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OPENSEQ.org
hs_alpha-V-hs_gamma
Genes: A B A+B
Length: 305 452 731
Sequences: 2820 791 169
Seq/Len: 9.25 1.75 0.23
MirrorTree (Pazo et al. 2001) 0.19
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 0.02 0.00
2 0.06 0.02 0.00
5 0.06 0.02 0.00
10 0.06 0.02 0.00
20 0.07 0.03 0.01
100 0.07 0.03 0.05
∞ 0.11 0.04 0.22
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 398_V 1.48 0.34 0.00
224_K 398_V 1.46 0.33 0.00
95_E 392_L 1.37 0.28 0.00
164_M 402_S 1.22 0.21 0.00
76_I 352_V 1.16 0.19 0.00
284_L 387_I 1.14 0.18 0.00
124_T 51_V 1.13 0.17 0.00
57_C 367_K 1.13 0.17 0.00
101_L 392_L 1.12 0.17 0.00
165_A 379_C 1.12 0.17 0.00
207_I 384_R 1.12 0.17 0.00
78_L 102_L 1.11 0.17 0.00
187_M 89_S 1.08 0.16 0.00
173_V 55_T 1.06 0.15 0.00
155_S 229_I 1.06 0.15 0.00
178_V 375_I 1.06 0.15 0.00
119_I 135_G 1.05 0.15 0.00
97_G 399_E 1.04 0.15 0.00
149_S 109_I 1.04 0.15 0.00
175_V 304_I 1.04 0.14 0.00
285_F 438_R 1.03 0.14 0.00
190_A 336_E 1.03 0.14 0.00
168_L 5_A 1.03 0.14 0.00
34_L 90_L 1.02 0.14 0.00
34_L 160_V 1.01 0.14 0.00
283_L 217_E 1.00 0.14 0.00
263_G 387_I 1.00 0.13 0.00
281_I 364_I 0.99 0.13 0.00
243_Q 370_I 0.99 0.13 0.00
184_G 122_R 0.99 0.13 0.00
188_E 409_I 0.99 0.13 0.00
88_K 412_N 0.98 0.13 0.00
220_K 413_A 0.98 0.13 0.00
173_V 327_P 0.97 0.13 0.00
193_V 358_I 0.97 0.13 0.00
216_A 404_I 0.97 0.13 0.00
190_A 122_R 0.97 0.12 0.00
220_K 369_S 0.96 0.12 0.00
90_K 433_E 0.96 0.12 0.00
76_I 118_V 0.96 0.12 0.00
68_G 204_L 0.96 0.12 0.00
290_V 432_I 0.96 0.12 0.00
94_I 30_V 0.96 0.12 0.00
184_G 346_I 0.96 0.12 0.00
224_K 8_M 0.95 0.12 0.00
278_P 375_I 0.95 0.12 0.00
220_K 401_G 0.95 0.12 0.00
119_I 397_T 0.94 0.12 0.00
228_V 370_I 0.94 0.12 0.00
220_K 89_S 0.94 0.12 0.00
38_K 415_I 0.94 0.12 0.00
58_G 36_I 0.94 0.12 0.00
46_R 81_D 0.93 0.12 0.00
141_A 376_G 0.93 0.12 0.00
274_D 29_P 0.93 0.12 0.00
56_L 16_M 0.93 0.11 0.00
98_E 36_I 0.93 0.11 0.00
208_N 392_L 0.92 0.11 0.00
208_N 426_I 0.92 0.11 0.00
194_I 316_L 0.92 0.11 0.00
230_A 381_I 0.92 0.11 0.00
78_L 159_G 0.92 0.11 0.00
278_P 429_G 0.92 0.11 0.00
54_E 369_S 0.91 0.11 0.00
103_R 72_K 0.91 0.11 0.00
279_S 406_G 0.91 0.11 0.00
186_I 49_E 0.91 0.11 0.00
213_N 363_Q 0.90 0.11 0.00
66_S 73_P 0.90 0.11 0.00
30_L 370_I 0.89 0.11 0.00
251_K 226_S 0.89 0.10 0.00
151_Y 378_S 0.89 0.10 0.00
194_I 384_R 0.89 0.10 0.00
125_I 368_S 0.89 0.10 0.00
136_R 364_I 0.88 0.10 0.00
215_M 378_S 0.88 0.10 0.00
197_A 390_C 0.88 0.10 0.00
227_Y 19_L 0.88 0.10 0.00
151_Y 415_I 0.88 0.10 0.00
97_G 227_E 0.88 0.10 0.00
184_G 342_S 0.87 0.10 0.00
138_L 319_Y 0.87 0.10 0.00
220_K 125_D 0.87 0.10 0.00
216_A 375_I 0.87 0.10 0.00
284_L 35_L 0.87 0.10 0.00
109_N 217_E 0.87 0.10 0.00
125_I 415_I 0.87 0.10 0.00
280_L 304_I 0.86 0.10 0.00
285_F 89_S 0.86 0.10 0.00
266_L 40_L 0.86 0.10 0.00
223_N 435_K 0.86 0.10 0.00
122_G 385_V 0.86 0.10 0.00
190_A 120_L 0.86 0.10 0.00
54_E 415_I 0.86 0.10 0.00
95_E 185_S 0.85 0.10 0.00
197_A 406_G 0.85 0.10 0.00
51_S 53_V 0.85 0.10 0.00
140_A 352_V 0.85 0.10 0.00
125_I 224_I 0.85 0.10 0.00
187_M 6_V 0.85 0.10 0.00
34_L 415_I 0.85 0.10 0.00
279_S 180_L 0.85 0.10 0.00
178_V 159_G 0.84 0.10 0.00
177_V 5_A 0.84 0.09 0.00
49_L 22_S 0.84 0.09 0.00
56_L 408_V 0.84 0.09 0.00
84_S 51_V 0.84 0.09 0.00
94_I 385_V 0.84 0.09 0.00
172_N 88_D 0.84 0.09 0.00
279_S 7_V 0.84 0.09 0.00
194_I 409_I 0.84 0.09 0.00
185_Y 373_S 0.84 0.09 0.00
221_A 37_W 0.83 0.09 0.00
228_V 205_Y 0.83 0.09 0.00
224_K 356_S 0.83 0.09 0.00
93_M 229_I 0.83 0.09 0.00
125_I 381_I 0.82 0.09 0.00
172_N 165_K 0.82 0.09 0.00
43_Q 138_S 0.82 0.09 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
7716 0.23 hs_alpha-V-hs_gamma Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.00 Done - Shared
7704 0.01 hs_alpha-V-hs_gamma Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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