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OPENSEQ.org
MinDE
Genes: A B A+B
Length: 270 88 353
Sequences: 13894 374 313
Seq/Len: 51.46 4.25 0.89
MirrorTree (Pazo et al. 2001) 0.73
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 0.03 0.00 0.87
2 0.04 0.00 0.87
5 0.05 0.00 0.87
10 0.07 0.00 0.87
20 0.08 0.00 0.87
100 0.12 0.00 0.89
∞ 0.17 0.00 0.91
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
246_L 73_S 1.80 0.89 0.28
4_I 14_T 1.79 0.89 0.27
219_R 73_S 1.64 0.82 0.19
236_G 26_V 1.59 0.79 0.17
58_Y 25_I 1.57 0.78 0.16
141_I 51_C 1.50 0.73 0.13
37_I 24_I 1.48 0.72 0.12
7_V 11_K 1.38 0.65 0.09
79_R 26_V 1.38 0.64 0.09
19_S 73_S 1.31 0.59 0.07
142_T 43_R 1.26 0.54 0.06
242_T 29_R 1.22 0.51 0.06
41_I 25_I 1.21 0.50 0.05
192_D 27_A 1.21 0.50 0.05
253_F 72_I 1.20 0.48 0.05
267_L 79_V 1.19 0.48 0.05
247_L 53_Y 1.18 0.47 0.05
161_A 38_Y 1.18 0.47 0.05
76_K 39_L 1.17 0.46 0.05
138_E 79_V 1.15 0.44 0.04
87_P 78_N 1.12 0.42 0.04
219_R 66_E 1.11 0.41 0.04
133_L 42_L 1.11 0.40 0.04
131_M 10_R 1.10 0.40 0.04
52_C 40_P 1.09 0.39 0.04
103_A 79_V 1.08 0.38 0.03
244_E 47_L 1.08 0.38 0.03
34_T 43_R 1.07 0.37 0.03
236_G 51_C 1.06 0.36 0.03
52_C 38_Y 1.06 0.36 0.03
261_K 26_V 1.05 0.36 0.03
253_F 7_F 1.05 0.36 0.03
235_A 78_N 1.04 0.35 0.03
141_I 61_V 1.04 0.35 0.03
184_N 67_Q 1.04 0.34 0.03
3_R 67_Q 1.01 0.33 0.03
60_F 51_C 0.98 0.30 0.02
199_V 10_R 0.98 0.30 0.02
106_L 38_Y 0.98 0.30 0.02
157_L 41_Q 0.98 0.30 0.02
106_L 34_A 0.97 0.29 0.02
184_N 26_V 0.97 0.29 0.02
208_V 6_F 0.97 0.29 0.02
237_K 26_V 0.96 0.29 0.02
61_V 62_T 0.96 0.28 0.02
195_S 73_S 0.95 0.28 0.02
236_G 20_E 0.95 0.28 0.02
164_S 67_Q 0.95 0.28 0.02
131_M 60_M 0.94 0.27 0.02
98_T 34_A 0.94 0.27 0.02
140_I 78_N 0.94 0.27 0.02
3_R 59_E 0.94 0.27 0.02
246_L 29_R 0.94 0.27 0.02
261_K 52_K 0.94 0.27 0.02
130_L 25_I 0.93 0.27 0.02
205_I 25_I 0.93 0.26 0.02
61_V 43_R 0.93 0.26 0.02
81_E 34_A 0.92 0.26 0.02
202_I 20_E 0.91 0.25 0.02
211_I 8_L 0.91 0.25 0.02
19_S 71_D 0.90 0.25 0.02
33_K 36_P 0.90 0.24 0.02
210_V 64_Q 0.90 0.24 0.02
229_L 4_L 0.89 0.24 0.02
208_V 26_V 0.88 0.23 0.01
230_D 3_L 0.88 0.23 0.01
117_I 54_V 0.88 0.23 0.01
242_T 73_S 0.88 0.23 0.01
246_L 72_I 0.88 0.23 0.01
264_L 3_L 0.87 0.23 0.01
134_Y 38_Y 0.87 0.23 0.01
235_A 26_V 0.87 0.23 0.01
35_V 56_I 0.87 0.22 0.01
223_Q 73_S 0.86 0.22 0.01
