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OPENSEQ.org
HbpS SenS (A, 50-188) (B, 150-398)
Genes: A B A+B
Length: 139 249 377
Sequences: 1039 50547 273
Seq/Len: 7.47 203 0.72
MirrorTree (Pazo et al. 2001) 0.36
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 0.03 0.09
2 0.00 0.06 0.26
5 0.01 0.09 0.34
10 0.01 0.12 0.47
20 0.01 0.15 0.70
100 0.01 0.27 1.68
∞ 0.09 0.31 2.28
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
115_I 221_L 1.49 0.67 0.00
36_S 244_I 1.25 0.47 0.00
100_A 73_T 1.21 0.44 0.00
77_T 156_A 1.17 0.40 0.00
115_I 137_E 1.15 0.39 0.00
131_R 195_D 1.03 0.30 0.00
115_I 229_T 0.99 0.27 0.00
90_L 155_I 0.97 0.25 0.00
15_E 215_P 0.97 0.25 0.00
15_E 139_S 0.96 0.25 0.00
131_R 215_P 0.96 0.25 0.00
134_A 214_L 0.96 0.25 0.00
26_E 242_A 0.95 0.24 0.00
109_G 129_R 0.95 0.24 0.00
63_A 60_Q 0.94 0.23 0.00
34_H 172_A 0.92 0.22 0.00
38_A 216_A 0.92 0.22 0.00
39_V 107_D 0.91 0.22 0.00
39_V 179_L 0.91 0.22 0.00
95_G 55_Q 0.90 0.21 0.00
118_A 66_A 0.90 0.21 0.00
115_I 124_R 0.89 0.21 0.00
137_L 28_E 0.88 0.20 0.00
111_P 228_L 0.88 0.20 0.00
77_T 45_L 0.88 0.20 0.00
20_A 155_I 0.86 0.19 0.00
77_T 187_V 0.86 0.19 0.00
112_V 178_C 0.86 0.19 0.00
12_L 171_T 0.85 0.18 0.00
117_V 214_L 0.85 0.18 0.00
78_S 121_V 0.84 0.18 0.00
73_W 60_Q 0.84 0.18 0.00
79_E 166_H 0.83 0.18 0.00
109_G 155_I 0.83 0.17 0.00
108_K 98_R 0.83 0.17 0.00
105_V 179_L 0.82 0.17 0.00
133_G 171_T 0.82 0.17 0.00
77_T 139_S 0.81 0.17 0.00
105_V 67_A 0.81 0.16 0.00
10_T 214_L 0.81 0.16 0.00
103_T 179_L 0.80 0.16 0.00
47_L 224_L 0.80 0.16 0.00
129_Y 160_L 0.79 0.16 0.00
134_A 55_Q 0.79 0.16 0.00
62_S 219_A 0.79 0.15 0.00
69_T 226_G 0.78 0.15 0.00
103_T 59_S 0.78 0.15 0.00
127_E 149_E 0.78 0.15 0.00
52_G 92_S 0.78 0.15 0.00
110_A 185_L 0.78 0.15 0.00
76_P 132_V 0.78 0.15 0.00
111_P 156_A 0.77 0.15 0.00
80_L 49_I 0.77 0.15 0.00
40_V 126_T 0.77 0.15 0.00
30_K 87_A 0.77 0.15 0.00
44_G 245_P 0.77 0.15 0.00
32_G 113_G 0.76 0.14 0.00
36_S 80_D 0.76 0.14 0.00
29_E 86_A 0.76 0.14 0.00
34_H 164_R 0.76 0.14 0.00
77_T 68_D 0.76 0.14 0.00
113_A 34_R 0.75 0.14 0.00
57_P 174_L 0.75 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
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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