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OPENSEQ.org
cytb_40_cIV_A_20_human
Genes: A B A+B
Length: 378 513 888
Sequences: 3773 3112 1641
Seq/Len: 9.98 6.07 1.85
MirrorTree (Pazo et al. 2001) 0.73
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 0.45
10 0.02 0.01 1.43
20 0.02 0.01 1.53
100 0.02 0.01 1.58
∞ 0.02 0.04 1.84
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
318_R 270_Y 1.28 0.77 0.04
269_K 204_A 1.19 0.69 0.03
243_T 314_I 1.10 0.61 0.02
197_L 359_A 1.05 0.56 0.02
362_I 172_K 1.04 0.54 0.02
254_D 231_Y 1.04 0.54 0.02
258_L 182_P 1.02 0.53 0.02
21_L 340_W 1.02 0.52 0.02
47_T 311_I 1.02 0.52 0.02
239_L 166_T 1.01 0.51 0.02
152_A 182_P 1.00 0.50 0.02
224_Y 346_F 1.00 0.50 0.02
308_H 363_L 0.98 0.48 0.01
176_T 359_A 0.96 0.46 0.01
27_I 53_I 0.96 0.46 0.01
322_Q 356_I 0.96 0.46 0.01
37_L 328_H 0.96 0.46 0.01
209_L 274_V 0.95 0.45 0.01
251_G 314_I 0.95 0.44 0.01
262_L 254_I 0.94 0.44 0.01
193_A 27_G 0.94 0.44 0.01
105_G 193_I 0.93 0.42 0.01
351_G 286_I 0.93 0.42 0.01
119_L 335_S 0.92 0.42 0.01
355_S 172_K 0.92 0.41 0.01
79_I 297_M 0.92 0.41 0.01
37_L 340_W 0.92 0.41 0.01
362_I 204_A 0.91 0.41 0.01
43_L 29_L 0.91 0.40 0.01
297_S 297_M 0.91 0.40 0.01
318_R 274_V 0.90 0.39 0.01
156_I 39_A 0.90 0.39 0.01
318_R 330_S 0.90 0.39 0.01
184_I 146_T 0.90 0.39 0.01
163_W 81_W 0.89 0.39 0.01
129_M 413_H 0.89 0.38 0.01
343_V 81_W 0.89 0.38 0.01
177_R 439_R 0.89 0.38 0.01
43_L 416_I 0.88 0.38 0.01
115_I 350_V 0.88 0.38 0.01
160_L 133_A 0.88 0.37 0.01
317_F 142_S 0.88 0.37 0.01
140_F 112_L 0.88 0.37 0.01
40_C 109_L 0.87 0.36 0.01
269_K 172_K 0.86 0.35 0.01
206_N 211_T 0.86 0.35 0.01
211_I 139_P 0.86 0.35 0.01
102_L 174_P 0.86 0.35 0.01
49_L 50_N 0.85 0.35 0.01
267_H 12_H 0.85 0.34 0.01
70_T 215_L 0.85 0.34 0.01
313_Q 205_G 0.85 0.34 0.01
322_Q 320_V 0.83 0.33 0.01
269_K 491_N 0.83 0.32 0.01
224_Y 218_T 0.83 0.32 0.01
185_L 229_I 0.83 0.32 0.01
324_L 342_L 0.82 0.32 0.01
82_L 471_M 0.82 0.32 0.01
242_L 359_A 0.82 0.31 0.01
279_T 159_L 0.81 0.31 0.01
292_L 53_I 0.81 0.31 0.01
180_T 492_L 0.81 0.30 0.01
41_L 90_P 0.81 0.30 0.01
70_T 279_S 0.81 0.30 0.01
292_L 21_L 0.81 0.30 0.01
28_S 83_V 0.81 0.30 0.01
323_S 472_I 0.81 0.30 0.01
368_T 463_T 0.81 0.30 0.01
193_A 356_I 0.81 0.30 0.01
134_P 227_D 0.80 0.30 0.01
105_G 357_V 0.80 0.30 0.01
153_I 453_L 0.80 0.30 0.01
263_N 83_V 0.80 0.29 0.01
251_G 505_F 0.80 0.29 0.01
75_Y 178_Q 0.79 0.29 0.01
25_S 24_A 0.79 0.29 0.01
160_L 18_L 0.79 0.28 0.01
269_K 275_W 0.79 0.28 0.01
348_T 505_F 0.79 0.28 0.01
279_T 198_S 0.79 0.28 0.01
119_L 20_L 0.78 0.28 0.01
