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OPENSEQ.org
MAZF_ECOLI_MAZE_ECOLI
Genes: A B A+B
Length: 111 82 191
Sequences: 1300 151 128
Seq/Len: 11.71 1.84 0.67
MirrorTree (Pazo et al. 2001) 0.66
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 0.66
2 0.00 0.00 0.67
5 0.01 0.00 0.66
10 0.01 0.00 0.66
20 0.02 0.00 0.66
100 0.04 0.00 0.66
∞ 0.08 0.00 0.67
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
79_K 73_W 1.77 0.82 0.06
104_A 53_F 1.63 0.74 0.04
59_P 62_I 1.61 0.73 0.04
43_T 62_I 1.48 0.63 0.03
6_V 43_I 1.44 0.61 0.03
105_K 53_F 1.35 0.53 0.02
34_L 4_S 1.34 0.52 0.02
54_Q 14_A 1.33 0.51 0.02
13_I 44_I 1.28 0.48 0.02
71_G 14_A 1.27 0.47 0.02
93_T 3_H 1.25 0.45 0.01
89_T 6_V 1.25 0.45 0.01
58_Y 62_I 1.24 0.44 0.01
77_Q 71_I 1.22 0.43 0.01
6_V 20_T 1.22 0.43 0.01
54_Q 61_D 1.21 0.41 0.01
64_L 76_P 1.19 0.40 0.01
45_M 33_V 1.17 0.38 0.01
45_M 32_E 1.17 0.38 0.01
101_L 27_L 1.15 0.37 0.01
55_S 21_L 1.14 0.36 0.01
94_V 32_E 1.12 0.35 0.01
45_M 52_V 1.12 0.34 0.01
38_M 59_V 1.10 0.33 0.01
58_Y 66_N 1.10 0.33 0.01
103_K 13_P 1.09 0.33 0.01
5_Y 67_L 1.09 0.32 0.01
93_T 27_L 1.08 0.31 0.01
92_G 35_I 1.08 0.31 0.01
110_I 62_I 1.06 0.30 0.01
101_L 53_F 1.05 0.29 0.01
21_K 56_A 1.05 0.29 0.01
93_T 14_A 1.05 0.29 0.01
32_V 33_V 1.04 0.29 0.01
71_G 13_P 1.03 0.28 0.01
45_M 8_R 1.02 0.27 0.01
48_C 30_D 1.02 0.27 0.01
83_W 66_N 1.01 0.27 0.01
58_Y 63_T 1.01 0.27 0.01
99_L 30_D 1.00 0.26 0.01
81_I 73_W 1.00 0.26 0.01
111_G 65_E 1.00 0.26 0.01
44_G 40_G 0.99 0.26 0.01
41_N 43_I 0.99 0.25 0.01
72_V 25_L 0.98 0.25 0.01
54_Q 76_P 0.97 0.24 0.01
81_I 8_R 0.96 0.24 0.01
61_E 66_N 0.96 0.23 0.01
9_M 30_D 0.95 0.23 0.01
102_I 39_D 0.95 0.23 0.01
92_G 7_K 0.94 0.23 0.01
16_D 79_K 0.94 0.22 0.01
28_H 71_I 0.93 0.22 0.01
61_E 68_H 0.93 0.22 0.01
52_T 68_H 0.92 0.21 0.01
75_A 66_N 0.92 0.21 0.01
105_K 43_I 0.92 0.21 0.01
13_I 14_A 0.91 0.21 0.01
76_D 68_H 0.91 0.21 0.01
71_G 22_M 0.90 0.20 0.01
18_D 39_D 0.90 0.20 0.01
17_F 45_E 0.89 0.20 0.00
102_I 82_W 0.88 0.19 0.00
45_M 67_L 0.88 0.19 0.00
31_A 43_I 0.88 0.19 0.00
65_S 64_P 0.88 0.19 0.00
41_N 41_K 0.88 0.19 0.00
3_S 72_D 0.88 0.19 0.00
76_D 66_N 0.87 0.18 0.00
59_P 66_N 0.87 0.18 0.00
47_L 39_D 0.86 0.18 0.00
95_A 21_L 0.85 0.18 0.00
29_R 55_L 0.85 0.18 0.00
94_V 49_K 0.85 0.17 0.00
5_Y 44_I 0.85 0.17 0.00
106_I 71_I 0.85 0.17 0.00
72_V 57_E 0.84 0.17 0.00
55_S 30_D 0.84 0.17 0.00
75_A 7_K 0.84 0.17 0.00
108_V 61_D 0.83 0.17 0.00
106_I 82_W 0.83 0.17 0.00
16_D 39_D 0.83 0.17 0.00
48_C 73_W 0.83 0.17 0.00
110_I 51_P 0.83 0.17 0.00
105_K 20_T 0.83 0.17 0.00
101_L 5_S 0.83 0.17 0.00
88_A 43_I 0.81 0.16 0.00
64_L 72_D 0.81 0.16 0.00
47_L 14_A 0.81 0.16 0.00
51_C 13_P 0.81 0.16 0.00
87_G 65_E 0.81 0.16 0.00
38_M 49_K 0.81 0.16 0.00
49_V 52_V 0.80 0.15 0.00
65_S 13_P 0.80 0.15 0.00
49_V 59_V 0.80 0.15 0.00
78_V 64_P 0.80 0.15 0.00
52_T 63_T 0.80 0.15 0.00
104_A 76_P 0.80 0.15 0.00
47_L 60_N 0.80 0.15 0.00
87_G 23_Q 0.79 0.15 0.00
42_K 66_N 0.79 0.15 0.00
44_G 5_S 0.79 0.15 0.00
81_I 70_N 0.79 0.15 0.00
12_L 30_D 0.79 0.15 0.00
50_P 80_E 0.79 0.15 0.00
97_E 65_E 0.78 0.15 0.00
13_I 31_D 0.78 0.15 0.00
98_E 57_E 0.78 0.14 0.00
39_Y 68_H 0.78 0.14 0.00
74_L 66_N 0.78 0.14 0.00
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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