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OPENSEQ.org
ds1
Genes: A B A+B
Length: 724 543 1159
Sequences: 2474 2994 506
Seq/Len: 3.42 5.51 0.44
MirrorTree (Pazo et al. 2001) 0.53
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 0.02 0.00
10 0.05 0.02 0.01
20 0.05 0.02 0.01
100 0.05 0.03 0.05
∞ 0.06 0.11 0.40
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
73_I 113_Q 1.41 0.46 0.00
398_S 472_M 1.21 0.32 0.00
181_V 86_N 1.20 0.31 0.00
136_A 387_I 1.14 0.27 0.00
381_V 395_K 1.11 0.26 0.00
96_A 307_G 1.11 0.26 0.00
513_M 265_Q 1.11 0.26 0.00
202_V 479_H 1.09 0.25 0.00
84_L 28_S 1.09 0.25 0.00
295_D 343_E 1.09 0.25 0.00
213_I 57_A 1.08 0.24 0.00
181_V 309_S 1.07 0.24 0.00
469_L 269_Y 1.07 0.23 0.00
99_I 11_G 1.06 0.23 0.00
44_I 316_Y 1.03 0.21 0.00
282_L 18_G 1.03 0.21 0.00
102_L 225_A 1.02 0.21 0.00
78_N 408_L 1.01 0.20 0.00
76_I 19_N 1.00 0.20 0.00
199_K 374_G 1.00 0.20 0.00
297_T 91_A 1.00 0.20 0.00
84_L 56_K 0.99 0.19 0.00
96_A 51_K 0.97 0.18 0.00
602_M 182_L 0.96 0.18 0.00
145_V 225_A 0.96 0.18 0.00
504_R 66_D 0.96 0.18 0.00
445_S 523_K 0.95 0.18 0.00
114_M 266_A 0.94 0.17 0.00
187_E 469_Q 0.94 0.17 0.00
478_E 55_Q 0.92 0.16 0.00
44_I 226_L 0.92 0.16 0.00
82_R 61_G 0.91 0.16 0.00
405_R 340_Q 0.91 0.16 0.00
314_D 437_A 0.91 0.16 0.00
557_K 57_A 0.90 0.16 0.00
595_T 10_K 0.90 0.15 0.00
145_V 307_G 0.90 0.15 0.00
215_L 218_L 0.90 0.15 0.00
84_L 451_Y 0.89 0.15 0.00
82_R 376_Y 0.89 0.15 0.00
181_V 343_E 0.89 0.15 0.00
580_I 117_A 0.89 0.15 0.00
679_R 323_Y 0.89 0.15 0.00
165_F 398_S 0.88 0.15 0.00
580_I 70_D 0.88 0.15 0.00
660_E 13_K 0.87 0.14 0.00
96_A 426_T 0.87 0.14 0.00
147_T 398_S 0.87 0.14 0.00
73_I 411_Q 0.87 0.14 0.00
191_E 113_Q 0.86 0.14 0.00
165_F 410_F 0.86 0.14 0.00
44_I 79_A 0.86 0.14 0.00
193_L 340_Q 0.86 0.14 0.00
73_I 53_D 0.86 0.14 0.00
314_D 413_A 0.86 0.14 0.00
353_I 487_R 0.85 0.14 0.00
370_I 378_Q 0.85 0.14 0.00
676_H 367_G 0.84 0.14 0.00
102_L 282_C 0.84 0.13 0.00
409_V 307_G 0.84 0.13 0.00
181_V 32_K 0.84 0.13 0.00
199_K 303_Y 0.84 0.13 0.00
102_L 307_G 0.84 0.13 0.00
659_F 239_K 0.84 0.13 0.00
421_E 350_E 0.83 0.13 0.00
147_T 289_G 0.83 0.13 0.00
424_E 314_E 0.83 0.13 0.00
44_I 119_L 0.82 0.13 0.00
213_I 246_K 0.82 0.13 0.00
165_F 46_A 0.82 0.13 0.00
165_F 80_A 0.82 0.13 0.00
684_I 311_F 0.82 0.13 0.00
502_R 340_Q 0.82 0.13 0.00
292_N 443_D 0.82 0.12 0.00
102_L 268_V 0.82 0.12 0.00
282_L 418_E 0.82 0.12 0.00
605_I 56_K 0.81 0.12 0.00
473_V 47_A 0.81 0.12 0.00
295_D 20_I 0.81 0.12 0.00
93_M 426_T 0.81 0.12 0.00
517_I 5_N 0.81 0.12 0.00
288_I 374_G 0.81 0.12 0.00
579_T 91_A 0.81 0.12 0.00
166_T 266_A 0.81 0.12 0.00
281_E 266_A 0.81 0.12 0.00
412_C 278_C 0.81 0.12 0.00
167_V 397_Y 0.81 0.12 0.00
75_I 10_K 0.80 0.12 0.00
550_K 251_A 0.80 0.12 0.00
672_D 333_P 0.80 0.12 0.00
414_E 85_L 0.80 0.12 0.00
191_E 375_D 0.80 0.12 0.00
181_V 59_E 0.80 0.12 0.00
187_E 242_D 0.80 0.12 0.00
513_M 341_Q 0.80 0.12 0.00
295_D 19_N 0.80 0.12 0.00
96_A 258_N 0.80 0.12 0.00
485_Y 91_A 0.80 0.12 0.00
445_S 477_N 0.79 0.12 0.00
591_I 266_A 0.79 0.12 0.00
187_E 98_G 0.79 0.12 0.00
75_I 362_E 0.79 0.12 0.00
181_V 24_L 0.79 0.12 0.00
314_D 421_I 0.79 0.12 0.00
496_N 342_A 0.79 0.12 0.00
380_V 228_E 0.79 0.12 0.00
580_I 243_T 0.79 0.12 0.00
142_K 351_R 0.79 0.12 0.00
410_K 375_D 0.79 0.12 0.00
635_V 45_S 0.79 0.12 0.00
354_K 433_R 0.79 0.12 0.00
99_I 87_R 0.79 0.12 0.00
84_L 29_E 0.79 0.12 0.00
628_I 321_H 0.79 0.12 0.00
529_D 424_E 0.78 0.12 0.00
563_L 390_N 0.78 0.12 0.00
334_F 271_E 0.78 0.11 0.00
505_K 256_P 0.78 0.11 0.00
381_V 21_D 0.78 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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