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OPENSEQ.org
RhoRNAP Omega
Genes: A B A+B
Length: 419 91 452
Sequences: 1133 448 165
Seq/Len: 2.7 4.92 0.37
MirrorTree (Pazo et al. 2001) 0.84
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 0.00
10 0.01 0.09 0.00
20 0.01 0.09 0.01
100 0.01 0.09 0.06
∞ 0.02 0.09 0.32
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
385_K 57_G 1.58 0.53 0.00
271_A 30_M 1.43 0.43 0.00
351_E 25_R 1.34 0.36 0.00
369_E 13_I 1.31 0.34 0.00
56_E 16_R 1.24 0.30 0.00
181_K 46_T 1.21 0.28 0.00
119_V 28_R 1.21 0.28 0.00
181_K 27_A 1.19 0.27 0.00
182_A 46_T 1.18 0.27 0.00
181_K 22_V 1.18 0.27 0.00
350_A 10_V 1.16 0.25 0.00
199_H 49_I 1.12 0.23 0.00
276_T 15_N 1.10 0.23 0.00
186_M 13_I 1.10 0.22 0.00
354_V 57_G 1.06 0.21 0.00
89_F 30_M 1.06 0.20 0.00
286_T 47_T 1.05 0.20 0.00
406_T 12_K 1.05 0.20 0.00
106_E 60_N 1.04 0.20 0.00
74_A 46_T 1.03 0.19 0.00
369_E 4_V 1.03 0.19 0.00
276_T 17_F 1.03 0.19 0.00
188_L 13_I 1.03 0.19 0.00
186_M 54_I 1.02 0.19 0.00
360_Y 30_M 1.02 0.19 0.00
134_E 46_T 1.01 0.18 0.00
249_K 17_F 1.01 0.18 0.00
378_Q 44_D 1.00 0.18 0.00
283_K 17_F 1.00 0.18 0.00
321_I 67_R 1.00 0.18 0.00
355_F 49_I 0.99 0.17 0.00
147_M 6_V 0.98 0.17 0.00
367_K 65_D 0.98 0.17 0.00
385_K 56_E 0.97 0.17 0.00
286_T 44_D 0.97 0.16 0.00
381_W 10_V 0.96 0.16 0.00
348_K 12_K 0.95 0.16 0.00
374_Q 25_R 0.95 0.16 0.00
68_A 14_G 0.94 0.15 0.00
51_G 17_F 0.94 0.15 0.00
299_R 8_D 0.93 0.15 0.00
372_T 25_R 0.93 0.15 0.00
166_S 66_V 0.93 0.15 0.00
321_I 70_Q 0.93 0.15 0.00
166_S 21_L 0.92 0.15 0.00
390_M 6_V 0.92 0.15 0.00
326_K 67_R 0.92 0.15 0.00
392_E 67_R 0.92 0.14 0.00
341_M 69_R 0.91 0.14 0.00
144_R 28_R 0.91 0.14 0.00
394_D 35_K 0.91 0.14 0.00
222_L 40_P 0.91 0.14 0.00
395_A 54_I 0.90 0.14 0.00
395_A 21_L 0.90 0.14 0.00
246_V 1_M 0.90 0.14 0.00
67_S 17_F 0.90 0.14 0.00
202_C 63_I 0.89 0.14 0.00
326_K 24_A 0.89 0.14 0.00
351_E 30_M 0.89 0.14 0.00
238_R 5_T 0.89 0.14 0.00
62_F 15_N 0.88 0.13 0.00
403_L 40_P 0.88 0.13 0.00
81_V 39_V 0.87 0.13 0.00
147_M 10_V 0.87 0.13 0.00
228_V 59_I 0.87 0.13 0.00
291_A 15_N 0.87 0.13 0.00
286_T 15_N 0.87 0.13 0.00
101_I 51_L 0.87 0.13 0.00
143_S 66_V 0.86 0.13 0.00
262_I 3_R 0.86 0.13 0.00
229_A 58_L 0.86 0.13 0.00
221_R 54_I 0.85 0.12 0.00
258_K 54_I 0.85 0.12 0.00
274_Y 20_V 0.85 0.12 0.00
63_G 1_M 0.85 0.12 0.00
207_L 1_M 0.85 0.12 0.00
236_A 59_I 0.85 0.12 0.00
205_M 59_I 0.84 0.12 0.00
46_G 27_A 0.84 0.12 0.00
189_Q 5_T 0.84 0.12 0.00
194_S 72_Q 0.84 0.12 0.00
181_K 47_T 0.84 0.12 0.00
127_A 20_V 0.83 0.12 0.00
77_D 51_L 0.83 0.12 0.00
373_T 70_Q 0.83 0.12 0.00
88_R 12_K 0.82 0.12 0.00
111_F 7_Q 0.82 0.12 0.00
188_L 32_V 0.82 0.11 0.00
243_A 10_V 0.82 0.11 0.00
332_Y 46_T 0.81 0.11 0.00
387_I 17_F 0.81 0.11 0.00
379_K 44_D 0.81 0.11 0.00
127_A 11_E 0.81 0.11 0.00
367_K 22_V 0.81 0.11 0.00
322_D 14_G 0.81 0.11 0.00
119_V 39_V 0.81 0.11 0.00
276_T 6_V 0.81 0.11 0.00
121_F 15_N 0.81 0.11 0.00
292_N 2_A 0.81 0.11 0.00
281_S 23_A 0.81 0.11 0.00
383_L 52_R 0.81 0.11 0.00
280_A 31_Q 0.80 0.11 0.00
194_S 43_N 0.80 0.11 0.00
132_L 29_Q 0.80 0.11 0.00
204_L 45_K 0.80 0.11 0.00
61_G 1_M 0.79 0.11 0.00
390_M 2_A 0.79 0.11 0.00
406_T 29_Q 0.79 0.11 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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