May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cI_2_10_cI_5_10_tt
Genes: A B A+B
Length: 181 207 362
Sequences: 2578 1025 673
Seq/Len: 14.24 4.95 1.86
MirrorTree (Pazo et al. 2001) 0.82
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 0.34
2 0.00 0.00 1.23
5 0.01 0.01 1.55
10 0.01 0.01 1.58
20 0.02 0.01 1.58
100 0.04 0.02 1.60
∞ 0.10 0.06 1.73
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 1.59 0.93 0.57
139_E 119_Y 1.38 0.84 0.39
28_M 50_A 1.30 0.79 0.32
102_E 29_L 1.21 0.71 0.25
80_L 114_L 1.18 0.69 0.23
119_V 146_L 1.02 0.52 0.14
148_A 103_T 0.99 0.49 0.12
9_D 105_T 0.98 0.48 0.12
67_Y 151_P 0.97 0.47 0.11
118_S 77_L 0.96 0.46 0.11
30_L 130_P 0.96 0.46 0.11
73_V 12_A 0.95 0.44 0.10
77_K 11_R 0.94 0.44 0.10
46_I 108_W 0.92 0.42 0.09
16_A 101_L 0.92 0.41 0.09
90_L 38_M 0.91 0.40 0.09
54_G 106_D 0.90 0.40 0.09
80_L 65_P 0.90 0.39 0.09
74_P 49_L 0.88 0.37 0.08
106_I 122_F 0.88 0.37 0.08
5_D 128_G 0.88 0.37 0.08
49_I 106_D 0.88 0.37 0.08
4_F 112_N 0.88 0.37 0.08
95_E 16_P 0.87 0.36 0.07
109_G 48_F 0.86 0.36 0.07
137_N 107_L 0.86 0.35 0.07
149_R 65_P 0.85 0.34 0.07
154_L 128_G 0.85 0.34 0.07
4_F 122_F 0.84 0.34 0.07
158_R 135_I 0.84 0.33 0.07
105_G 23_G 0.83 0.33 0.06
65_S 73_E 0.83 0.32 0.06
25_A 171_R 0.83 0.32 0.06
115_G 23_G 0.82 0.32 0.06
94_E 45_G 0.80 0.30 0.06
146_T 25_L 0.80 0.30 0.06
42_R 125_V 0.80 0.30 0.06
113_P 32_E 0.80 0.29 0.06
108_P 121_L 0.80 0.29 0.06
164_E 124_I 0.80 0.29 0.06
172_C 180_G 0.79 0.29 0.05
144_C 175_T 0.79 0.29 0.05
4_F 34_F 0.79 0.29 0.05
72_F 91_R 0.79 0.28 0.05
78_Y 97_E 0.79 0.28 0.05
101_T 65_P 0.79 0.28 0.05
69_Y 140_D 0.78 0.28 0.05
162_R 124_I 0.78 0.28 0.05
62_G 75_V 0.78 0.28 0.05
147_R 30_P 0.78 0.28 0.05
28_M 11_R 0.78 0.28 0.05
123_E 67_R 0.78 0.28 0.05
16_A 74_L 0.77 0.27 0.05
137_N 119_Y 0.77 0.27 0.05
46_I 107_L 0.77 0.27 0.05
52_L 69_A 0.77 0.27 0.05
73_V 37_E 0.76 0.26 0.05
42_R 174_L 0.76 0.26 0.05
90_L 53_V 0.76 0.26 0.05
157_L 167_P 0.76 0.26 0.04
68_S 89_F 0.76 0.26 0.04
61_M 152_L 0.75 0.26 0.04
164_E 128_G 0.75 0.25 0.04
19_P 67_R 0.75 0.25 0.04
9_D 13_K 0.75 0.25 0.04
16_A 8_E 0.75 0.25 0.04
102_E 77_L 0.74 0.25 0.04
172_C 32_E 0.74 0.25 0.04
137_N 92_V 0.74 0.24 0.04
169_P 124_I 0.74 0.24 0.04
40_W 66_E 0.73 0.24 0.04
51_R 8_E 0.73 0.24 0.04
13_E 35_K 0.73 0.23 0.04
6_D 28_V 0.73 0.23 0.04
26_A 46_F 0.73 0.23 0.04
105_G 163_R 0.73 0.23 0.04
132_P 56_D 0.73 0.23 0.04
141_Y 72_Y 0.73 0.23 0.04
65_S 146_L 0.72 0.23 0.04
156_G 121_L 0.72 0.23 0.04
60_V 108_W 0.72 0.23 0.04
57_P 101_L 0.72 0.23 0.04
152_A 8_E 0.72 0.23 0.04
106_I 73_E 0.72 0.23 0.04
125_L 146_L 0.72 0.23 0.04
80_L 135_I 0.72 0.23 0.04
136_V 38_M 0.71 0.22 0.04
89_K 73_E 0.71 0.22 0.04
123_E 57_Y 0.71 0.22 0.04
28_M 22_L 0.71 0.22 0.04
69_Y 190_K 0.71 0.22 0.04
172_C 176_G 0.70 0.22 0.04
82_V 136_L 0.70 0.22 0.04
116_L 31_R 0.70 0.22 0.04
46_I 34_F 0.70 0.21 0.04
12_E 101_L 0.70 0.21 0.04
37_E 160_R 0.70 0.21 0.03
79_H 99_P 0.69 0.21 0.03
54_G 68_F 0.69 0.21 0.03
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
Page generated in 2.1314 seconds.