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OPENSEQ.org

FliP FliQ camju jh

Genes: A B A+B
Length: 244 89 315
Sequences: 3294 3178 2793
Seq/Len: 13.5 35.71 8.87
MirrorTree (Pazo et al. 2001) 0.68
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 6.65
2 0.00 0.00 6.69
5 0.00 0.00 6.97
10 0.00 0.00 7.21
20 0.00 0.00 7.80
100 0.01 0.00 8.17
0.06 0.05 8.39
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
228_V 77_T 3.11 1.00 1.00
184_I 84_I 2.85 1.00 1.00
202_V 24_M 2.25 1.00 0.99
190_L 13_T 1.91 1.00 0.98
187_L 80_I 1.79 1.00 0.98
197_M 17_T 1.37 0.99 0.89
194_V 17_T 1.34 0.99 0.88
71_S 43_Q 1.24 0.98 0.82
194_V 13_T 1.24 0.98 0.82
204_M 66_M 1.23 0.98 0.82
187_L 9_L 1.16 0.97 0.77
198_V 20_L 1.13 0.96 0.74
209_M 47_M 1.13 0.96 0.74
228_V 74_I 1.06 0.94 0.68
90_T 66_M 1.02 0.92 0.63
212_P 25_L 1.01 0.92 0.62
212_P 55_I 0.95 0.88 0.55
234_L 81_L 0.95 0.88 0.55
227_L 6_L 0.94 0.87 0.54
188_I 81_L 0.93 0.86 0.52
228_V 81_L 0.92 0.85 0.51
53_A 55_I 0.89 0.83 0.47
218_L 43_Q 0.88 0.81 0.46
139_K 34_V 0.88 0.81 0.45
190_L 9_L 0.88 0.81 0.45
215_M 36_S 0.85 0.78 0.42
190_L 76_F 0.81 0.74 0.37
148_L 67_P 0.80 0.72 0.36
103_V 49_L 0.77 0.67 0.31
79_T 58_V 0.76 0.67 0.31
72_F 43_Q 0.75 0.66 0.30
56_I 79_N 0.74 0.63 0.28
212_P 17_T 0.73 0.63 0.28
218_L 73_M 0.73 0.62 0.27
198_V 28_G 0.71 0.59 0.25
39_T 43_Q 0.71 0.59 0.25
197_M 55_I 0.71 0.59 0.25
190_L 77_T 0.70 0.57 0.24
39_T 41_T 0.69 0.56 0.23
201_S 25_L 0.67 0.52 0.21
108_Y 3_E 0.67 0.52 0.21
32_N 34_V 0.67 0.52 0.21
45_I 9_L 0.67 0.51 0.20
201_S 21_S 0.66 0.51 0.20
80_Q 47_M 0.66 0.50 0.20
227_L 3_E 0.66 0.50 0.20
71_S 84_I 0.66 0.50 0.20
81_S 40_A 0.66 0.50 0.20
241_S 85_P 0.66 0.50 0.19
75_Q 43_Q 0.66 0.50 0.19
123_E 60_V 0.65 0.49 0.19
190_L 6_L 0.65 0.49 0.19
198_V 17_T 0.65 0.49 0.19
170_V 16_I 0.65 0.48 0.19
179_K 40_A 0.65 0.48 0.18
41_L 37_I 0.64 0.47 0.18
151_R 85_P 0.64 0.47 0.18
91_L 36_S 0.64 0.47 0.18
227_L 84_I 0.64 0.46 0.17
180_T 88_I 0.63 0.46 0.17
122_Y 47_M 0.63 0.46 0.17
190_L 27_A 0.63 0.46 0.17
53_A 62_L 0.63 0.45 0.17
197_M 29_L 0.62 0.44 0.17
80_Q 58_V 0.62 0.44 0.16
189_Y 33_L 0.62 0.43 0.16
82_M 77_T 0.62 0.43 0.16
95_L 69_M 0.62 0.43 0.16
222_L 37_I 0.61 0.43 0.16
240_E 60_V 0.61 0.42 0.15
224_I 68_W 0.61 0.42 0.15
47_L 21_S 0.61 0.42 0.15
163_D 79_N 0.61 0.42 0.15
224_I 77_T 0.61 0.42 0.15
80_Q 56_I 0.60 0.41 0.15
87_I 33_L 0.60 0.41 0.15
107_S 65_L 0.60 0.41 0.15
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
10517 4.27 PvQ Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
7211 8.63 FliP FliQ camju jh 2 Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 1.00 Done
7208 8.87 FliP FliQ camju jh Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 1.00 Done
7152 4.62 FliP FliQ camju Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done
3578 3.72 PxQ Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 1.00 Done - Shared

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