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OPENSEQ.org
cI_A_6_cIII_isp_10_Pdenitr
Genes: A B A+B
Length: 147 190 305
Sequences: 3938 1539 474
Seq/Len: 26.79 8.1 1.55
MirrorTree (Pazo et al. 2001) 0.62
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 0.00 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.01
10 0.00 0.01 0.02
20 0.01 0.01 0.03
100 0.01 0.01 0.12
∞ 0.02 0.04 1.41
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
16_F 131_V 2.20 0.99 0.97
18_I 42_M 1.45 0.84 0.69
33_G 176_I 1.42 0.83 0.66
36_F 22_A 1.36 0.78 0.60
33_G 67_L 1.33 0.77 0.58
37_L 112_A 1.31 0.75 0.56
94_E 22_A 1.20 0.65 0.44
108_F 32_G 1.20 0.65 0.43
77_I 126_L 1.13 0.58 0.36
18_I 65_T 1.12 0.58 0.36
24_I 23_T 1.11 0.57 0.34
40_R 19_L 1.10 0.56 0.34
33_G 36_W 1.10 0.55 0.33
20_L 58_V 1.02 0.47 0.25
37_L 24_A 1.01 0.46 0.25
90_T 23_T 0.98 0.43 0.22
41_A 174_L 0.98 0.43 0.22
80_V 179_A 0.98 0.43 0.22
108_F 93_D 0.93 0.38 0.18
25_G 47_D 0.91 0.36 0.17
98_V 38_L 0.91 0.36 0.16
23_A 18_F 0.90 0.35 0.16
29_L 24_A 0.90 0.34 0.16
90_T 159_Y 0.89 0.34 0.15
44_R 9_G 0.88 0.33 0.15
117_L 156_G 0.87 0.33 0.14
32_V 101_S 0.87 0.32 0.14
31_L 47_D 0.86 0.32 0.14
34_G 47_D 0.86 0.31 0.14
22_V 165_I 0.86 0.31 0.13
23_A 125_W 0.85 0.31 0.13
56_S 188_K 0.85 0.30 0.13
26_L 48_V 0.85 0.30 0.13
90_T 13_A 0.85 0.30 0.13
16_F 42_M 0.84 0.30 0.12
38_G 65_T 0.84 0.29 0.12
9_V 107_K 0.84 0.29 0.12
119_R 40_N 0.83 0.29 0.12
29_L 31_A 0.83 0.28 0.12
20_L 10_D 0.82 0.28 0.11
33_G 131_V 0.82 0.28 0.11
89_S 172_Q 0.82 0.28 0.11
29_L 60_G 0.82 0.28 0.11
56_S 185_T 0.81 0.27 0.11
103_A 89_G 0.81 0.27 0.11
86_F 71_W 0.81 0.27 0.10
41_A 189_L 0.81 0.27 0.10
29_L 184_D 0.80 0.27 0.10
86_F 78_I 0.80 0.26 0.10
50_F 125_W 0.80 0.26 0.10
72_A 53_S 0.80 0.26 0.10
24_I 90_R 0.80 0.26 0.10
21_I 11_H 0.80 0.26 0.10
24_I 29_V 0.79 0.26 0.10
22_V 70_K 0.79 0.26 0.10
50_F 166_R 0.79 0.25 0.10
97_W 83_E 0.79 0.25 0.10
108_F 48_V 0.79 0.25 0.10
24_I 174_L 0.79 0.25 0.10
108_F 35_A 0.78 0.25 0.10
92_I 10_D 0.78 0.25 0.09
124_D 107_K 0.78 0.25 0.09
20_L 24_A 0.78 0.25 0.09
40_R 70_K 0.78 0.24 0.09
29_L 96_Q 0.78 0.24 0.09
119_R 175_H 0.77 0.24 0.09
109_V 25_G 0.77 0.24 0.09
12_H 31_A 0.77 0.24 0.09
88_W 159_Y 0.77 0.24 0.09
55_D 26_A 0.77 0.24 0.09
17_A 94_L 0.77 0.24 0.09
16_F 10_D 0.77 0.24 0.09
40_R 32_G 0.76 0.23 0.09
67_K 157_S 0.76 0.23 0.09
124_D 65_T 0.76 0.23 0.08
58_G 78_I 0.76 0.23 0.08
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
2955 1.6 cI_A_10_cIII_isp_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.94 Done - Shared
2954 1.55 cI_A_6_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.97 Done - Shared
2953 1.53 cI_A_10_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.98 Done - Shared
2952 0.99 cI_A_10_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.54 Done - Shared
2951 0.1 cI_A_40_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
2950 0.99 cI_A_20_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.35 Done - Shared
2434 1.48 cI_E_cIII_isp_6 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (2015_03) 0.97 Done - Shared
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