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OPENSEQ.org
cytb_80_cIV_A_80_human
Genes: A B A+B
Length: 378 513 888
Sequences: 3718 3112 1615
Seq/Len: 9.84 6.07 1.82
MirrorTree (Pazo et al. 2001) 0.71
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 0.02 0.01 0.08
2 0.02 0.01 0.15
5 0.02 0.01 0.44
10 0.02 0.01 1.43
20 0.02 0.01 1.52
100 0.02 0.01 1.56
∞ 0.02 0.04 1.81
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
269_K 204_A 1.21 0.71 0.01
318_R 270_Y 1.13 0.63 0.01
243_T 314_I 1.12 0.62 0.01
197_L 359_A 1.11 0.62 0.01
152_A 182_P 1.08 0.58 0.01
254_D 231_Y 1.05 0.55 0.01
209_L 274_V 1.04 0.54 0.01
47_T 311_I 1.03 0.53 0.01
322_Q 356_I 1.03 0.52 0.01
27_I 53_I 1.02 0.52 0.01
262_L 254_I 1.01 0.51 0.01
211_I 139_P 1.01 0.51 0.01
308_H 363_L 1.00 0.50 0.01
362_I 172_K 1.00 0.50 0.01
224_Y 346_F 0.99 0.49 0.01
105_G 193_I 0.99 0.48 0.01
79_I 297_M 0.98 0.48 0.01
21_L 340_W 0.97 0.46 0.01
129_M 413_H 0.96 0.45 0.01
343_V 81_W 0.96 0.45 0.01
176_T 359_A 0.95 0.44 0.01
351_G 286_I 0.95 0.44 0.01
317_F 142_S 0.95 0.44 0.01
292_L 53_I 0.94 0.43 0.01
49_L 50_N 0.94 0.43 0.01
239_L 166_T 0.93 0.42 0.01
140_F 112_L 0.93 0.42 0.01
40_C 109_L 0.92 0.41 0.01
62_A 152_L 0.92 0.41 0.01
102_L 174_P 0.92 0.41 0.01
115_I 350_V 0.91 0.40 0.01
267_H 12_H 0.91 0.40 0.01
258_L 182_P 0.91 0.40 0.01
362_I 204_A 0.91 0.40 0.01
156_I 39_A 0.90 0.38 0.01
160_L 133_A 0.89 0.38 0.01
194_T 193_I 0.89 0.38 0.01
324_L 342_L 0.89 0.38 0.01
184_I 146_T 0.89 0.38 0.01
163_W 81_W 0.89 0.37 0.01
137_Q 234_L 0.89 0.37 0.01
70_T 279_S 0.88 0.37 0.01
43_L 416_I 0.88 0.36 0.01
224_Y 389_I 0.87 0.36 0.01
279_T 198_S 0.87 0.36 0.01
119_L 20_L 0.87 0.36 0.01
301_L 314_I 0.86 0.35 0.01
25_S 24_A 0.86 0.35 0.01
37_L 328_H 0.86 0.35 0.01
119_L 412_I 0.86 0.35 0.01
206_N 211_T 0.85 0.34 0.01
224_Y 218_T 0.85 0.34 0.01
251_G 314_I 0.85 0.34 0.01
189_I 469_I 0.85 0.33 0.01
41_L 90_P 0.84 0.33 0.01
297_S 297_M 0.84 0.33 0.01
160_L 18_L 0.84 0.33 0.01
318_R 274_V 0.84 0.33 0.01
92_I 89_A 0.84 0.33 0.01
309_M 258_V 0.84 0.33 0.01
119_L 335_S 0.84 0.33 0.01
105_G 357_V 0.84 0.32 0.01
47_T 17_T 0.83 0.32 0.01
107_F 401_S 0.83 0.32 0.01
37_L 340_W 0.83 0.32 0.01
355_S 172_K 0.83 0.32 0.01
322_Q 320_V 0.83 0.32 0.01
71_R 172_K 0.83 0.32 0.01
197_L 274_V 0.83 0.32 0.01
135_W 12_H 0.82 0.31 0.00
279_T 159_L 0.82 0.31 0.00
180_T 492_L 0.82 0.31 0.00
239_L 253_M 0.82 0.31 0.00
190_A 218_T 0.82 0.31 0.00
150_L 388_A 0.81 0.30 0.00
156_I 113_L 0.81 0.30 0.00
30_W 507_E 0.81 0.30 0.00
356_V 464_A 0.81 0.30 0.00
185_L 229_I 0.81 0.30 0.00
318_R 330_S 0.81 0.30 0.00
153_I 453_L 0.81 0.30 0.00
269_K 491_N 0.81 0.30 0.00
70_T 215_L 0.81 0.30 0.00
45_I 33_L 0.80 0.29 0.00
82_L 471_M 0.80 0.29 0.00
153_I 97_M 0.80 0.29 0.00
62_A 311_I 0.80 0.29 0.00
368_T 463_T 0.79 0.29 0.00
152_A 70_V 0.79 0.29 0.00
118_I 419_I 0.79 0.29 0.00
153_I 460_I 0.79 0.28 0.00
234_L 320_V 0.79 0.28 0.00
140_F 253_M 0.79 0.28 0.00
269_K 172_K 0.79 0.28 0.00
184_I 83_V 0.79 0.28 0.00
313_Q 205_G 0.79 0.28 0.00
164_I 93_A 0.79 0.28 0.00
55_Y 267_P 0.79 0.28 0.00
254_D 468_M 0.79 0.28 0.00
