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OPENSEQ.org
3sgf_H_K
Genes: A B A+B
Length: 165 121 271
Sequences: 2373 2284 2121
Seq/Len: 14.38 18.88 7.83
MirrorTree (Pazo et al. 2001) 0.64
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 0.09 0.09 7.40
2 0.09 0.09 7.41
5 0.09 0.09 7.42
10 0.09 0.09 7.42
20 0.09 0.09 7.42
100 0.09 0.09 7.42
∞ 0.09 0.09 7.48
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
158_V 27_M 1.29 0.98 0.54
147_S 20_V 1.26 0.98 0.50
140_M 27_M 1.19 0.96 0.44
136_I 31_F 1.17 0.96 0.42
143_M 27_M 1.14 0.95 0.39
153_R 34_S 1.10 0.94 0.36
152_V 27_M 1.07 0.93 0.33
139_L 15_M 0.94 0.84 0.22
78_G 87_L 0.93 0.83 0.21
162_K 15_M 0.92 0.82 0.21
158_V 31_F 0.88 0.79 0.18
146_A 17_V 0.82 0.72 0.15
143_M 20_V 0.82 0.71 0.14
151_L 20_V 0.79 0.67 0.13
142_T 24_I 0.78 0.65 0.12
125_R 18_M 0.78 0.65 0.12
132_Y 31_F 0.76 0.63 0.11
136_I 27_M 0.74 0.60 0.10
135_A 21_V 0.72 0.56 0.09
114_E 16_S 0.71 0.55 0.09
129_L 21_V 0.69 0.51 0.08
144_K 32_G 0.67 0.48 0.07
159_R 21_V 0.67 0.48 0.07
143_M 15_M 0.66 0.46 0.07
138_R 28_E 0.64 0.44 0.07
125_R 25_S 0.64 0.43 0.07
157_A 35_A 0.63 0.41 0.06
90_G 18_M 0.62 0.40 0.06
147_S 17_V 0.62 0.40 0.06
132_Y 20_V 0.62 0.40 0.06
132_Y 27_M 0.61 0.39 0.06
101_K 47_E 0.60 0.38 0.05
83_A 54_E 0.59 0.36 0.05
72_L 120_V 0.59 0.36 0.05
139_L 20_V 0.58 0.34 0.05
139_L 23_L 0.58 0.34 0.05
140_M 20_V 0.58 0.34 0.05
151_L 24_I 0.57 0.34 0.05
157_A 33_V 0.57 0.33 0.05
94_R 25_S 0.57 0.33 0.04
129_L 40_A 0.57 0.32 0.04
141_A 38_A 0.56 0.32 0.04
136_I 20_V 0.56 0.32 0.04
137_A 34_S 0.56 0.31 0.04
138_R 39_V 0.55 0.30 0.04
139_L 24_I 0.55 0.30 0.04
121_S 56_D 0.54 0.29 0.04
47_E 86_D 0.54 0.29 0.04
138_R 93_A 0.54 0.29 0.04
40_E 102_D 0.54 0.29 0.04
130_P 23_L 0.53 0.27 0.04
142_T 21_V 0.52 0.27 0.04
142_T 27_M 0.52 0.26 0.04
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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