May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
PPI check
Genes: A B A+B
Length: 483 356 746
Sequences: 521 4282 169
Seq/Len: 1.08 12.03 0.23
MirrorTree (Pazo et al. 2001) 0.36
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 0.04 0.01
2 0.03 0.04 0.01
5 0.03 0.04 0.01
10 0.03 0.05 0.01
20 0.03 0.05 0.01
100 0.03 0.06 0.04
∞ 0.04 0.11 0.20
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
302_Y 214_V 1.25 0.22 0.00
358_V 217_V 1.23 0.21 0.00
192_L 281_A 1.23 0.21 0.00
170_K 159_L 1.22 0.21 0.00
308_A 181_Y 1.18 0.19 0.00
331_V 72_V 1.14 0.18 0.00
147_T 184_K 1.08 0.16 0.00
53_Q 329_N 1.08 0.16 0.00
328_I 336_L 1.08 0.16 0.00
354_S 292_V 1.08 0.16 0.00
76_Q 159_L 1.07 0.15 0.00
328_I 272_A 1.04 0.15 0.00
140_L 272_A 1.03 0.14 0.00
59_P 343_L 1.03 0.14 0.00
247_N 152_C 1.02 0.14 0.00
171_A 85_T 1.00 0.13 0.00
162_A 312_V 1.00 0.13 0.00
353_N 159_L 0.99 0.13 0.00
396_L 157_V 0.98 0.13 0.00
342_E 49_I 0.98 0.13 0.00
72_Y 307_F 0.98 0.13 0.00
72_Y 113_M 0.97 0.13 0.00
154_L 145_C 0.96 0.12 0.00
290_T 340_K 0.96 0.12 0.00
247_N 217_V 0.96 0.12 0.00
470_M 159_L 0.95 0.12 0.00
380_A 70_V 0.95 0.12 0.00
185_F 185_R 0.95 0.12 0.00
306_A 157_V 0.94 0.12 0.00
146_P 57_G 0.94 0.12 0.00
306_A 152_C 0.93 0.11 0.00
60_E 259_Q 0.92 0.11 0.00
229_V 151_C 0.91 0.11 0.00
295_A 293_V 0.91 0.11 0.00
54_L 212_V 0.91 0.11 0.00
110_F 161_S 0.90 0.11 0.00
414_W 235_P 0.89 0.10 0.00
113_M 281_A 0.89 0.10 0.00
229_V 348_Q 0.89 0.10 0.00
345_K 317_R 0.89 0.10 0.00
367_R 233_K 0.88 0.10 0.00
423_V 47_V 0.88 0.10 0.00
82_V 338_R 0.88 0.10 0.00
250_L 318_G 0.87 0.10 0.00
324_V 161_S 0.87 0.10 0.00
226_V 202_A 0.86 0.10 0.00
147_T 296_A 0.86 0.10 0.00
391_Q 117_I 0.86 0.10 0.00
399_V 334_V 0.86 0.10 0.00
333_E 246_L 0.86 0.10 0.00
332_V 212_V 0.86 0.10 0.00
149_E 280_D 0.86 0.10 0.00
462_L 161_S 0.86 0.10 0.00
149_E 150_K 0.85 0.10 0.00
429_G 137_N 0.85 0.10 0.00
178_T 186_L 0.85 0.10 0.00
443_S 141_V 0.85 0.10 0.00
52_S 322_V 0.84 0.09 0.00
280_D 201_V 0.83 0.09 0.00
157_E 99_G 0.82 0.09 0.00
462_L 348_Q 0.82 0.09 0.00
430_L 244_E 0.82 0.09 0.00
154_L 201_V 0.82 0.09 0.00
188_G 107_E 0.82 0.09 0.00
205_G 123_P 0.82 0.09 0.00
82_V 247_T 0.82 0.09 0.00
403_V 259_Q 0.82 0.09 0.00
462_L 128_M 0.82 0.09 0.00
340_T 330_E 0.81 0.09 0.00
214_P 161_S 0.81 0.09 0.00
231_S 216_V 0.81 0.09 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 0.6229 seconds.