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OPENSEQ.org
Hsp70_lid-GRLBD (B, 40-235)
Genes: A B A+B
Length: 219 196 410
Sequences: 4806 1585 102
Seq/Len: 21.95 8.09 0.25
MirrorTree (Pazo et al. 2001) 0.04
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 0.02 0.09 0.00
2 0.03 0.10 0.01
5 0.05 0.11 0.02
10 0.06 0.12 0.03
20 0.06 0.13 0.04
100 0.08 0.15 0.13
∞ 0.14 0.17 0.25
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
145_V 163_L 1.53 0.39 0.00
172_D 164_L 1.12 0.18 0.00
196_I 38_L 1.12 0.18 0.00
94_G 29_L 1.08 0.17 0.00
137_A 21_K 1.05 0.16 0.00
87_T 112_L 1.03 0.15 0.00
142_D 112_L 0.99 0.14 0.00
171_A 29_L 0.98 0.14 0.00
196_I 160_L 0.96 0.13 0.00
194_A 74_Q 0.95 0.12 0.00
144_L 122_L 0.94 0.12 0.00
42_E 47_A 0.92 0.12 0.00
137_A 160_L 0.90 0.11 0.00
42_E 99_Q 0.90 0.11 0.00
84_I 183_L 0.90 0.11 0.00
215_Q 170_V 0.90 0.11 0.00
95_I 113_L 0.88 0.11 0.00
23_L 126_E 0.88 0.11 0.00
171_A 97_R 0.88 0.11 0.00
23_L 48_F 0.88 0.11 0.00
90_I 88_M 0.85 0.10 0.00
148_R 131_I 0.84 0.10 0.00
165_A 160_L 0.84 0.10 0.00
198_A 124_S 0.83 0.10 0.00
175_T 126_E 0.83 0.10 0.00
59_R 9_G 0.83 0.10 0.00
189_K 108_M 0.83 0.10 0.00
194_A 34_Q 0.82 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)
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