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OPENSEQ.org
IQGAP1 GRD Cdc42
Genes: A B A+B
Length: 384 191 545
Sequences: 1107 12030 737
Seq/Len: 2.88 62.98 1.35
MirrorTree (Pazo et al. 2001) 0.09
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 0.02
2 0.06 0.09 0.03
5 0.07 0.11 0.06
10 0.07 0.12 0.12
20 0.07 0.15 0.25
100 0.08 0.23 0.78
∞ 0.11 0.28 1.28
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
325_D 82_F 1.11 0.52 0.00
111_L 19_L 0.95 0.37 0.00
267_I 89_S 0.85 0.28 0.00
171_D 51_Y 0.81 0.25 0.00
108_R 150_K 0.80 0.24 0.00
304_F 137_I 0.79 0.23 0.00
258_T 23_Y 0.77 0.22 0.00
41_M 79_L 0.76 0.21 0.00
119_M 106_P 0.74 0.20 0.00
275_A 111_L 0.74 0.20 0.00
65_F 138_T 0.74 0.20 0.00
300_K 42_V 0.73 0.20 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
7045 1.35 IQGAP1 GRD Cdc42 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
7033 0.27 IQGAP1 GRD Cdc42 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
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