211_I 45_D 0.86 0.22 0.01
267_L 34_A 0.86 0.22 0.01
79_R 8_L 0.86 0.21 0.01
60_F 19_K 0.85 0.21 0.01
205_I 47_L 0.85 0.21 0.01
159_I 9_S 0.85 0.21 0.01
118_V 32_S 0.85 0.21 0.01
35_V 73_S 0.84 0.21 0.01
157_L 38_Y 0.84 0.20 0.01
35_V 31_R 0.84 0.20 0.01
161_A 79_V 0.84 0.20 0.01
165_R 53_Y 0.83 0.20 0.01
135_F 52_K 0.83 0.20 0.01
79_R 57_D 0.83 0.20 0.01
100_E 24_I 0.83 0.20 0.01
223_Q 6_F 0.83 0.20 0.01
169_N 63_V 0.83 0.20 0.01
192_D 48_E 0.82 0.20 0.01
116_F 2_A 0.82 0.20 0.01
204_R 28_E 0.82 0.20 0.01
98_T 13_N 0.82 0.20 0.01
215_Q 63_V 0.82 0.20 0.01
19_S 72_I 0.82 0.19 0.01
180_L 14_T 0.82 0.19 0.01
214_D 28_E 0.82 0.19 0.01
104_K 79_V 0.81 0.19 0.01
143_T 23_Q 0.81 0.19 0.01
233_A 52_K 0.81 0.19 0.01
61_V 32_S 0.81 0.19 0.01
196_M 10_R 0.81 0.19 0.01
24_A 52_K 0.81 0.19 0.01
242_T 37_H 0.81 0.19 0.01
81_E 50_I 0.81 0.19 0.01
67_D 5_D 0.81 0.19 0.01
118_V 66_E 0.81 0.19 0.01
25_T 80_T 0.81 0.19 0.01
147_V 82_P 0.81 0.19 0.01
162_S 20_E 0.80 0.18 0.01
208_V 44_K 0.80 0.18 0.01
112_M 28_E 0.80 0.18 0.01
143_T 56_I 0.80 0.18 0.01
159_I 80_T 0.80 0.18 0.01
133_L 28_E 0.79 0.18 0.01
199_V 78_N 0.79 0.18 0.01
215_Q 17_I 0.79 0.18 0.01
234_D 6_F 0.79 0.18 0.01
25_T 79_V 0.79 0.18 0.01
263_F 27_A 0.79 0.18 0.01
106_L 36_P 0.79 0.17 0.01
192_D 43_R 0.78 0.17 0.01
106_L 56_I 0.78 0.17 0.01
61_V 6_F 0.78 0.17 0.01
147_V 46_I 0.78 0.17 0.01
117_I 55_Q 0.78 0.17 0.01
4_I 26_V 0.78 0.17 0.01
49_I 36_P 0.78 0.17 0.01
159_I 50_I 0.78 0.17 0.01
118_V 33_D 0.78 0.17 0.01
207_L 78_N 0.78 0.17 0.01
188_V 40_P 0.78 0.17 0.01
1_M 7_F 0.78 0.17 0.01
178_L 7_F 0.77 0.17 0.01
157_L 36_P 0.77 0.17 0.01
183_Y 45_D 0.77 0.17 0.01
7_V 79_V 0.77 0.17 0.01
114_F 56_I 0.77 0.17 0.01
82_N 63_V 0.77 0.17 0.01
118_V 5_D 0.77 0.17 0.01
49_I 79_V 0.76 0.16 0.01
166_R 4_L 0.76 0.16 0.01
61_V 26_V 0.76 0.16 0.01
201_E 11_K 0.75 0.16 0.01
216_S 50_I 0.75 0.16 0.01
204_R 58_P 0.75 0.16 0.01
115_E 4_L 0.75 0.16 0.01
32_K 43_R 0.74 0.15 0.01
61_V 33_D 0.74 0.15 0.01
178_L 65_L 0.74 0.15 0.01
164_S 41_Q 0.74 0.15 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)
ID Seq/Len Name Options I_Prob Status
14313 MinD_MinE Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Running - Shared
2962 0.89 MinDE Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.28 Done
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