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OPENSEQ.org
1RM6_A_B
Genes: A B A+B
Length: 769 324 1023
Sequences: 4230 3456 2573
Seq/Len: 5.5 10.67 2.52
MirrorTree (Pazo et al. 2001) 0.79
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 1.69
2 0.03 0.01 2.29
5 0.04 0.02 2.34
10 0.05 0.03 2.35
20 0.11 0.10 2.35
100 0.14 0.13 2.37
∞ 0.22 0.22 2.39
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
633_D 315_K 2.07 1.00 0.98
763_D 307_R 1.55 0.95 0.88
635_I 311_A 1.55 0.95 0.88
635_I 314_R 1.53 0.95 0.87
635_I 315_K 1.40 0.91 0.80
695_R 232_D 1.36 0.89 0.77
759_T 307_R 1.28 0.84 0.70
756_D 301_G 1.28 0.84 0.70
759_T 308_V 0.96 0.55 0.36
760_E 303_K 0.95 0.54 0.35
698_T 228_R 0.87 0.44 0.26
291_K 14_T 0.82 0.38 0.21
464_L 171_D 0.77 0.32 0.17
209_L 321_W 0.76 0.32 0.16
66_E 240_A 0.76 0.32 0.16
638_K 223_S 0.74 0.29 0.15
755_P 304_Y 0.73 0.29 0.15
755_P 227_I 0.72 0.28 0.14
504_I 287_L 0.71 0.27 0.13
638_K 225_V 0.70 0.26 0.12
690_N 42_R 0.68 0.24 0.11
755_P 308_V 0.68 0.24 0.11
504_I 8_R 0.68 0.24 0.11
432_P 315_K 0.67 0.24 0.11
294_I 116_L 0.67 0.24 0.11
124_K 180_A 0.67 0.23 0.11
155_I 252_L 0.65 0.21 0.09
237_I 51_V 0.64 0.21 0.09
70_A 212_V 0.64 0.21 0.09
71_V 320_L 0.63 0.20 0.09
30_Y 54_T 0.63 0.20 0.09
740_V 186_P 0.63 0.20 0.09
11_V 12_P 0.63 0.20 0.09
224_A 74_A 0.62 0.20 0.08
499_V 191_F 0.62 0.20 0.08
522_S 316_V 0.62 0.20 0.08
42_G 31_G 0.62 0.19 0.08
119_A 16_A 0.62 0.19 0.08
123_I 62_I 0.62 0.19 0.08
367_A 112_L 0.61 0.19 0.08
237_I 254_V 0.61 0.19 0.08
191_M 112_L 0.61 0.18 0.08
64_A 275_N 0.61 0.18 0.07
740_V 93_A 0.61 0.18 0.07
61_A 58_G 0.60 0.18 0.07
210_N 55_G 0.60 0.18 0.07
59_T 292_S 0.60 0.18 0.07
52_A 238_V 0.60 0.18 0.07
312_A 12_P 0.60 0.18 0.07
557_E 80_A 0.60 0.18 0.07
120_L 74_A 0.60 0.18 0.07
50_A 282_E 0.59 0.17 0.07
701_E 228_R 0.59 0.17 0.07
502_S 209_A 0.59 0.17 0.07
100_Y 313_S 0.59 0.17 0.07
139_A 111_T 0.59 0.17 0.07
512_A 72_I 0.59 0.17 0.07
462_V 20_N 0.58 0.17 0.06
695_R 228_R 0.57 0.16 0.06
695_R 227_I 0.57 0.16 0.06
128_E 190_L 0.57 0.16 0.06
213_T 308_V 0.57 0.16 0.06
520_S 234_P 0.57 0.16 0.06
691_I 215_T 0.57 0.16 0.06
301_K 186_P 0.56 0.15 0.06
131_P 320_L 0.56 0.15 0.06
21_V 50_L 0.56 0.15 0.06
696_V 24_A 0.56 0.15 0.06
640_T 229_D 0.56 0.15 0.06
532_A 12_P 0.56 0.15 0.06
124_K 243_Q 0.56 0.15 0.06
131_P 17_D 0.55 0.15 0.06
359_G 191_F 0.55 0.15 0.05
180_T 184_T 0.55 0.14 0.05
667_V 98_A 0.55 0.14 0.05
759_T 311_A 0.55 0.14 0.05
390_I 280_A 0.55 0.14 0.05
118_K 43_G 0.54 0.14 0.05
155_I 17_D 0.54 0.14 0.05
30_Y 12_P 0.54 0.14 0.05
391_N 30_L 0.54 0.14 0.05
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)
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