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OPENSEQ.org
bub1_mad1
Genes: A B A+B
Length: 20 238 254
Sequences: 87 2226 52
Seq/Len: 4.35 9.35 0.2
MirrorTree (Pazo et al. 2001) 0.28
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 0.03 0.03 0.00
2 0.03 0.04 0.00
5 0.03 0.04 0.00
10 0.03 0.04 0.00
20 0.03 0.04 0.00
100 0.03 0.05 0.02
∞ 0.03 0.07 0.20
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
6_K 127_Q 1.56 0.35 0.00
4_N 120_E 1.48 0.31 0.00
11_D 95_L 1.42 0.28 0.00
15_M 118_S 1.39 0.27 0.00
7_E 22_R 1.37 0.26 0.00
15_M 151_K 1.36 0.25 0.00
20_L 155_T 1.33 0.24 0.00
11_D 94_L 1.26 0.21 0.00
6_K 149_F 1.23 0.20 0.00
6_K 52_Q 1.17 0.18 0.00
9_M 22_R 1.16 0.17 0.00
15_M 152_A 1.14 0.17 0.00
3_I 227_L 1.12 0.16 0.00
20_L 145_K 1.10 0.15 0.00
6_K 105_P 1.09 0.15 0.00
3_I 131_A 1.08 0.15 0.00
10_D 152_A 1.08 0.14 0.00
6_K 170_R 1.05 0.14 0.00
6_K 42_L 1.02 0.13 0.00
15_M 182_C 1.02 0.13 0.00
7_E 204_H 1.00 0.12 0.00
6_K 181_D 1.00 0.12 0.00
3_I 117_S 0.99 0.12 0.00
4_N 117_S 0.99 0.12 0.00
7_E 211_E 0.99 0.12 0.00
17_Q 83_Q 0.97 0.12 0.00
15_M 159_Y 0.96 0.12 0.00
15_M 146_I 0.96 0.11 0.00
14_S 55_Y 0.96 0.11 0.00
10_D 122_A 0.94 0.11 0.00
15_M 169_Y 0.93 0.11 0.00
11_D 41_M 0.93 0.11 0.00
9_M 211_E 0.92 0.10 0.00
14_S 98_M 0.92 0.10 0.00
3_I 120_E 0.91 0.10 0.00
11_D 10_S 0.90 0.10 0.00
9_M 204_H 0.88 0.10 0.00
13_N 110_A 0.87 0.09 0.00
9_M 134_K 0.87 0.09 0.00
6_K 53_G 0.87 0.09 0.00
7_E 90_R 0.87 0.09 0.00
7_E 134_K 0.86 0.09 0.00
11_D 150_R 0.86 0.09 0.00
6_K 176_A 0.86 0.09 0.00
20_L 173_S 0.85 0.09 0.00
14_S 59_R 0.85 0.09 0.00
12_I 21_L 0.84 0.09 0.00
7_E 127_Q 0.84 0.09 0.00
9_M 120_E 0.83 0.09 0.00
7_E 76_R 0.83 0.09 0.00
15_M 70_T 0.83 0.09 0.00
18_K 209_L 0.83 0.09 0.00
11_D 102_G 0.83 0.09 0.00
14_S 236_T 0.83 0.09 0.00
20_L 121_V 0.82 0.08 0.00
17_Q 101_G 0.82 0.08 0.00
10_D 215_R 0.82 0.08 0.00
6_K 153_C 0.82 0.08 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
5224 0.09 bub1_mad1 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-10, 4) msa: Jackhmmer (2016_06) Killed - Shared
5208 0.09 bub1_mad1 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-10, 2) msa: Jackhmmer (2015_06) Killed - Shared
4680 0.09 mad1_CDI Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 4) msa: Jackhmmer (2015_06) Killed - Shared
4679 0.2 bub1_mad1 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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