May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cI_A_cIII_isp_ecoli
Genes: A B A+B
Length: 147 183 296
Sequences: 3696 2217 595
Seq/Len: 25.14 12.11 2.01
MirrorTree (Pazo et al. 2001) 0.51
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 0.01 0.02
20 0.00 0.01 0.04
100 0.01 0.01 0.16
∞ 0.01 0.04 1.80
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 1.40 0.87 0.22
115_V 35_V 1.20 0.73 0.12
98_V 174_Q 1.14 0.68 0.10
34_G 47_K 1.00 0.53 0.07
49_P 175_I 1.00 0.52 0.06
23_A 23_T 0.98 0.50 0.06
23_A 18_C 0.96 0.48 0.06
20_L 10_E 0.96 0.48 0.06
112_A 87_I 0.94 0.46 0.05
41_A 162_L 0.94 0.46 0.05
100_F 121_Y 0.90 0.42 0.04
83_L 154_T 0.89 0.40 0.04
16_F 42_L 0.88 0.40 0.04
27_C 147_F 0.88 0.39 0.04
25_G 94_D 0.88 0.39 0.04
39_G 99_I 0.86 0.38 0.04
18_I 180_T 0.86 0.37 0.04
120_I 176_V 0.86 0.37 0.04
33_G 121_Y 0.86 0.37 0.04
21_I 39_V 0.85 0.37 0.04
18_I 94_D 0.85 0.36 0.04
28_C 48_T 0.84 0.35 0.04
108_F 48_T 0.84 0.35 0.04
22_V 28_A 0.84 0.35 0.04
94_E 22_L 0.83 0.34 0.03
40_R 19_L 0.83 0.34 0.03
29_L 134_G 0.83 0.34 0.03
20_L 118_V 0.83 0.34 0.03
45_S 145_S 0.82 0.33 0.03
34_G 40_S 0.82 0.33 0.03
18_I 42_L 0.81 0.32 0.03
24_I 23_T 0.81 0.32 0.03
68_F 59_L 0.80 0.31 0.03
16_F 80_H 0.80 0.31 0.03
23_A 128_V 0.80 0.31 0.03
44_R 9_G 0.80 0.31 0.03
80_V 167_Y 0.80 0.31 0.03
66_A 28_A 0.80 0.31 0.03
26_L 171_S 0.79 0.30 0.03
112_A 91_R 0.79 0.30 0.03
28_C 59_L 0.79 0.30 0.03
14_W 25_F 0.79 0.30 0.03
73_M 121_Y 0.79 0.30 0.03
26_L 121_Y 0.78 0.29 0.03
101_V 81_H 0.78 0.29 0.03
20_L 59_L 0.78 0.29 0.03
98_V 60_A 0.78 0.29 0.03
15_A 145_S 0.77 0.29 0.03
18_I 66_Q 0.77 0.29 0.03
90_T 23_T 0.77 0.28 0.03
21_I 95_L 0.77 0.28 0.03
77_I 80_H 0.77 0.28 0.03
64_L 37_P 0.77 0.28 0.03
58_G 79_I 0.77 0.28 0.03
24_I 88_V 0.76 0.28 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
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 0.047 seconds.