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OPENSEQ.org
EmrB-TolC interface
Genes: A B A+B
Length: 512 493 902
Sequences: 20463 12959 1254
Seq/Len: 39.97 26.29 1.39
MirrorTree (Pazo et al. 2001) 0.45
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 0.02 0.00 0.25
2 0.02 0.00 0.86
5 0.04 0.02 1.00
10 0.06 0.04 1.10
20 0.08 0.06 1.25
100 0.15 0.14 2.01
∞ 0.24 0.20 3.00
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
91_I 132_A 1.13 0.55 0.00
432_L 32_A 1.07 0.49 0.00
486_G 261_Q 0.98 0.41 0.00
483_M 27_Q 0.97 0.39 0.00
95_A 48_A 0.95 0.37 0.00
246_C 401_L 0.94 0.36 0.00
318_V 56_A 0.92 0.34 0.00
242_V 152_K 0.92 0.34 0.00
59_G 259_I 0.91 0.34 0.00
21_L 138_V 0.91 0.33 0.00
30_S 209_G 0.90 0.33 0.00
21_L 311_S 0.90 0.32 0.00
275_L 117_D 0.89 0.32 0.00
263_S 64_L 0.88 0.31 0.00
153_C 190_E 0.87 0.30 0.00
95_A 159_L 0.87 0.30 0.00
153_C 214_E 0.87 0.30 0.00
88_A 58_S 0.86 0.29 0.00
101_S 245_L 0.86 0.29 0.00
486_G 393_D 0.86 0.29 0.00
275_L 245_L 0.85 0.29 0.00
160_Y 55_E 0.85 0.29 0.00
290_L 65_G 0.84 0.28 0.00
175_V 34_L 0.84 0.28 0.00
370_I 127_L 0.84 0.27 0.00
32_I 47_D 0.83 0.27 0.00
128_L 208_T 0.83 0.27 0.00
144_S 121_Q 0.82 0.26 0.00
102_L 53_I 0.82 0.26 0.00
334_R 49_A 0.81 0.26 0.00
460_A 314_I 0.81 0.25 0.00
472_G 152_K 0.81 0.25 0.00
286_G 400_T 0.81 0.25 0.00
73_A 64_L 0.81 0.25 0.00
286_G 118_V 0.81 0.25 0.00
114_I 407_E 0.79 0.24 0.00
483_M 166_F 0.79 0.24 0.00
433_T 352_S 0.79 0.24 0.00
374_A 373_A 0.79 0.23 0.00
239_V 156_Y 0.78 0.23 0.00
257_N 36_N 0.77 0.22 0.00
481_F 91_L 0.76 0.22 0.00
179_V 153_E 0.76 0.21 0.00
88_A 258_Q 0.76 0.21 0.00
377_C 30_Q 0.75 0.21 0.00
342_I 27_Q 0.75 0.21 0.00
275_L 160_D 0.75 0.21 0.00
416_I 127_L 0.75 0.21 0.00
377_C 39_L 0.75 0.21 0.00
180_A 89_A 0.74 0.20 0.00
405_T 51_E 0.74 0.20 0.00
306_A 55_E 0.74 0.20 0.00
377_C 208_T 0.74 0.20 0.00
373_F 149_Q 0.74 0.20 0.00
87_I 272_L 0.74 0.20 0.00
327_F 69_D 0.73 0.20 0.00
395_L 379_A 0.73 0.20 0.00
54_V 397_A 0.73 0.20 0.00
490_V 107_T 0.73 0.20 0.00
46_S 166_F 0.73 0.20 0.00
283_L 270_L 0.73 0.20 0.00
293_Q 203_Q 0.73 0.20 0.00
323_I 265_G 0.73 0.20 0.00
319_I 89_A 0.73 0.19 0.00
163_D 66_L 0.73 0.19 0.00
189_L 265_G 0.73 0.19 0.00
398_A 159_L 0.73 0.19 0.00
416_I 349_V 0.72 0.19 0.00
187_Q 127_L 0.72 0.19 0.00
259_I 149_Q 0.72 0.19 0.00
377_C 153_E 0.72 0.19 0.00
386_T 175_D 0.72 0.19 0.00
134_A 39_L 0.71 0.19 0.00
279_L 397_A 0.71 0.19 0.00
87_I 261_Q 0.71 0.18 0.00
432_L 109_Q 0.71 0.18 0.00
247_F 327_A 0.71 0.18 0.00
358_G 401_L 0.71 0.18 0.00
441_P 420_L 0.71 0.18 0.00
386_T 399_T 0.71 0.18 0.00
79_V 427_G 0.71 0.18 0.00
86_T 383_G 0.71 0.18 0.00
27_V 314_I 0.71 0.18 0.00
173_I 116_Q 0.70 0.18 0.00
170_I 305_K 0.70 0.18 0.00
472_G 348_T 0.70 0.18 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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