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OPENSEQ.org
mfd (570) rnap (1342) ecoli
Genes: A B A+B
Length: 570 672 1223
Sequences: 3809 1008 816
Seq/Len: 6.68 1.5 0.67
MirrorTree (Pazo et al. 2001) 0.20
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 0.00
10 0.03 0.09 0.00
20 0.03 0.09 0.01
100 0.05 0.09 0.07
∞ 0.19 0.09 0.66
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
169_L 554_P 1.44 0.61 0.00
277_P 64_I 1.36 0.54 0.00
556_K 98_M 1.30 0.49 0.00
507_E 3_H 1.23 0.43 0.00
329_S 417_Y 1.22 0.42 0.00
321_W 24_R 1.08 0.32 0.00
531_R 136_P 1.06 0.30 0.00
106_L 642_N 1.05 0.29 0.00
531_R 257_T 1.03 0.28 0.00
528_L 120_D 1.03 0.28 0.00
15_E 203_I 1.02 0.27 0.00
190_D 649_M 1.02 0.27 0.00
159_H 568_L 1.01 0.27 0.00
226_L 59_A 1.01 0.27 0.00
402_L 614_A 1.01 0.27 0.00
162_Y 155_E 1.01 0.27 0.00
479_I 188_G 1.00 0.26 0.00
190_D 463_K 1.00 0.26 0.00
344_L 259_I 0.99 0.26 0.00
190_D 384_L 0.99 0.26 0.00
208_A 201_V 0.99 0.25 0.00
275_Y 130_M 0.97 0.24 0.00
445_C 86_Y 0.96 0.24 0.00
169_L 149_S 0.96 0.24 0.00
184_F 217_V 0.95 0.23 0.00
141_L 155_E 0.95 0.23 0.00
387_F 34_M 0.94 0.23 0.00
490_V 642_N 0.94 0.22 0.00
60_S 46_A 0.94 0.22 0.00
248_V 49_K 0.93 0.22 0.00
162_Y 426_I 0.93 0.22 0.00
39_A 54_V 0.93 0.22 0.00
221_K 131_R 0.93 0.22 0.00
45_I 547_T 0.92 0.21 0.00
283_V 188_G 0.92 0.21 0.00
192_L 412_I 0.91 0.21 0.00
197_V 13_A 0.91 0.21 0.00
542_L 407_S 0.91 0.21 0.00
369_A 23_L 0.91 0.20 0.00
526_L 130_M 0.91 0.20 0.00
85_Q 419_E 0.90 0.20 0.00
481_Q 640_D 0.89 0.20 0.00
186_D 167_A 0.89 0.20 0.00
338_Q 409_I 0.89 0.20 0.00
511_L 412_I 0.88 0.19 0.00
188_E 439_I 0.88 0.19 0.00
188_E 13_A 0.87 0.19 0.00
77_P 226_T 0.87 0.19 0.00
192_L 208_T 0.87 0.19 0.00
488_H 148_V 0.87 0.18 0.00
70_L 88_R 0.86 0.18 0.00
250_K 188_G 0.86 0.18 0.00
430_A 410_N 0.86 0.18 0.00
272_L 201_V 0.86 0.18 0.00
374_L 660_I 0.85 0.18 0.00
283_V 113_L 0.85 0.18 0.00
322_L 54_V 0.85 0.18 0.00
477_L 132_V 0.85 0.18 0.00
197_V 439_I 0.85 0.18 0.00
89_S 142_F 0.84 0.17 0.00
430_A 46_A 0.84 0.17 0.00
50_Q 188_G 0.83 0.17 0.00
184_F 348_Y 0.83 0.17 0.00
192_L 155_E 0.83 0.17 0.00
211_L 103_L 0.83 0.17 0.00
93_S 113_L 0.83 0.17 0.00
217_F 59_A 0.83 0.17 0.00
130_M 193_S 0.82 0.17 0.00
185_F 188_G 0.82 0.16 0.00
159_H 244_K 0.82 0.16 0.00
86_D 120_D 0.82 0.16 0.00
42_V 25_A 0.82 0.16 0.00
154_D 580_S 0.82 0.16 0.00
79_D 86_Y 0.81 0.16 0.00
133_G 59_A 0.81 0.16 0.00
487_E 227_P 0.81 0.16 0.00
117_V 217_V 0.81 0.16 0.00
417_E 384_L 0.81 0.16 0.00
76_L 559_Y 0.81 0.16 0.00
481_Q 636_K 0.81 0.16 0.00
481_Q 580_S 0.81 0.16 0.00
183_D 212_I 0.81 0.16 0.00
157_M 410_N 0.81 0.16 0.00
179_P 433_V 0.81 0.16 0.00
271_P 443_L 0.80 0.15 0.00
487_E 26_D 0.80 0.15 0.00
481_Q 566_N 0.80 0.15 0.00
151_R 203_I 0.80 0.15 0.00
87_I 391_Q 0.80 0.15 0.00
190_D 223_T 0.80 0.15 0.00
172_F 23_L 0.80 0.15 0.00
106_L 422_T 0.80 0.15 0.00
232_R 647_P 0.80 0.15 0.00
131_K 633_K 0.80 0.15 0.00
493_Y 155_E 0.79 0.15 0.00
292_A 390_I 0.79 0.15 0.00
105_V 3_H 0.79 0.15 0.00
216_E 175_L 0.79 0.15 0.00
517_A 100_C 0.79 0.15 0.00
529_I 148_V 0.79 0.15 0.00
523_V 407_S 0.79 0.15 0.00
117_V 64_I 0.79 0.15 0.00
163_A 63_V 0.79 0.15 0.00
132_K 103_L 0.79 0.15 0.00
475_A 406_I 0.79 0.15 0.00
561_V 349_D 0.79 0.15 0.00
401_L 151_R 0.79 0.15 0.00
528_L 37_A 0.78 0.15 0.00
185_F 89_S 0.78 0.15 0.00
169_L 341_L 0.78 0.15 0.00
25_A 100_C 0.78 0.15 0.00
188_E 217_V 0.78 0.15 0.00
186_D 22_T 0.78 0.14 0.00
196_D 83_L 0.78 0.14 0.00
93_S 616_T 0.78 0.14 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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