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OPENSEQ.org
Ch_BPTI_lowerEvalue
Genes: A B A+B
Length: 58 228 283
Sequences: 3158 15189 56
Seq/Len: 54.45 66.62 0.2
MirrorTree (Pazo et al. 2001) 0.04
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 0.18 0.17 0.02
2 0.20 0.18 0.02
5 0.22 0.19 0.04
10 0.23 0.20 0.10
20 0.23 0.21 0.20
100 0.24 0.23 0.48
∞ 0.26 0.26 0.63
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
23_Y 162_A 1.64 0.40 0.00
51_C 174_C 1.36 0.25 0.00
36_G 109_P 1.22 0.20 0.00
23_Y 31_L 1.17 0.17 0.00
34_V 51_V 1.16 0.17 0.00
48_A 211_Y 1.15 0.17 0.00
47_S 143_L 1.14 0.16 0.00
23_Y 185_K 1.10 0.15 0.00
47_S 52_V 1.09 0.15 0.00
51_C 125_G 1.07 0.14 0.00
40_A 14_W 1.07 0.14 0.00
23_Y 95_T 1.05 0.14 0.00
39_R 106_V 1.04 0.13 0.00
44_N 183_V 1.02 0.13 0.00
21_Y 91_L 1.01 0.13 0.00
21_Y 72_K 1.01 0.13 0.00
26_K 63_E 1.01 0.12 0.00
51_C 87_D 0.99 0.12 0.00
44_N 225_L 0.98 0.12 0.00
39_R 121_C 0.98 0.12 0.00
48_A 86_N 0.98 0.12 0.00
45_F 125_G 0.97 0.12 0.00
21_Y 195_I 0.97 0.12 0.00
55_C 174_C 0.96 0.11 0.00
20_R 96_A 0.96 0.11 0.00
30_C 27_C 0.94 0.11 0.00
43_N 27_C 0.94 0.11 0.00
54_T 114_D 0.94 0.11 0.00
30_C 151_C 0.93 0.11 0.00
43_N 151_C 0.93 0.11 0.00
35_Y 32_I 0.93 0.11 0.00
51_C 127_G 0.92 0.10 0.00
37_G 181_P 0.91 0.10 0.00
28_G 223_Q 0.91 0.10 0.00
55_C 54_G 0.91 0.10 0.00
30_C 179_G 0.90 0.10 0.00
43_N 179_G 0.90 0.10 0.00
19_I 89_T 0.90 0.10 0.00
30_C 194_G 0.89 0.10 0.00
43_N 194_G 0.89 0.10 0.00
22_F 103_V 0.89 0.10 0.00
30_C 43_C 0.89 0.10 0.00
43_N 43_C 0.89 0.10 0.00
21_Y 217_L 0.88 0.10 0.00
7_E 30_S 0.88 0.09 0.00
21_Y 182_L 0.87 0.09 0.00
29_L 74_F 0.87 0.09 0.00
36_G 209_G 0.87 0.09 0.00
45_F 145_L 0.87 0.09 0.00
51_C 126_W 0.87 0.09 0.00
35_Y 126_W 0.87 0.09 0.00
30_C 174_C 0.87 0.09 0.00
43_N 174_C 0.87 0.09 0.00
50_D 98_S 0.87 0.09 0.00
44_N 96_A 0.86 0.09 0.00
51_C 177_D 0.86 0.09 0.00
31_Q 182_L 0.86 0.09 0.00
44_N 25_H 0.85 0.09 0.00
11_T 141_A 0.85 0.09 0.00
51_C 176_G 0.85 0.09 0.00
24_N 78_K 0.84 0.09 0.00
44_N 167_G 0.84 0.09 0.00
23_Y 150_N 0.84 0.09 0.00
37_G 109_P 0.84 0.09 0.00
8_P 208_P 0.83 0.09 0.00
10_Y 183_V 0.83 0.09 0.00
48_A 36_W 0.83 0.09 0.00
24_N 119_T 0.83 0.09 0.00
35_Y 39_T 0.83 0.09 0.00
29_L 33_N 0.82 0.08 0.00
41_K 79_Y 0.82 0.08 0.00
28_G 141_A 0.82 0.08 0.00
28_G 11_S 0.82 0.08 0.00
44_N 115_F 0.82 0.08 0.00
9_P 63_E 0.82 0.08 0.00
10_Y 40_A 0.81 0.08 0.00
24_N 132_A 0.81 0.08 0.00
30_C 54_G 0.81 0.08 0.00
43_N 54_G 0.81 0.08 0.00
14_C 87_D 0.80 0.08 0.00
38_C 87_D 0.80 0.08 0.00
34_V 16_V 0.80 0.08 0.00
22_F 93_L 0.80 0.08 0.00
28_G 57_D 0.80 0.08 0.00
35_Y 41_A 0.80 0.08 0.00
27_A 53_A 0.80 0.08 0.00
20_R 183_V 0.80 0.08 0.00
39_R 173_S 0.79 0.08 0.00
8_P 121_C 0.79 0.08 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
8252 0.2 Ch_BPTI_lowerEvalue Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8250 0.06 Ch_BPTI Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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