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OPENSEQ.org
zf_cox1-zf_cox2
Genes: A B A+B
Length: 516 230 739
Sequences: 3117 4273 2018
Seq/Len: 6.04 18.58 2.73
MirrorTree (Pazo et al. 2001) 0.87
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 0.01 2.32
2 0.01 0.01 2.39
5 0.01 0.01 2.53
10 0.01 0.01 2.66
20 0.01 0.01 2.71
100 0.01 0.02 2.76
∞ 0.04 0.07 2.90
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
229_I 175_V 3.00 1.00 1.00
369_D 198_E 2.96 1.00 1.00
369_D 171_K 2.08 1.00 0.98
369_D 173_D 2.07 1.00 0.98
434_A 6_Q 1.99 0.99 0.98
440_Y 205_S 1.79 0.99 0.96
441_S 205_S 1.72 0.98 0.95
227_D 178_R 1.68 0.98 0.94
353_L 35_S 1.57 0.96 0.91
319_K 62_E 1.51 0.95 0.89
449_L 5_A 1.41 0.92 0.84
447_Y 2_A 1.40 0.92 0.84
369_D 197_S 1.24 0.84 0.73
359_A 76_I 1.21 0.82 0.70
232_Q 160_L 1.18 0.80 0.67
295_V 180_N 1.17 0.79 0.66
311_I 70_A 1.17 0.79 0.66
374_V 198_E 1.14 0.76 0.63
372_Y 24_H 1.12 0.75 0.61
268_F 66_T 1.11 0.73 0.60
428_Q 14_S 1.07 0.69 0.55
324_L 41_I 1.05 0.68 0.53
280_I 62_E 1.03 0.65 0.51
97_M 213_A 1.03 0.65 0.51
334_W 46_V 1.02 0.64 0.49
423_L 146_K 1.00 0.61 0.47
294_T 162_S 0.98 0.60 0.45
314_I 38_V 0.97 0.59 0.43
369_D 162_S 0.97 0.58 0.43
353_L 31_V 0.95 0.56 0.40
340_W 205_S 0.94 0.55 0.40
58_V 199_I 0.92 0.53 0.37
316_T 69_P 0.92 0.52 0.37
324_L 45_M 0.90 0.49 0.34
132_L 199_I 0.89 0.49 0.34
372_Y 144_V 0.87 0.47 0.32
307_S 81_L 0.87 0.47 0.32
51_D 205_S 0.87 0.46 0.31
200_P 104_W 0.87 0.46 0.31
268_F 62_E 0.87 0.46 0.31
313_A 62_E 0.86 0.46 0.31
320_V 17_M 0.86 0.45 0.30
410_T 125_T 0.86 0.45 0.30
393_F 155_S 0.86 0.45 0.30
400_F 71_I 0.85 0.44 0.29
296_G 180_N 0.85 0.44 0.29
475_A 6_Q 0.84 0.43 0.28
284_G 219_F 0.84 0.43 0.28
51_D 203_N 0.84 0.43 0.28
374_V 171_K 0.81 0.40 0.25
492_V 168_L 0.81 0.39 0.25
356_I 93_P 0.81 0.39 0.24
370_T 21_L 0.80 0.38 0.24
345_I 58_S 0.80 0.38 0.24
229_I 68_L 0.80 0.38 0.24
430_F 73_L 0.80 0.37 0.23
314_I 70_A 0.78 0.36 0.22
262_A 41_I 0.78 0.35 0.22
233_H 173_D 0.78 0.35 0.22
317_G 69_P 0.77 0.35 0.21
321_F 66_T 0.77 0.34 0.21
172_K 110_Y 0.76 0.34 0.20
54_Y 152_I 0.76 0.34 0.20
325_A 87_M 0.76 0.33 0.20
268_F 65_W 0.75 0.33 0.19
338_M 168_L 0.75 0.32 0.19
322_S 62_E 0.75 0.32 0.19
177_S 99_A 0.75 0.32 0.19
230_L 178_R 0.74 0.32 0.19
