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OPENSEQ.org
IQGAP1 GRD Cdc42
Genes: A B A+B
Length: 384 191 542
Sequences: 1107 12030 146
Seq/Len: 2.88 62.98 0.27
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 0.06 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 1.27
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
294_L 13_A 1.41 0.34 0.00
348_L 137_I 1.34 0.29 0.00
115_V 142_A 1.28 0.26 0.00
296_Q 36_V 1.18 0.21 0.00
65_F 142_A 1.13 0.20 0.00
196_P 118_D 1.11 0.19 0.00
294_L 165_L 1.08 0.18 0.00
118_I 90_F 1.07 0.17 0.00
123_S 144_K 1.06 0.17 0.00
192_V 113_V 1.06 0.17 0.00
274_A 28_F 1.06 0.17 0.00
196_P 15_G 1.05 0.17 0.00
335_Y 89_S 1.05 0.17 0.00
239_I 97_W 1.04 0.16 0.00
52_A 112_L 1.04 0.16 0.00
367_L 79_L 1.02 0.15 0.00
308_A 17_T 1.02 0.15 0.00
280_F 114_G 1.01 0.15 0.00
226_I 146_A 0.97 0.14 0.00
81_Q 161_T 0.96 0.14 0.00
248_I 141_T 0.96 0.13 0.00
196_P 116_Q 0.96 0.13 0.00
119_M 55_L 0.95 0.13 0.00
60_L 86_S 0.95 0.13 0.00
363_I 26_N 0.94 0.13 0.00
264_L 169_F 0.92 0.12 0.00
238_A 22_S 0.92 0.12 0.00
83_I 143_E 0.91 0.12 0.00
186_S 84_V 0.91 0.12 0.00
117_E 93_V 0.90 0.12 0.00
267_I 106_P 0.90 0.12 0.00
311_V 82_F 0.90 0.12 0.00
367_L 140_E 0.88 0.11 0.00
130_P 118_D 0.87 0.11 0.00
275_A 137_I 0.87 0.11 0.00
111_L 6_C 0.86 0.11 0.00
196_P 158_S 0.86 0.11 0.00
305_F 75_T 0.85 0.10 0.00
238_A 101_I 0.85 0.10 0.00
274_A 155_V 0.85 0.10 0.00
302_R 17_T 0.85 0.10 0.00
173_S 36_V 0.83 0.10 0.00
221_E 23_Y 0.83 0.10 0.00
49_Y 112_L 0.83 0.10 0.00
219_E 164_G 0.81 0.10 0.00
65_F 4_I 0.81 0.10 0.00
344_T 114_G 0.81 0.10 0.00
48_L 48_G 0.81 0.10 0.00
69_L 144_K 0.80 0.09 0.00
118_I 143_E 0.80 0.09 0.00
212_E 18_C 0.80 0.09 0.00
304_F 140_E 0.80 0.09 0.00
351_H 6_C 0.80 0.09 0.00
63_R 112_L 0.80 0.09 0.00
257_T 38_D 0.79 0.09 0.00
355_I 106_P 0.79 0.09 0.00
109_Q 46_I 0.79 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
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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