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OPENSEQ.org
13
Genes: A B A+B
Length: 840 340 1096
Sequences: 868 4321 133
Seq/Len: 1.03 12.71 0.12
MirrorTree (Pazo et al. 2001) 0.33
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 0.03 0.06 0.00
2 0.03 0.06 0.00
5 0.04 0.06 0.00
10 0.04 0.06 0.01
20 0.04 0.06 0.01
100 0.04 0.07 0.04
∞ 0.05 0.12 0.11
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
261_R 171_S 2.14 0.53 0.03
662_D 297_V 1.68 0.30 0.01
261_R 11_L 1.48 0.22 0.01
674_K 302_L 1.35 0.18 0.00
203_M 19_E 1.31 0.17 0.00
396_D 254_V 1.29 0.16 0.00
261_R 174_E 1.28 0.16 0.00
190_A 64_F 1.26 0.15 0.00
207_A 276_L 1.24 0.15 0.00
25_T 260_I 1.23 0.14 0.00
662_D 67_Y 1.22 0.14 0.00
306_F 278_G 1.20 0.14 0.00
261_R 243_P 1.20 0.14 0.00
25_T 48_I 1.17 0.13 0.00
685_I 174_E 1.17 0.13 0.00
661_E 253_D 1.15 0.12 0.00
23_I 243_P 1.15 0.12 0.00
119_A 16_S 1.14 0.12 0.00
604_M 20_I 1.12 0.12 0.00
122_L 266_L 1.12 0.12 0.00
156_V 206_I 1.09 0.11 0.00
313_L 206_I 1.08 0.11 0.00
276_L 13_R 1.07 0.11 0.00
97_G 11_L 1.07 0.11 0.00
119_A 253_D 1.07 0.11 0.00
261_R 8_T 1.06 0.11 0.00
113_T 297_V 1.06 0.10 0.00
52_A 250_D 1.06 0.10 0.00
202_D 32_H 1.05 0.10 0.00
301_M 235_I 1.05 0.10 0.00
236_F 19_E 1.04 0.10 0.00
258_S 206_I 1.04 0.10 0.00
37_A 239_L 1.04 0.10 0.00
594_L 54_V 1.03 0.10 0.00
51_A 11_L 1.03 0.10 0.00
126_K 174_E 1.02 0.10 0.00
337_A 260_I 1.02 0.10 0.00
229_T 276_L 1.02 0.10 0.00
661_E 66_R 1.02 0.10 0.00
224_A 174_E 1.02 0.10 0.00
464_V 334_L 1.01 0.10 0.00
646_N 19_E 1.00 0.09 0.00
39_I 245_N 0.99 0.09 0.00
664_E 323_P 0.98 0.09 0.00
316_R 180_T 0.98 0.09 0.00
87_L 261_S 0.98 0.09 0.00
215_F 208_V 0.97 0.09 0.00
199_V 155_P 0.97 0.09 0.00
276_L 67_Y 0.97 0.09 0.00
87_L 297_V 0.97 0.09 0.00
513_D 260_I 0.97 0.09 0.00
233_G 303_P 0.97 0.09 0.00
1_M 174_E 0.97 0.09 0.00
325_L 61_R 0.97 0.09 0.00
642_E 147_G 0.97 0.09 0.00
338_V 253_D 0.97 0.09 0.00
623_E 329_T 0.97 0.09 0.00
317_V 273_V 0.96 0.09 0.00
202_D 34_D 0.96 0.09 0.00
258_S 273_V 0.96 0.09 0.00
99_T 320_V 0.96 0.09 0.00
274_K 48_I 0.96 0.09 0.00
15_V 299_G 0.96 0.09 0.00
153_R 249_R 0.94 0.08 0.00
261_R 119_R 0.94 0.08 0.00
642_E 334_L 0.94 0.08 0.00
202_D 312_G 0.94 0.08 0.00
204_G 178_G 0.94 0.08 0.00
342_G 178_G 0.94 0.08 0.00
622_E 178_G 0.94 0.08 0.00
658_W 178_G 0.94 0.08 0.00
476_S 318_F 0.94 0.08 0.00
449_P 174_E 0.94 0.08 0.00
402_I 16_S 0.93 0.08 0.00
155_S 8_T 0.93 0.08 0.00
330_L 273_V 0.93 0.08 0.00
589_I 239_L 0.93 0.08 0.00
343_G 61_R 0.93 0.08 0.00
47_S 106_F 0.92 0.08 0.00
202_D 33_P 0.92 0.08 0.00
274_K 303_P 0.92 0.08 0.00
628_M 269_C 0.92 0.08 0.00
288_I 37_K 0.92 0.08 0.00
293_N 174_E 0.91 0.08 0.00
41_F 211_G 0.91 0.08 0.00
141_V 265_A 0.91 0.08 0.00
326_E 254_V 0.91 0.08 0.00
