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OPENSEQ.org
idr
Genes: A B A+B
Length: 111 82 193
Sequences: 3252 646 518
Seq/Len: 29.3 7.88 2.68
MirrorTree (Pazo et al. 2001) 0.65
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 0.00 0.00 2.66
2 0.01 0.00 2.65
5 0.01 0.00 2.66
10 0.01 0.01 2.68
20 0.02 0.02 2.68
100 0.05 0.02 2.72
∞ 0.11 0.05 2.82
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
38_M 56_A 1.80 0.99 0.93
104_A 53_F 1.40 0.92 0.77
79_K 73_W 1.21 0.81 0.60
49_V 2_I 1.20 0.80 0.59
108_V 54_T 1.16 0.77 0.55
105_K 58_L 1.12 0.74 0.51
10_G 58_L 1.09 0.71 0.47
39_Y 23_Q 1.08 0.70 0.46
73_A 38_V 1.02 0.64 0.39
6_V 43_I 1.01 0.62 0.38
4_R 25_L 1.00 0.61 0.37
60_F 62_I 0.99 0.61 0.36
105_K 53_F 0.96 0.56 0.32
45_M 54_T 0.95 0.55 0.32
59_P 62_I 0.93 0.53 0.30
62_V 39_D 0.93 0.53 0.30
101_L 53_F 0.92 0.52 0.29
75_A 22_M 0.92 0.52 0.28
16_D 5_S 0.92 0.51 0.28
42_K 62_I 0.91 0.51 0.28
101_L 5_S 0.91 0.51 0.28
16_D 17_I 0.91 0.51 0.28
45_M 32_E 0.90 0.49 0.26
83_W 68_H 0.89 0.49 0.26
34_L 60_N 0.89 0.48 0.25
38_M 59_V 0.88 0.47 0.24
108_V 58_L 0.88 0.46 0.24
66_G 23_Q 0.87 0.45 0.23
12_L 20_T 0.86 0.45 0.23
35_S 21_L 0.85 0.44 0.22
106_I 31_D 0.85 0.43 0.22
93_T 45_E 0.85 0.43 0.22
73_A 32_E 0.82 0.39 0.19
58_Y 62_I 0.81 0.39 0.19
64_L 76_P 0.81 0.39 0.19
38_M 65_E 0.80 0.38 0.18
94_V 49_K 0.79 0.37 0.17
43_T 7_K 0.79 0.37 0.17
90_K 37_L 0.78 0.35 0.16
59_P 59_V 0.77 0.34 0.16
99_L 28_N 0.77 0.34 0.16
53_T 51_P 0.76 0.33 0.15
41_N 38_V 0.76 0.33 0.15
48_C 73_W 0.76 0.33 0.15
108_V 53_F 0.76 0.33 0.15
107_N 52_V 0.75 0.32 0.14
90_K 57_E 0.75 0.32 0.14
47_L 81_V 0.75 0.32 0.14
106_I 69_E 0.75 0.32 0.14
37_F 55_L 0.74 0.31 0.14
36_P 59_V 0.74 0.31 0.14
1_M 21_L 0.74 0.31 0.14
23_S 8_R 0.74 0.31 0.14
40_N 58_L 0.74 0.31 0.14
39_Y 68_H 0.74 0.31 0.14
93_T 27_L 0.73 0.30 0.13
54_Q 52_V 0.73 0.30 0.13
15_V 24_A 0.73 0.30 0.13
58_Y 66_N 0.73 0.30 0.13
14_W 49_K 0.73 0.30 0.13
3_S 72_D 0.72 0.29 0.13
46_C 3_H 0.72 0.29 0.13
54_Q 14_A 0.72 0.29 0.12
78_V 19_A 0.72 0.29 0.12
109_L 39_D 0.72 0.29 0.12
27_G 12_S 0.72 0.29 0.12
99_L 42_L 0.72 0.29 0.12
81_I 5_S 0.72 0.29 0.12
82_A 78_D 0.72 0.29 0.12
110_I 4_S 0.72 0.29 0.12
33_V 14_A 0.72 0.29 0.12
76_D 9_W 0.72 0.29 0.12
61_E 66_N 0.72 0.29 0.12
100_Q 3_H 0.72 0.29 0.12
13_I 11_N 0.71 0.28 0.12
76_D 8_R 0.71 0.28 0.12
93_T 30_D 0.71 0.28 0.12
59_P 66_N 0.71 0.28 0.12
46_C 37_L 0.70 0.28 0.12
18_D 41_K 0.70 0.27 0.12
76_D 14_A 0.70 0.27 0.12
48_C 25_L 0.70 0.27 0.11
51_C 23_Q 0.70 0.27 0.11
62_V 58_L 0.70 0.27 0.11
94_V 20_T 0.70 0.27 0.11
68_E 75_E 0.69 0.27 0.11
84_R 79_K 0.69 0.26 0.11
96_P 44_I 0.69 0.26 0.11
32_V 33_V 0.69 0.26 0.11
81_I 31_D 0.69 0.26 0.11
57_G 6_V 0.68 0.26 0.10
2_V 20_T 0.68 0.25 0.10
4_R 3_H 0.68 0.25 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
13058 2.68 idr Δgene:(1, 20) A:(1E-06, 4) B:(1E-06, 8) msa: HHblits (2015_06) 0.93 Done - Shared
6413 2.62 MazEF_lower_thresholds Δgene:(1, 20) A:(1E-20, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.92 Done - Shared
3423 0.67 MAZF_ECOLI_MAZE_ECOLI Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.06 Done
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