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m2_gnaq

Genes: A B A+B
Length: 466 359 777
Sequences: 455 2174 78
Seq/Len: 0.98 6.06 0.1
MirrorTree (Pazo et al. 2001) 0.14
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 0.06 0.09 0.00
2 0.06 0.10 0.00
5 0.07 0.11 0.00
10 0.07 0.11 0.00
20 0.08 0.12 0.01
100 0.08 0.14 0.02
0.11 0.17 0.09
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
96_C 155_D 1.01 0.09 0.00
432_N 206_V 1.00 0.09 0.00
153_I 252_K 1.00 0.09 0.00
96_C 82_N 0.97 0.08 0.00
307_T 26_E 0.96 0.08 0.00
75_F 90_M 0.96 0.08 0.00
439_C 206_V 0.94 0.08 0.00
65_L 58_Q 0.93 0.08 0.00
349_S 97_L 0.92 0.07 0.00
24_V 160_Y 0.90 0.07 0.00
70_L 79_V 0.89 0.07 0.00
65_L 46_G 0.88 0.07 0.00
65_L 51_G 0.88 0.07 0.00
65_L 54_T 0.88 0.07 0.00
196_Y 87_M 0.87 0.07 0.00
183_N 145_Y 0.87 0.07 0.00
309_S 294_E 0.86 0.07 0.00
159_I 173_L 0.84 0.06 0.00
125_V 328_F 0.84 0.06 0.00
77_M 101_Y 0.84 0.06 0.00
150_L 167_V 0.84 0.06 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
7098 0.1 m2_gnaq Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
6126 ACM2_GNAQ_HUMAN Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) Running - Shared
6044 0 ACM2_GNAQ_HUMAN Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared

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