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OPENSEQ.org
cI_M_H_Ecoli
Genes: A B A+B
Length: 509 325 808
Sequences: 2110 4760 1615
Seq/Len: 4.15 14.65 2
MirrorTree (Pazo et al. 2001) 0.65
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.00 0.06
2 0.01 0.00 0.08
5 0.01 0.00 1.46
10 0.02 0.01 1.73
20 0.02 0.01 1.79
100 0.03 0.02 1.85
∞ 0.06 0.05 1.94
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
397_G 136_S 1.02 0.54 0.00
233_V 306_L 1.01 0.54 0.00
228_F 193_F 0.98 0.50 0.00
398_M 99_A 0.97 0.49 0.00
429_L 41_G 0.96 0.48 0.00
347_A 244_G 0.95 0.47 0.00
246_D 301_G 0.94 0.46 0.00
137_F 193_F 0.93 0.45 0.00
278_L 306_L 0.93 0.45 0.00
98_G 257_F 0.93 0.44 0.00
315_I 15_V 0.92 0.43 0.00
83_I 23_L 0.92 0.43 0.00
368_T 61_V 0.91 0.43 0.00
309_T 201_I 0.91 0.43 0.00
151_Y 188_N 0.91 0.42 0.00
99_V 231_G 0.91 0.42 0.00
440_L 139_N 0.90 0.41 0.00
36_M 118_F 0.89 0.40 0.00
374_M 139_N 0.89 0.40 0.00
242_G 34_F 0.88 0.40 0.00
218_G 197_I 0.88 0.39 0.00
143_W 235_G 0.88 0.39 0.00
63_W 273_L 0.87 0.38 0.00
337_A 38_R 0.86 0.37 0.00
331_Y 128_Y 0.85 0.36 0.00
342_V 81_V 0.85 0.36 0.00
321_S 267_P 0.84 0.35 0.00
279_F 306_L 0.83 0.34 0.00
468_I 197_I 0.83 0.34 0.00
327_L 165_M 0.83 0.34 0.00
416_Q 154_L 0.82 0.33 0.00
400_G 260_W 0.82 0.33 0.00
368_T 225_Y 0.81 0.32 0.00
130_V 74_I 0.81 0.32 0.00
157_W 231_G 0.80 0.31 0.00
351_S 132_F 0.80 0.31 0.00
193_V 165_M 0.80 0.31 0.00
422_T 171_A 0.79 0.30 0.00
42_L 109_V 0.79 0.30 0.00
423_V 89_I 0.79 0.30 0.00
38_L 12_L 0.79 0.30 0.00
311_I 136_S 0.78 0.29 0.00
359_C 163_S 0.78 0.29 0.00
441_H 98_F 0.78 0.29 0.00
44_L 252_M 0.78 0.29 0.00
292_W 318_A 0.78 0.29 0.00
116_F 261_Q 0.78 0.29 0.00
262_I 251_L 0.78 0.29 0.00
105_S 154_L 0.77 0.28 0.00
318_T 205_A 0.77 0.28 0.00
184_V 173_S 0.77 0.28 0.00
143_W 312_N 0.77 0.28 0.00
420_V 197_I 0.77 0.28 0.00
275_S 160_L 0.76 0.28 0.00
247_A 256_F 0.76 0.28 0.00
438_A 193_F 0.76 0.28 0.00
432_A 225_Y 0.76 0.27 0.00
41_A 89_I 0.76 0.27 0.00
352_A 262_G 0.76 0.27 0.00
107_K 130_V 0.76 0.27 0.00
489_S 67_M 0.75 0.26 0.00
344_Q 138_N 0.75 0.26 0.00
116_F 41_G 0.75 0.26 0.00
424_I 281_M 0.75 0.26 0.00
272_L 320_I 0.75 0.26 0.00
289_I 202_A 0.75 0.26 0.00
362_L 164_L 0.74 0.26 0.00
326_V 25_V 0.74 0.26 0.00
474_L 278_F 0.74 0.26 0.00
104_C 33_S 0.74 0.26 0.00
223_L 155_S 0.74 0.26 0.00
126_G 316_T 0.73 0.25 0.00
69_M 16_L 0.72 0.24 0.00
394_A 300_F 0.72 0.24 0.00
137_F 225_Y 0.72 0.24 0.00
371_M 217_A 0.72 0.24 0.00
390_F 173_S 0.72 0.24 0.00
79_I 196_F 0.72 0.24 0.00
194_F 288_S 0.71 0.23 0.00
302_A 202_A 0.71 0.23 0.00
366_I 150_S 0.71 0.23 0.00
120_L 65_I 0.71 0.23 0.00
146_M 153_T 0.71 0.23 0.00
318_T 140_K 0.71 0.23 0.00
474_L 107_W 0.71 0.23 0.00
171_A 243_I 0.71 0.23 0.00
146_M 98_F 0.71 0.23 0.00
146_M 90_A 0.71 0.23 0.00
114_G 89_I 0.71 0.23 0.00
358_L 131_L 0.70 0.23 0.00
299_F 15_V 0.70 0.23 0.00
434_V 173_S 0.70 0.22 0.00
214_P 154_L 0.70 0.22 0.00
351_S 160_L 0.70 0.22 0.00
443_A 60_L 0.70 0.22 0.00
424_I 39_L 0.70 0.22 0.00
120_L 164_L 0.69 0.22 0.00
474_L 308_L 0.69 0.22 0.00
9_I 269_I 0.69 0.22 0.00
246_D 244_G 0.69 0.22 0.00
263_L 225_Y 0.69 0.22 0.00
422_T 99_A 0.69 0.22 0.00
395_T 189_V 0.69 0.22 0.00
429_L 51_R 0.69 0.22 0.00
368_T 313_L 0.69 0.22 0.00
352_A 247_T 0.69 0.22 0.00
410_I 253_V 0.69 0.22 0.00
321_S 127_V 0.69 0.22 0.00
229_I 16_L 0.69 0.21 0.00
9_I 15_V 0.69 0.21 0.00
91_V 101_V 0.69 0.21 0.00
57_S 78_S 0.69 0.21 0.00
152_F 313_L 0.69 0.21 0.00
442_R 73_W 0.69 0.21 0.00
187_I 41_G 0.69 0.21 0.00
388_S 162_L 0.69 0.21 0.00
492_A 146_A 0.68 0.21 0.00
196_H 240_G 0.68 0.21 0.00
332_T 285_I 0.68 0.21 0.00
299_F 273_L 0.68 0.21 0.00
296_I 12_L 0.68 0.21 0.00
481_Y 155_S 0.68 0.21 0.00
416_Q 80_R 0.68 0.21 0.00
398_M 165_M 0.68 0.21 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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