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DNAN_DPO3B_BACSU-DINB1_DPO41_BACSU HHBlits
Genes: A B A+B
Length: 378 414 757
Sequences: 2691 6745 1426
Seq/Len: 7.12 16.29 1.88
MirrorTree (Pazo et al. 2001) 0.13
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.02 0.00
2 0.01 0.02 0.00
5 0.01 0.02 0.01
10 0.01 0.03 0.01
20 0.01 0.03 0.03
100 0.01 0.04 0.19
∞ 0.02 0.14 1.80
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
10_L 207_L 0.94 0.44 0.00
35_I 255_L 0.90 0.39 0.00
179_T 357_L 0.88 0.37 0.00
349_V 349_E 0.84 0.34 0.00
274_A 280_L 0.81 0.31 0.00
340_K 50_S 0.80 0.30 0.00
271_F 233_I 0.76 0.26 0.00
349_V 34_A 0.76 0.26 0.00
302_I 146_I 0.76 0.26 0.00
123_Y 346_V 0.75 0.26 0.00
267_N 116_D 0.75 0.25 0.00
347_I 98_Y 0.75 0.25 0.00
271_F 134_L 0.74 0.25 0.00
267_N 230_A 0.73 0.24 0.00
185_A 69_R 0.73 0.23 0.00
292_L 343_T 0.72 0.23 0.00
163_T 345_L 0.72 0.23 0.00
208_L 290_L 0.72 0.23 0.00
51_I 338_L 0.72 0.23 0.00
84_E 225_R 0.72 0.23 0.00
82_F 384_L 0.71 0.23 0.00
294_A 328_K 0.70 0.22 0.00
258_Q 294_I 0.70 0.22 0.00
96_I 211_D 0.70 0.21 0.00
342_L 182_V 0.70 0.21 0.00
351_F 192_T 0.70 0.21 0.00
266_V 134_L 0.69 0.21 0.00
99_Q 78_P 0.69 0.21 0.00
203_I 226_L 0.69 0.21 0.00
123_Y 76_V 0.69 0.21 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
7086 1.88 DNAN_DPO3B_BACSU-DINB1_DPO41_BACSU HHBlits Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
7082 3.81 DNAN_DPO3B_BACSU-DINB1_DPO41_BACSU Jackhammer Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
6934 0.03 DNAN_DPO3B_BACSU-DINB1_DPO41_BACSU HHBlits Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
6894 0.1 DNAN_DPO3B_BACSU-DINB1_DPO41_BACSU Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
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