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OPENSEQ.org
L4-L22
Genes: A B A+B
Length: 201 110 306
Sequences: 2818 2079 1867
Seq/Len: 14.02 18.9 6.1
MirrorTree (Pazo et al. 2001) 0.72
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 0.00 0.00 0.00
2 0.00 0.00 0.05
5 0.00 0.00 5.92
10 0.00 0.00 5.95
20 0.00 0.00 6.00
100 0.00 0.00 6.02
∞ 0.00 0.00 6.14
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
61_R 92_R 0.91 0.75 0.01
97_N 63_G 0.82 0.64 0.01
41_Q 27_K 0.66 0.40 0.00
160_A 96_I 0.64 0.38 0.00
72_S 93_A 0.64 0.37 0.00
188_M 21_A 0.64 0.37 0.00
127_E 24_I 0.63 0.36 0.00
88_R 44_A 0.61 0.33 0.00
61_R 90_K 0.60 0.32 0.00
154_D 73_K 0.60 0.32 0.00
35_Y 88_R 0.60 0.32 0.00
103_G 107_V 0.60 0.31 0.00
196_V 23_L 0.59 0.30 0.00
193_V 23_L 0.58 0.29 0.00
150_T 92_R 0.58 0.29 0.00
149_I 99_R 0.58 0.29 0.00
47_K 38_Y 0.57 0.29 0.00
79_R 42_K 0.56 0.27 0.00
14_V 109_D 0.56 0.27 0.00
175_I 37_T 0.56 0.27 0.00
167_V 24_I 0.56 0.27 0.00
200_L 21_A 0.55 0.26 0.00
97_N 82_M 0.55 0.26 0.00
132_K 83_K 0.54 0.24 0.00
101_Y 90_K 0.53 0.23 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
1898 6.06 L4-L22 Δgene:(1, 20) A:(1E-06, 4) B:(1E-06, 2) msa: Jackhmmer (2015_03) 0.01 Done - Shared
1878 6.1 L4-L22 Δgene:(1, 20) A:(1E-06, 4) B:(1E-06, 4) msa: Jackhmmer (2015_03) 0.01 Done - Shared
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