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OPENSEQ.org
1A4R_A CDC42 GTPase GDP 1RGP_ CDC42 GAP
Genes: A B A+B
Length: 191 242 411
Sequences: 7707 2691 367
Seq/Len: 40.35 11.12 0.89
MirrorTree (Pazo et al. 2001) 0.18
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 0.11 0.07 0.06
2 0.12 0.08 0.15
5 0.14 0.08 0.33
10 0.16 0.09 0.55
20 0.17 0.10 0.85
100 0.22 0.12 2.18
∞ 0.26 0.16 3.20
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
90_F 192_N 1.27 0.55 0.00
91_E 124_F 1.22 0.51 0.00
84_V 204_L 1.11 0.41 0.00
165_L 204_L 0.93 0.27 0.00
145_L 133_L 0.90 0.24 0.00
140_E 65_V 0.84 0.20 0.00
47_G 230_Q 0.83 0.20 0.00
153_K 73_L 0.82 0.19 0.00
84_V 136_D 0.82 0.19 0.00
46_I 181_I 0.81 0.19 0.00
165_L 195_L 0.81 0.19 0.00
55_L 185_S 0.79 0.18 0.00
92_N 133_L 0.78 0.17 0.00
8_V 203_L 0.76 0.16 0.00
19_L 138_Y 0.76 0.16 0.00
48_G 70_V 0.75 0.16 0.00
112_L 170_V 0.75 0.16 0.00
94_K 132_L 0.75 0.16 0.00
140_E 223_T 0.75 0.16 0.00
116_Q 122_K 0.74 0.15 0.00
119_L 198_V 0.74 0.15 0.00
64_Y 109_D 0.74 0.15 0.00
75_T 103_G 0.73 0.15 0.00
84_V 83_I 0.72 0.15 0.00
80_V 55_K 0.72 0.15 0.00
55_L 75_A 0.72 0.14 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
9111 0.81 1GRN Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
4113 0.89 1A4R_A CDC42 GTPase GDP 1RGP_ CDC42 GAP Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4076 1.51 1A4R_A CDC42 GTPase GDP 1RGP_ CDC42 GAP Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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