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OPENSEQ.org
DHAK_DHAL
Genes: A B A+B
Length: 356 210 540
Sequences: 1269 1447 712
Seq/Len: 3.56 6.89 1.32
MirrorTree (Pazo et al. 2001) 0.69
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 0.01 1.21
2 0.10 0.06 1.23
5 0.16 0.07 1.26
10 0.16 0.08 1.26
20 0.16 0.08 1.26
100 0.17 0.08 1.26
∞ 0.19 0.11 1.28
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
122_D 89_I 1.45 0.81 0.05
119_L 89_I 1.32 0.71 0.04
79_T 72_L 1.26 0.66 0.03
79_T 79_A 1.18 0.58 0.02
114_E 120_R 1.14 0.55 0.02
83_P 38_H 1.09 0.49 0.02
118_E 120_R 1.08 0.49 0.02
203_S 31_R 1.05 0.46 0.02
57_E 78_G 1.03 0.44 0.01
151_A 36_A 1.03 0.43 0.01
57_E 38_H 1.00 0.41 0.01
57_E 77_G 1.00 0.41 0.01
296_V 199_F 1.00 0.40 0.01
79_T 33_I 0.99 0.40 0.01
10_D 139_E 0.98 0.39 0.01
114_E 122_K 0.98 0.39 0.01
122_D 93_Q 0.98 0.39 0.01
107_T 181_Y 0.98 0.38 0.01
60_H 181_Y 0.97 0.38 0.01
201_K 28_G 0.97 0.38 0.01
76_E 72_L 0.95 0.36 0.01
124_G 96_Q 0.94 0.35 0.01
79_T 44_R 0.93 0.34 0.01
291_S 82_P 0.92 0.33 0.01
83_P 196_S 0.92 0.33 0.01
76_E 44_R 0.91 0.32 0.01
291_S 38_H 0.90 0.32 0.01
72_A 80_S 0.90 0.32 0.01
104_K 181_Y 0.89 0.31 0.01
57_E 82_P 0.87 0.29 0.01
157_E 41_N 0.86 0.28 0.01
48_L 57_A 0.85 0.28 0.01
84_D 74_S 0.85 0.27 0.01
104_K 80_S 0.84 0.27 0.01
113_F 121_G 0.82 0.25 0.01
57_E 196_S 0.82 0.25 0.01
82_T 82_P 0.82 0.25 0.01
126_K 164_S 0.82 0.25 0.01
104_K 176_K 0.82 0.25 0.01
153_T 181_Y 0.82 0.25 0.01
60_H 80_S 0.82 0.25 0.01
155_L 12_L 0.81 0.25 0.01
351_A 78_G 0.81 0.24 0.01
124_G 93_Q 0.81 0.24 0.01
118_E 127_D 0.81 0.24 0.01
104_K 41_N 0.81 0.24 0.01
70_S 162_A 0.80 0.24 0.01
323_L 180_S 0.80 0.23 0.01
114_E 79_A 0.80 0.23 0.01
146_G 180_S 0.80 0.23 0.01
57_E 80_S 0.79 0.23 0.01
211_M 42_M 0.79 0.23 0.01
335_V 101_L 0.78 0.22 0.01
80_S 180_S 0.78 0.22 0.01
47_A 52_K 0.78 0.22 0.01
153_T 80_S 0.78 0.22 0.01
79_T 41_N 0.77 0.21 0.01
50_S 77_G 0.77 0.21 0.01
153_T 41_N 0.76 0.21 0.01
188_G 185_R 0.76 0.21 0.01
326_T 201_M 0.76 0.21 0.01
111_L 60_D 0.76 0.21 0.01
154_V 125_P 0.76 0.21 0.01
88_E 124_E 0.76 0.20 0.01
217_I 80_S 0.76 0.20 0.01
153_T 78_G 0.75 0.20 0.01
297_Y 172_M 0.75 0.20 0.01
107_T 38_H 0.75 0.20 0.01
118_E 90_R 0.74 0.20 0.01
138_V 74_S 0.74 0.20 0.01
60_H 41_N 0.74 0.20 0.01
165_E 21_T 0.74 0.19 0.01
196_V 179_A 0.73 0.19 0.01
330_I 48_K 0.73 0.19 0.01
146_G 181_Y 0.73 0.19 0.01
155_L 203_M 0.73 0.19 0.01
235_V 19_F 0.73 0.19 0.01
80_S 41_N 0.72 0.19 0.01
79_T 196_S 0.72 0.18 0.01
60_H 176_K 0.72 0.18 0.01
71_G 19_F 0.72 0.18 0.01
138_V 181_Y 0.71 0.18 0.01
69_L 181_Y 0.71 0.17 0.01
97_E 117_V 0.71 0.17 0.01
49_L 198_M 0.71 0.17 0.01
306_Q 104_E 0.70 0.17 0.01
77_I 160_S 0.70 0.17 0.01
137_A 192_P 0.70 0.17 0.01
85_K 83_L 0.70 0.17 0.01
115_T 116_G 0.70 0.17 0.00
199_A 40_L 0.70 0.17 0.00
57_E 84_F 0.70 0.17 0.00
79_T 176_K 0.70 0.17 0.00
123_S 100_S 0.69 0.17 0.00
152_N 36_A 0.69 0.17 0.00
171_D 156_E 0.69 0.17 0.00
132_I 80_S 0.69 0.17 0.00
157_E 78_G 0.69 0.16 0.00
243_L 106_L 0.69 0.16 0.00
83_P 130_M 0.68 0.16 0.00
71_G 62_G 0.68 0.16 0.00
68_M 199_F 0.68 0.16 0.00
50_S 179_A 0.68 0.16 0.00
130_V 173_Q 0.68 0.16 0.00
310_T 110_F 0.68 0.16 0.00
49_L 98_R 0.67 0.16 0.00
110_I 83_L 0.67 0.15 0.00
50_S 80_S 0.67 0.15 0.00
228_F 131_C 0.67 0.15 0.00
71_G 77_G 0.67 0.15 0.00
245_N 134_W 0.67 0.15 0.00
79_T 38_H 0.67 0.15 0.00
341_A 150_S 0.67 0.15 0.00
114_E 33_I 0.67 0.15 0.00
12_L 155_L 0.67 0.15 0.00
154_V 181_Y 0.66 0.15 0.00
12_L 69_G 0.66 0.15 0.00
313_R 172_M 0.66 0.15 0.00
103_I 181_Y 0.66 0.15 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)
ID Seq/Len Name Options I_Prob Status
0186 1.01 DHAK_DHAL Δgene:(0, 0) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.93 Done - Shared
0179 2.34 DHAK_DHAL Δgene:(0, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.10 Done - Shared
0178 1.32 DHAK_DHAL Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.05 Done - Shared
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