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OPENSEQ.org
DHAK_DHAL
Genes: A B A+B
Length: 356 210 542
Sequences: 1269 1447 1269
Seq/Len: 3.56 6.89 2.34
MirrorTree (Pazo et al. 2001) 0.74
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 2.17
2 0.10 0.06 2.19
5 0.16 0.07 2.22
10 0.16 0.08 2.22
20 0.16 0.08 2.22
100 0.17 0.08 2.23
∞ 0.19 0.11 2.24
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
107_T 181_Y 1.27 0.82 0.10
119_L 89_I 1.14 0.72 0.07
122_D 93_Q 1.11 0.69 0.06
84_D 74_S 1.09 0.67 0.06
114_E 120_R 1.09 0.67 0.06
122_D 89_I 1.04 0.61 0.05
118_E 120_R 1.02 0.60 0.05
76_E 72_L 0.95 0.52 0.04
146_G 181_Y 0.95 0.51 0.04
153_T 80_S 0.95 0.51 0.04
151_A 36_A 0.93 0.49 0.03
186_S 183_G 0.91 0.46 0.03
57_E 78_G 0.89 0.44 0.03
114_E 122_K 0.88 0.43 0.03
104_K 80_S 0.87 0.42 0.03
83_P 38_H 0.83 0.37 0.02
131_V 83_L 0.82 0.36 0.02
186_S 205_A 0.81 0.36 0.02
79_T 44_R 0.81 0.35 0.02
211_M 42_M 0.81 0.35 0.02
69_L 181_Y 0.81 0.35 0.02
48_L 42_M 0.81 0.35 0.02
178_R 55_A 0.80 0.35 0.02
57_E 77_G 0.79 0.33 0.02
146_G 180_S 0.78 0.32 0.02
126_K 164_S 0.78 0.32 0.02
132_I 80_S 0.78 0.32 0.02
60_H 80_S 0.78 0.32 0.02
60_H 181_Y 0.77 0.32 0.02
119_L 70_M 0.77 0.31 0.02
79_T 72_L 0.77 0.31 0.02
110_I 122_K 0.77 0.31 0.02
114_E 79_A 0.75 0.29 0.02
186_S 68_T 0.75 0.29 0.02
351_A 78_G 0.74 0.29 0.02
83_P 196_S 0.74 0.29 0.02
25_S 117_V 0.74 0.29 0.02
193_A 31_R 0.74 0.28 0.02
66_Q 95_T 0.74 0.28 0.02
79_T 41_N 0.73 0.28 0.02
203_S 31_R 0.73 0.28 0.02
323_L 110_F 0.73 0.27 0.02
72_A 80_S 0.72 0.26 0.01
107_T 38_H 0.71 0.26 0.01
235_V 19_F 0.71 0.26 0.01
11_V 76_V 0.71 0.26 0.01
225_R 61_I 0.71 0.26 0.01
104_K 181_Y 0.70 0.25 0.01
118_E 90_R 0.70 0.24 0.01
12_L 204_L 0.69 0.24 0.01
296_V 199_F 0.69 0.24 0.01
124_G 96_Q 0.69 0.24 0.01
152_N 36_A 0.69 0.24 0.01
291_S 82_P 0.68 0.23 0.01
330_I 52_K 0.68 0.23 0.01
210_E 93_Q 0.68 0.23 0.01
217_I 80_S 0.67 0.22 0.01
150_V 46_F 0.67 0.22 0.01
153_T 181_Y 0.67 0.22 0.01
137_A 192_P 0.66 0.22 0.01
119_L 74_S 0.66 0.21 0.01
103_I 181_Y 0.66 0.21 0.01
110_I 83_L 0.66 0.21 0.01
77_I 102_T 0.65 0.21 0.01
57_E 82_P 0.65 0.21 0.01
293_L 201_M 0.65 0.20 0.01
79_T 176_K 0.65 0.20 0.01
63_Y 92_A 0.65 0.20 0.01
171_D 156_E 0.65 0.20 0.01
110_I 44_R 0.64 0.20 0.01
18_G 77_G 0.64 0.20 0.01
199_A 40_L 0.64 0.20 0.01
143_Y 79_A 0.64 0.20 0.01
211_M 92_A 0.64 0.20 0.01
171_D 14_R 0.64 0.20 0.01
244_V 152_P 0.64 0.20 0.01
74_P 44_R 0.64 0.20 0.01
60_H 41_N 0.63 0.19 0.01
207_A 3_L 0.63 0.19 0.01
107_T 196_S 0.63 0.19 0.01
306_Q 140_S 0.62 0.19 0.01
301_T 12_L 0.62 0.19 0.01
331_T 145_S 0.62 0.18 0.01
154_V 92_A 0.62 0.18 0.01
157_E 80_S 0.61 0.18 0.01
118_E 127_D 0.61 0.18 0.01
110_I 196_S 0.61 0.18 0.01
153_T 78_G 0.61 0.18 0.01
114_E 33_I 0.61 0.18 0.01
142_L 79_A 0.61 0.18 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
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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