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OPENSEQ.org
PCRA_RNAPbeta_Bsubtilis 1
Genes: A B A+B
Length: 739 550 1145
Sequences: 3698 1344 1082
Seq/Len: 5 2.44 0.94
MirrorTree (Pazo et al. 2001) 0.26
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 0.12
∞ 0.16 0.09 0.84
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
558_D 549_R 1.20 0.51 0.00
323_Y 127_I 1.16 0.47 0.00
76_V 549_R 1.02 0.34 0.00
371_L 88_Y 1.00 0.33 0.00
375_G 88_Y 1.00 0.32 0.00
323_Y 126_I 0.97 0.30 0.00
89_I 231_K 0.96 0.30 0.00
509_L 257_S 0.95 0.29 0.00
220_I 545_T 0.94 0.28 0.00
59_I 534_Y 0.94 0.28 0.00
337_A 20_I 0.93 0.27 0.00
461_L 535_A 0.93 0.27 0.00
461_L 127_I 0.91 0.26 0.00
246_L 478_A 0.91 0.26 0.00
598_M 31_E 0.90 0.25 0.00
74_E 88_Y 0.89 0.25 0.00
356_I 88_Y 0.89 0.25 0.00
229_N 162_V 0.89 0.25 0.00
618_L 375_N 0.89 0.24 0.00
421_G 459_K 0.89 0.24 0.00
430_I 534_Y 0.88 0.24 0.00
337_A 534_Y 0.88 0.24 0.00
355_A 375_N 0.88 0.23 0.00
613_E 126_I 0.87 0.23 0.00
410_S 497_E 0.87 0.23 0.00
600_E 501_M 0.87 0.23 0.00
184_L 162_V 0.86 0.22 0.00
517_S 537_V 0.86 0.22 0.00
29_L 57_D 0.85 0.22 0.00
578_L 134_I 0.85 0.22 0.00
125_I 179_V 0.85 0.22 0.00
178_A 221_L 0.85 0.22 0.00
352_S 68_D 0.84 0.22 0.00
190_L 162_V 0.84 0.21 0.00
562_L 545_T 0.84 0.21 0.00
398_Y 449_I 0.84 0.21 0.00
81_G 49_F 0.83 0.21 0.00
55_A 192_V 0.82 0.20 0.00
613_E 89_S 0.82 0.20 0.00
281_L 456_A 0.82 0.20 0.00
188_Q 249_E 0.82 0.20 0.00
536_T 454_V 0.82 0.20 0.00
185_L 385_I 0.82 0.20 0.00
557_K 436_S 0.82 0.20 0.00
96_C 182_V 0.80 0.19 0.00
95_M 126_I 0.80 0.19 0.00
143_S 549_R 0.80 0.19 0.00
174_S 262_P 0.80 0.19 0.00
493_Y 134_I 0.79 0.18 0.00
195_L 442_T 0.79 0.18 0.00
74_E 18_A 0.79 0.18 0.00
564_T 126_I 0.78 0.18 0.00
265_T 126_I 0.78 0.18 0.00
498_K 126_I 0.78 0.18 0.00
50_A 126_I 0.78 0.18 0.00
560_I 146_F 0.78 0.18 0.00
259_W 66_F 0.78 0.18 0.00
108_G 206_E 0.77 0.17 0.00
20_V 537_V 0.77 0.17 0.00
248_V 250_N 0.77 0.17 0.00
616_L 549_R 0.77 0.17 0.00
522_F 195_L 0.77 0.17 0.00
426_S 19_R 0.77 0.17 0.00
196_I 284_R 0.76 0.17 0.00
235_L 158_F 0.76 0.17 0.00
532_V 230_D 0.76 0.17 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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