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OPENSEQ.org
Grasx4
Genes: A B A+B
Length: 307 346 554
Sequences: 683 12508 378
Seq/Len: 2.22 36.15 0.68
MirrorTree (Pazo et al. 2001) 0.32
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.00
2 0.00 0.00 0.03
5 0.00 0.01 0.04
10 0.00 0.03 0.08
20 0.00 0.05 0.09
100 0.00 0.11 0.19
∞ 0.02 0.20 0.58
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
188_F 235_L 1.07 0.32 0.00
91_L 308_L 1.06 0.31 0.00
107_K 218_N 1.05 0.30 0.00
240_G 211_D 1.00 0.27 0.00
127_A 262_I 0.97 0.25 0.00
38_K 173_R 0.97 0.25 0.00
240_G 312_L 0.96 0.24 0.00
124_R 255_D 0.95 0.23 0.00
97_F 258_V 0.95 0.23 0.00
30_T 235_L 0.94 0.23 0.00
118_D 262_I 0.92 0.22 0.00
249_E 105_A 0.88 0.19 0.00
205_K 250_S 0.87 0.19 0.00
247_I 250_S 0.87 0.19 0.00
106_V 215_K 0.87 0.19 0.00
123_E 247_V 0.86 0.19 0.00
11_T 56_I 0.86 0.18 0.00
9_G 237_N 0.86 0.18 0.00
9_G 297_G 0.86 0.18 0.00
240_G 311_Q 0.84 0.17 0.00
127_A 188_L 0.83 0.17 0.00
5_V 138_M 0.83 0.17 0.00
236_T 262_I 0.82 0.17 0.00
177_F 101_R 0.81 0.16 0.00
109_V 60_L 0.81 0.16 0.00
11_T 148_Q 0.81 0.16 0.00
5_V 326_L 0.80 0.16 0.00
136_N 235_L 0.80 0.15 0.00
136_N 165_L 0.79 0.15 0.00
111_Y 101_R 0.79 0.15 0.00
44_E 260_L 0.79 0.15 0.00
153_Y 220_V 0.79 0.15 0.00
14_I 315_T 0.78 0.15 0.00
12_G 237_N 0.78 0.15 0.00
12_G 297_G 0.78 0.15 0.00
4_K 271_K 0.78 0.15 0.00
172_N 58_L 0.78 0.14 0.00
87_R 299_Y 0.77 0.14 0.00
109_V 72_F 0.77 0.14 0.00
60_A 271_K 0.77 0.14 0.00
107_K 169_L 0.76 0.14 0.00
235_Y 248_D 0.76 0.14 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
10137 0.09 grasx10 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10135 0.09 Grasx9 Δgene:(1, ∞) A:(1E-60, 8) B:(1E-06, 4) msa: HHblits (2015_06) 0.01 Done - Shared
10134 0 Grasx8 Δgene:(1, 1) A:(1E-60, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
10133 0 Grasx7 Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 4) msa: HHblits (2015_06) Killed - Shared
10131 1.18 Grasx6 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 2) msa: HHblits (2015_06) 0.00 Done - Shared
10130 1.2 Grasx5 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 4) msa: HHblits (2015_06) 0.00 Done - Shared
10129 0.68 Grasx4 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10128 0.16 Grasx3 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10127 0.09 grasx2 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10126 0.72 grasx1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10124 1.16 Grasx Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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