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OPENSEQ.org
PcrAsubtilis_RNAP(4GZY)500
Genes: A B A+B
Length: 739 500 1138
Sequences: 3698 1810 1111
Seq/Len: 5 3.62 0.98
MirrorTree (Pazo et al. 2001) 0.21
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 0.90
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
323_Y 129_I 1.09 0.42 0.00
558_D 473_R 1.04 0.37 0.00
375_G 90_Y 0.98 0.32 0.00
371_L 90_Y 0.97 0.31 0.00
509_L 128_I 0.94 0.29 0.00
76_V 473_R 0.93 0.28 0.00
461_L 459_A 0.93 0.28 0.00
89_I 233_E 0.92 0.28 0.00
461_L 129_I 0.92 0.27 0.00
220_I 469_T 0.91 0.26 0.00
613_E 128_I 0.91 0.26 0.00
337_A 458_Y 0.90 0.26 0.00
512_I 26_Y 0.90 0.26 0.00
174_S 264_P 0.88 0.25 0.00
52_K 128_I 0.88 0.25 0.00
509_L 259_G 0.87 0.24 0.00
246_L 402_S 0.87 0.23 0.00
280_I 322_V 0.84 0.22 0.00
125_I 181_V 0.84 0.22 0.00
376_L 128_I 0.83 0.21 0.00
399_L 500_N 0.82 0.21 0.00
108_G 129_I 0.82 0.20 0.00
557_K 360_L 0.81 0.20 0.00
355_A 297_E 0.81 0.20 0.00
600_E 425_F 0.81 0.20 0.00
598_M 20_E 0.81 0.20 0.00
185_L 307_L 0.81 0.20 0.00
299_V 356_R 0.81 0.20 0.00
229_N 164_P 0.81 0.20 0.00
562_L 469_T 0.81 0.20 0.00
191_D 68_F 0.81 0.20 0.00
337_A 9_I 0.80 0.20 0.00
259_W 355_V 0.80 0.20 0.00
421_G 383_R 0.80 0.19 0.00
642_I 496_I 0.79 0.19 0.00
352_S 70_E 0.78 0.18 0.00
167_G 160_A 0.78 0.18 0.00
617_Y 233_E 0.78 0.18 0.00
398_Y 373_V 0.78 0.18 0.00
270_F 461_V 0.78 0.18 0.00
472_T 469_T 0.77 0.18 0.00
45_I 469_T 0.77 0.17 0.00
143_S 473_R 0.77 0.17 0.00
498_K 128_I 0.76 0.17 0.00
190_L 164_P 0.76 0.17 0.00
184_L 164_P 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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