May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cI_G_cIII_cytb_Pdenitr
Genes: A B A+B
Length: 674 440 1075
Sequences: 1936 3290 530
Seq/Len: 2.87 7.48 0.49
MirrorTree (Pazo et al. 2001) 0.35
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 0.00
2 0.00 0.00 0.01
5 0.01 0.00 0.01
10 0.01 0.00 0.01
20 0.01 0.00 0.01
100 0.03 0.00 0.07
∞ 0.09 0.01 0.48
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
520_Q 93_L 1.27 0.38 0.00
393_I 379_W 1.21 0.34 0.00
14_I 196_S 1.20 0.33 0.00
525_I 343_M 1.18 0.32 0.00
299_S 264_F 1.16 0.30 0.00
72_D 176_I 1.13 0.29 0.00
280_R 172_V 1.13 0.29 0.00
389_L 172_V 1.12 0.28 0.00
296_R 130_I 1.11 0.27 0.00
510_N 25_I 1.09 0.27 0.00
125_A 172_V 1.09 0.26 0.00
406_V 398_A 1.08 0.26 0.00
31_I 376_V 1.08 0.26 0.00
151_V 385_A 1.07 0.25 0.00
248_K 207_A 1.07 0.25 0.00
588_L 61_T 1.06 0.24 0.00
72_D 376_V 1.05 0.24 0.00
98_V 180_L 1.05 0.24 0.00
525_I 123_A 1.04 0.24 0.00
457_G 187_D 1.03 0.23 0.00
503_D 285_P 1.02 0.23 0.00
430_S 180_L 1.02 0.22 0.00
500_A 407_I 1.02 0.22 0.00
500_A 254_F 1.01 0.22 0.00
83_E 60_A 0.99 0.21 0.00
390_N 333_V 0.99 0.21 0.00
470_N 172_V 0.99 0.21 0.00
630_L 60_A 0.98 0.20 0.00
602_R 341_L 0.97 0.20 0.00
18_P 405_L 0.96 0.20 0.00
93_K 59_I 0.96 0.20 0.00
503_D 392_I 0.96 0.19 0.00
575_K 227_V 0.96 0.19 0.00
255_I 63_I 0.95 0.19 0.00
525_I 370_L 0.95 0.19 0.00
525_I 207_A 0.95 0.19 0.00
305_E 369_L 0.95 0.19 0.00
274_F 296_W 0.94 0.18 0.00
599_G 141_G 0.94 0.18 0.00
55_V 345_L 0.93 0.18 0.00
581_L 56_V 0.92 0.18 0.00
56_V 286_L 0.92 0.18 0.00
97_G 200_L 0.92 0.18 0.00
553_L 201_L 0.92 0.17 0.00
15_E 180_L 0.92 0.17 0.00
596_S 345_L 0.91 0.17 0.00
177_M 342_V 0.91 0.17 0.00
252_V 270_M 0.91 0.17 0.00
149_P 298_F 0.90 0.17 0.00
599_G 171_G 0.90 0.17 0.00
9_I 64_V 0.90 0.17 0.00
181_G 75_L 0.89 0.16 0.00
445_V 265_A 0.89 0.16 0.00
241_S 93_L 0.89 0.16 0.00
504_G 334_I 0.88 0.16 0.00
14_I 28_L 0.88 0.16 0.00
188_I 374_F 0.88 0.16 0.00
520_Q 362_L 0.88 0.16 0.00
316_I 169_I 0.88 0.16 0.00
54_E 254_F 0.88 0.16 0.00
204_I 342_V 0.87 0.15 0.00
503_D 380_V 0.87 0.15 0.00
371_D 61_T 0.87 0.15 0.00
510_N 392_I 0.87 0.15 0.00
418_H 334_I 0.86 0.15 0.00
460_V 269_F 0.86 0.15 0.00
32_E 201_L 0.86 0.15 0.00
84_I 61_T 0.86 0.15 0.00
467_L 112_I 0.85 0.15 0.00
255_I 172_V 0.85 0.15 0.00
429_L 60_A 0.84 0.14 0.00
302_E 227_V 0.84 0.14 0.00
251_E 180_L 0.84 0.14 0.00
581_L 71_P 0.84 0.14 0.00
457_G 402_A 0.84 0.14 0.00
433_E 227_V 0.84 0.14 0.00
268_I 269_F 0.84 0.14 0.00
437_E 136_Y 0.84 0.14 0.00
443_S 385_A 0.83 0.14 0.00
151_V 210_V 0.83 0.14 0.00
552_G 282_E 0.83 0.14 0.00
127_A 406_I 0.83 0.14 0.00
10_D 375_V 0.83 0.14 0.00
406_V 14_G 0.83 0.14 0.00
98_V 379_W 0.82 0.14 0.00
92_K 93_L 0.82 0.14 0.00
292_N 394_L 0.82 0.14 0.00
135_Y 176_I 0.82 0.14 0.00
599_G 397_S 0.82 0.13 0.00
627_R 20_H 0.82 0.13 0.00
521_G 333_V 0.82 0.13 0.00
380_T 86_D 0.82 0.13 0.00
567_A 108_V 0.81 0.13 0.00
79_G 22_R 0.81 0.13 0.00
567_A 156_F 0.81 0.13 0.00
232_S 103_L 0.81 0.13 0.00
502_I 397_S 0.81 0.13 0.00
507_V 397_S 0.80 0.13 0.00
70_V 353_R 0.80 0.13 0.00
457_G 110_I 0.80 0.13 0.00
388_V 56_V 0.80 0.13 0.00
375_I 379_W 0.80 0.13 0.00
316_I 410_L 0.80 0.13 0.00
607_A 213_I 0.80 0.13 0.00
135_Y 15_F 0.79 0.13 0.00
551_S 310_A 0.79 0.12 0.00
62_P 86_D 0.79 0.12 0.00
248_K 106_L 0.79 0.12 0.00
602_R 133_M 0.79 0.12 0.00
400_G 258_V 0.79 0.12 0.00
125_A 106_L 0.78 0.12 0.00
530_H 103_L 0.78 0.12 0.00
316_I 201_L 0.78 0.12 0.00
57_G 122_K 0.78 0.12 0.00
597_L 211_V 0.78 0.12 0.00
507_V 63_I 0.78 0.12 0.00
9_I 344_A 0.78 0.12 0.00
299_S 345_L 0.78 0.12 0.00
262_G 258_V 0.78 0.12 0.00
132_F 93_L 0.78 0.12 0.00
646_N 242_L 0.78 0.12 0.00
607_A 172_V 0.78 0.12 0.00
341_G 418_D 0.78 0.12 0.00
315_K 168_A 0.78 0.12 0.00
194_Q 136_Y 0.77 0.12 0.00
457_G 395_A 0.77 0.12 0.00
91_V 96_L 0.77 0.12 0.00
31_I 211_V 0.77 0.12 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 0.1149 seconds.