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OPENSEQ.org
PCRA_RNAP1120
Genes: A B A+B
Length: 435 619 911
Sequences: 1621 1323 487
Seq/Len: 3.73 2.14 0.53
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 0.01 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 0.46
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
107_L 230_S 1.39 0.50 0.00
103_I 245_I 1.29 0.42 0.00
87_I 106_V 1.28 0.41 0.00
91_I 327_V 1.21 0.36 0.00
91_I 326_Y 1.20 0.35 0.00
345_P 251_P 1.13 0.30 0.00
82_L 152_G 1.13 0.30 0.00
141_L 351_K 1.13 0.30 0.00
67_V 2_P 1.12 0.29 0.00
179_L 486_P 1.11 0.29 0.00
103_I 540_L 1.10 0.29 0.00
147_D 184_F 1.08 0.27 0.00
47_V 268_T 1.06 0.26 0.00
230_T 268_T 1.06 0.26 0.00
103_I 552_M 1.06 0.26 0.00
103_I 149_V 1.05 0.26 0.00
250_A 43_N 1.05 0.25 0.00
295_I 349_V 1.04 0.25 0.00
48_A 148_R 1.04 0.24 0.00
87_I 300_V 1.03 0.24 0.00
349_L 52_H 1.02 0.24 0.00
293_E 7_R 1.01 0.23 0.00
8_N 252_G 1.00 0.23 0.00
257_E 113_V 1.00 0.23 0.00
51_I 578_E 1.00 0.23 0.00
99_D 369_V 0.99 0.22 0.00
293_E 4_E 0.99 0.22 0.00
335_T 29_V 0.98 0.22 0.00
328_L 46_L 0.96 0.20 0.00
108_A 360_H 0.96 0.20 0.00
141_L 272_R 0.94 0.20 0.00
141_L 6_N 0.94 0.19 0.00
32_I 175_A 0.94 0.19 0.00
122_L 225_D 0.94 0.19 0.00
125_I 140_R 0.93 0.19 0.00
67_V 321_E 0.93 0.19 0.00
352_I 113_V 0.93 0.19 0.00
323_E 211_E 0.91 0.18 0.00
339_N 487_I 0.90 0.17 0.00
208_L 349_V 0.90 0.17 0.00
271_M 193_E 0.90 0.17 0.00
47_V 175_A 0.88 0.17 0.00
106_I 245_I 0.88 0.17 0.00
315_A 248_E 0.88 0.17 0.00
294_G 268_T 0.87 0.16 0.00
79_E 162_E 0.87 0.16 0.00
113_I 10_A 0.87 0.16 0.00
52_R 230_S 0.87 0.16 0.00
294_G 2_P 0.87 0.16 0.00
112_V 487_I 0.86 0.16 0.00
10_V 104_A 0.86 0.16 0.00
66_A 42_V 0.86 0.16 0.00
231_K 360_H 0.86 0.16 0.00
203_G 193_E 0.85 0.15 0.00
118_D 125_L 0.85 0.15 0.00
296_F 170_Q 0.85 0.15 0.00
220_L 286_K 0.85 0.15 0.00
221_E 288_T 0.84 0.15 0.00
318_G 500_M 0.84 0.15 0.00
103_I 197_R 0.84 0.15 0.00
226_F 96_Y 0.84 0.15 0.00
87_I 42_V 0.84 0.15 0.00
327_V 197_R 0.83 0.15 0.00
43_E 251_P 0.83 0.15 0.00
133_I 487_I 0.83 0.15 0.00
82_L 200_Y 0.83 0.14 0.00
265_A 166_L 0.83 0.14 0.00
157_G 113_V 0.83 0.14 0.00
306_D 153_D 0.83 0.14 0.00
107_L 206_E 0.82 0.14 0.00
82_L 170_Q 0.82 0.14 0.00
6_A 417_L 0.82 0.14 0.00
41_A 300_V 0.82 0.14 0.00
48_A 581_V 0.82 0.14 0.00
235_N 35_S 0.82 0.14 0.00
294_G 540_L 0.82 0.14 0.00
78_M 594_A 0.82 0.14 0.00
101_K 385_I 0.82 0.14 0.00
193_E 140_R 0.81 0.14 0.00
323_E 114_R 0.81 0.14 0.00
180_E 72_I 0.81 0.14 0.00
3_I 503_D 0.81 0.14 0.00
243_I 147_Q 0.81 0.14 0.00
207_M 180_D 0.81 0.14 0.00
133_I 111_I 0.80 0.14 0.00
178_Q 52_H 0.80 0.13 0.00
125_I 128_F 0.80 0.13 0.00
315_A 20_E 0.80 0.13 0.00
225_E 45_N 0.80 0.13 0.00
332_Q 230_S 0.80 0.13 0.00
349_L 9_A 0.80 0.13 0.00
307_E 532_F 0.79 0.13 0.00
141_L 34_V 0.79 0.13 0.00
138_I 532_F 0.79 0.13 0.00
53_E 239_E 0.79 0.13 0.00
192_T 155_L 0.79 0.13 0.00
230_T 316_K 0.79 0.13 0.00
349_L 552_M 0.79 0.13 0.00
111_R 46_L 0.79 0.13 0.00
61_R 73_R 0.79 0.13 0.00
118_D 141_P 0.79 0.13 0.00
88_P 103_V 0.79 0.13 0.00
9_E 95_L 0.79 0.13 0.00
293_E 78_V 0.79 0.13 0.00
270_V 140_R 0.79 0.13 0.00
175_F 128_F 0.79 0.13 0.00
266_E 178_P 0.79 0.13 0.00
44_A 95_L 0.79 0.13 0.00
305_D 487_I 0.79 0.13 0.00
238_D 362_P 0.78 0.13 0.00
195_V 388_T 0.78 0.13 0.00
78_M 351_K 0.78 0.13 0.00
319_I 574_E 0.78 0.13 0.00
223_L 203_I 0.78 0.13 0.00
252_I 369_V 0.78 0.13 0.00
329_T 6_N 0.78 0.12 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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