181_T 95_V 0.74 0.32 0.19
324_L 42_I 0.74 0.31 0.18
419_I 100_V 0.74 0.31 0.18
293_F 176_P 0.73 0.31 0.18
278_M 197_S 0.73 0.30 0.18
310_M 195_Q 0.73 0.30 0.17
317_G 73_L 0.73 0.30 0.17
370_T 155_S 0.73 0.30 0.17
342_L 42_I 0.73 0.30 0.17
197_L 192_F 0.73 0.30 0.17
365_I 144_V 0.72 0.29 0.17
59_T 219_F 0.72 0.29 0.16
365_I 182_T 0.72 0.29 0.16
369_D 199_I 0.71 0.29 0.16
255_S 62_E 0.71 0.29 0.16
160_G 28_L 0.71 0.29 0.16
440_Y 195_Q 0.71 0.28 0.16
319_K 66_T 0.71 0.28 0.16
349_T 38_V 0.71 0.28 0.16
295_V 175_V 0.71 0.28 0.16
91_D 69_P 0.71 0.28 0.16
346_F 42_I 0.71 0.28 0.16
405_L 20_L 0.71 0.28 0.16
369_D 204_H 0.71 0.28 0.16
313_A 63_I 0.70 0.28 0.15
116_S 154_V 0.70 0.28 0.15
350_V 35_S 0.70 0.28 0.15
43_Q 163_W 0.70 0.28 0.15
392_G 87_M 0.70 0.28 0.15
421_V 180_N 0.70 0.27 0.15
251_F 62_E 0.70 0.27 0.15
437_P 161_H 0.69 0.27 0.15
467_M 75_L 0.69 0.27 0.15
247_I 62_E 0.69 0.26 0.14
380_V 211_V 0.69 0.26 0.14
206_I 140_H 0.69 0.26 0.14
39_A 95_V 0.69 0.26 0.14
437_P 200_C 0.69 0.26 0.14
62_A 170_I 0.69 0.26 0.14
460_I 44_A 0.69 0.26 0.14
363_L 27_A 0.69 0.26 0.14
463_V 32_F 0.69 0.26 0.14
245_I 198_E 0.68 0.26 0.14
202_L 195_Q 0.68 0.26 0.14
139_A 33_L 0.68 0.26 0.14
354_T 219_F 0.68 0.25 0.14
233_H 171_K 0.68 0.25 0.14
312_I 80_S 0.68 0.25 0.14
170_N 199_I 0.68 0.25 0.13
166_T 17_M 0.68 0.25 0.13
248_L 144_V 0.67 0.25 0.13
54_Y 137_E 0.67 0.25 0.13
232_Q 173_D 0.67 0.25 0.13
336_T 142_M 0.67 0.24 0.13
196_L 160_L 0.67 0.24 0.13
459_L 61_I 0.66 0.24 0.13
36_L 71_I 0.66 0.24 0.12
457_G 194_G 0.66 0.24 0.12
29_V 146_K 0.66 0.24 0.12
104_L 221_N 0.66 0.24 0.12
411_K 20_L 0.66 0.24 0.12
480_R 144_V 0.66 0.23 0.12
127_T 199_I 0.66 0.23 0.12
119_E 6_Q 0.66 0.23 0.12
20_L 203_N 0.66 0.23 0.12
83_V 95_V 0.66 0.23 0.12
455_S 88_D 0.66 0.23 0.12
276_A 34_I 0.66 0.23 0.12
303_A 85_Y 0.66 0.23 0.12
104_L 38_V 0.65 0.23 0.12
437_P 196_C 0.65 0.23 0.12
289_A 50_L 0.65 0.23 0.12
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
14380 AB_cox1_cox2 Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) Running - Shared
14375 rer_cox1_cox2 Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Running - Shared
13993 2.73 zf_cox1-zf_cox2 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
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