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OPENSEQ.org
PCRA_RNAPrpoA_bsubtilis
Genes: A B A+B
Length: 739 314 955
Sequences: 3698 1865 1131
Seq/Len: 5 5.94 1.18
MirrorTree (Pazo et al. 2001) 0.27
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 0.00
10 0.09 0.09 0.01
20 0.09 0.09 0.01
100 0.10 0.09 0.16
∞ 0.16 0.09 1.07
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
639_I 56_I 1.18 0.55 0.00
29_L 281_T 1.14 0.51 0.00
568_A 195_T 1.05 0.42 0.00
246_L 213_G 1.05 0.42 0.00
221_H 197_D 1.04 0.42 0.00
426_S 127_I 1.01 0.38 0.00
376_L 198_V 0.97 0.35 0.00
156_T 68_I 0.97 0.35 0.00
375_G 135_S 0.96 0.34 0.00
560_I 149_T 0.95 0.34 0.00
590_R 110_A 0.95 0.34 0.00
361_N 77_T 0.94 0.33 0.00
171_Q 68_I 0.94 0.33 0.00
622_K 281_T 0.92 0.31 0.00
480_I 195_T 0.91 0.30 0.00
35_S 22_K 0.91 0.30 0.00
129_L 78_I 0.90 0.29 0.00
517_S 281_T 0.89 0.29 0.00
198_T 170_Y 0.89 0.28 0.00
430_I 198_V 0.88 0.27 0.00
209_V 85_L 0.86 0.27 0.00
179_D 136_F 0.86 0.26 0.00
333_G 144_R 0.86 0.26 0.00
407_D 170_Y 0.86 0.26 0.00
484_T 127_I 0.86 0.26 0.00
187_N 253_I 0.85 0.26 0.00
466_Q 195_T 0.85 0.25 0.00
173_V 161_I 0.84 0.25 0.00
609_I 152_D 0.84 0.24 0.00
80_L 120_I 0.83 0.24 0.00
128_I 67_T 0.81 0.23 0.00
301_K 150_P 0.81 0.22 0.00
401_L 43_I 0.80 0.22 0.00
244_Q 219_E 0.80 0.22 0.00
414_I 182_N 0.79 0.21 0.00
492_E 190_N 0.79 0.21 0.00
145_L 170_Y 0.78 0.21 0.00
100_L 120_I 0.78 0.20 0.00
599_E 19_K 0.78 0.20 0.00
352_S 271_I 0.77 0.20 0.00
181_Q 82_I 0.77 0.20 0.00
625_T 130_L 0.77 0.20 0.00
395_I 40_L 0.77 0.20 0.00
577_F 203_S 0.76 0.20 0.00
444_A 36_L 0.76 0.19 0.00
26_P 201_D 0.76 0.19 0.00
361_N 257_D 0.76 0.19 0.00
396_L 59_D 0.76 0.19 0.00
592_L 193_K 0.76 0.19 0.00
66_N 25_V 0.76 0.19 0.00
191_D 76_T 0.75 0.19 0.00
323_Y 152_D 0.75 0.19 0.00
211_E 231_A 0.75 0.19 0.00
292_I 287_K 0.75 0.18 0.00
598_M 96_T 0.74 0.18 0.00
264_I 77_T 0.74 0.18 0.00
58_N 88_K 0.74 0.18 0.00
534_F 271_I 0.74 0.18 0.00
151_A 166_I 0.74 0.18 0.00
321_I 22_K 0.74 0.18 0.00
430_I 205_G 0.74 0.18 0.00
269_S 280_K 0.74 0.18 0.00
465_R 127_I 0.73 0.18 0.00
425_T 68_I 0.73 0.18 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)
ID Seq/Len Name Options I_Prob Status
5629 1.18 PCRA_RNAPrpoA_bsubtilis Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5628 0.01 PCRA_RNAPrpoA_bsubtilis Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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