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DNAN_DPO3B_BACSU-DINB2_DPO42_BACSU HHBlits

Genes: A B A+B
Length: 378 412 756
Sequences: 2691 6819 1437
Seq/Len: 7.12 16.55 1.9
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 1.82
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 210_L 0.92 0.42 0.00
340_K 49_C 0.83 0.33 0.00
179_T 362_L 0.82 0.32 0.00
35_I 258_L 0.81 0.31 0.00
82_F 387_A 0.79 0.29 0.00
266_V 134_I 0.77 0.27 0.00
341_V 347_V 0.77 0.27 0.00
349_V 33_I 0.76 0.26 0.00
208_L 294_V 0.76 0.26 0.00
267_N 115_G 0.75 0.26 0.00
80_R 342_V 0.74 0.25 0.00
31_T 256_M 0.74 0.25 0.00
302_I 146_I 0.73 0.24 0.00
347_I 97_Y 0.73 0.24 0.00
44_F 32_V 0.73 0.24 0.00
44_F 175_N 0.73 0.24 0.00
123_Y 353_S 0.73 0.24 0.00
292_L 350_S 0.72 0.23 0.00
263_E 325_V 0.72 0.23 0.00
123_Y 75_V 0.72 0.23 0.00
203_I 229_L 0.72 0.23 0.00
267_N 233_A 0.72 0.23 0.00
294_A 335_T 0.71 0.23 0.00
99_Q 77_R 0.71 0.22 0.00
84_E 228_V 0.71 0.22 0.00
347_I 133_R 0.71 0.22 0.00
258_Q 298_C 0.70 0.22 0.00
274_A 284_S 0.70 0.22 0.00
342_L 185_V 0.70 0.22 0.00
185_A 68_E 0.69 0.21 0.00
294_A 16_Y 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
7085 1.9 DNAN_DPO3B_BACSU-DINB2_DPO42_BACSU HHBlits Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
7081 3.82 DNAN_DPO3B_BACSU-DINB2_DPO42_BACSU Jackhammer Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
6933 0.03 DNAN_DPO3B_BACSU-DINB2_DPO42_BACSU HHBlits Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
6893 0.1 DNAN_DPO3B_BACSU-DINB2_DPO42_BACSU Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared

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