235_K 61_R 0.90 0.08 0.00
143_S 334_L 0.90 0.08 0.00
288_I 30_R 0.90 0.08 0.00
112_F 253_D 0.90 0.08 0.00
212_V 154_E 0.89 0.08 0.00
321_L 131_F 0.89 0.08 0.00
662_D 174_E 0.89 0.08 0.00
178_A 48_I 0.89 0.08 0.00
396_D 302_L 0.89 0.08 0.00
600_N 239_L 0.89 0.08 0.00
250_K 281_I 0.89 0.07 0.00
25_T 262_L 0.88 0.07 0.00
485_N 229_N 0.88 0.07 0.00
242_N 246_I 0.88 0.07 0.00
338_V 48_I 0.88 0.07 0.00
604_M 61_R 0.88 0.07 0.00
289_E 303_P 0.88 0.07 0.00
280_N 253_D 0.88 0.07 0.00
126_K 316_I 0.88 0.07 0.00
293_N 210_K 0.88 0.07 0.00
662_D 295_R 0.88 0.07 0.00
113_T 218_I 0.87 0.07 0.00
145_P 51_A 0.87 0.07 0.00
626_Y 268_G 0.87 0.07 0.00
334_D 14_G 0.87 0.07 0.00
629_R 232_P 0.87 0.07 0.00
155_S 266_L 0.87 0.07 0.00
378_L 5_Y 0.87 0.07 0.00
678_L 265_A 0.87 0.07 0.00
97_G 222_K 0.87 0.07 0.00
14_Y 174_E 0.87 0.07 0.00
202_D 301_G 0.86 0.07 0.00
679_K 168_L 0.86 0.07 0.00
99_T 277_D 0.86 0.07 0.00
67_F 266_L 0.86 0.07 0.00
117_V 167_D 0.86 0.07 0.00
112_F 205_T 0.86 0.07 0.00
202_D 249_R 0.86 0.07 0.00
354_I 14_G 0.86 0.07 0.00
338_V 168_L 0.86 0.07 0.00
188_L 215_G 0.85 0.07 0.00
655_T 8_T 0.85 0.07 0.00
99_T 174_E 0.85 0.07 0.00
164_G 13_R 0.85 0.07 0.00
7_D 178_G 0.84 0.07 0.00
9_G 178_G 0.84 0.07 0.00
33_R 178_G 0.84 0.07 0.00
67_F 205_T 0.84 0.07 0.00
331_K 254_V 0.84 0.07 0.00
497_L 5_Y 0.84 0.07 0.00
97_G 267_C 0.84 0.07 0.00
346_R 178_G 0.84 0.07 0.00
370_E 178_G 0.84 0.07 0.00
375_G 178_G 0.84 0.07 0.00
306_F 313_D 0.84 0.07 0.00
411_E 19_E 0.84 0.07 0.00
173_E 302_L 0.84 0.07 0.00
122_L 276_L 0.84 0.07 0.00
309_M 62_E 0.84 0.07 0.00
64_V 19_E 0.84 0.07 0.00
207_A 261_S 0.84 0.07 0.00
208_Y 206_I 0.84 0.07 0.00
91_I 334_L 0.84 0.07 0.00
328_T 16_S 0.83 0.07 0.00
240_L 323_P 0.83 0.07 0.00
377_A 281_I 0.83 0.07 0.00
735_E 289_I 0.83 0.07 0.00
279_A 314_L 0.83 0.07 0.00
709_Y 54_V 0.83 0.07 0.00
729_A 26_R 0.83 0.07 0.00
209_Q 37_K 0.83 0.07 0.00
278_S 51_A 0.83 0.07 0.00
157_M 13_R 0.82 0.07 0.00
193_E 91_S 0.82 0.07 0.00
154_R 217_K 0.82 0.07 0.00
170_L 53_D 0.82 0.07 0.00
52_A 323_P 0.82 0.07 0.00
638_K 170_V 0.82 0.07 0.00
147_F 82_G 0.82 0.07 0.00
281_A 174_E 0.82 0.07 0.00
287_S 334_L 0.82 0.07 0.00
387_F 57_D 0.82 0.07 0.00
665_D 52_Y 0.82 0.07 0.00
419_V 35_K 0.82 0.07 0.00
253_K 14_G 0.82 0.07 0.00
680_N 269_C 0.82 0.07 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
8548 0.12 13 Δgene:(0, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.03 Done - Shared
8447 0 HSP74_HUMANDNJB1_HUMAN Δgene:(0, 0) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
8445 0 HSP74_HUMANDNJB1_HUMAN Δgene:(0, 0) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
8444 0.01 HSP74_HUMANDNJB1_HUMAN Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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