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OPENSEQ.org
UMUC_SALTY - UMUD_SALTY
Genes: A B A+B
Length: 422 139 547
Sequences: 15934 7987 2718
Seq/Len: 37.76 57.46 4.97
MirrorTree (Pazo et al. 2001) 0.67
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 3.68
2 0.00 0.00 4.32
5 0.00 0.00 4.49
10 0.01 0.00 4.68
20 0.01 0.01 4.84
100 0.02 0.02 5.53
∞ 0.07 0.05 8.77
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
415_Y 38_I 3.19 1.00 1.00
130_R 50_S 1.87 1.00 0.98
78_A 34_I 1.58 0.99 0.94
74_Y 33_Y 1.50 0.98 0.93
129_K 79_N 1.42 0.98 0.90
419_L 54_V 1.40 0.97 0.89
132_H 76_S 1.35 0.96 0.87
23_C 126_D 1.26 0.94 0.82
404_R 33_Y 1.20 0.92 0.78
86_T 49_S 1.10 0.87 0.69
420_R 55_K 1.03 0.81 0.61
419_L 94_F 1.01 0.80 0.59
420_R 57_S 1.01 0.80 0.59
421_V 54_V 0.97 0.76 0.55
79_D 37_R 0.94 0.73 0.51
130_R 47_H 0.94 0.73 0.51
418_L 53_F 0.89 0.67 0.45
415_Y 71_L 0.87 0.64 0.42
100_I 30_A 0.85 0.61 0.39
75_E 33_Y 0.81 0.56 0.34
129_K 80_A 0.77 0.50 0.29
277_K 31_A 0.72 0.44 0.24
75_E 35_E 0.71 0.41 0.23
369_G 127_I 0.71 0.41 0.23
415_Y 53_F 0.70 0.40 0.22
82_N 37_R 0.70 0.40 0.22
11_Y 30_A 0.70 0.40 0.22
87_T 49_S 0.69 0.40 0.22
419_L 74_V 0.69 0.39 0.21
418_L 71_L 0.68 0.38 0.20
386_K 127_I 0.68 0.38 0.20
130_R 76_S 0.67 0.36 0.19
417_D 57_S 0.66 0.35 0.18
115_D 90_I 0.64 0.33 0.17
72_S 33_Y 0.64 0.32 0.16
100_I 28_S 0.63 0.32 0.16
132_H 52_Y 0.62 0.30 0.15
270_Y 33_Y 0.61 0.29 0.14
23_C 128_F 0.60 0.28 0.14
385_G 69_G 0.60 0.28 0.13
410_R 83_G 0.60 0.28 0.13
187_V 115_R 0.59 0.27 0.13
131_T 52_Y 0.59 0.27 0.13
183_D 69_G 0.59 0.27 0.13
80_M 76_S 0.59 0.26 0.12
5_C 127_I 0.58 0.26 0.12
88_L 23_P 0.57 0.25 0.12
280_G 31_A 0.57 0.25 0.12
130_R 77_S 0.57 0.25 0.11
49_I 59_D 0.57 0.25 0.11
64_R 19_S 0.57 0.25 0.11
63_R 113_A 0.57 0.24 0.11
164_V 87_I 0.57 0.24 0.11
129_K 78_R 0.56 0.23 0.10
9_S 89_A 0.55 0.23 0.10
404_R 20_Y 0.55 0.23 0.10
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
7046 3.78 UMUC_SALTY - UMUD_SALTY Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 1.00 Done - Shared
6931 1.91 UMUC_SALTY - UMUD_SALTY HHBlits Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
6890 4.97 UMUC_SALTY - UMUD_SALTY Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 1.00 Done - Shared
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