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OPENSEQ.org
hs_alpha-V-hs_epsilon
Genes: A B A+B
Length: 305 721 937
Sequences: 2820 355 80
Seq/Len: 9.25 0.49 0.09
MirrorTree (Pazo et al. 2001) 0.42
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 0.06 0.03 0.00
2 0.06 0.03 0.00
5 0.06 0.03 0.00
10 0.06 0.03 0.00
20 0.07 0.03 0.00
100 0.07 0.03 0.02
∞ 0.11 0.04 0.08
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
34_L 681_I 1.87 0.33 0.00
50_T 432_T 1.60 0.22 0.00
94_I 389_V 1.30 0.14 0.00
281_I 75_L 1.28 0.13 0.00
87_S 707_I 1.25 0.13 0.00
173_V 314_I 1.24 0.12 0.00
178_V 143_L 1.23 0.12 0.00
33_F 423_V 1.22 0.12 0.00
200_V 49_A 1.20 0.12 0.00
119_I 271_D 1.18 0.11 0.00
151_Y 382_G 1.18 0.11 0.00
190_A 324_E 1.17 0.11 0.00
220_K 417_A 1.16 0.11 0.00
280_L 413_L 1.15 0.11 0.00
220_K 405_G 1.15 0.11 0.00
119_I 646_L 1.15 0.10 0.00
90_K 438_G 1.14 0.10 0.00
190_A 40_P 1.13 0.10 0.00
281_I 349_S 1.13 0.10 0.00
82_E 425_L 1.12 0.10 0.00
177_V 46_V 1.12 0.10 0.00
165_A 419_V 1.11 0.10 0.00
7_I 40_P 1.11 0.10 0.00
277_A 494_G 1.10 0.10 0.00
119_I 714_E 1.08 0.09 0.00
139_E 674_E 1.07 0.09 0.00
270_H 52_F 1.06 0.09 0.00
111_I 171_R 1.06 0.09 0.00
64_A 554_Q 1.06 0.09 0.00
193_V 398_Q 1.05 0.09 0.00
227_Y 632_F 1.05 0.09 0.00
157_P 69_P 1.04 0.09 0.00
82_E 92_F 1.04 0.09 0.00
105_S 391_L 1.03 0.09 0.00
181_A 172_R 1.02 0.09 0.00
55_T 399_G 1.02 0.08 0.00
182_A 171_R 1.00 0.08 0.00
64_A 621_L 1.00 0.08 0.00
243_Q 348_V 1.00 0.08 0.00
17_D 347_E 1.00 0.08 0.00
207_I 388_N 0.99 0.08 0.00
203_N 397_W 0.99 0.08 0.00
220_K 586_N 0.99 0.08 0.00
206_I 300_V 0.98 0.08 0.00
286_T 565_K 0.98 0.08 0.00
284_L 155_V 0.97 0.08 0.00
151_Y 319_Y 0.97 0.08 0.00
98_E 557_V 0.96 0.08 0.00
229_V 184_I 0.96 0.07 0.00
212_T 576_L 0.96 0.07 0.00
105_S 683_S 0.96 0.07 0.00
200_V 400_V 0.95 0.07 0.00
220_K 309_V 0.95 0.07 0.00
193_V 230_L 0.95 0.07 0.00
224_K 350_L 0.94 0.07 0.00
74_R 267_Q 0.94 0.07 0.00
207_I 368_I 0.94 0.07 0.00
127_T 158_N 0.94 0.07 0.00
181_A 274_R 0.94 0.07 0.00
139_E 377_S 0.93 0.07 0.00
119_I 263_N 0.93 0.07 0.00
203_N 492_G 0.93 0.07 0.00
178_V 696_Q 0.93 0.07 0.00
283_L 262_D 0.93 0.07 0.00
29_T 98_K 0.93 0.07 0.00
193_V 674_E 0.93 0.07 0.00
204_G 83_L 0.93 0.07 0.00
204_G 264_F 0.93 0.07 0.00
211_G 83_L 0.93 0.07 0.00
211_G 264_F 0.93 0.07 0.00
293_P 154_D 0.92 0.07 0.00
82_E 143_L 0.92 0.07 0.00
62_S 408_I 0.92 0.07 0.00
203_N 78_Y 0.92 0.07 0.00
199_G 627_A 0.92 0.07 0.00
17_D 39_P 0.92 0.07 0.00
44_G 37_E 0.92 0.07 0.00
182_A 253_S 0.91 0.07 0.00
221_A 186_K 0.91 0.07 0.00
145_K 402_V 0.91 0.07 0.00
34_L 418_E 0.91 0.07 0.00
98_E 440_N 0.90 0.07 0.00
45_L 563_R 0.90 0.07 0.00
151_Y 434_Q 0.90 0.07 0.00
48_N 425_L 0.90 0.07 0.00
110_K 226_F 0.89 0.07 0.00
72_F 411_S 0.89 0.07 0.00
51_S 679_E 0.88 0.07 0.00
215_M 372_C 0.88 0.07 0.00
285_F 184_I 0.88 0.07 0.00
50_T 559_G 0.88 0.07 0.00
268_E 374_I 0.88 0.07 0.00
168_L 215_F 0.88 0.07 0.00
40_E 46_V 0.88 0.07 0.00
127_T 133_D 0.88 0.07 0.00
49_L 192_H 0.88 0.07 0.00
10_F 546_Q 0.87 0.07 0.00
168_L 132_G 0.87 0.06 0.00
168_L 136_R 0.87 0.06 0.00
168_L 265_D 0.87 0.06 0.00
220_K 686_S 0.87 0.06 0.00
152_V 382_G 0.86 0.06 0.00
261_Q 351_G 0.86 0.06 0.00
168_L 45_A 0.86 0.06 0.00
149_S 587_I 0.86 0.06 0.00
172_N 149_L 0.86 0.06 0.00
50_T 151_V 0.86 0.06 0.00
49_L 75_L 0.86 0.06 0.00
113_D 588_S 0.86 0.06 0.00
215_M 144_V 0.86 0.06 0.00
176_T 366_T 0.86 0.06 0.00
170_H 397_W 0.86 0.06 0.00
173_V 245_L 0.86 0.06 0.00
144_A 718_S 0.85 0.06 0.00
151_Y 351_G 0.85 0.06 0.00
168_L 671_Y 0.85 0.06 0.00
88_K 416_N 0.85 0.06 0.00
124_T 405_G 0.85 0.06 0.00
228_V 431_L 0.85 0.06 0.00
57_C 205_V 0.85 0.06 0.00
165_A 144_V 0.85 0.06 0.00
6_L 230_L 0.85 0.06 0.00
175_V 291_V 0.85 0.06 0.00
82_E 528_E 0.84 0.06 0.00
201_V 586_N 0.84 0.06 0.00
168_L 553_F 0.84 0.06 0.00
56_L 215_F 0.84 0.06 0.00
102_R 679_E 0.84 0.06 0.00
8_E 399_G 0.84 0.06 0.00
144_A 437_V 0.84 0.06 0.00
172_N 356_L 0.84 0.06 0.00
200_V 408_I 0.84 0.06 0.00
199_G 574_L 0.84 0.06 0.00
109_N 436_V 0.84 0.06 0.00
95_E 719_E 0.84 0.06 0.00
184_G 688_R 0.83 0.06 0.00
178_V 349_S 0.83 0.06 0.00
119_I 592_V 0.83 0.06 0.00
193_V 409_H 0.83 0.06 0.00
165_A 383_C 0.83 0.06 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
7713 0.09 hs_alpha-V-hs_epsilon Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
7703 0 hs_alpha-V-hs_epsilon Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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