May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
xtRic8AxtGa13
Genes: A B A+B
Length: 539 374 855
Sequences: 409 1939 51
Seq/Len: 0.76 5.18 0.06
MirrorTree (Pazo et al. 2001) 0.37
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 0.06 0.03 0.00
2 0.06 0.03 0.00
5 0.06 0.03 0.00
10 0.06 0.03 0.00
20 0.06 0.04 0.00
100 0.06 0.04 0.01
∞ 0.07 0.05 0.06
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
121_G 30_K 1.49 0.14 0.00
288_V 77_D 1.45 0.14 0.00
258_L 184_L 1.29 0.11 0.00
336_R 149_I 1.23 0.10 0.00
388_L 86_A 1.19 0.09 0.00
504_I 186_D 1.19 0.09 0.00
284_V 24_E 1.16 0.09 0.00
361_R 196_I 1.15 0.09 0.00
237_N 153_W 1.14 0.09 0.00
286_L 297_E 1.12 0.08 0.00
464_V 64_F 1.12 0.08 0.00
365_L 72_H 1.10 0.08 0.00
504_I 188_D 1.08 0.08 0.00
289_N 38_L 1.07 0.08 0.00
336_R 47_R 1.07 0.08 0.00
91_T 305_I 1.06 0.07 0.00
365_L 71_I 1.06 0.07 0.00
136_A 93_I 1.05 0.07 0.00
292_L 184_L 1.05 0.07 0.00
468_V 261_Q 1.05 0.07 0.00
480_T 203_T 1.05 0.07 0.00
445_E 190_L 1.05 0.07 0.00
178_D 23_R 1.04 0.07 0.00
265_C 115_N 1.04 0.07 0.00
387_R 114_A 1.03 0.07 0.00
357_R 89_Y 1.03 0.07 0.00
124_N 287_I 1.02 0.07 0.00
365_L 272_F 1.02 0.07 0.00
481_E 38_L 1.02 0.07 0.00
461_I 139_T 1.02 0.07 0.00
471_K 43_T 1.01 0.07 0.00
514_R 47_R 0.99 0.07 0.00
81_S 156_T 0.98 0.07 0.00
424_A 170_L 0.98 0.07 0.00
118_A 153_W 0.98 0.07 0.00
424_A 287_I 0.98 0.07 0.00
116_V 77_D 0.98 0.07 0.00
388_L 295_L 0.98 0.07 0.00
404_L 168_F 0.97 0.07 0.00
361_R 154_A 0.97 0.07 0.00
172_L 177_F 0.97 0.06 0.00
68_E 35_D 0.97 0.06 0.00
368_L 340_K 0.97 0.06 0.00
93_A 47_R 0.97 0.06 0.00
489_M 300_V 0.96 0.06 0.00
500_R 89_Y 0.96 0.06 0.00
513_G 236_C 0.96 0.06 0.00
114_S 65_L 0.96 0.06 0.00
238_I 192_S 0.96 0.06 0.00
512_D 283_N 0.95 0.06 0.00
322_I 87_T 0.95 0.06 0.00
72_I 268_S 0.95 0.06 0.00
239_T 298_E 0.94 0.06 0.00
126_I 30_K 0.94 0.06 0.00
88_A 300_V 0.94 0.06 0.00
513_G 280_V 0.94 0.06 0.00
415_F 27_Q 0.94 0.06 0.00
48_E 35_D 0.93 0.06 0.00
126_I 312_F 0.93 0.06 0.00
121_G 47_R 0.93 0.06 0.00
108_S 282_S 0.93 0.06 0.00
395_D 33_E 0.93 0.06 0.00
435_A 301_R 0.93 0.06 0.00
266_L 184_L 0.93 0.06 0.00
480_T 243_I 0.93 0.06 0.00
428_L 34_I 0.93 0.06 0.00
70_I 252_Y 0.93 0.06 0.00
77_K 31_S 0.93 0.06 0.00
109_I 122_M 0.92 0.06 0.00
481_E 85_R 0.92 0.06 0.00
523_Q 333_K 0.92 0.06 0.00
81_S 24_E 0.92 0.06 0.00
345_L 98_V 0.92 0.06 0.00
333_H 190_L 0.91 0.06 0.00
73_L 298_E 0.91 0.06 0.00
514_R 30_K 0.91 0.06 0.00
290_L 242_S 0.91 0.06 0.00
299_L 26_E 0.91 0.06 0.00
322_I 151_S 0.91 0.06 0.00
357_R 218_F 0.91 0.06 0.00
517_P 145_H 0.90 0.06 0.00
61_S 184_L 0.90 0.06 0.00
521_A 297_E 0.90 0.06 0.00
235_L 75_D 0.89 0.06 0.00
464_V 273_E 0.89 0.06 0.00
75_R 170_L 0.89 0.06 0.00
225_T 99_L 0.89 0.06 0.00
428_L 62_S 0.89 0.06 0.00
334_K 168_F 0.89 0.06 0.00
92_L 59_S 0.89 0.06 0.00
288_V 278_N 0.88 0.06 0.00
169_L 152_L 0.88 0.06 0.00
402_E 181_L 0.88 0.06 0.00
237_N 62_S 0.88 0.06 0.00
284_V 78_L 0.88 0.06 0.00
365_L 76_F 0.88 0.06 0.00
482_E 287_I 0.88 0.06 0.00
501_E 46_K 0.87 0.06 0.00
67_L 211_F 0.87 0.06 0.00
148_R 30_K 0.87 0.06 0.00
444_S 357_V 0.87 0.05 0.00
93_A 101_D 0.87 0.05 0.00
410_E 186_D 0.87 0.05 0.00
433_L 181_L 0.87 0.05 0.00
428_L 153_W 0.86 0.05 0.00
514_R 311_D 0.86 0.05 0.00
72_I 70_I 0.86 0.05 0.00
501_E 178_L 0.86 0.05 0.00
476_M 122_M 0.86 0.05 0.00
414_R 99_L 0.86 0.05 0.00
426_G 287_I 0.86 0.05 0.00
184_A 192_S 0.86 0.05 0.00
122_L 152_L 0.86 0.05 0.00
257_H 190_L 0.86 0.05 0.00
470_E 69_R 0.86 0.05 0.00
470_E 76_F 0.86 0.05 0.00
325_L 305_I 0.86 0.05 0.00
483_Q 203_T 0.86 0.05 0.00
228_V 183_K 0.86 0.05 0.00
121_G 41_E 0.85 0.05 0.00
357_R 70_I 0.85 0.05 0.00
416_V 116_Q 0.85 0.05 0.00
346_L 68_M 0.85 0.05 0.00
47_G 156_T 0.85 0.05 0.00
380_T 181_L 0.85 0.05 0.00
258_L 88_I 0.85 0.05 0.00
178_D 79_R 0.85 0.05 0.00
45_K 320_E 0.85 0.05 0.00
238_I 113_P 0.85 0.05 0.00
407_L 226_Q 0.85 0.05 0.00
516_E 154_A 0.84 0.05 0.00
508_G 85_R 0.84 0.05 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
9708 0.07 xtric8AxtGa13 Δgene:(0, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
9621 0.01 xtric8AxtGa13 Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (r132) Killed - Shared
9342 0.06 xtRic8AxtGa13 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
9299 0 xtRic8AxtGa13 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
Page generated in 0.1339 seconds.