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OPENSEQ.org
PcrA(3PJR)_RNAP600(geobacillus)
Genes: A B A+B
Length: 724 600 1186
Sequences: 4096 1433 1151
Seq/Len: 5.66 2.39 0.97
MirrorTree (Pazo et al. 2001) 0.27
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 0.87
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
557_D 549_R 1.16 0.48 0.00
612_E 126_I 1.09 0.41 0.00
323_Y 126_I 1.05 0.38 0.00
410_S 497_E 0.97 0.31 0.00
419_K 581_L 0.96 0.30 0.00
461_L 121_E 0.96 0.30 0.00
159_E 231_K 0.94 0.29 0.00
262_A 540_F 0.94 0.28 0.00
355_A 375_H 0.92 0.27 0.00
125_M 179_V 0.92 0.27 0.00
340_I 379_A 0.92 0.27 0.00
41_L 459_K 0.91 0.26 0.00
356_V 558_T 0.91 0.26 0.00
599_E 501_F 0.90 0.26 0.00
337_A 592_V 0.87 0.24 0.00
356_V 127_I 0.86 0.23 0.00
323_Y 127_I 0.85 0.23 0.00
594_D 249_E 0.85 0.23 0.00
248_A 250_N 0.85 0.22 0.00
371_L 88_Y 0.85 0.22 0.00
81_G 49_F 0.84 0.22 0.00
512_L 37_Y 0.84 0.22 0.00
89_I 231_K 0.83 0.21 0.00
174_S 262_P 0.81 0.20 0.00
96_C 182_V 0.81 0.20 0.00
430_L 121_E 0.81 0.20 0.00
396_L 256_A 0.80 0.20 0.00
76_V 549_R 0.80 0.19 0.00
426_T 19_R 0.79 0.19 0.00
290_K 249_E 0.79 0.19 0.00
540_L 180_V 0.79 0.19 0.00
375_N 88_Y 0.79 0.18 0.00
187_N 158_Y 0.78 0.18 0.00
367_M 441_N 0.77 0.18 0.00
615_L 35_S 0.77 0.18 0.00
276_N 45_L 0.77 0.18 0.00
563_T 126_I 0.76 0.17 0.00
229_N 162_V 0.76 0.17 0.00
99_I 195_L 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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