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OPENSEQ.org
MFDecoli500RNAPthermus500
Genes: A B A+B
Length: 500 500 975
Sequences: 4285 1810 1222
Seq/Len: 8.57 3.62 1.25
MirrorTree (Pazo et al. 2001) -0.03
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 0.03 0.09 0.00
2 0.03 0.09 0.00
5 0.03 0.09 0.01
10 0.03 0.09 0.01
20 0.03 0.09 0.05
100 0.05 0.09 0.24
∞ 0.20 0.09 1.22
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
45_I 90_Y 1.54 0.85 0.11
186_D 355_V 1.46 0.80 0.09
162_Y 109_K 1.30 0.68 0.06
274_S 14_P 1.29 0.67 0.06
171_L 129_I 1.21 0.59 0.04
159_H 460_R 1.16 0.55 0.04
168_L 26_Y 1.15 0.54 0.04
41_P 251_D 1.15 0.54 0.04
107_I 264_P 1.12 0.51 0.03
406_K 404_L 1.08 0.47 0.03
45_I 304_L 1.07 0.46 0.03
481_Q 339_L 1.07 0.46 0.03
105_V 251_D 1.07 0.46 0.03
146_D 464_L 1.05 0.45 0.03
105_V 112_E 1.04 0.43 0.03
108_V 95_Y 1.04 0.43 0.03
70_L 233_E 1.03 0.42 0.02
192_L 160_A 1.02 0.42 0.02
199_S 24_E 1.01 0.40 0.02
25_A 425_F 1.00 0.40 0.02
25_A 492_D 0.99 0.39 0.02
239_R 126_S 0.99 0.39 0.02
308_V 360_L 0.99 0.39 0.02
170_D 19_T 0.99 0.38 0.02
70_L 469_T 0.99 0.38 0.02
374_L 398_T 0.99 0.38 0.02
160_G 196_L 0.99 0.38 0.02
106_L 71_Y 0.98 0.38 0.02
70_L 254_V 0.98 0.37 0.02
201_R 460_R 0.98 0.37 0.02
222_A 26_Y 0.96 0.36 0.02
44_L 91_Q 0.95 0.35 0.02
169_L 483_V 0.95 0.35 0.02
190_D 51_T 0.95 0.34 0.02
62_F 26_Y 0.95 0.34 0.02
56_H 111_D 0.94 0.34 0.02
59_I 113_V 0.94 0.34 0.02
43_V 184_M 0.94 0.34 0.02
36_E 207_L 0.93 0.33 0.02
191_S 421_E 0.93 0.33 0.02
378_L 382_I 0.92 0.32 0.02
44_L 21_I 0.92 0.32 0.02
374_L 196_L 0.91 0.32 0.02
496_M 148_F 0.91 0.31 0.01
169_L 164_P 0.90 0.31 0.01
232_R 73_L 0.90 0.31 0.01
189_I 457_A 0.90 0.30 0.01
479_I 14_P 0.90 0.30 0.01
233_D 182_V 0.89 0.30 0.01
255_A 433_T 0.89 0.30 0.01
133_G 381_A 0.89 0.30 0.01
410_Q 248_P 0.89 0.29 0.01
40_G 136_I 0.88 0.29 0.01
189_I 33_D 0.88 0.29 0.01
70_L 206_T 0.88 0.29 0.01
100_T 464_L 0.88 0.29 0.01
184_F 5_R 0.88 0.29 0.01
283_V 196_L 0.88 0.28 0.01
180_Y 183_S 0.87 0.28 0.01
161_E 307_L 0.87 0.28 0.01
86_D 19_T 0.87 0.28 0.01
106_L 251_D 0.87 0.28 0.01
492_R 304_L 0.86 0.27 0.01
258_E 148_F 0.86 0.27 0.01
409_P 388_R 0.86 0.27 0.01
183_D 239_F 0.86 0.27 0.01
490_V 45_Q 0.86 0.27 0.01
57_D 281_L 0.86 0.27 0.01
43_V 458_Y 0.86 0.27 0.01
184_F 245_G 0.85 0.27 0.01
31_V 160_A 0.85 0.27 0.01
