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OPENSEQ.org
PCRA_RNAPbeta_Bsubtilis 2
Genes: A B A+B
Length: 739 643 1227
Sequences: 3698 1455 1053
Seq/Len: 5 2.26 0.86
MirrorTree (Pazo et al. 2001) 0.24
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 0.03
100 0.10 0.09 0.10
∞ 0.16 0.09 0.76
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 337_I 1.32 0.58 0.00
125_I 104_E 1.16 0.44 0.00
331_G 282_I 1.12 0.40 0.00
148_I 63_V 1.10 0.39 0.00
336_V 282_I 1.00 0.31 0.00
173_V 350_E 0.95 0.27 0.00
430_I 58_V 0.95 0.27 0.00
313_T 140_V 0.95 0.27 0.00
558_D 60_Y 0.93 0.26 0.00
482_E 282_I 0.90 0.24 0.00
95_M 396_Y 0.90 0.24 0.00
642_I 55_R 0.89 0.23 0.00
22_T 140_V 0.89 0.23 0.00
335_F 56_N 0.88 0.23 0.00
130_K 403_I 0.88 0.23 0.00
419_K 31_L 0.88 0.23 0.00
246_L 60_Y 0.88 0.22 0.00
131_E 403_I 0.87 0.22 0.00
205_R 480_V 0.86 0.21 0.00
462_D 282_I 0.85 0.21 0.00
106_R 388_I 0.85 0.21 0.00
492_E 72_A 0.84 0.20 0.00
204_D 142_V 0.84 0.20 0.00
484_T 105_A 0.84 0.20 0.00
557_K 234_D 0.83 0.20 0.00
262_A 234_D 0.83 0.20 0.00
471_L 191_I 0.82 0.19 0.00
618_L 35_G 0.82 0.19 0.00
459_N 137_A 0.81 0.18 0.00
482_E 212_G 0.81 0.18 0.00
436_I 221_Y 0.81 0.18 0.00
512_I 545_I 0.81 0.18 0.00
211_E 475_P 0.81 0.18 0.00
206_V 337_I 0.80 0.18 0.00
425_T 350_E 0.80 0.18 0.00
641_E 203_L 0.80 0.18 0.00
556_G 418_I 0.79 0.18 0.00
176_V 234_D 0.79 0.17 0.00
613_E 186_V 0.79 0.17 0.00
434_A 234_D 0.79 0.17 0.00
58_N 107_F 0.79 0.17 0.00
176_V 352_P 0.79 0.17 0.00
273_D 165_F 0.77 0.17 0.00
531_L 462_D 0.77 0.17 0.00
377_N 133_E 0.77 0.17 0.00
581_L 39_D 0.77 0.17 0.00
216_K 124_V 0.77 0.17 0.00
220_I 101_M 0.77 0.16 0.00
598_M 184_D 0.77 0.16 0.00
236_V 468_Y 0.77 0.16 0.00
642_I 24_V 0.77 0.16 0.00
358_Y 306_A 0.77 0.16 0.00
204_D 342_V 0.77 0.16 0.00
344_H 221_Y 0.76 0.16 0.00
575_V 71_A 0.76 0.16 0.00
557_K 468_Y 0.76 0.16 0.00
122_L 140_V 0.76 0.16 0.00
613_E 143_R 0.75 0.16 0.00
293_L 540_Y 0.75 0.15 0.00
371_L 388_I 0.75 0.15 0.00
239_L 177_R 0.75 0.15 0.00
578_L 405_I 0.74 0.15 0.00
639_I 401_T 0.74 0.15 0.00
562_L 101_M 0.74 0.15 0.00
296_A 142_V 0.74 0.15 0.00
74_E 466_V 0.74 0.15 0.00
577_F 305_T 0.74 0.15 0.00
421_G 104_E 0.74 0.15 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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