May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cI_A_cIII_isp_ecoli_2
Genes: A B A+B
Length: 147 183 295
Sequences: 3696 2127 572
Seq/Len: 25.14 11.62 1.94
MirrorTree (Pazo et al. 2001) 0.53
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 0.00
2 0.00 0.00 0.00
5 0.00 0.00 0.02
10 0.00 0.00 0.02
20 0.00 0.01 0.04
100 0.01 0.01 0.15
∞ 0.01 0.04 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
16_F 121_Y 1.67 0.95 0.75
108_F 32_A 1.23 0.75 0.37
41_A 162_L 1.14 0.66 0.29
16_F 42_L 1.10 0.62 0.26
90_T 147_F 0.99 0.51 0.18
40_R 136_L 0.98 0.49 0.17
40_R 19_L 0.95 0.46 0.15
20_L 118_V 0.94 0.45 0.15
29_L 136_L 0.93 0.43 0.14
16_F 160_A 0.93 0.43 0.14
36_F 22_L 0.92 0.43 0.14
121_G 148_D 0.91 0.41 0.13
18_I 66_Q 0.90 0.40 0.12
26_L 171_S 0.90 0.40 0.12
67_K 145_S 0.90 0.40 0.12
115_V 35_V 0.90 0.40 0.12
27_C 147_F 0.89 0.40 0.12
29_L 39_V 0.89 0.39 0.12
32_V 102_Q 0.88 0.38 0.11
44_R 22_L 0.87 0.38 0.11
24_I 23_T 0.87 0.37 0.11
44_R 9_G 0.87 0.37 0.11
117_L 144_G 0.86 0.37 0.11
66_A 114_Q 0.86 0.36 0.10
24_I 171_S 0.86 0.36 0.10
23_A 23_T 0.86 0.36 0.10
115_V 28_A 0.85 0.35 0.10
73_M 121_Y 0.85 0.35 0.10
119_R 112_H 0.83 0.34 0.09
101_V 39_V 0.83 0.34 0.09
67_K 158_A 0.83 0.34 0.09
83_L 154_T 0.83 0.33 0.09
34_G 151_G 0.81 0.32 0.09
90_T 105_S 0.81 0.31 0.08
92_I 28_A 0.81 0.31 0.08
122_A 158_A 0.80 0.31 0.08
74_F 76_L 0.80 0.30 0.08
20_L 59_L 0.80 0.30 0.08
34_G 47_K 0.80 0.30 0.08
40_R 57_V 0.80 0.30 0.08
101_V 136_L 0.80 0.30 0.08
25_G 75_K 0.80 0.30 0.08
98_V 174_Q 0.80 0.30 0.08
33_G 68_I 0.80 0.30 0.08
100_F 144_G 0.80 0.30 0.08
33_G 121_Y 0.79 0.30 0.08
120_I 176_V 0.79 0.29 0.08
37_L 23_T 0.79 0.29 0.07
23_A 18_C 0.79 0.29 0.07
38_G 148_D 0.78 0.29 0.07
99_G 30_G 0.77 0.27 0.07
80_V 167_Y 0.77 0.27 0.07
37_L 163_A 0.77 0.27 0.07
91_S 105_S 0.77 0.27 0.07
14_W 25_F 0.76 0.27 0.07
33_G 164_I 0.76 0.27 0.07
45_S 145_S 0.76 0.27 0.07
18_I 42_L 0.76 0.27 0.07
49_P 74_G 0.76 0.27 0.07
20_L 10_E 0.76 0.27 0.07
66_A 28_A 0.76 0.27 0.07
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
2468 0.95 cI_A_cIII_isp_ecoli Δgene:(1, ∞) A:(1E-20, 8) B:(1E-02, 1) msa: Jackhmmer (2015_03) 0.29 Done - Shared
2467 1.18 cI_A_cIII_isp_ecoli_2hhblits Δgene:(1, ∞) A:(1E-20, 8) B:(1E-02, 8) msa: HHblits (2013_03) 0.07 Done - Shared
2466 1.94 cI_A_cIII_isp_ecoli_2 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-02, 8) msa: Jackhmmer (2015_03) 0.75 Done - Shared
2457 1.95 cI_A_cIII_isp_ecoli_4 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: Jackhmmer (2015_03) 0.40 Done - Shared
2454 1.94 cI_A_cIII_isp_ecoli_6 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_03) 0.03 Done - Shared
2453 2.01 cI_A_cIII_isp_ecoli Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (2015_03) 0.22 Done - Shared
Page generated in 0.0829 seconds.