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OPENSEQ.org
ds1
Genes: A B A+B
Length: 724 543 1168
Sequences: 2473 4000 653
Seq/Len: 3.42 7.37 0.56
MirrorTree (Pazo et al. 2001) 0.47
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 0.01 0.01
20 0.05 0.02 0.02
100 0.05 0.03 0.08
∞ 0.06 0.10 0.52
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
343_L 79_A 1.30 0.44 0.00
181_V 66_D 1.16 0.34 0.00
335_I 394_A 1.15 0.33 0.00
165_F 334_D 1.14 0.32 0.00
314_D 413_A 1.11 0.30 0.00
155_Y 435_A 1.10 0.30 0.00
181_V 118_R 1.07 0.27 0.00
167_V 79_A 1.05 0.26 0.00
529_D 78_K 1.02 0.24 0.00
84_L 96_E 1.00 0.23 0.00
84_L 19_N 1.00 0.23 0.00
147_T 309_S 0.99 0.23 0.00
44_I 316_Y 0.98 0.22 0.00
628_I 110_E 0.98 0.22 0.00
605_I 495_V 0.97 0.22 0.00
672_D 63_K 0.97 0.22 0.00
181_V 351_R 0.97 0.22 0.00
210_G 323_Y 0.96 0.21 0.00
86_L 306_I 0.96 0.21 0.00
288_I 310_Y 0.96 0.21 0.00
187_E 87_R 0.96 0.21 0.00
191_E 445_T 0.95 0.20 0.00
424_E 273_G 0.94 0.20 0.00
141_E 435_A 0.94 0.20 0.00
81_E 86_N 0.94 0.20 0.00
44_I 19_N 0.92 0.19 0.00
97_D 388_K 0.92 0.19 0.00
96_A 29_E 0.91 0.19 0.00
147_T 266_A 0.91 0.18 0.00
635_V 134_Y 0.90 0.18 0.00
192_Y 305_R 0.89 0.18 0.00
635_V 191_D 0.89 0.17 0.00
114_M 461_C 0.87 0.17 0.00
202_V 383_Y 0.87 0.17 0.00
97_D 183_L 0.87 0.17 0.00
633_P 347_K 0.86 0.16 0.00
82_R 134_Y 0.86 0.16 0.00
295_D 380_M 0.86 0.16 0.00
595_T 30_A 0.86 0.16 0.00
295_D 495_V 0.85 0.16 0.00
74_D 409_E 0.85 0.16 0.00
86_L 435_A 0.85 0.16 0.00
554_E 87_R 0.84 0.16 0.00
165_F 353_A 0.84 0.15 0.00
586_S 27_Y 0.84 0.15 0.00
84_L 81_A 0.84 0.15 0.00
628_I 96_E 0.83 0.15 0.00
295_D 79_A 0.83 0.15 0.00
517_I 417_C 0.83 0.15 0.00
70_E 375_D 0.83 0.15 0.00
70_E 369_E 0.82 0.15 0.00
638_L 112_L 0.82 0.15 0.00
427_K 273_G 0.82 0.15 0.00
44_I 235_A 0.82 0.14 0.00
137_Y 387_I 0.81 0.14 0.00
96_A 321_H 0.81 0.14 0.00
297_T 246_K 0.81 0.14 0.00
282_L 341_Q 0.80 0.14 0.00
96_A 307_G 0.80 0.14 0.00
191_E 183_L 0.80 0.14 0.00
202_V 70_D 0.80 0.14 0.00
86_L 347_K 0.80 0.14 0.00
398_S 524_N 0.80 0.14 0.00
97_D 455_L 0.80 0.14 0.00
84_L 82_L 0.79 0.14 0.00
419_L 141_P 0.79 0.14 0.00
58_S 408_L 0.79 0.14 0.00
522_V 276_N 0.79 0.13 0.00
558_A 275_Y 0.79 0.13 0.00
170_D 47_A 0.79 0.13 0.00
198_V 134_Y 0.79 0.13 0.00
167_V 323_Y 0.78 0.13 0.00
335_I 336_L 0.78 0.13 0.00
509_E 417_C 0.78 0.13 0.00
188_D 426_T 0.78 0.13 0.00
469_L 196_I 0.78 0.13 0.00
181_V 137_L 0.78 0.13 0.00
335_I 220_E 0.77 0.13 0.00
608_A 495_V 0.77 0.13 0.00
605_I 11_G 0.77 0.13 0.00
541_L 248_Y 0.77 0.13 0.00
677_S 442_K 0.77 0.13 0.00
220_E 279_R 0.77 0.13 0.00
469_L 477_N 0.77 0.13 0.00
482_S 58_Y 0.77 0.12 0.00
377_I 11_G 0.77 0.12 0.00
628_I 388_K 0.76 0.12 0.00
97_D 97_E 0.76 0.12 0.00
211_Y 239_K 0.76 0.12 0.00
44_I 328_A 0.76 0.12 0.00
313_E 307_G 0.76 0.12 0.00
142_K 456_D 0.76 0.12 0.00
314_D 134_Y 0.76 0.12 0.00
202_V 480_D 0.76 0.12 0.00
308_L 517_A 0.76 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)
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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