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OPENSEQ.org
4A-4Gmin
Genes: A B A+B
Length: 406 350 735
Sequences: 13334 513 109
Seq/Len: 32.84 1.47 0.15
MirrorTree (Pazo et al. 2001) 0.29
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 0.05 0.10 0.00
2 0.07 0.11 0.00
5 0.09 0.18 0.01
10 0.10 0.18 0.02
20 0.11 0.19 0.04
100 0.15 0.19 0.14
∞ 0.22 0.20 0.35
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
105_V 136_T 1.39 0.22 0.00
357_I 309_I 1.31 0.19 0.00
325_V 292_L 1.28 0.18 0.00
375_M 283_R 1.24 0.17 0.00
292_M 70_R 1.11 0.13 0.00
345_I 295_S 1.09 0.13 0.00
155_I 108_I 1.07 0.12 0.00
259_K 131_A 1.07 0.12 0.00
156_V 279_S 1.07 0.12 0.00
383_T 291_D 1.05 0.12 0.00
180_V 230_L 1.05 0.12 0.00
83_T 122_Y 1.01 0.11 0.00
80_T 282_I 1.00 0.11 0.00
104_L 206_I 1.00 0.10 0.00
126_Y 262_M 0.99 0.10 0.00
76_A 144_V 0.98 0.10 0.00
105_V 121_A 0.98 0.10 0.00
318_F 112_A 0.97 0.10 0.00
161_R 218_L 0.97 0.10 0.00
125_D 292_L 0.97 0.10 0.00
90_I 86_L 0.97 0.10 0.00
345_I 109_F 0.96 0.10 0.00
397_E 73_S 0.95 0.10 0.00
123_L 190_E 0.95 0.10 0.00
105_V 317_E 0.93 0.09 0.00
156_V 14_G 0.93 0.09 0.00
83_T 79_T 0.92 0.09 0.00
76_A 231_L 0.92 0.09 0.00
70_Y 97_T 0.91 0.09 0.00
288_L 199_R 0.91 0.09 0.00
72_V 101_L 0.90 0.09 0.00
336_I 82_M 0.90 0.09 0.00
214_A 293_R 0.90 0.09 0.00
358_H 293_R 0.90 0.09 0.00
63_I 213_F 0.89 0.09 0.00
199_I 207_K 0.89 0.08 0.00
83_T 111_K 0.88 0.08 0.00
118_K 199_R 0.88 0.08 0.00
73_I 218_L 0.87 0.08 0.00
270_L 269_M 0.87 0.08 0.00
156_V 109_F 0.87 0.08 0.00
230_D 249_I 0.87 0.08 0.00
86_F 118_F 0.87 0.08 0.00
154_I 122_Y 0.86 0.08 0.00
318_F 212_L 0.86 0.08 0.00
83_T 210_G 0.86 0.08 0.00
361_G 150_L 0.86 0.08 0.00
375_M 141_T 0.86 0.08 0.00
106_L 52_K 0.86 0.08 0.00
80_T 291_D 0.85 0.08 0.00
67_I 226_C 0.85 0.08 0.00
39_L 20_R 0.85 0.08 0.00
156_V 313_H 0.85 0.08 0.00
154_I 110_E 0.85 0.08 0.00
361_G 281_R 0.85 0.08 0.00
59_Q 250_G 0.85 0.08 0.00
79_G 250_G 0.85 0.08 0.00
81_G 250_G 0.85 0.08 0.00
82_K 250_G 0.85 0.08 0.00
182_D 250_G 0.85 0.08 0.00
183_E 250_G 0.85 0.08 0.00
185_D 250_G 0.85 0.08 0.00
215_T 250_G 0.85 0.08 0.00
334_R 250_G 0.85 0.08 0.00
335_G 250_G 0.85 0.08 0.00
362_R 250_G 0.85 0.08 0.00
365_R 250_G 0.85 0.08 0.00
370_G 250_G 0.85 0.08 0.00
137_G 158_F 0.84 0.08 0.00
108_P 283_R 0.84 0.08 0.00
45_R 239_L 0.84 0.08 0.00
350_P 212_L 0.83 0.07 0.00
64_L 290_L 0.83 0.07 0.00
109_T 201_R 0.83 0.07 0.00
277_I 29_T 0.83 0.07 0.00
104_L 67_L 0.83 0.07 0.00
148_Q 222_I 0.83 0.07 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
4215 0.15 4A-4Gmin Δgene:(1, 100) A:(1E-80, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4064 0.36 4A-4Gmin Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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