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OPENSEQ.org
DRD1_GNAI3
Genes: A B A+B
Length: 446 354 754
Sequences: 1253 1497 132
Seq/Len: 2.81 4.23 0.18
MirrorTree (Pazo et al. 2001) 0.16
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 0.07 0.08 0.01
2 0.08 0.09 0.01
5 0.08 0.09 0.01
10 0.09 0.10 0.02
20 0.10 0.10 0.04
100 0.13 0.13 0.09
∞ 0.15 0.15 0.17
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
125_I 343_I 1.27 0.20 0.00
96_C 219_T 1.18 0.17 0.00
35_L 343_I 1.09 0.14 0.00
337_F 353_L 0.98 0.11 0.00
67_A 59_D 0.96 0.11 0.00
330_I 162_I 0.96 0.11 0.00
145_S 160_D 0.94 0.10 0.00
125_I 54_K 0.93 0.10 0.00
327_N 221_I 0.93 0.10 0.00
62_F 17_K 0.90 0.09 0.00
334_N 93_I 0.89 0.09 0.00
261_K 283_L 0.89 0.09 0.00
125_I 162_I 0.88 0.09 0.00
33_L 32_K 0.88 0.09 0.00
118_S 86_R 0.87 0.09 0.00
27_A 97_E 0.83 0.08 0.00
39_L 264_I 0.82 0.08 0.00
214_Y 147_Q 0.82 0.08 0.00
159_V 146_Y 0.82 0.08 0.00
153_L 264_I 0.82 0.08 0.00
75_V 351_C 0.82 0.08 0.00
128_P 23_L 0.81 0.08 0.00
62_F 65_E 0.81 0.08 0.00
54_L 290_Y 0.80 0.08 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
6274 0.12 DRD1_GNAI3 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
6273 0.18 DRD1_GNAI3 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-80, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
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