May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
PCC Me (A, 1-450) (B, 30-495)
Genes: A B A+B
Length: 450 466 909
Sequences: 11784 3788 1707
Seq/Len: 26.19 8.13 1.88
MirrorTree (Pazo et al. 2001) 0.44
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 0.02 0.01 0.87
2 0.02 0.01 1.34
5 0.03 0.01 1.64
10 0.05 0.02 1.79
20 0.07 0.02 1.86
100 0.12 0.04 2.08
∞ 0.22 0.13 2.68
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
445_F 185_A 0.95 0.45 0.00
287_L 164_T 0.95 0.45 0.00
7_I 293_V 0.90 0.39 0.00
277_V 189_T 0.89 0.38 0.00
100_I 329_F 0.88 0.37 0.00
374_D 240_L 0.87 0.37 0.00
68_D 261_V 0.86 0.36 0.00
195_D 8_E 0.86 0.36 0.00
103_I 417_D 0.85 0.35 0.00
351_S 368_I 0.84 0.34 0.00
108_G 367_I 0.83 0.32 0.00
131_V 8_E 0.83 0.32 0.00
375_T 257_L 0.82 0.31 0.00
426_F 202_D 0.80 0.29 0.00
395_V 327_V 0.78 0.28 0.00
339_V 451_H 0.78 0.28 0.00
107_P 323_S 0.78 0.28 0.00
433_H 109_A 0.77 0.27 0.00
406_E 46_V 0.77 0.27 0.00
146_T 94_I 0.76 0.26 0.00
5_I 460_A 0.76 0.26 0.00
239_I 221_I 0.74 0.24 0.00
242_A 153_F 0.74 0.24 0.00
419_G 177_V 0.73 0.24 0.00
130_T 303_V 0.73 0.24 0.00
189_S 11_E 0.73 0.24 0.00
394_L 133_V 0.73 0.24 0.00
239_I 368_I 0.72 0.23 0.00
57_A 88_K 0.72 0.23 0.00
5_I 327_V 0.72 0.23 0.00
384_A 22_F 0.72 0.23 0.00
221_V 213_L 0.71 0.22 0.00
228_E 174_N 0.71 0.22 0.00
313_I 199_F 0.70 0.21 0.00
100_I 396_A 0.70 0.21 0.00
414_A 201_N 0.70 0.21 0.00
304_T 368_I 0.69 0.21 0.00
66_I 243_L 0.69 0.21 0.00
82_Y 129_P 0.69 0.20 0.00
254_K 186_K 0.68 0.20 0.00
78_V 292_F 0.68 0.20 0.00
349_L 335_F 0.68 0.20 0.00
421_R 46_V 0.68 0.20 0.00
402_L 279_I 0.67 0.19 0.00
432_A 94_I 0.67 0.19 0.00
327_Q 94_I 0.67 0.19 0.00
384_A 90_R 0.67 0.19 0.00
5_I 14_L 0.67 0.19 0.00
86_S 313_A 0.67 0.19 0.00
385_I 348_K 0.66 0.19 0.00
44_M 293_V 0.66 0.19 0.00
250_E 243_L 0.66 0.19 0.00
278_A 57_V 0.66 0.19 0.00
244_S 24_M 0.66 0.18 0.00
379_E 46_V 0.66 0.18 0.00
267_N 212_L 0.65 0.18 0.00
120_K 372_A 0.65 0.18 0.00
217_K 447_V 0.65 0.18 0.00
93_K 365_V 0.65 0.18 0.00
86_S 100_G 0.65 0.18 0.00
284_F 164_T 0.65 0.18 0.00
299_V 46_V 0.64 0.18 0.00
110_I 94_I 0.64 0.18 0.00
198_F 250_K 0.64 0.17 0.00
420_I 59_L 0.64 0.17 0.00
17_I 223_G 0.64 0.17 0.00
347_N 94_I 0.64 0.17 0.00
391_I 178_T 0.64 0.17 0.00
156_M 169_V 0.64 0.17 0.00
179_E 323_S 0.64 0.17 0.00
131_V 52_V 0.64 0.17 0.00
7_I 257_L 0.64 0.17 0.00
198_F 404_K 0.64 0.17 0.00
126_A 47_T 0.63 0.17 0.00
66_I 17_G 0.63 0.17 0.00
173_S 16_H 0.63 0.17 0.00
7_I 340_A 0.63 0.17 0.00
159_A 251_P 0.63 0.17 0.00
280_Q 447_V 0.63 0.17 0.00
203_I 313_A 0.63 0.17 0.00
255_M 404_K 0.62 0.16 0.00
78_V 420_K 0.62 0.16 0.00
231_I 209_I 0.62 0.16 0.00
231_I 132_S 0.62 0.16 0.00
355_L 11_E 0.62 0.16 0.00
231_I 154_M 0.62 0.16 0.00
398_A 447_V 0.62 0.16 0.00
378_E 243_L 0.62 0.16 0.00
106_N 255_G 0.61 0.16 0.00
335_V 16_H 0.61 0.16 0.00
126_A 373_F 0.61 0.16 0.00
339_V 246_D 0.61 0.16 0.00
121_K 94_I 0.61 0.16 0.00
108_G 447_V 0.61 0.16 0.00
203_I 156_R 0.61 0.16 0.00
213_V 313_A 0.61 0.15 0.00
425_P 94_I 0.61 0.15 0.00
376_G 285_V 0.61 0.15 0.00
209_I 316_V 0.61 0.15 0.00
78_V 235_R 0.61 0.15 0.00
161_A 89_M 0.61 0.15 0.00
327_Q 290_V 0.61 0.15 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)
Page generated in 0.5612 seconds.