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OPENSEQ.org
cIm_L_20_cytb_20_human
Genes: A B A+B
Length: 603 378 974
Sequences: 4892 3804 3007
Seq/Len: 8.11 10.06 3.09
MirrorTree (Pazo et al. 2001) 0.65
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 0.01 0.02 0.26
2 0.01 0.02 1.34
5 0.01 0.02 2.45
10 0.01 0.02 2.65
20 0.01 0.02 2.72
100 0.01 0.02 2.77
∞ 0.02 0.03 3.07
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
267_A 120_L 1.25 0.87 0.19
182_F 56_S 1.21 0.85 0.17
235_S 254_D 1.02 0.68 0.10
181_G 299_L 1.01 0.67 0.09
111_D 173_P 1.01 0.67 0.09
341_M 244_L 1.01 0.67 0.09
461_S 160_L 0.99 0.64 0.09
337_A 173_P 0.98 0.64 0.08
172_I 169_S 0.98 0.64 0.08
545_S 47_T 0.97 0.62 0.08
378_L 355_S 0.95 0.60 0.08
182_F 314_S 0.95 0.59 0.07
184_L 234_L 0.94 0.58 0.07
302_V 59_A 0.93 0.57 0.07
116_Q 251_G 0.92 0.56 0.07
483_P 45_I 0.91 0.55 0.07
528_F 322_Q 0.91 0.54 0.06
266_L 42_I 0.90 0.54 0.06
554_D 92_I 0.90 0.53 0.06
475_A 184_I 0.90 0.53 0.06
314_M 122_A 0.90 0.53 0.06
101_M 112_T 0.90 0.53 0.06
142_I 355_S 0.90 0.53 0.06
453_P 320_L 0.88 0.50 0.06
112_P 347_F 0.88 0.50 0.06
288_A 315_M 0.86 0.49 0.06
383_M 322_Q 0.86 0.48 0.05
346_I 303_M 0.86 0.48 0.05
283_I 89_M 0.86 0.48 0.05
267_A 98_I 0.85 0.47 0.05
378_L 233_L 0.85 0.47 0.05
341_M 121_L 0.85 0.47 0.05
562_L 248_D 0.85 0.47 0.05
76_L 94_L 0.85 0.47 0.05
429_L 298_I 0.85 0.47 0.05
428_L 49_L 0.85 0.47 0.05
572_S 46_T 0.84 0.47 0.05
467_L 96_L 0.84 0.46 0.05
123_I 262_L 0.84 0.46 0.05
424_T 162_Q 0.83 0.45 0.05
464_A 105_G 0.83 0.44 0.05
435_P 298_I 0.83 0.44 0.05
134_A 119_L 0.82 0.44 0.05
131_L 303_M 0.82 0.44 0.05
461_S 322_Q 0.82 0.44 0.05
387_T 29_A 0.82 0.44 0.05
338_M 169_S 0.82 0.44 0.05
173_L 99_G 0.82 0.43 0.05
500_T 156_I 0.82 0.43 0.05
338_M 58_D 0.81 0.43 0.04
532_I 191_A 0.81 0.42 0.04
198_P 75_Y 0.81 0.42 0.04
386_L 329_A 0.81 0.42 0.04
167_A 350_I 0.81 0.42 0.04
379_A 232_L 0.81 0.42 0.04
459_A 224_Y 0.80 0.41 0.04
311_G 217_K 0.80 0.41 0.04
553_L 198_L 0.80 0.41 0.04
76_L 11_M 0.80 0.41 0.04
341_M 93_C 0.80 0.41 0.04
174_Y 294_L 0.79 0.40 0.04
231_P 55_Y 0.79 0.40 0.04
394_H 192_L 0.79 0.40 0.04
111_D 107_F 0.79 0.40 0.04
495_F 11_M 0.79 0.40 0.04
416_T 301_L 0.79 0.40 0.04
184_L 283_S 0.79 0.40 0.04
217_L 164_I 0.79 0.40 0.04
430_T 191_A 0.79 0.40 0.04
95_F 257_T 0.79 0.39 0.04
103_F 222_P 0.79 0.39 0.04
49_F 296_L 0.78 0.39 0.04