193_A 27_G 0.79 0.28 0.00
84_A 119_E 0.79 0.28 0.00
292_L 21_L 0.78 0.28 0.00
121_L 83_V 0.78 0.28 0.00
209_L 267_P 0.78 0.28 0.00
104_Y 141_A 0.78 0.28 0.00
138_M 65_M 0.78 0.28 0.00
50_F 416_I 0.78 0.27 0.00
120_L 360_N 0.78 0.27 0.00
47_T 36_L 0.78 0.27 0.00
140_F 64_V 0.78 0.27 0.00
188_I 155_V 0.78 0.27 0.00
193_A 356_I 0.78 0.27 0.00
251_G 505_F 0.78 0.27 0.00
327_L 469_I 0.78 0.27 0.00
327_L 161_A 0.77 0.27 0.00
197_L 73_I 0.77 0.27 0.00
242_L 359_A 0.77 0.27 0.00
47_T 253_M 0.77 0.27 0.00
267_H 158_I 0.77 0.27 0.00
284_V 149_S 0.77 0.27 0.00
28_S 83_V 0.77 0.26 0.00
156_I 458_S 0.76 0.26 0.00
92_I 460_I 0.76 0.26 0.00
163_W 250_G 0.76 0.26 0.00
114_N 116_A 0.76 0.25 0.00
243_T 175_A 0.76 0.25 0.00
172_S 390_M 0.75 0.25 0.00
340_G 117_M 0.75 0.25 0.00
193_A 28_V 0.75 0.25 0.00
156_I 476_F 0.75 0.25 0.00
129_M 254_I 0.75 0.25 0.00
177_R 439_R 0.75 0.25 0.00
61_T 286_I 0.75 0.25 0.00
55_Y 472_I 0.75 0.24 0.00
288_L 460_I 0.74 0.24 0.00
218_I 35_L 0.74 0.24 0.00
327_L 229_I 0.74 0.24 0.00
119_L 135_N 0.74 0.24 0.00
262_L 462_L 0.74 0.24 0.00
348_T 505_F 0.74 0.24 0.00
75_Y 178_Q 0.74 0.24 0.00
314_S 161_A 0.74 0.24 0.00
295_L 57_I 0.74 0.24 0.00
194_T 423_L 0.73 0.24 0.00
328_L 397_F 0.73 0.23 0.00
303_M 134_G 0.73 0.23 0.00
21_L 362_S 0.73 0.23 0.00
252_D 340_W 0.73 0.23 0.00
180_T 39_A 0.73 0.23 0.00
269_K 275_W 0.73 0.23 0.00
245_F 363_L 0.73 0.23 0.00
231_G 54_Y 0.73 0.23 0.00
234_L 53_I 0.73 0.23 0.00
194_T 475_A 0.73 0.23 0.00
179_F 260_Y 0.72 0.23 0.00
199_F 73_I 0.72 0.23 0.00
43_L 29_L 0.72 0.23 0.00
206_N 353_L 0.72 0.23 0.00
179_F 398_P 0.72 0.23 0.00
117_I 178_Q 0.72 0.23 0.00
367_P 44_P 0.72 0.23 0.00
79_I 278_M 0.72 0.23 0.00
126_T 444_P 0.72 0.23 0.00
177_R 285_F 0.72 0.22 0.00
323_S 472_I 0.72 0.22 0.00
176_T 29_L 0.72 0.22 0.00
211_I 48_L 0.72 0.22 0.00
185_L 412_I 0.72 0.22 0.00
82_L 87_I 0.71 0.22 0.00
98_I 481_K 0.71 0.22 0.00
239_L 63_F 0.71 0.22 0.00
215_S 406_D 0.71 0.22 0.00
260_N 7_L 0.71 0.22 0.00
356_V 447_Y 0.71 0.22 0.00
211_I 185_V 0.71 0.22 0.00
263_N 83_V 0.71 0.21 0.00
347_F 89_A 0.71 0.21 0.00
330_A 390_M 0.70 0.21 0.00
294_L 81_W 0.70 0.21 0.00
170_V 188_V 0.70 0.21 0.00
62_A 27_G 0.70 0.21 0.00
229_A 460_I 0.70 0.21 0.00
296_L 453_L 0.70 0.21 0.00
75_Y 359_A 0.70 0.21 0.00
266_P 262_S 0.70 0.21 0.00
361_T 181_T 0.70 0.21 0.00
107_F 225_G 0.70 0.21 0.00
254_D 73_I 0.70 0.21 0.00
164_I 333_K 0.70 0.21 0.00
189_I 467_L 0.70 0.21 0.00
37_L 469_I 0.70 0.21 0.00
25_S 339_L 0.70 0.21 0.00
160_L 334_W 0.70 0.21 0.00
226_I 253_M 0.70 0.21 0.00
37_L 362_S 0.70 0.21 0.00
104_Y 419_I 0.70 0.21 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
5431 1.82 cytb_80_cIV_A_80_human Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2015_06) 0.01 Done - Shared
5422 1.87 cytb_4_cIV_A_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.03 Done - Shared
5405 1.85 cytb_40_cIV_A_20_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.04 Done - Shared
5400 1.85 cytb_40_cIV_A_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.04 Done - Shared
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