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OPENSEQ.org
ds1
Genes: A B A+B
Length: 724 543 1163
Sequences: 2477 2554 496
Seq/Len: 3.42 4.7 0.43
MirrorTree (Pazo et al. 2001) 0.49
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 0.05 0.01 0.00
2 0.05 0.01 0.00
5 0.05 0.01 0.00
10 0.05 0.02 0.01
20 0.05 0.02 0.01
100 0.05 0.02 0.05
∞ 0.06 0.07 0.39
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
181_V 118_R 1.31 0.38 0.00
381_V 395_K 1.26 0.35 0.00
638_L 112_L 1.14 0.27 0.00
96_A 135_Q 1.14 0.27 0.00
335_I 116_E 1.05 0.22 0.00
61_D 266_A 1.03 0.21 0.00
165_F 115_M 1.03 0.21 0.00
562_N 11_G 0.99 0.19 0.00
517_I 417_C 0.98 0.19 0.00
605_I 11_G 0.98 0.19 0.00
377_I 11_G 0.98 0.19 0.00
165_F 334_D 0.97 0.18 0.00
167_V 85_L 0.96 0.18 0.00
684_I 70_D 0.96 0.18 0.00
353_I 20_I 0.96 0.18 0.00
154_Q 11_G 0.96 0.18 0.00
504_R 112_L 0.95 0.17 0.00
473_V 424_E 0.95 0.17 0.00
343_L 79_A 0.95 0.17 0.00
181_V 66_D 0.95 0.17 0.00
420_A 495_V 0.94 0.17 0.00
308_L 517_A 0.94 0.17 0.00
202_V 218_L 0.94 0.17 0.00
13_E 86_N 0.94 0.17 0.00
335_I 336_L 0.93 0.17 0.00
166_T 409_E 0.93 0.17 0.00
554_E 87_R 0.93 0.16 0.00
414_E 285_A 0.93 0.16 0.00
563_L 35_P 0.91 0.16 0.00
295_D 15_L 0.90 0.15 0.00
577_K 167_G 0.90 0.15 0.00
663_L 383_Y 0.89 0.15 0.00
97_D 97_E 0.89 0.15 0.00
314_D 266_A 0.89 0.15 0.00
302_G 97_E 0.88 0.14 0.00
419_L 141_P 0.88 0.14 0.00
659_F 386_A 0.88 0.14 0.00
460_S 306_I 0.87 0.14 0.00
680_I 239_K 0.87 0.14 0.00
167_V 237_K 0.87 0.14 0.00
469_L 438_L 0.86 0.14 0.00
672_D 380_M 0.86 0.14 0.00
529_D 471_C 0.86 0.14 0.00
75_I 194_E 0.86 0.14 0.00
489_E 495_V 0.86 0.14 0.00
142_K 90_E 0.85 0.14 0.00
202_V 480_D 0.85 0.14 0.00
44_I 94_T 0.85 0.14 0.00
213_I 230_E 0.85 0.13 0.00
473_V 273_G 0.85 0.13 0.00
197_R 63_K 0.84 0.13 0.00
197_R 239_K 0.84 0.13 0.00
381_V 401_A 0.84 0.13 0.00
72_K 328_A 0.84 0.13 0.00
628_I 80_A 0.84 0.13 0.00
536_V 278_C 0.84 0.13 0.00
153_E 446_K 0.83 0.13 0.00
426_Y 195_E 0.83 0.13 0.00
209_I 325_K 0.83 0.13 0.00
529_D 465_A 0.83 0.13 0.00
335_I 220_E 0.83 0.13 0.00
296_I 460_S 0.83 0.13 0.00
460_S 350_E 0.82 0.13 0.00
529_D 78_K 0.82 0.12 0.00
580_I 112_L 0.82 0.12 0.00
72_K 423_L 0.82 0.12 0.00
485_Y 340_Q 0.81 0.12 0.00
147_T 35_P 0.81 0.12 0.00
75_I 451_Y 0.81 0.12 0.00
97_D 388_K 0.81 0.12 0.00
358_R 58_Y 0.81 0.12 0.00
97_D 183_L 0.81 0.12 0.00
595_T 477_N 0.81 0.12 0.00
167_V 323_Y 0.81 0.12 0.00
158_E 300_A 0.81 0.12 0.00
44_I 19_N 0.81 0.12 0.00
291_R 198_T 0.81 0.12 0.00
147_T 273_G 0.80 0.12 0.00
202_V 58_Y 0.80 0.12 0.00
295_D 426_T 0.80 0.12 0.00
529_D 429_K 0.80 0.12 0.00
86_L 23_A 0.80 0.12 0.00
469_L 196_I 0.80 0.12 0.00
75_I 50_K 0.80 0.12 0.00
522_V 465_A 0.80 0.12 0.00
297_T 423_L 0.80 0.12 0.00
213_I 112_L 0.79 0.12 0.00
587_S 425_P 0.79 0.12 0.00
101_N 92_K 0.79 0.12 0.00
312_W 320_I 0.79 0.12 0.00
167_V 186_D 0.79 0.12 0.00
288_I 283_E 0.79 0.12 0.00
300_E 111_G 0.79 0.12 0.00
37_E 69_P 0.79 0.12 0.00
147_T 266_A 0.79 0.12 0.00
473_V 72_G 0.79 0.12 0.00
107_K 87_R 0.79 0.11 0.00
486_I 345_I 0.79 0.11 0.00
202_V 272_K 0.79 0.11 0.00
296_I 273_G 0.78 0.11 0.00
165_F 362_E 0.78 0.11 0.00
188_D 349_Q 0.78 0.11 0.00
297_T 78_K 0.78 0.11 0.00
300_E 526_V 0.78 0.11 0.00
72_K 63_K 0.78 0.11 0.00
685_K 323_Y 0.78 0.11 0.00
272_I 350_E 0.78 0.11 0.00
79_P 249_D 0.78 0.11 0.00
676_H 262_I 0.78 0.11 0.00
663_L 89_E 0.78 0.11 0.00
295_D 422_Q 0.77 0.11 0.00
80_Q 468_Y 0.77 0.11 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
2769 0.44 ds1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
2768 0.52 ds1 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
2767 0.56 ds1 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared
2765 0.43 ds1 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
2761 0.02 ds1 Δgene:(0, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) Killed - Shared
2758 0.02 ds1 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) Killed - Shared
2757 0.03 ds1 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) Killed - Shared
2756 0.03 ds1 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) Killed - Shared
2754 0 ds1 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
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