123_T 324_L 0.78 0.28 0.01
257_T 87_I 0.78 0.28 0.01
224_Y 389_I 0.78 0.28 0.01
189_I 469_I 0.78 0.28 0.01
62_A 152_L 0.78 0.27 0.01
188_I 155_V 0.78 0.27 0.01
260_N 7_L 0.78 0.27 0.01
301_L 314_I 0.78 0.27 0.01
121_L 83_V 0.78 0.27 0.01
135_W 12_H 0.78 0.27 0.01
92_I 89_A 0.77 0.27 0.01
102_L 190_I 0.77 0.27 0.01
303_M 134_G 0.77 0.27 0.01
164_I 93_A 0.77 0.27 0.01
140_F 253_M 0.77 0.27 0.01
55_Y 472_I 0.77 0.27 0.01
156_I 476_F 0.77 0.27 0.01
190_A 218_T 0.77 0.26 0.01
137_Q 234_L 0.77 0.26 0.01
62_A 311_I 0.77 0.26 0.01
55_Y 267_P 0.77 0.26 0.01
252_D 340_W 0.77 0.26 0.01
336_T 293_F 0.76 0.26 0.01
104_Y 141_A 0.76 0.26 0.01
258_L 42_G 0.76 0.26 0.01
30_W 507_E 0.76 0.26 0.01
185_L 412_I 0.76 0.26 0.01
47_T 36_L 0.76 0.26 0.01
184_I 467_L 0.76 0.26 0.01
71_R 172_K 0.76 0.26 0.01
176_T 410_A 0.76 0.26 0.01
153_I 97_M 0.76 0.26 0.01
254_D 468_M 0.76 0.26 0.01
172_S 390_M 0.76 0.26 0.01
114_N 116_A 0.76 0.26 0.01
231_G 54_Y 0.76 0.26 0.01
69_I 327_L 0.75 0.25 0.01
177_R 285_F 0.75 0.25 0.01
209_L 118_V 0.75 0.25 0.01
184_I 83_V 0.75 0.25 0.01
267_H 158_I 0.75 0.25 0.01
107_F 133_A 0.75 0.25 0.01
125_A 29_L 0.75 0.25 0.01
314_S 161_A 0.75 0.25 0.01
84_A 119_E 0.75 0.25 0.01
82_L 262_S 0.75 0.25 0.01
45_I 33_L 0.74 0.25 0.01
119_L 135_N 0.74 0.24 0.01
232_L 341_A 0.74 0.24 0.01
361_T 181_T 0.74 0.24 0.01
152_A 70_V 0.74 0.24 0.01
21_L 362_S 0.74 0.24 0.01
96_L 332_M 0.74 0.24 0.01
313_Q 39_A 0.74 0.24 0.01
356_V 464_A 0.74 0.24 0.01
179_F 260_Y 0.74 0.24 0.01
234_L 320_V 0.73 0.24 0.01
19_I 254_I 0.73 0.24 0.01
367_P 44_P 0.73 0.24 0.01
107_F 401_S 0.73 0.23 0.01
254_D 73_I 0.73 0.23 0.01
120_L 162_I 0.73 0.23 0.01
183_F 389_I 0.72 0.23 0.01
189_I 359_A 0.72 0.23 0.01
107_F 225_G 0.72 0.23 0.01
340_G 117_M 0.72 0.23 0.01
266_P 262_S 0.72 0.23 0.01
119_L 412_I 0.72 0.23 0.01
332_L 215_L 0.72 0.23 0.01
243_T 175_A 0.72 0.23 0.01
82_L 134_G 0.72 0.23 0.01
226_I 162_I 0.72 0.23 0.01
328_L 397_F 0.72 0.23 0.01
197_L 73_I 0.72 0.23 0.01
126_T 444_P 0.72 0.23 0.01
189_I 467_L 0.72 0.23 0.01
327_L 469_I 0.72 0.23 0.01
229_A 460_I 0.72 0.23 0.01
156_I 458_S 0.72 0.22 0.01
98_I 481_K 0.72 0.22 0.01
153_I 460_I 0.71 0.22 0.01
61_T 286_I 0.71 0.22 0.01
49_L 257_I 0.71 0.22 0.01
215_S 406_D 0.71 0.22 0.01
120_L 360_N 0.71 0.22 0.01
356_V 447_Y 0.71 0.22 0.01
209_L 267_P 0.71 0.22 0.01
82_L 87_I 0.71 0.22 0.01
184_I 152_L 0.71 0.22 0.01
108_L 161_A 0.71 0.22 0.01
55_Y 43_Q 0.70 0.22 0.01
222_P 48_L 0.70 0.21 0.01
192_L 90_P 0.70 0.21 0.01
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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