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OPENSEQ.org

FliP FliQ camju jh 2

Genes: A B A+B
Length: 244 89 315
Sequences: 3294 3178 2719
Seq/Len: 13.5 35.71 8.63
MirrorTree (Pazo et al. 2001) 0.69
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 6.61
2 0.00 0.00 6.68
5 0.00 0.00 6.98
10 0.00 0.00 7.20
20 0.00 0.00 7.81
100 0.01 0.00 8.17
0.06 0.05 8.40
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 3.05 1.00 1.00
184_I 84_I 2.95 1.00 1.00
202_V 24_M 2.25 1.00 0.99
190_L 13_T 1.89 1.00 0.98
187_L 80_I 1.82 1.00 0.98
197_M 17_T 1.37 0.99 0.89
194_V 17_T 1.35 0.99 0.88
204_M 66_M 1.27 0.98 0.84
71_S 43_Q 1.22 0.98 0.81
194_V 13_T 1.20 0.97 0.80
209_M 47_M 1.18 0.97 0.78
198_V 20_L 1.16 0.96 0.77
187_L 9_L 1.13 0.96 0.74
212_P 55_I 1.07 0.94 0.69
212_P 25_L 1.02 0.91 0.63
227_L 6_L 0.99 0.90 0.60
90_T 66_M 0.98 0.89 0.58
228_V 81_L 0.98 0.89 0.58
228_V 74_I 0.97 0.89 0.57
218_L 43_Q 0.94 0.86 0.54
234_L 81_L 0.94 0.86 0.53
215_M 36_S 0.91 0.84 0.49
53_A 55_I 0.88 0.81 0.45
188_I 81_L 0.84 0.77 0.41
148_L 67_P 0.83 0.76 0.40
190_L 9_L 0.82 0.73 0.37
103_V 49_L 0.80 0.71 0.35
79_T 58_V 0.80 0.71 0.35
190_L 76_F 0.78 0.68 0.33
218_L 73_M 0.77 0.67 0.32
72_F 43_Q 0.75 0.64 0.29
139_K 34_V 0.75 0.64 0.29
197_M 55_I 0.73 0.61 0.27
212_P 17_T 0.72 0.60 0.26
205_A 36_S 0.71 0.58 0.25
39_T 41_T 0.71 0.58 0.25
39_T 43_Q 0.71 0.57 0.24
108_Y 3_E 0.70 0.57 0.24
56_I 79_N 0.70 0.56 0.23
75_Q 43_Q 0.69 0.55 0.23
32_N 34_V 0.69 0.55 0.23
87_I 33_L 0.69 0.54 0.22
71_S 84_I 0.69 0.54 0.22
180_T 88_I 0.68 0.54 0.22
41_L 37_I 0.68 0.53 0.22
227_L 84_I 0.68 0.53 0.22
201_S 25_L 0.68 0.53 0.21
80_Q 47_M 0.67 0.52 0.21
201_S 21_S 0.67 0.51 0.20
198_V 17_T 0.67 0.51 0.20
227_L 3_E 0.66 0.50 0.20
151_R 85_P 0.66 0.50 0.20
179_K 40_A 0.66 0.50 0.20
175_I 41_T 0.66 0.50 0.20
81_S 40_A 0.66 0.49 0.20
198_V 28_G 0.66 0.49 0.20
91_L 36_S 0.66 0.49 0.19
90_T 20_L 0.65 0.48 0.19
95_L 69_M 0.65 0.48 0.19
47_L 55_I 0.65 0.47 0.18
241_S 85_P 0.64 0.47 0.18
224_I 77_T 0.64 0.46 0.18
149_F 40_A 0.64 0.46 0.18
73_L 47_M 0.64 0.46 0.18
190_L 77_T 0.64 0.46 0.17
224_I 68_W 0.63 0.45 0.17
75_Q 4_S 0.63 0.45 0.17
80_Q 58_V 0.63 0.44 0.17
205_A 64_F 0.62 0.44 0.17
122_Y 47_M 0.62 0.43 0.16
190_L 6_L 0.62 0.42 0.16
170_V 16_I 0.61 0.42 0.15
233_L 78_E 0.60 0.41 0.15
74_R 58_V 0.60 0.41 0.15
82_M 77_T 0.60 0.41 0.15
80_Q 56_I 0.60 0.40 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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