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OPENSEQ.org
HbpS SenS (A, 50-188) (B, 150-398)
Genes: A B A+B
Length: 139 249 363
Sequences: 1017 6212 472
Seq/Len: 7.32 24.95 1.3
MirrorTree (Pazo et al. 2001) 0.15
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.07
2 0.00 0.01 0.07
5 0.01 0.01 0.08
10 0.01 0.02 0.10
20 0.01 0.03 0.14
100 0.01 0.08 0.38
∞ 0.09 0.16 1.22
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
115_I 156_A 0.95 0.36 0.00
28_A 187_V 0.93 0.34 0.00
112_V 187_V 0.87 0.28 0.00
63_A 88_I 0.85 0.27 0.00
70_A 227_T 0.83 0.26 0.00
115_I 221_L 0.81 0.24 0.00
54_G 212_H 0.79 0.23 0.00
36_S 172_A 0.78 0.22 0.00
26_E 174_L 0.77 0.21 0.00
39_V 156_A 0.76 0.21 0.00
121_P 240_L 0.75 0.20 0.00
63_A 240_L 0.74 0.20 0.00
39_V 126_T 0.74 0.19 0.00
113_A 158_G 0.73 0.19 0.00
127_E 163_V 0.73 0.19 0.00
112_V 139_S 0.73 0.19 0.00
37_V 190_D 0.72 0.18 0.00
44_G 160_L 0.70 0.17 0.00
70_A 232_S 0.69 0.17 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
0159 1.3 HbpS SenS (A, 50-188) (B, 150-398) Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.00 Done - Shared
0158 0.72 HbpS SenS (A, 50-188) (B, 150-398) Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2013_03) 0.00 Done - Shared
0156 0.15 HbpS SenS (A, 50-188) (B, 150-398) Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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