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OPENSEQ.org
2xdf_B_D
Genes: A B A+B
Length: 573 85 651
Sequences: 2534 3242 1189
Seq/Len: 4.42 38.14 1.83
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 0.01 0.01 1.62
2 0.01 0.01 1.66
5 0.01 0.01 1.77
10 0.01 0.01 1.79
20 0.01 0.01 1.81
100 0.05 0.06 1.89
∞ 0.12 0.14 2.35
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
79_L 47_L 1.30 0.79 0.05
75_G 16_T 1.27 0.76 0.04
133_I 16_T 1.10 0.60 0.03
75_G 20_A 1.04 0.54 0.02
7_A 48_F 1.03 0.53 0.02
123_L 51_Q 0.97 0.47 0.02
330_I 36_T 0.95 0.44 0.02
83_E 47_L 0.93 0.42 0.02
167_E 42_A 0.90 0.39 0.01
537_I 3_Q 0.90 0.39 0.01
232_T 63_I 0.86 0.35 0.01
257_K 48_F 0.85 0.34 0.01
56_T 71_Q 0.82 0.31 0.01
481_V 22_F 0.82 0.31 0.01
250_K 33_I 0.81 0.31 0.01
220_L 24_K 0.81 0.30 0.01
324_C 81_M 0.81 0.30 0.01
104_A 42_A 0.81 0.30 0.01
178_G 38_N 0.80 0.29 0.01
142_L 50_L 0.80 0.29 0.01
180_I 5_E 0.79 0.28 0.01
74_E 20_A 0.79 0.28 0.01
115_L 51_Q 0.78 0.27 0.01
55_E 42_A 0.78 0.27 0.01
81_E 27_K 0.78 0.27 0.01
235_V 61_V 0.77 0.27 0.01
525_M 8_I 0.76 0.26 0.01
381_S 29_F 0.75 0.25 0.01
83_E 27_K 0.75 0.25 0.01
83_E 46_S 0.75 0.25 0.01
157_I 42_A 0.74 0.24 0.01
319_A 8_I 0.74 0.24 0.01
84_E 43_S 0.73 0.24 0.01
59_T 71_Q 0.73 0.23 0.01
99_T 47_L 0.73 0.23 0.01
301_F 16_T 0.72 0.23 0.01
277_T 12_N 0.72 0.23 0.01
118_L 51_Q 0.72 0.22 0.01
496_G 30_T 0.71 0.22 0.01
81_E 47_L 0.70 0.21 0.01
432_T 21_Q 0.70 0.21 0.01
311_E 76_H 0.70 0.21 0.01
215_D 34_T 0.70 0.21 0.01
77_I 4_Q 0.70 0.21 0.01
238_K 50_L 0.70 0.21 0.01
430_V 5_E 0.69 0.21 0.01
212_V 8_I 0.69 0.20 0.01
132_D 18_P 0.69 0.20 0.01
14_G 10_A 0.69 0.20 0.01
450_S 45_K 0.68 0.20 0.01
185_G 14_L 0.68 0.20 0.01
317_Y 1_M 0.68 0.20 0.01
199_L 74_V 0.68 0.20 0.01
215_D 63_I 0.68 0.20 0.01
74_E 24_K 0.68 0.20 0.01
484_L 26_A 0.68 0.19 0.01
124_K 22_F 0.67 0.19 0.01
269_V 77_L 0.67 0.19 0.01
480_S 5_E 0.67 0.19 0.01
475_Q 47_L 0.67 0.19 0.01
76_H 61_V 0.67 0.19 0.01
83_E 45_K 0.66 0.18 0.01
14_G 44_A 0.66 0.18 0.01
108_I 54_G 0.66 0.18 0.01
252_E 33_I 0.66 0.18 0.01
115_L 50_L 0.66 0.18 0.01
235_V 33_I 0.66 0.18 0.01
115_L 16_T 0.66 0.18 0.01
490_D 44_A 0.65 0.18 0.01
311_E 33_I 0.65 0.18 0.01
72_I 21_Q 0.65 0.18 0.01
406_I 81_M 0.65 0.18 0.01
83_E 24_K 0.65 0.17 0.01
301_F 57_Q 0.65 0.17 0.01
77_I 61_V 0.65 0.17 0.01
227_V 59_T 0.64 0.17 0.01
507_G 57_Q 0.64 0.17 0.01
303_D 80_L 0.64 0.17 0.01
84_E 23_V 0.64 0.17 0.01
157_I 34_T 0.64 0.17 0.01
14_G 57_Q 0.63 0.17 0.01
547_V 71_Q 0.63 0.17 0.01
525_M 22_F 0.63 0.17 0.01
411_Q 79_K 0.63 0.17 0.01
360_I 51_Q 0.63 0.17 0.01
52_A 71_Q 0.63 0.17 0.01
218_L 30_T 0.63 0.17 0.01
381_S 65_A 0.63 0.16 0.01
417_G 5_E 0.63 0.16 0.01
377_I 27_K 0.63 0.16 0.01
501_M 46_S 0.62 0.16 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)
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