136_V 0.75 0.16 0.00
127_G 5_R 0.74 0.16 0.00
333_G 336_S 0.74 0.16 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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