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OPENSEQ.org
PCRAC_RNAP2
Genes: A B A+B
Length: 435 559 852
Sequences: 1621 1202 482
Seq/Len: 3.73 2.15 0.57
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 0.03
100 0.02 0.09 0.08
∞ 0.04 0.09 0.48
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
87_I 46_V 1.29 0.44 0.00
103_I 185_I 1.29 0.44 0.00
345_P 191_P 1.25 0.40 0.00
91_I 267_V 1.21 0.37 0.00
82_L 92_G 1.18 0.35 0.00
107_L 170_S 1.15 0.33 0.00
91_I 266_Y 1.14 0.32 0.00
103_I 480_L 1.09 0.29 0.00
141_L 291_K 1.08 0.28 0.00
295_I 289_V 1.06 0.27 0.00
103_I 492_M 1.05 0.27 0.00
179_L 426_P 1.05 0.26 0.00
47_V 208_T 1.04 0.26 0.00
103_I 89_V 1.02 0.25 0.00
230_T 208_T 1.02 0.24 0.00
48_A 88_R 1.01 0.24 0.00
352_I 53_V 0.99 0.23 0.00
257_E 53_V 0.99 0.23 0.00
32_I 115_A 0.98 0.23 0.00
8_N 192_G 0.98 0.22 0.00
108_A 300_H 0.95 0.21 0.00
99_D 309_V 0.95 0.21 0.00
87_I 240_V 0.94 0.20 0.00
306_D 93_D 0.93 0.20 0.00
305_D 427_I 0.92 0.19 0.00
147_D 124_F 0.91 0.19 0.00
122_L 165_D 0.89 0.18 0.00
141_L 212_R 0.89 0.18 0.00
231_K 300_H 0.89 0.18 0.00
125_I 68_F 0.88 0.17 0.00
51_I 518_E 0.88 0.17 0.00
339_N 427_I 0.88 0.17 0.00
208_L 289_V 0.87 0.17 0.00
67_V 261_E 0.87 0.17 0.00
180_E 12_I 0.86 0.17 0.00
271_M 133_E 0.86 0.16 0.00
47_V 115_A 0.85 0.16 0.00
125_I 80_R 0.85 0.16 0.00
6_A 357_L 0.84 0.15 0.00
294_G 208_T 0.83 0.15 0.00
52_R 170_S 0.83 0.15 0.00
315_A 188_E 0.83 0.15 0.00
53_E 13_R 0.83 0.15 0.00
349_L 492_M 0.82 0.15 0.00
323_E 54_R 0.82 0.15 0.00
159_L 325_I 0.81 0.14 0.00
133_I 102_E 0.81 0.14 0.00
43_E 191_P 0.81 0.14 0.00
328_L 106_L 0.81 0.14 0.00
296_F 110_Q 0.81 0.14 0.00
10_V 44_A 0.81 0.14 0.00
323_E 151_E 0.81 0.14 0.00
207_M 120_D 0.80 0.14 0.00
233_F 519_P 0.80 0.14 0.00
107_L 146_E 0.80 0.14 0.00
220_L 226_K 0.80 0.14 0.00
118_D 81_P 0.80 0.14 0.00
226_F 82_R 0.80 0.14 0.00
265_A 106_L 0.80 0.14 0.00
213_T 82_R 0.79 0.14 0.00
203_G 133_E 0.79 0.14 0.00
78_M 534_A 0.79 0.14 0.00
61_R 13_R 0.79 0.14 0.00
206_E 90_R 0.79 0.14 0.00
118_D 65_L 0.79 0.13 0.00
92_V 142_S 0.79 0.13 0.00
351_E 239_I 0.78 0.13 0.00
318_G 440_M 0.78 0.13 0.00
329_T 231_R 0.78 0.13 0.00
36_E 35_L 0.78 0.13 0.00
192_T 95_L 0.78 0.13 0.00
297_P 134_L 0.77 0.13 0.00
226_F 307_V 0.77 0.13 0.00
174_A 434_I 0.77 0.13 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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