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OPENSEQ.org
PcrA(3PJR)_RNAPrest1119(4GZY)
Genes: A B A+B
Length: 724 619 1194
Sequences: 4122 1309 1110
Seq/Len: 5.69 2.11 0.93
MirrorTree (Pazo et al. 2001) 0.31
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 0.10 0.09 0.04
100 0.11 0.09 0.11
∞ 0.17 0.09 0.83
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
220_I 300_V 1.12 0.42 0.00
331_D 245_I 1.04 0.36 0.00
95_M 360_H 1.00 0.33 0.00
246_I 31_F 1.00 0.33 0.00
335_F 27_E 1.00 0.33 0.00
148_I 34_V 0.94 0.28 0.00
125_M 75_Q 0.94 0.28 0.00
430_L 29_V 0.92 0.27 0.00
392_I 352_I 0.92 0.27 0.00
640_E 166_L 0.92 0.26 0.00
333_A 350_A 0.89 0.24 0.00
484_V 76_A 0.87 0.23 0.00
371_L 352_I 0.87 0.23 0.00
531_L 469_Q 0.86 0.23 0.00
58_N 78_V 0.86 0.23 0.00
340_I 149_V 0.85 0.22 0.00
99_I 349_V 0.85 0.22 0.00
612_E 149_V 0.84 0.21 0.00
580_M 10_A 0.84 0.21 0.00
106_R 385_I 0.83 0.21 0.00
480_V 416_E 0.83 0.21 0.00
94_S 326_Y 0.83 0.20 0.00
643_A 29_V 0.83 0.20 0.00
402_I 203_I 0.82 0.20 0.00
465_R 29_V 0.82 0.20 0.00
356_V 482_P 0.82 0.20 0.00
557_D 31_F 0.82 0.20 0.00
195_L 251_P 0.81 0.19 0.00
577_L 333_L 0.80 0.19 0.00
239_L 140_R 0.79 0.18 0.00
239_L 484_E 0.79 0.18 0.00
358_Y 269_P 0.79 0.18 0.00
617_L 6_N 0.79 0.18 0.00
74_E 473_V 0.79 0.18 0.00
616_V 100_D 0.79 0.18 0.00
576_F 268_T 0.79 0.18 0.00
377_P 104_A 0.78 0.18 0.00
465_R 314_E 0.78 0.18 0.00
272_R 6_N 0.78 0.18 0.00
176_V 83_L 0.78 0.18 0.00
641_I 26_P 0.78 0.18 0.00
534_F 560_I 0.77 0.17 0.00
459_G 108_G 0.76 0.17 0.00
263_D 29_V 0.76 0.17 0.00
176_V 316_K 0.75 0.16 0.00
211_H 482_P 0.75 0.16 0.00
115_I 15_A 0.75 0.16 0.00
286_Y 95_L 0.75 0.16 0.00
380_I 327_V 0.75 0.16 0.00
559_V 236_D 0.75 0.16 0.00
106_R 352_I 0.75 0.16 0.00
22_T 111_I 0.75 0.16 0.00
582_E 243_V 0.74 0.16 0.00
334_Q 73_R 0.74 0.16 0.00
518_V 62_S 0.74 0.15 0.00
419_K 3_L 0.73 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)
ID Seq/Len Name Options I_Prob Status
5574 0.93 PcrA(3PJR)_RNAPrest1119(4GZY) Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5559 0.93 PcrA(3PJR)_RNAPrest1119(4GZY) Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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