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OPENSEQ.org
ds1
Genes: A B A+B
Length: 724 543 1177
Sequences: 2474 5145 612
Seq/Len: 3.42 9.48 0.52
MirrorTree (Pazo et al. 2001) 0.41
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 0.02 0.00
2 0.05 0.02 0.01
5 0.05 0.03 0.01
10 0.05 0.03 0.01
20 0.05 0.03 0.03
100 0.05 0.06 0.10
∞ 0.06 0.13 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
469_L 413_A 1.14 0.30 0.00
97_D 97_E 1.13 0.30 0.00
80_Q 37_N 1.05 0.25 0.00
165_F 334_D 0.99 0.21 0.00
471_E 468_Y 0.99 0.21 0.00
198_V 134_Y 0.97 0.21 0.00
335_I 394_A 0.96 0.20 0.00
80_Q 367_G 0.96 0.20 0.00
199_K 303_Y 0.95 0.20 0.00
213_I 309_S 0.95 0.20 0.00
381_V 190_M 0.95 0.20 0.00
473_V 273_G 0.94 0.19 0.00
638_L 112_L 0.93 0.18 0.00
73_I 315_K 0.92 0.18 0.00
75_I 95_Y 0.91 0.18 0.00
63_S 350_E 0.91 0.18 0.00
635_V 57_A 0.88 0.17 0.00
314_D 413_A 0.88 0.16 0.00
295_D 495_V 0.88 0.16 0.00
192_Y 270_F 0.87 0.16 0.00
318_V 406_K 0.87 0.16 0.00
187_E 19_N 0.87 0.16 0.00
314_D 238_K 0.87 0.16 0.00
82_R 134_Y 0.86 0.15 0.00
539_E 307_G 0.86 0.15 0.00
381_V 393_D 0.85 0.15 0.00
202_V 395_K 0.85 0.15 0.00
191_E 445_T 0.85 0.15 0.00
91_I 86_N 0.85 0.15 0.00
605_I 263_T 0.85 0.15 0.00
184_H 74_G 0.84 0.15 0.00
57_E 306_I 0.84 0.15 0.00
70_E 99_L 0.84 0.15 0.00
124_S 248_Y 0.84 0.15 0.00
192_Y 305_R 0.84 0.15 0.00
299_E 333_P 0.83 0.14 0.00
147_T 196_I 0.83 0.14 0.00
44_I 94_T 0.82 0.14 0.00
482_S 58_Y 0.82 0.14 0.00
580_I 10_K 0.82 0.14 0.00
91_I 482_P 0.81 0.14 0.00
408_I 319_A 0.81 0.14 0.00
184_H 340_Q 0.81 0.14 0.00
213_I 82_L 0.81 0.14 0.00
142_K 407_L 0.80 0.13 0.00
102_L 304_A 0.80 0.13 0.00
84_L 107_Q 0.80 0.13 0.00
96_A 404_Y 0.80 0.13 0.00
26_S 340_Q 0.80 0.13 0.00
380_V 86_N 0.80 0.13 0.00
605_I 495_V 0.80 0.13 0.00
165_F 452_Q 0.80 0.13 0.00
201_V 58_Y 0.80 0.13 0.00
295_D 380_M 0.80 0.13 0.00
314_D 108_L 0.79 0.13 0.00
460_S 314_E 0.79 0.13 0.00
44_I 453_K 0.79 0.13 0.00
86_L 235_A 0.79 0.13 0.00
473_V 421_I 0.79 0.13 0.00
147_T 79_A 0.79 0.13 0.00
420_A 338_K 0.79 0.13 0.00
79_P 254_L 0.79 0.13 0.00
684_I 103_A 0.79 0.13 0.00
337_R 453_K 0.78 0.13 0.00
381_V 199_P 0.78 0.13 0.00
471_E 232_G 0.78 0.13 0.00
547_E 61_G 0.78 0.13 0.00
202_V 341_Q 0.78 0.13 0.00
313_E 459_S 0.78 0.13 0.00
381_V 89_E 0.78 0.12 0.00
295_D 53_D 0.78 0.12 0.00
144_V 460_S 0.78 0.12 0.00
470_S 421_I 0.78 0.12 0.00
181_V 351_R 0.77 0.12 0.00
579_T 367_G 0.77 0.12 0.00
628_I 110_E 0.77 0.12 0.00
44_I 321_H 0.77 0.12 0.00
622_A 383_Y 0.77 0.12 0.00
211_Y 413_A 0.77 0.12 0.00
142_K 332_T 0.77 0.12 0.00
222_E 23_A 0.77 0.12 0.00
154_Q 392_K 0.76 0.12 0.00
586_S 386_A 0.76 0.12 0.00
197_R 437_A 0.76 0.12 0.00
147_T 50_K 0.76 0.12 0.00
165_F 275_Y 0.76 0.12 0.00
563_L 320_I 0.76 0.12 0.00
608_A 495_V 0.76 0.12 0.00
44_I 377_P 0.76 0.12 0.00
413_L 387_I 0.76 0.12 0.00
167_V 393_D 0.75 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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