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OPENSEQ.org
UMUC_SALTY - UMUD_SALTY
Genes: A B A+B
Length: 422 139 546
Sequences: 15934 7987 2064
Seq/Len: 37.76 57.46 3.78
MirrorTree (Pazo et al. 2001) 0.68
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 4.69
20 0.01 0.01 4.84
100 0.02 0.02 5.52
∞ 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 3.38 1.00 1.00
130_R 50_S 2.13 1.00 0.99
78_A 34_I 1.77 0.99 0.97
132_H 76_S 1.76 0.99 0.97
74_Y 33_Y 1.65 0.99 0.95
129_K 79_N 1.65 0.99 0.95
23_C 126_D 1.41 0.96 0.88
404_R 33_Y 1.33 0.94 0.84
419_L 54_V 1.30 0.93 0.83
86_T 49_S 1.29 0.92 0.82
79_D 37_R 1.16 0.85 0.72
420_R 55_K 1.15 0.85 0.71
420_R 57_S 1.08 0.80 0.64
421_V 54_V 1.08 0.79 0.64
419_L 94_F 1.06 0.78 0.62
100_I 30_A 1.06 0.77 0.61
130_R 47_H 1.02 0.73 0.57
75_E 33_Y 0.96 0.67 0.49
418_L 53_F 0.93 0.64 0.46
277_K 31_A 0.93 0.63 0.45
87_T 49_S 0.91 0.61 0.43
132_H 52_Y 0.89 0.58 0.41
129_K 80_A 0.83 0.51 0.34
130_R 76_S 0.81 0.48 0.32
415_Y 71_L 0.81 0.48 0.31
419_L 74_V 0.80 0.47 0.30
280_G 31_A 0.80 0.46 0.30
100_I 28_S 0.79 0.45 0.29
415_Y 53_F 0.78 0.44 0.28
23_C 128_F 0.77 0.42 0.26
403_K 35_E 0.76 0.41 0.26
386_K 127_I 0.76 0.41 0.25
82_N 37_R 0.72 0.36 0.21
270_Y 33_Y 0.72 0.36 0.21
5_C 127_I 0.71 0.35 0.21
410_R 83_G 0.71 0.35 0.20
417_D 57_S 0.70 0.34 0.20
418_L 71_L 0.70 0.34 0.20
131_T 52_Y 0.69 0.33 0.19
87_T 50_S 0.67 0.30 0.17
72_S 33_Y 0.67 0.30 0.17
369_G 127_I 0.65 0.28 0.15
418_L 38_I 0.65 0.28 0.15
130_R 77_S 0.64 0.28 0.15
129_K 78_R 0.64 0.27 0.15
90_E 49_S 0.64 0.27 0.14
252_S 29_P 0.64 0.27 0.14
9_S 39_D 0.63 0.27 0.14
115_D 90_I 0.63 0.26 0.14
25_R 101_L 0.63 0.26 0.14
9_S 89_A 0.63 0.26 0.14
410_R 35_E 0.62 0.25 0.13
75_E 35_E 0.61 0.25 0.13
385_G 69_G 0.61 0.24 0.13
192_S 31_A 0.61 0.24 0.12
91_M 101_L 0.60 0.24 0.12
5_C 131_V 0.60 0.23 0.12
63_R 113_A 0.60 0.23 0.12
415_Y 43_L 0.60 0.23 0.12
132_H 128_F 0.59 0.22 0.11
212_W 119_V 0.58 0.22 0.11
38_I 85_I 0.58 0.21 0.11
415_Y 42_E 0.58 0.21 0.10
11_Y 29_P 0.57 0.21 0.10
191_I 80_A 0.57 0.21 0.10
394_Q 119_V 0.55 0.19 0.09
88_L 23_P 0.55 0.19 0.09
404_R 20_Y 0.55 0.19 0.09
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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