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OPENSEQ.org
PCRA_RNAP1193bsubtilis
Genes: A B A+B
Length: 739 693 1273
Sequences: 3698 1308 1019
Seq/Len: 5 1.89 0.8
MirrorTree (Pazo et al. 2001) 0.32
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 0.02
20 0.09 0.09 0.03
100 0.10 0.09 0.10
∞ 0.16 0.09 0.71
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
125_I 154_E 1.22 0.47 0.00
331_G 332_I 1.09 0.36 0.00
220_I 387_I 1.03 0.32 0.00
173_V 400_E 1.00 0.29 0.00
337_A 34_Y 0.99 0.29 0.00
336_V 332_I 0.99 0.29 0.00
558_D 110_Y 0.98 0.28 0.00
430_I 108_V 0.97 0.27 0.00
95_M 446_Y 0.96 0.26 0.00
220_I 45_T 0.95 0.26 0.00
558_D 49_R 0.95 0.26 0.00
557_K 284_D 0.93 0.24 0.00
459_N 187_A 0.92 0.24 0.00
517_S 37_V 0.91 0.23 0.00
130_K 453_I 0.91 0.23 0.00
618_L 85_G 0.91 0.23 0.00
22_T 190_V 0.90 0.23 0.00
642_I 105_R 0.90 0.23 0.00
205_R 530_V 0.88 0.21 0.00
220_I 151_M 0.88 0.21 0.00
482_E 332_I 0.88 0.21 0.00
131_E 453_I 0.87 0.21 0.00
211_E 525_P 0.87 0.21 0.00
148_I 113_V 0.87 0.21 0.00
76_V 49_R 0.85 0.20 0.00
99_I 435_I 0.85 0.20 0.00
512_I 595_I 0.84 0.20 0.00
246_L 110_Y 0.84 0.19 0.00
461_L 35_A 0.83 0.19 0.00
377_N 183_E 0.83 0.19 0.00
419_K 81_L 0.83 0.19 0.00
236_V 518_Y 0.83 0.18 0.00
471_L 241_I 0.83 0.18 0.00
600_E 1_M 0.82 0.18 0.00
356_I 407_Q 0.81 0.17 0.00
492_E 122_A 0.80 0.17 0.00
217_F 387_I 0.80 0.17 0.00
270_F 37_V 0.80 0.17 0.00
462_D 332_I 0.79 0.17 0.00
239_L 227_R 0.79 0.17 0.00
106_R 438_I 0.79 0.17 0.00
581_L 153_P 0.79 0.17 0.00
216_K 174_V 0.79 0.17 0.00
208_E 34_Y 0.79 0.16 0.00
562_L 151_M 0.78 0.16 0.00
335_F 106_N 0.78 0.16 0.00
273_D 215_F 0.78 0.16 0.00
333_G 436_S 0.78 0.16 0.00
577_F 355_T 0.78 0.16 0.00
344_H 271_Y 0.77 0.16 0.00
421_G 154_E 0.77 0.16 0.00
217_F 242_L 0.77 0.16 0.00
556_G 468_I 0.77 0.16 0.00
313_T 190_V 0.77 0.16 0.00
562_L 204_K 0.77 0.16 0.00
196_I 603_V 0.77 0.16 0.00
392_I 438_I 0.77 0.16 0.00
93_H 275_I 0.77 0.15 0.00
382_G 317_G 0.77 0.15 0.00
58_N 157_F 0.77 0.15 0.00
296_A 192_V 0.76 0.15 0.00
176_V 402_P 0.76 0.15 0.00
436_I 271_Y 0.76 0.15 0.00
242_R 59_G 0.76 0.15 0.00
262_A 284_D 0.76 0.15 0.00
340_I 236_V 0.76 0.15 0.00
74_E 516_V 0.76 0.15 0.00
515_F 591_T 0.76 0.15 0.00
579_M 435_I 0.75 0.15 0.00
617_Y 179_P 0.75 0.15 0.00
356_I 516_V 0.75 0.15 0.00
642_I 74_V 0.75 0.15 0.00
531_L 512_D 0.75 0.15 0.00
371_L 407_Q 0.75 0.15 0.00
581_L 89_D 0.75 0.15 0.00
581_L 435_I 0.74 0.14 0.00
641_E 253_L 0.74 0.14 0.00
127_G 105_R 0.74 0.14 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
5572 0.81 PCRA_RNAP1193bsubtilis Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5562 0.8 PCRA_RNAP1193bsubtilis Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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