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OPENSEQ.org
PcrA(3PJR)_RNAPfirst500(4GZY)
Genes: A B A+B
Length: 724 500 1137
Sequences: 4096 1810 1191
Seq/Len: 5.66 3.62 1.05
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 0.13
∞ 0.17 0.09 0.97
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 473_R 1.18 0.52 0.00
612_E 128_I 1.08 0.42 0.00
371_L 90_Y 0.95 0.31 0.00
262_A 464_L 0.93 0.29 0.00
125_M 181_V 0.93 0.29 0.00
323_Y 129_I 0.91 0.28 0.00
563_T 128_I 0.91 0.28 0.00
512_L 26_Y 0.90 0.27 0.00
89_I 233_E 0.89 0.26 0.00
410_S 421_E 0.89 0.26 0.00
376_I 128_I 0.88 0.26 0.00
594_D 251_D 0.86 0.24 0.00
159_E 233_E 0.85 0.23 0.00
41_L 383_R 0.83 0.22 0.00
375_N 90_Y 0.83 0.22 0.00
81_G 48_F 0.83 0.22 0.00
441_L 91_Q 0.82 0.22 0.00
52_K 128_I 0.82 0.22 0.00
355_A 297_E 0.81 0.21 0.00
396_L 258_Y 0.81 0.21 0.00
259_W 355_V 0.79 0.20 0.00
387_Y 483_V 0.79 0.20 0.00
461_L 123_E 0.79 0.20 0.00
187_N 160_A 0.79 0.20 0.00
280_I 461_V 0.79 0.20 0.00
248_A 252_K 0.78 0.19 0.00
246_I 402_S 0.78 0.19 0.00
144_I 473_R 0.78 0.19 0.00
356_V 480_T 0.78 0.19 0.00
159_E 478_V 0.77 0.18 0.00
599_E 425_F 0.77 0.18 0.00
222_I 36_P 0.76 0.18 0.00
540_L 182_V 0.75 0.17 0.00
29_I 79_P 0.75 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)
ID Seq/Len Name Options I_Prob Status
5573 1.05 PcrA(3PJR)_RNAPfirst500(4GZY) Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5558 1.05 PcrA(3PJR)_RNAPfirst500(4GZY) Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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