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OPENSEQ.org
ARRB1-Rho2
Genes: A B A+B
Length: 418 348 714
Sequences: 528 15908 168
Seq/Len: 1.26 45.71 0.24
MirrorTree (Pazo et al. 2001) 0.31
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 0.03 0.20 0.01
2 0.03 0.22 0.02
5 0.03 0.24 0.03
10 0.03 0.26 0.04
20 0.03 0.28 0.05
100 0.03 0.32 0.12
∞ 0.05 0.33 0.22
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
57_L 115_F 1.30 0.25 0.00
43_V 109_G 1.23 0.22 0.00
124_P 79_L 1.20 0.21 0.00
231_I 49_V 1.15 0.19 0.00
126_S 214_I 1.11 0.17 0.00
126_S 56_F 1.02 0.14 0.00
220_V 138_V 0.98 0.13 0.00
224_T 87_V 0.98 0.13 0.00
272_Y 158_A 0.93 0.12 0.00
37_V 54_I 0.93 0.12 0.00
378_E 158_A 0.92 0.12 0.00
43_V 166_A 0.91 0.11 0.00
341_S 304_V 0.90 0.11 0.00
80_F 149_G 0.90 0.11 0.00
220_V 277_T 0.90 0.11 0.00
222_N 135_R 0.89 0.11 0.00
120_P 249_E 0.89 0.11 0.00
235_V 277_T 0.88 0.10 0.00
113_Y 123_I 0.87 0.10 0.00
312_R 186_S 0.86 0.10 0.00
344_A 151_N 0.86 0.10 0.00
105_I 317_M 0.86 0.10 0.00
214_I 56_F 0.86 0.10 0.00
197_L 154_I 0.85 0.10 0.00
220_V 91_F 0.85 0.10 0.00
124_P 139_V 0.84 0.10 0.00
344_A 192_Y 0.83 0.09 0.00
214_I 166_A 0.83 0.09 0.00
102_E 112_L 0.83 0.09 0.00
163_S 205_I 0.82 0.09 0.00
359_E 304_V 0.81 0.09 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
5684 0.25 ARRB1-Rho4 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-10, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5678 0.02 ARRB1-Rho3 Δgene:(1, 10) A:(1E-02, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
5677 0.24 ARRB1-Rho2 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5675 0.13 ARRB1-Rho Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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