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OPENSEQ.org
cI_2_2_cI_5_6_tt
Genes: A B A+B
Length: 181 207 361
Sequences: 2502 1086 734
Seq/Len: 13.82 5.25 2.03
MirrorTree (Pazo et al. 2001) 0.81
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 0.00 0.36
2 0.00 0.00 1.37
5 0.01 0.01 1.70
10 0.01 0.01 1.72
20 0.02 0.01 1.73
100 0.04 0.01 1.77
∞ 0.09 0.02 1.89
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
46_I 135_I 1.39 0.87 0.21
28_M 50_A 1.26 0.78 0.14
139_E 119_Y 1.25 0.78 0.14
80_L 114_L 1.17 0.71 0.11
102_E 29_L 1.04 0.57 0.07
5_D 128_G 1.02 0.55 0.07
103_T 52_I 1.01 0.54 0.07
30_L 130_P 1.01 0.54 0.07
119_V 146_L 1.00 0.53 0.06
73_V 12_A 0.98 0.51 0.06
109_G 48_F 0.97 0.49 0.06
106_I 73_E 0.94 0.47 0.05
86_L 178_D 0.90 0.42 0.04
16_A 118_V 0.89 0.41 0.04
24_R 146_L 0.89 0.41 0.04
90_L 38_M 0.89 0.40 0.04
72_F 111_A 0.88 0.40 0.04
107_G 35_K 0.88 0.40 0.04
67_Y 151_P 0.87 0.39 0.04
158_R 135_I 0.87 0.38 0.04
115_G 23_G 0.86 0.38 0.04
118_S 77_L 0.86 0.38 0.04
116_L 97_E 0.84 0.36 0.04
141_Y 180_G 0.84 0.35 0.04
137_N 107_L 0.84 0.35 0.03
4_F 112_N 0.84 0.35 0.03
101_T 65_P 0.83 0.34 0.03
141_Y 135_I 0.83 0.34 0.03
15_F 73_E 0.82 0.34 0.03
3_F 92_V 0.82 0.33 0.03
144_C 10_A 0.82 0.33 0.03
147_R 30_P 0.82 0.33 0.03
21_E 91_R 0.81 0.32 0.03
28_M 157_T 0.81 0.32 0.03
62_G 137_T 0.81 0.32 0.03
125_L 146_L 0.80 0.32 0.03
4_F 122_F 0.80 0.31 0.03
125_L 49_L 0.80 0.31 0.03
126_G 157_T 0.80 0.31 0.03
165_E 55_L 0.79 0.30 0.03
69_Y 140_D 0.79 0.30 0.03
80_L 135_I 0.79 0.30 0.03
102_E 188_S 0.79 0.30 0.03
9_D 105_T 0.79 0.30 0.03
46_I 108_W 0.78 0.30 0.03
62_G 139_E 0.77 0.28 0.03
60_V 108_W 0.77 0.28 0.03
12_E 105_T 0.76 0.28 0.03
132_P 56_D 0.76 0.27 0.02
125_L 56_D 0.76 0.27 0.02
49_I 146_L 0.76 0.27 0.02
62_G 75_V 0.75 0.27 0.02
173_G 112_N 0.75 0.27 0.02
65_S 26_W 0.75 0.27 0.02
95_E 16_P 0.75 0.27 0.02
102_E 77_L 0.75 0.27 0.02
12_E 92_V 0.75 0.26 0.02
15_F 42_K 0.74 0.26 0.02
39_G 23_G 0.74 0.26 0.02
149_R 65_P 0.73 0.25 0.02
42_R 125_V 0.73 0.25 0.02
144_C 175_T 0.73 0.25 0.02
137_N 119_Y 0.72 0.24 0.02
12_E 101_L 0.72 0.24 0.02
26_A 118_V 0.72 0.24 0.02
137_N 112_N 0.72 0.24 0.02
122_V 151_P 0.72 0.24 0.02
9_D 13_K 0.72 0.24 0.02
54_G 106_D 0.71 0.24 0.02
123_E 150_Y 0.71 0.24 0.02
6_D 28_V 0.71 0.24 0.02
145_V 139_E 0.71 0.24 0.02
21_E 96_E 0.71 0.23 0.02
11_L 112_N 0.71 0.23 0.02
21_E 58_L 0.71 0.23 0.02
13_E 35_K 0.71 0.23 0.02
113_P 32_E 0.71 0.23 0.02
34_V 15_Y 0.70 0.23 0.02
65_S 73_E 0.70 0.23 0.02
72_F 91_R 0.70 0.23 0.02
142_V 160_R 0.70 0.23 0.02
116_L 31_R 0.70 0.23 0.02
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
4857 2.03 cI_2_2_cI_5_6_tt Δgene:(1, ∞) A:(1E-02, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.21 Done - Shared
4856 1.86 cI_2_2_cI_5_10_tt Δgene:(1, ∞) A:(1E-02, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.79 Done - Shared
4855 1.98 cI_2_4_cI_5_20_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
4854 1.88 cI_2_4_cI_5_10_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.70 Done - Shared
4844 1.86 cI_2_6_cI_5_10_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.67 Done - Shared
4843 1.98 cI_2_20_cI_5_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
4842 1.86 cI_2_10_cI_5_10_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.57 Done - Shared
4841 2.02 cI_2_6_cI_5_6_tt Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.27 Done - Shared
4840 1.99 cI_2_4_cI_5_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
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