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OPENSEQ.org
3RPF_A_C
Genes: A B A+B
Length: 148 74 198
Sequences: 1759 3244 1209
Seq/Len: 11.89 43.84 6.11
MirrorTree (Pazo et al. 2001) 0.78
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 4.55
2 0.01 0.01 4.92
5 0.01 0.01 5.25
10 0.01 0.01 5.34
20 0.01 0.02 5.45
100 0.01 0.03 5.53
∞ 0.02 0.10 6.27
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
52_D 12_K 2.37 1.00 1.00
60_T 50_H 1.97 1.00 0.99
54_Y 66_S 1.15 0.93 0.74
124_Y 13_E 1.13 0.92 0.72
57_L 46_A 1.09 0.90 0.69
53_I 72_C 1.09 0.90 0.68
56_A 49_D 1.07 0.89 0.67
58_L 71_V 1.00 0.84 0.59
60_T 49_D 1.00 0.84 0.59
61_W 51_L 0.95 0.79 0.53
39_I 10_P 0.94 0.79 0.52
64_K 50_H 0.93 0.77 0.50
40_V 71_V 0.92 0.76 0.49
62_F 9_G 0.90 0.73 0.46
57_L 68_L 0.88 0.72 0.45
57_L 49_D 0.88 0.72 0.44
70_K 3_V 0.86 0.70 0.42
73_G 3_V 0.86 0.69 0.41
54_Y 46_A 0.83 0.65 0.37
81_S 9_G 0.81 0.62 0.35
54_Y 49_D 0.79 0.59 0.32
89_Q 42_V 0.78 0.58 0.32
76_L 45_I 0.77 0.56 0.30
57_L 66_S 0.76 0.55 0.29
89_Q 39_W 0.74 0.53 0.28
128_H 28_A 0.71 0.48 0.24
54_Y 64_V 0.71 0.48 0.24
108_Y 43_C 0.71 0.48 0.24
16_E 28_A 0.70 0.47 0.23
46_I 71_V 0.69 0.45 0.22
91_S 72_C 0.69 0.44 0.21
19_K 58_P 0.68 0.42 0.20
51_F 68_L 0.67 0.42 0.20
19_K 17_F 0.67 0.42 0.20
91_S 68_L 0.67 0.42 0.20
93_L 29_I 0.67 0.41 0.20
16_E 19_K 0.67 0.41 0.19
39_I 11_I 0.66 0.40 0.19
65_W 19_K 0.66 0.40 0.19
96_S 6_R 0.66 0.40 0.19
49_L 50_H 0.65 0.39 0.18
121_I 64_V 0.65 0.39 0.18
51_F 72_C 0.65 0.39 0.18
125_D 11_I 0.65 0.39 0.18
125_D 66_S 0.65 0.38 0.17
19_K 20_A 0.64 0.37 0.17
52_D 68_L 0.64 0.37 0.17
57_L 64_V 0.63 0.36 0.17
35_V 61_D 0.63 0.36 0.16
55_E 9_G 0.63 0.35 0.16
7_I 72_C 0.62 0.34 0.15
121_I 72_C 0.61 0.33 0.15
89_Q 53_D 0.61 0.33 0.15
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
7271 6.11 3RPF_A_C Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 1.00 Done - Shared
7265 0.31 3RPF_A_C Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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