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PCRA_RNAPbeta1120
Genes: A B A+B
Length: 724 559 1135
Sequences: 4096 1202 1105
Seq/Len: 5.66 2.15 0.97
MirrorTree (Pazo et al. 2001) 0.32
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
∞ 0.17 0.09 0.86
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
340_I 89_V 1.02 0.35 0.00
331_D 185_I 1.00 0.34 0.00
125_M 15_Q 0.99 0.33 0.00
95_M 300_H 0.96 0.30 0.00
484_V 16_A 0.95 0.30 0.00
220_I 240_V 0.95 0.29 0.00
640_E 106_L 0.92 0.27 0.00
333_A 290_A 0.91 0.26 0.00
612_E 89_V 0.91 0.26 0.00
392_I 292_I 0.90 0.26 0.00
531_L 409_Q 0.90 0.26 0.00
402_I 143_I 0.87 0.24 0.00
106_R 325_I 0.85 0.23 0.00
480_V 356_E 0.85 0.22 0.00
58_N 18_V 0.85 0.22 0.00
99_I 289_V 0.85 0.22 0.00
371_L 292_I 0.84 0.21 0.00
74_E 413_V 0.83 0.21 0.00
515_F 488_T 0.83 0.21 0.00
195_L 191_P 0.82 0.20 0.00
239_L 80_R 0.82 0.20 0.00
94_S 266_Y 0.81 0.20 0.00
358_Y 209_P 0.81 0.20 0.00
534_F 500_I 0.80 0.19 0.00
207_P 185_I 0.79 0.19 0.00
334_Q 13_R 0.79 0.19 0.00
125_M 325_I 0.79 0.19 0.00
616_V 40_D 0.79 0.19 0.00
356_V 413_V 0.78 0.18 0.00
356_V 261_E 0.78 0.18 0.00
159_E 240_V 0.77 0.18 0.00
377_P 44_A 0.77 0.18 0.00
176_V 23_L 0.77 0.18 0.00
313_T 51_I 0.77 0.18 0.00
465_R 254_E 0.77 0.18 0.00
165_A 185_I 0.77 0.18 0.00
130_K 307_V 0.77 0.18 0.00
577_L 273_L 0.77 0.17 0.00
356_V 92_G 0.76 0.17 0.00
459_G 48_G 0.76 0.17 0.00
369_E 300_H 0.76 0.17 0.00
179_E 289_V 0.76 0.17 0.00
216_K 35_L 0.76 0.17 0.00
576_F 208_T 0.75 0.17 0.00
259_W 73_Q 0.75 0.17 0.00
239_L 424_E 0.75 0.17 0.00
559_V 176_D 0.75 0.17 0.00
94_S 2_S 0.75 0.17 0.00
427_I 240_V 0.75 0.17 0.00
356_V 422_P 0.75 0.17 0.00
248_A 179_E 0.74 0.16 0.00
556_G 137_R 0.74 0.16 0.00
380_I 267_V 0.74 0.16 0.00
612_E 54_R 0.74 0.16 0.00
440_S 240_V 0.74 0.16 0.00
106_R 292_I 0.74 0.16 0.00
363_Q 124_F 0.74 0.16 0.00
204_D 53_V 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)
ID Seq/Len Name Options I_Prob Status
5416 0.97 PCRA_RNAPbeta1120 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5389 0.97 PCRA_RNAPbeta1120 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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