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OPENSEQ.org
PCRA_RNAPbeta1524
Genes: A B A+B
Length: 724 764 1300
Sequences: 4096 2025 1094
Seq/Len: 5.66 2.65 0.84
MirrorTree (Pazo et al. 2001) 0.30
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 0.10
∞ 0.17 0.08 0.74
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
356_V 104_V 1.20 0.47 0.00
235_L 297_V 1.08 0.37 0.00
567_A 455_V 1.06 0.35 0.00
356_V 515_S 1.01 0.31 0.00
594_D 621_V 1.00 0.30 0.00
185_L 393_V 0.97 0.28 0.00
182_Q 414_L 0.96 0.28 0.00
207_P 621_V 0.96 0.27 0.00
430_L 155_V 0.95 0.27 0.00
41_L 454_P 0.92 0.25 0.00
46_A 401_E 0.92 0.25 0.00
325_E 189_I 0.92 0.24 0.00
617_L 521_V 0.91 0.24 0.00
461_L 449_L 0.90 0.23 0.00
559_V 389_L 0.89 0.23 0.00
289_T 104_V 0.89 0.23 0.00
638_L 407_S 0.88 0.22 0.00
124_V 400_L 0.88 0.22 0.00
557_D 647_L 0.87 0.22 0.00
430_L 241_E 0.86 0.21 0.00
144_I 36_R 0.86 0.21 0.00
614_E 101_Q 0.85 0.21 0.00
124_V 306_T 0.85 0.20 0.00
101_R 619_V 0.85 0.20 0.00
611_A 461_V 0.84 0.20 0.00
567_A 624_P 0.83 0.19 0.00
567_A 240_T 0.83 0.19 0.00
341_R 233_L 0.83 0.19 0.00
94_S 350_A 0.82 0.19 0.00
185_L 242_K 0.81 0.18 0.00
559_V 145_P 0.80 0.17 0.00
190_L 306_T 0.80 0.17 0.00
425_S 98_V 0.80 0.17 0.00
159_E 400_L 0.80 0.17 0.00
515_F 436_T 0.79 0.17 0.00
536_T 114_E 0.79 0.17 0.00
222_I 415_I 0.79 0.17 0.00
186_R 621_V 0.79 0.17 0.00
560_M 612_V 0.78 0.17 0.00
557_D 389_L 0.78 0.17 0.00
466_S 423_I 0.77 0.16 0.00
246_I 624_P 0.77 0.16 0.00
561_L 621_V 0.77 0.16 0.00
336_V 423_I 0.77 0.16 0.00
85_E 423_I 0.77 0.16 0.00
263_D 185_S 0.76 0.16 0.00
538_L 384_L 0.76 0.16 0.00
289_T 347_V 0.76 0.16 0.00
301_E 248_F 0.76 0.16 0.00
527_D 401_E 0.76 0.16 0.00
356_V 401_E 0.76 0.15 0.00
302_H 174_L 0.75 0.15 0.00
59_I 121_L 0.75 0.15 0.00
376_I 5_S 0.75 0.15 0.00
388_D 382_A 0.75 0.15 0.00
440_S 104_V 0.75 0.15 0.00
515_F 196_I 0.75 0.15 0.00
336_V 191_I 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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