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OPENSEQ.org
PCRA_RNAPbeta500
Genes: A B A+B
Length: 435 500 853
Sequences: 1621 1810 520
Seq/Len: 3.73 3.62 0.61
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 0.01 0.09 0.00
2 0.01 0.09 0.00
5 0.01 0.09 0.01
10 0.01 0.09 0.02
20 0.01 0.09 0.04
100 0.02 0.09 0.10
∞ 0.04 0.09 0.56
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
164_L 91_Q 1.46 0.59 0.00
349_L 136_I 1.43 0.56 0.00
329_T 5_R 1.24 0.42 0.00
175_F 458_Y 1.23 0.40 0.00
250_A 421_E 1.20 0.39 0.00
108_A 76_P 1.15 0.34 0.00
107_L 136_I 1.12 0.33 0.00
284_P 356_R 1.10 0.31 0.00
323_E 90_Y 1.08 0.29 0.00
329_T 193_L 1.06 0.28 0.00
67_V 305_P 1.05 0.28 0.00
164_L 24_E 1.05 0.28 0.00
47_V 47_A 1.04 0.27 0.00
288_L 26_Y 1.03 0.26 0.00
196_E 123_E 1.01 0.25 0.00
315_A 215_G 1.01 0.25 0.00
351_E 157_R 1.01 0.25 0.00
329_T 421_E 0.98 0.24 0.00
247_T 355_V 0.98 0.24 0.00
47_V 46_A 0.98 0.23 0.00
355_H 473_R 0.97 0.23 0.00
121_S 14_P 0.96 0.22 0.00
139_D 21_I 0.96 0.22 0.00
337_F 279_E 0.95 0.22 0.00
301_S 90_Y 0.95 0.22 0.00
125_I 309_Y 0.95 0.22 0.00
209_K 26_Y 0.94 0.21 0.00
51_I 264_P 0.94 0.21 0.00
278_A 307_L 0.93 0.20 0.00
284_P 23_V 0.93 0.20 0.00
98_Y 303_F 0.92 0.20 0.00
277_A 164_P 0.92 0.20 0.00
249_L 433_T 0.91 0.20 0.00
318_G 206_T 0.91 0.20 0.00
329_T 86_K 0.91 0.19 0.00
27_P 421_E 0.91 0.19 0.00
202_S 304_L 0.91 0.19 0.00
249_L 200_L 0.90 0.19 0.00
65_F 457_A 0.90 0.19 0.00
32_I 118_I 0.90 0.19 0.00
226_F 129_I 0.90 0.19 0.00
247_T 370_A 0.90 0.19 0.00
245_F 191_F 0.90 0.19 0.00
88_P 481_D 0.90 0.19 0.00
329_T 496_I 0.90 0.19 0.00
270_V 473_R 0.90 0.19 0.00
93_G 237_R 0.89 0.19 0.00
65_F 17_P 0.89 0.19 0.00
319_I 252_K 0.89 0.18 0.00
323_E 356_R 0.89 0.18 0.00
195_V 457_A 0.89 0.18 0.00
91_I 232_E 0.88 0.18 0.00
72_N 271_E 0.88 0.18 0.00
82_L 136_I 0.88 0.18 0.00
291_M 192_P 0.88 0.18 0.00
87_I 482_E 0.88 0.18 0.00
130_K 487_T 0.87 0.17 0.00
285_V 481_D 0.87 0.17 0.00
103_I 467_I 0.87 0.17 0.00
315_A 237_R 0.86 0.17 0.00
91_I 79_P 0.86 0.17 0.00
247_T 182_V 0.86 0.17 0.00
67_V 301_E 0.86 0.17 0.00
297_P 68_F 0.85 0.17 0.00
3_I 20_E 0.85 0.17 0.00
233_F 277_A 0.85 0.17 0.00
268_D 486_M 0.84 0.16 0.00
125_I 469_T 0.84 0.16 0.00
358_E 92_A 0.84 0.16 0.00
141_L 101_I 0.84 0.16 0.00
10_V 467_I 0.83 0.16 0.00
272_L 441_V 0.83 0.16 0.00
121_S 342_D 0.83 0.16 0.00
172_L 265_R 0.83 0.16 0.00
144_Y 304_L 0.83 0.16 0.00
107_L 123_E 0.83 0.16 0.00
111_R 124_D 0.82 0.15 0.00
238_D 483_V 0.82 0.15 0.00
74_Q 456_A 0.82 0.15 0.00
231_K 473_R 0.82 0.15 0.00
137_T 66_L 0.82 0.15 0.00
315_A 333_I 0.82 0.15 0.00
113_I 441_V 0.81 0.15 0.00
241_S 164_P 0.81 0.15 0.00
51_I 84_R 0.81 0.15 0.00
80_E 160_A 0.81 0.15 0.00
211_E 160_A 0.81 0.15 0.00
349_L 216_E 0.81 0.15 0.00
46_F 190_K 0.81 0.15 0.00
329_T 497_A 0.81 0.15 0.00
64_D 128_I 0.81 0.15 0.00
329_T 161_S 0.81 0.15 0.00
260_G 26_Y 0.81 0.15 0.00
67_V 461_V 0.81 0.15 0.00
308_M 307_L 0.80 0.15 0.00
270_V 365_D 0.80 0.15 0.00
43_E 351_L 0.80 0.14 0.00
201_K 253_A 0.80 0.14 0.00
190_S 490_E 0.80 0.14 0.00
113_I 58_D 0.80 0.14 0.00
111_R 94_L 0.80 0.14 0.00
24_T 129_I 0.80 0.14 0.00
261_T 473_R 0.80 0.14 0.00
114_A 469_T 0.79 0.14 0.00
107_L 483_V 0.79 0.14 0.00
35_Y 469_T 0.79 0.14 0.00
288_L 457_A 0.79 0.14 0.00
159_L 26_Y 0.79 0.14 0.00
339_N 123_E 0.79 0.14 0.00
198_V 186_V 0.79 0.14 0.00
65_F 84_R 0.79 0.14 0.00
68_L 26_Y 0.79 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)
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