May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
GyrA
Genes: A B A+B
Length: 821 269 1047
Sequences: 2969 2805 1125
Seq/Len: 3.62 10.43 1.07
MirrorTree (Pazo et al. 2001) 0.15
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.01 0.04 0.00
2 0.01 0.04 0.00
5 0.01 0.04 0.01
10 0.01 0.04 0.01
20 0.01 0.04 0.02
100 0.02 0.04 0.12
∞ 0.10 0.06 1.03
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
502_E 182_I 1.13 0.48 0.00
566_V 113_V 1.06 0.41 0.00
104_V 9_V 0.95 0.32 0.00
132_S 90_P 0.95 0.31 0.00
207_P 254_F 0.92 0.29 0.00
113_V 238_L 0.91 0.28 0.00
135_I 9_V 0.90 0.27 0.00
700_V 214_R 0.89 0.27 0.00
578_G 209_G 0.86 0.25 0.00
368_Y 173_L 0.84 0.23 0.00
264_L 145_C 0.83 0.22 0.00
511_T 145_C 0.81 0.21 0.00
293_R 206_I 0.81 0.21 0.00
194_G 81_V 0.81 0.21 0.00
215_G 14_V 0.80 0.21 0.00
169_V 33_I 0.80 0.20 0.00
65_K 22_E 0.79 0.20 0.00
750_L 59_T 0.79 0.20 0.00
264_L 33_I 0.78 0.19 0.00
118_A 25_R 0.77 0.19 0.00
70_I 181_L 0.76 0.18 0.00
418_E 171_Q 0.76 0.18 0.00
622_S 117_G 0.75 0.18 0.00
283_D 181_L 0.75 0.18 0.00
118_A 247_K 0.74 0.17 0.00
132_S 238_L 0.73 0.17 0.00
307_I 182_I 0.73 0.17 0.00
355_L 122_V 0.73 0.17 0.00
557_I 148_F 0.73 0.16 0.00
354_Y 212_T 0.73 0.16 0.00
615_F 225_M 0.72 0.16 0.00
401_Q 49_E 0.72 0.16 0.00
337_L 117_G 0.72 0.16 0.00
118_A 205_L 0.72 0.16 0.00
127_R 188_Y 0.71 0.16 0.00
417_T 78_T 0.71 0.16 0.00
260_I 247_K 0.71 0.15 0.00
417_T 91_I 0.71 0.15 0.00
249_I 21_K 0.70 0.15 0.00
321_Y 160_E 0.70 0.15 0.00
638_L 46_R 0.70 0.15 0.00
362_I 115_I 0.70 0.15 0.00
586_I 240_T 0.70 0.15 0.00
761_D 69_M 0.70 0.15 0.00
553_T 182_I 0.70 0.15 0.00
494_T 18_T 0.69 0.15 0.00
684_T 144_A 0.69 0.15 0.00
649_L 122_V 0.69 0.15 0.00
324_T 146_P 0.69 0.15 0.00
333_N 77_A 0.69 0.14 0.00
256_K 109_N 0.69 0.14 0.00
358_Q 212_T 0.69 0.14 0.00
262_T 71_V 0.68 0.14 0.00
418_E 9_V 0.68 0.14 0.00
480_N 113_V 0.68 0.14 0.00
495_I 124_S 0.68 0.14 0.00
209_L 94_V 0.68 0.14 0.00
139_I 117_G 0.68 0.14 0.00
666_K 21_K 0.67 0.14 0.00
276_K 133_S 0.67 0.14 0.00
601_I 123_K 0.67 0.14 0.00
368_Y 198_V 0.67 0.14 0.00
565_K 152_V 0.67 0.14 0.00
354_Y 211_E 0.67 0.14 0.00
431_R 19_V 0.67 0.13 0.00
194_G 59_T 0.66 0.13 0.00
541_E 49_E 0.66 0.13 0.00
31_V 140_V 0.66 0.13 0.00
86_V 50_E 0.66 0.13 0.00
369_E 67_I 0.66 0.13 0.00
316_I 190_I 0.66 0.13 0.00
314_N 182_I 0.66 0.13 0.00
666_K 182_I 0.65 0.13 0.00
308_R 32_I 0.65 0.13 0.00
260_I 129_E 0.65 0.13 0.00
602_I 47_S 0.65 0.13 0.00
750_L 200_G 0.65 0.13 0.00
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
6548 1.07 GyrA Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
6547 0.02 GyrA Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
6546 0.02 GyrA Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed - Shared
6545 0.03 GyrA Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
6526 0.02 GyrA Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
Page generated in 0.136 seconds.