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OPENSEQ.org
PCRA_RNAPrpoC_bsubtilis1199
Genes: A B A+B
Length: 739 599 1215
Sequences: 3698 2298 1089
Seq/Len: 5 3.84 0.9
MirrorTree (Pazo et al. 2001) 0.28
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 0.08 0.00
2 0.09 0.08 0.00
5 0.09 0.08 0.01
10 0.09 0.08 0.03
20 0.09 0.08 0.04
100 0.10 0.08 0.11
∞ 0.16 0.08 0.81
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
618_L 378_V 1.12 0.42 0.00
430_I 24_I 0.99 0.31 0.00
568_A 437_V 0.94 0.28 0.00
568_A 109_K 0.94 0.27 0.00
41_L 312_D 0.93 0.27 0.00
186_K 71_E 0.92 0.26 0.00
568_A 313_V 0.92 0.26 0.00
430_I 110_D 0.91 0.25 0.00
598_M 178_I 0.88 0.23 0.00
408_D 471_V 0.88 0.23 0.00
153_N 281_I 0.87 0.23 0.00
278_S 480_V 0.87 0.23 0.00
235_L 163_I 0.86 0.22 0.00
568_A 483_A 0.86 0.22 0.00
612_A 30_R 0.86 0.22 0.00
560_I 279_A 0.84 0.21 0.00
461_L 307_L 0.84 0.21 0.00
108_G 550_A 0.83 0.20 0.00
76_V 321_I 0.82 0.20 0.00
182_K 480_V 0.82 0.19 0.00
482_E 165_S 0.81 0.19 0.00
222_V 277_V 0.81 0.19 0.00
568_A 282_E 0.81 0.19 0.00
367_I 284_V 0.81 0.19 0.00
236_V 291_T 0.81 0.19 0.00
171_Q 480_V 0.80 0.18 0.00
340_I 102_I 0.80 0.18 0.00
101_R 478_V 0.79 0.18 0.00
246_L 483_A 0.79 0.18 0.00
596_A 261_L 0.79 0.18 0.00
567_A 418_I 0.78 0.18 0.00
214_Q 208_A 0.78 0.17 0.00
560_I 248_A 0.77 0.17 0.00
567_A 208_A 0.77 0.17 0.00
538_L 243_L 0.77 0.17 0.00
612_A 319_V 0.77 0.17 0.00
54_V 472_R 0.76 0.17 0.00
539_A 24_I 0.76 0.17 0.00
97_V 208_A 0.76 0.16 0.00
545_D 277_V 0.76 0.16 0.00
317_E 241_E 0.75 0.16 0.00
461_L 15_F 0.75 0.16 0.00
128_I 118_K 0.75 0.16 0.00
173_V 442_T 0.75 0.16 0.00
266_N 307_L 0.75 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)
ID Seq/Len Name Options I_Prob Status
5654 0.89 PCRA_RNAPrpoC_bsubtilis1199 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5631 0.9 PCRA_RNAPrpoC_bsubtilis1199 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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