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OPENSEQ.org
DH
Genes: A B A+B
Length: 492 290 758
Sequences: 2516 610 716
Seq/Len: 5.11 2.1 0.94
MirrorTree (Pazo et al. 2001) 0.82
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 0.62 0.02 0.57
2 0.63 0.02 0.72
5 0.64 0.03 0.89
10 0.64 0.04 0.91
20 0.65 0.07 0.92
100 0.74 0.11 0.93
∞ 0.76 0.18 0.94
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
160_G 104_I 1.78 0.89 0.29
260_S 239_D 1.32 0.61 0.09
307_E 51_H 1.28 0.57 0.07
249_C 48_L 1.24 0.54 0.07
267_K 84_V 1.21 0.51 0.06
244_E 195_E 1.21 0.51 0.06
198_A 158_A 1.17 0.47 0.05
334_E 28_A 1.16 0.47 0.05
223_V 74_E 1.14 0.45 0.05
312_I 206_T 1.12 0.43 0.04
295_M 64_E 1.10 0.41 0.04
301_G 163_N 1.08 0.39 0.04
291_G 75_D 1.07 0.39 0.04
317_D 202_N 1.07 0.39 0.04
324_C 152_C 1.05 0.36 0.03
247_L 183_L 1.03 0.35 0.03
330_K 202_N 1.03 0.35 0.03
353_L 159_M 1.02 0.34 0.03
165_S 250_D 1.02 0.34 0.03
332_K 81_Y 1.01 0.33 0.03
198_A 183_L 1.00 0.33 0.03
122_D 117_E 1.00 0.33 0.03
202_V 57_T 0.98 0.31 0.03
126_G 164_N 0.97 0.31 0.03
261_E 243_A 0.97 0.30 0.02
322_K 258_N 0.97 0.30 0.02
126_G 102_G 0.96 0.30 0.02
133_K 64_E 0.96 0.30 0.02
13_I 262_M 0.96 0.29 0.02
126_G 153_S 0.96 0.29 0.02
119_Q 140_I 0.95 0.29 0.02
194_G 149_Y 0.95 0.29 0.02
270_L 60_E 0.95 0.29 0.02
175_S 158_A 0.94 0.28 0.02
317_D 84_V 0.94 0.28 0.02
414_K 146_Q 0.94 0.28 0.02
37_P 189_N 0.94 0.28 0.02
386_D 213_P 0.94 0.28 0.02
257_G 34_V 0.94 0.28 0.02
379_Y 248_V 0.94 0.28 0.02
225_I 169_I 0.93 0.27 0.02
286_M 48_L 0.93 0.27 0.02
473_K 166_S 0.93 0.27 0.02
463_M 166_S 0.93 0.27 0.02
160_G 148_I 0.92 0.27 0.02
377_T 238_A 0.92 0.27 0.02
148_I 75_D 0.92 0.26 0.02
175_S 236_K 0.92 0.26 0.02
198_A 137_A 0.91 0.26 0.02
439_R 84_V 0.91 0.26 0.02
289_K 202_N 0.91 0.26 0.02
146_K 33_K 0.91 0.26 0.02
471_C 117_E 0.90 0.26 0.02
405_T 196_L 0.90 0.25 0.02
342_Y 76_V 0.90 0.25 0.02
272_L 217_V 0.89 0.25 0.02
160_G 164_N 0.89 0.24 0.02
265_T 226_M 0.89 0.24 0.02
242_L 70_D 0.89 0.24 0.02
160_G 145_A 0.89 0.24 0.02
212_E 84_V 0.89 0.24 0.02
177_T 179_R 0.88 0.24 0.02
105_G 258_N 0.88 0.23 0.02
39_V 74_E 0.87 0.23 0.02
160_G 102_G 0.87 0.23 0.02
150_V 252_K 0.87 0.23 0.02
87_G 107_I 0.87 0.23 0.02
116_S 260_I 0.86 0.23 0.02
145_N 127_V 0.86 0.23 0.02
423_S 270_M 0.86 0.23 0.02
294_W 264_E 0.86 0.23 0.02
241_L 64_E 0.85 0.22 0.01
480_E 34_V 0.85 0.22 0.01
225_I 24_V 0.85 0.22 0.01