396_I 254_D 0.78 0.39 0.04
382_G 274_F 0.78 0.39 0.04
102_E 179_F 0.78 0.38 0.04
172_I 343_V 0.78 0.38 0.04
90_I 55_Y 0.77 0.38 0.04
431_L 74_N 0.77 0.38 0.04
301_I 223_Y 0.77 0.38 0.04
267_A 314_S 0.77 0.38 0.04
471_N 262_L 0.77 0.38 0.04
489_T 42_I 0.77 0.37 0.04
542_L 350_I 0.77 0.37 0.04
113_N 164_I 0.77 0.37 0.04
312_L 305_P 0.77 0.37 0.04
378_L 49_L 0.77 0.37 0.04
399_A 96_L 0.76 0.37 0.04
177_I 329_A 0.76 0.36 0.04
587_Y 184_I 0.76 0.36 0.04
453_P 222_P 0.76 0.36 0.04
399_A 156_I 0.76 0.36 0.04
319_I 246_S 0.75 0.35 0.04
137_L 314_S 0.75 0.35 0.04
182_F 28_S 0.75 0.35 0.04
542_L 170_V 0.74 0.35 0.03
181_G 341_Q 0.74 0.34 0.03
261_I 252_D 0.74 0.34 0.03
457_L 101_G 0.74 0.34 0.03
427_I 362_I 0.74 0.34 0.03
169_I 279_T 0.74 0.34 0.03
457_L 250_L 0.74 0.34 0.03
174_Y 308_H 0.74 0.34 0.03
337_A 239_L 0.74 0.34 0.03
183_I 111_E 0.74 0.34 0.03
87_M 27_I 0.74 0.34 0.03
517_L 160_L 0.73 0.34 0.03
409_L 322_Q 0.73 0.34 0.03
360_G 293_A 0.73 0.34 0.03
174_Y 181_F 0.73 0.33 0.03
190_I 39_A 0.73 0.33 0.03
198_P 225_T 0.73 0.33 0.03
162_A 197_L 0.73 0.33 0.03
479_Q 129_M 0.73 0.33 0.03
441_T 254_D 0.73 0.33 0.03
126_I 66_I 0.73 0.33 0.03
364_K 102_L 0.73 0.33 0.03
220_A 236_I 0.72 0.32 0.03
401_M 50_F 0.72 0.32 0.03
129_L 59_A 0.72 0.32 0.03
431_L 229_A 0.72 0.32 0.03
267_A 115_I 0.72 0.32 0.03
72_Q 226_I 0.72 0.32 0.03
431_L 62_A 0.72 0.32 0.03
82_L 314_S 0.72 0.31 0.03
459_A 363_L 0.71 0.31 0.03
103_F 248_D 0.71 0.31 0.03
132_V 331_D 0.71 0.31 0.03
311_G 126_T 0.71 0.31 0.03
100_I 171_D 0.71 0.31 0.03
218_L 153_I 0.71 0.31 0.03
555_L 102_L 0.71 0.31 0.03
544_T 64_S 0.71 0.31 0.03
153_L 314_S 0.71 0.31 0.03
544_T 123_T 0.71 0.30 0.03
172_I 316_M 0.71 0.30 0.03
469_T 222_P 0.71 0.30 0.03
188_W 225_T 0.71 0.30 0.03
382_G 267_H 0.71 0.30 0.03
112_P 119_L 0.71 0.30 0.03
428_L 249_L 0.70 0.30 0.03
419_T 53_M 0.70 0.30 0.03
302_V 112_T 0.70 0.30 0.03
436_R 47_T 0.70 0.30 0.03
182_F 262_L 0.70 0.30 0.03
537_I 329_A 0.70 0.30 0.03
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
5728 3.09 cIm_L_20_cytb_20_human Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.19 Done - Shared
5727 3.06 cIm_L_60_cytb_60_human Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: HHblits (2015_06) 0.18 Done - Shared
5726 3.09 cIm_L_40_cytb_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.20 Done - Shared
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