161_E 461_V 0.85 0.26 0.01
192_L 475_V 0.85 0.26 0.01
396_E 474_V 0.84 0.26 0.01
171_L 65_V 0.84 0.26 0.01
393_G 469_T 0.84 0.26 0.01
350_N 128_I 0.84 0.26 0.01
197_V 270_G 0.84 0.26 0.01
184_F 275_Y 0.84 0.26 0.01
186_D 487_T 0.84 0.26 0.01
350_N 473_R 0.84 0.26 0.01
87_I 72_R 0.83 0.25 0.01
496_M 285_L 0.83 0.25 0.01
141_L 486_M 0.83 0.25 0.01
122_F 188_K 0.83 0.25 0.01
207_E 356_R 0.83 0.25 0.01
184_F 175_E 0.83 0.25 0.01
42_V 307_L 0.83 0.25 0.01
159_H 432_R 0.83 0.25 0.01
143_T 356_R 0.82 0.24 0.01
500_E 251_D 0.82 0.24 0.01
152_H 251_D 0.82 0.24 0.01
479_I 128_I 0.82 0.24 0.01
171_L 8_R 0.82 0.24 0.01
272_L 112_E 0.82 0.24 0.01
251_G 128_I 0.81 0.24 0.01
391_S 433_T 0.81 0.24 0.01
189_I 492_D 0.81 0.24 0.01
284_N 196_L 0.81 0.23 0.01
340_K 301_E 0.81 0.23 0.01
67_V 209_R 0.81 0.23 0.01
97_Q 85_E 0.81 0.23 0.01
130_M 101_I 0.80 0.23 0.01
239_R 196_L 0.80 0.23 0.01
184_F 65_V 0.80 0.23 0.01
86_D 220_G 0.80 0.23 0.01
493_Y 34_V 0.80 0.23 0.01
194_V 359_M 0.80 0.23 0.01
97_Q 458_Y 0.80 0.23 0.01
148_A 487_T 0.80 0.23 0.01
355_F 402_S 0.80 0.23 0.01
422_G 136_I 0.80 0.23 0.01
290_T 363_S 0.80 0.23 0.01
186_D 136_I 0.80 0.22 0.01
182_L 138_S 0.80 0.22 0.01
162_Y 469_T 0.79 0.22 0.01
45_I 98_L 0.79 0.22 0.01
387_F 123_E 0.79 0.22 0.01
45_I 495_T 0.79 0.22 0.01
300_L 248_P 0.79 0.22 0.01
34_I 112_E 0.79 0.22 0.01
397_A 168_R 0.78 0.22 0.01
28_A 51_T 0.78 0.21 0.01
338_Q 484_V 0.78 0.21 0.01
200_Q 389_S 0.78 0.21 0.01
399_G 104_D 0.78 0.21 0.01
374_L 44_I 0.78 0.21 0.01
83_P 307_L 0.78 0.21 0.01
406_K 382_I 0.77 0.21 0.01
318_Q 90_Y 0.77 0.21 0.01
453_R 149_T 0.77 0.21 0.01
195_F 246_D 0.77 0.21 0.01
393_G 310_L 0.77 0.21 0.01
94_T 456_A 0.77 0.21 0.01
443_L 335_T 0.77 0.21 0.01
123_L 257_V 0.77 0.21 0.01
169_L 7_G 0.77 0.20 0.01
275_Y 89_T 0.77 0.20 0.01
327_L 7_G 0.77 0.20 0.01
292_A 104_D 0.77 0.20 0.01
171_L 492_D 0.77 0.20 0.01
230_Q 21_I 0.76 0.20 0.01
395_R 246_D 0.76 0.20 0.01
497_T 164_P 0.76 0.20 0.01
147_S 482_E 0.76 0.20 0.01
344_L 138_S 0.76 0.20 0.01
106_L 193_L 0.76 0.20 0.01
255_A 353_R 0.76 0.20 0.01
71_A 373_V 0.76 0.20 0.01
301_A 24_E 0.76 0.20 0.01
481_Q 398_T 0.76 0.20 0.01
361_L 383_R 0.76 0.20 0.01
62_F 283_I 0.76 0.20 0.01
192_L 97_R 0.76 0.20 0.01
250_K 68_F 0.76 0.20 0.01
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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