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OPENSEQ.org
GNAS2-Rho
Genes: A B A+B
Length: 394 348 666
Sequences: 1271 17504 157
Seq/Len: 3.23 50.3 0.24
MirrorTree (Pazo et al. 2001) 0.14
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 0.06 0.13 0.01
2 0.06 0.15 0.01
5 0.07 0.18 0.03
10 0.07 0.20 0.04
20 0.07 0.23 0.06
100 0.10 0.27 0.15
∞ 0.13 0.28 0.21
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
376_F 267_P 1.27 0.24 0.00
145_E 134_E 1.11 0.17 0.00
62_I 55_N 1.08 0.16 0.00
193_S 123_I 1.04 0.15 0.00
18_A 260_A 0.96 0.13 0.00
31_Q 248_K 0.91 0.11 0.00
23_N 155_M 0.89 0.11 0.00
340_F 219_I 0.89 0.11 0.00
142_F 242_T 0.88 0.11 0.00
185_I 300_I 0.88 0.10 0.00
183_D 220_F 0.86 0.10 0.00
372_I 309_M 0.84 0.10 0.00
155_E 139_V 0.84 0.10 0.00
296_L 164_A 0.84 0.10 0.00
183_D 221_F 0.84 0.10 0.00
372_I 317_M 0.83 0.09 0.00
197_L 163_M 0.82 0.09 0.00
156_D 55_N 0.82 0.09 0.00
270_L 245_K 0.81 0.09 0.00
178_F 143_M 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
5687 0.66 GNAS2-Rho2 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5680 0.24 GNAS2-Rho Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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