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PCRA_RNAPrpoC_bsubtilis600
Genes: A B A+B
Length: 739 600 1217
Sequences: 3698 1342 1076
Seq/Len: 5 2.24 0.88
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 0.04
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
534_F 411_L 1.31 0.58 0.00
94_S 237_E 1.21 0.49 0.00
356_I 537_V 1.09 0.38 0.00
461_L 582_T 0.98 0.30 0.00
80_L 175_I 0.97 0.29 0.00
356_I 304_P 0.97 0.29 0.00
80_L 213_L 0.97 0.29 0.00
209_V 231_L 0.96 0.28 0.00
94_S 202_R 0.96 0.28 0.00
104_I 202_R 0.95 0.28 0.00
178_A 537_V 0.95 0.28 0.00
559_A 128_V 0.93 0.26 0.00
178_A 231_L 0.88 0.23 0.00
364_S 18_D 0.87 0.22 0.00
371_L 208_K 0.86 0.21 0.00
356_I 90_E 0.86 0.21 0.00
642_I 175_I 0.85 0.21 0.00
279_V 537_V 0.84 0.20 0.00
49_M 216_F 0.83 0.20 0.00
290_K 557_L 0.83 0.20 0.00
258_R 128_V 0.83 0.20 0.00
581_L 373_E 0.82 0.20 0.00
618_L 558_L 0.82 0.19 0.00
572_E 389_K 0.82 0.19 0.00
93_H 481_N 0.82 0.19 0.00
115_I 227_I 0.81 0.19 0.00
379_N 438_L 0.81 0.19 0.00
272_K 74_V 0.81 0.19 0.00
367_I 390_I 0.81 0.19 0.00
285_N 404_V 0.81 0.19 0.00
593_M 175_I 0.81 0.18 0.00
62_I 43_K 0.80 0.18 0.00
396_L 459_V 0.80 0.18 0.00
235_L 228_L 0.80 0.18 0.00
231_A 227_I 0.80 0.18 0.00
59_I 541_A 0.79 0.18 0.00
220_I 237_E 0.79 0.18 0.00
285_N 43_K 0.79 0.18 0.00
376_L 557_L 0.79 0.18 0.00
567_A 174_A 0.79 0.17 0.00
423_G 175_I 0.78 0.17 0.00
29_L 539_V 0.78 0.17 0.00
292_I 566_V 0.77 0.17 0.00
241_E 127_E 0.77 0.17 0.00
89_I 115_G 0.77 0.17 0.00
49_M 55_T 0.77 0.16 0.00
304_S 85_A 0.76 0.16 0.00
422_V 176_H 0.76 0.16 0.00
492_E 137_T 0.76 0.16 0.00
538_L 352_M 0.76 0.16 0.00
222_V 150_L 0.76 0.16 0.00
308_P 128_V 0.75 0.16 0.00
578_L 539_V 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
5653 0.88 PCRA_RNAPrpoC_bsubtilis600 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5630 0.89 PCRA_RNAPrpoC_bsubtilis600 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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