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OPENSEQ.org
test-cua-sco
Genes: A B A+B
Length: 135 172 282
Sequences: 2002 16219 243
Seq/Len: 14.83 94.3 0.86
MirrorTree (Pazo et al. 2001) 0.40
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 0.01 0.01 0.05
2 0.01 0.01 0.27
5 0.01 0.02 0.40
10 0.01 0.03 0.56
20 0.02 0.04 0.79
100 0.02 0.08 1.88
∞ 0.09 0.17 4.23
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
62_I 113_E 1.34 0.60 0.00
94_V 149_L 1.20 0.48 0.00
47_T 40_L 1.12 0.41 0.00
118_Q 55_L 1.10 0.39 0.00
71_V 73_V 1.03 0.33 0.00
62_I 118_F 1.00 0.31 0.00
109_P 92_R 0.99 0.30 0.00
104_Y 35_D 0.94 0.27 0.00
83_F 55_L 0.93 0.26 0.00
72_F 118_F 0.93 0.26 0.00
75_T 39_L 0.91 0.25 0.00
134_K 50_V 0.90 0.24 0.00
35_A 168_L 0.85 0.21 0.00
55_F 28_V 0.85 0.21 0.00
44_N 58_L 0.85 0.20 0.00
31_W 124_K 0.84 0.20 0.00
132_V 120_V 0.84 0.20 0.00
94_V 142_F 0.82 0.19 0.00
57_Y 25_Q 0.82 0.19 0.00
73_K 40_L 0.82 0.19 0.00
111_E 76_I 0.81 0.19 0.00
133_V 168_L 0.81 0.18 0.00
133_V 117_T 0.80 0.18 0.00
32_A 124_K 0.78 0.17 0.00
101_T 143_V 0.78 0.17 0.00
87_G 48_P 0.78 0.17 0.00
97_G 115_A 0.77 0.17 0.00
101_T 45_T 0.76 0.16 0.00
94_V 23_G 0.76 0.16 0.00
64_V 157_K 0.75 0.16 0.00
70_I 162_D 0.75 0.15 0.00
79_V 50_V 0.74 0.15 0.00
73_K 88_E 0.74 0.15 0.00
76_S 35_D 0.74 0.15 0.00
76_S 147_G 0.73 0.15 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
0771 4.59 test-cua-sco Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.00 Done
0764 0.86 test-cua-sco Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 0.00 Done - Shared
0763 0.21 test-cua-sco Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
0762 0.13 test-cua-sco Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2013_03) Killed - Shared
0761 0.09 test-cua-sco Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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