376_G 82_G 0.85 0.22 0.01
103_T 34_V 0.85 0.22 0.01
84_G 140_I 0.85 0.22 0.01
211_D 215_D 0.85 0.22 0.01
420_L 112_E 0.85 0.22 0.01
272_L 229_I 0.85 0.22 0.01
324_C 250_D 0.85 0.22 0.01
449_P 178_V 0.85 0.22 0.01
37_P 230_E 0.85 0.22 0.01
219_T 75_D 0.85 0.22 0.01
178_I 34_V 0.84 0.22 0.01
324_C 26_A 0.84 0.21 0.01
262_I 206_T 0.84 0.21 0.01
37_P 34_V 0.84 0.21 0.01
238_S 119_D 0.84 0.21 0.01
14_Q 83_G 0.83 0.21 0.01
306_I 34_V 0.83 0.21 0.01
85_P 80_G 0.83 0.21 0.01
241_L 28_A 0.83 0.21 0.01
362_H 179_R 0.83 0.21 0.01
423_S 248_V 0.83 0.20 0.01
127_G 158_A 0.82 0.20 0.01
261_E 6_C 0.82 0.20 0.01
322_K 57_T 0.82 0.20 0.01
47_I 49_I 0.82 0.20 0.01
129_K 220_R 0.82 0.20 0.01
243_E 246_R 0.82 0.20 0.01
83_H 107_I 0.82 0.20 0.01
252_Q 260_I 0.82 0.20 0.01
122_D 172_Y 0.82 0.20 0.01
337_A 74_E 0.82 0.20 0.01
36_D 250_D 0.82 0.20 0.01
170_K 250_D 0.82 0.20 0.01
110_V 183_L 0.81 0.20 0.01
24_A 270_M 0.81 0.20 0.01
75_I 57_T 0.81 0.20 0.01
94_A 49_I 0.81 0.20 0.01
360_P 158_A 0.81 0.20 0.01
85_P 213_P 0.81 0.20 0.01
254_S 119_D 0.81 0.19 0.01
436_I 202_N 0.80 0.19 0.01
188_G 96_V 0.80 0.19 0.01
227_G 5_Q 0.80 0.19 0.01
337_A 152_C 0.80 0.19 0.01
126_G 101_R 0.80 0.19 0.01
217_A 234_K 0.80 0.19 0.01
264_L 33_K 0.80 0.19 0.01
162_D 127_V 0.80 0.19 0.01
360_P 58_I 0.80 0.19 0.01
289_K 192_R 0.80 0.19 0.01
310_R 114_G 0.80 0.19 0.01
292_I 152_C 0.79 0.19 0.01
107_N 258_N 0.79 0.18 0.01
39_V 263_D 0.79 0.18 0.01
411_E 215_D 0.79 0.18 0.01
238_S 247_K 0.79 0.18 0.01
216_F 117_E 0.79 0.18 0.01
84_G 183_L 0.79 0.18 0.01
160_G 101_R 0.79 0.18 0.01
332_K 212_V 0.79 0.18 0.01
480_E 23_L 0.79 0.18 0.01
317_D 109_F 0.79 0.18 0.01
179_V 212_V 0.79 0.18 0.01
258_S 34_V 0.79 0.18 0.01
159_I 241_Y 0.79 0.18 0.01
248_R 81_Y 0.78 0.18 0.01
341_K 220_R 0.78 0.18 0.01
178_I 118_D 0.78 0.18 0.01
209_K 82_G 0.78 0.18 0.01
217_A 64_E 0.78 0.18 0.01
301_G 158_A 0.78 0.18 0.01
313_A 75_D 0.78 0.18 0.01
25_R 175_S 0.78 0.18 0.01
35_N 152_C 0.78 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)
WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.65 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
3938 0.48 DH Δgene:(1, 20) A:(1E-60, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done
3675 0.94 DH Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.29 Done
3671 1 DH Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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