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OPENSEQ.org
DI4200001
Genes: A B A+B
Length: 30 138 166
Sequences: 399 9681 126
Seq/Len: 13.3 70.15 0.76
MirrorTree (Pazo et al. 2001) 0.10
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 0.00 0.01
2 0.01 0.00 0.01
5 0.01 0.01 0.01
10 0.01 0.01 0.02
20 0.01 0.01 0.04
100 0.01 0.02 0.13
∞ 0.07 0.08 0.75
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
29_D 56_Y 1.93 0.91 0.41
21_D 32_S 1.39 0.61 0.11
5_K 53_V 1.37 0.59 0.10
11_F 53_V 1.29 0.52 0.08
22_A 62_D 1.23 0.47 0.06
9_E 135_T 1.09 0.35 0.04
21_D 18_V 1.00 0.28 0.03
12_F 48_G 0.96 0.26 0.02
7_E 134_T 0.95 0.25 0.02
17_S 36_Q 0.90 0.22 0.02
21_D 68_E 0.89 0.21 0.02
4_Q 113_I 0.87 0.20 0.01
29_D 92_D 0.87 0.20 0.01
21_D 2_D 0.86 0.20 0.01
17_S 8_L 0.86 0.20 0.01
23_A 3_R 0.84 0.19 0.01
30_D 99_G 0.84 0.18 0.01
27_I 86_V 0.83 0.18 0.01
3_Q 87_A 0.83 0.18 0.01
2_R 21_S 0.82 0.17 0.01
14_D 132_V 0.81 0.17 0.01
6_S 92_D 0.81 0.17 0.01
18_E 113_I 0.81 0.17 0.01
17_S 29_E 0.81 0.17 0.01
15_Y 68_E 0.79 0.16 0.01
9_E 62_D 0.79 0.16 0.01
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
7788 0.76 DI4200001 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 4) msa: Jackhmmer (r132) 0.41 Done - Shared
7778 0.01 DI4200001 Δgene:(1, ∞) A:(1E-06, 4) B:(1E-06, 4) msa: Jackhmmer (r132) Killed - Shared
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