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OPENSEQ.org
DH
Genes: A B A+B
Length: 492 290 755
Sequences: 2537 13821 752
Seq/Len: 5.16 47.66 1
MirrorTree (Pazo et al. 2001) 0.71
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 0.61 0.03 0.57
2 0.62 0.04 0.73
5 0.63 0.05 0.91
10 0.65 0.07 0.93
20 0.65 0.08 0.96
100 0.75 0.12 1.03
∞ 0.76 0.18 1.10
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 1.38 0.68 0.00
223_V 74_E 1.17 0.49 0.00
244_E 195_E 1.14 0.46 0.00
307_E 51_H 1.10 0.43 0.00
238_S 119_D 1.09 0.42 0.00
249_C 48_L 1.09 0.42 0.00
312_I 206_T 1.03 0.37 0.00
165_S 250_D 1.02 0.36 0.00
261_E 6_C 1.02 0.35 0.00
317_D 202_N 1.01 0.35 0.00
395_G 202_N 1.00 0.34 0.00
260_S 239_D 0.99 0.34 0.00
353_L 159_M 0.98 0.32 0.00
291_G 75_D 0.97 0.32 0.00
119_Q 140_I 0.95 0.30 0.00
122_D 117_E 0.95 0.30 0.00
201_A 8_I 0.94 0.29 0.00
324_C 152_C 0.93 0.28 0.00
148_I 172_Y 0.92 0.28 0.00
71_V 61_M 0.92 0.28 0.00
138_V 60_E 0.92 0.28 0.00
263_E 71_L 0.91 0.27 0.00
270_L 60_E 0.91 0.27 0.00
439_R 84_V 0.90 0.26 0.00
24_A 270_M 0.90 0.26 0.00
146_K 33_K 0.90 0.26 0.00
473_K 166_S 0.90 0.26 0.00
133_K 239_D 0.89 0.25 0.00
388_D 248_V 0.88 0.24 0.00
267_K 84_V 0.88 0.24 0.00
159_I 104_I 0.86 0.24 0.00
475_L 269_L 0.86 0.24 0.00
179_V 119_D 0.86 0.24 0.00
25_R 175_S 0.86 0.23 0.00
395_G 241_Y 0.85 0.23 0.00
305_T 57_T 0.84 0.22 0.00
324_C 26_A 0.84 0.22 0.00
322_K 57_T 0.84 0.22 0.00
202_V 57_T 0.84 0.22 0.00
475_L 6_C 0.83 0.22 0.00
14_Q 6_C 0.83 0.22 0.00
181_V 172_Y 0.83 0.22 0.00
198_A 158_A 0.83 0.21 0.00
436_I 202_N 0.83 0.21 0.00
254_S 119_D 0.83 0.21 0.00
420_L 112_E 0.82 0.21 0.00
377_T 238_A 0.82 0.21 0.00
178_I 34_V 0.82 0.21 0.00
132_A 166_S 0.82 0.21 0.00
307_E 64_E 0.82 0.21 0.00
178_I 6_C 0.81 0.20 0.00
415_R 250_D 0.81 0.20 0.00
25_R 270_M 0.81 0.20 0.00
244_E 198_I 0.80 0.20 0.00
39_V 74_E 0.80 0.20 0.00
257_G 34_V 0.80 0.20 0.00
372_M 84_V 0.79 0.19 0.00
160_G 148_I 0.79 0.19 0.00
105_G 23_L 0.79 0.19 0.00
414_K 146_Q 0.79 0.19 0.00
437_P 23_L 0.79 0.19 0.00
107_N 261_T 0.78 0.19 0.00
14_Q 83_G 0.78 0.19 0.00
22_E 267_E 0.78 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)
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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