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OPENSEQ.org
ntd p52_1_130
Genes: A B A+B
Length: 130 130 235
Sequences: 969 240 201
Seq/Len: 7.45 1.85 0.86
MirrorTree (Pazo et al. 2001) 0.75
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 0.50 0.02 0.77
2 0.54 0.02 0.77
5 0.56 0.02 0.78
10 0.57 0.02 0.78
20 0.57 0.02 0.78
100 0.58 0.02 0.78
∞ 0.59 0.02 0.78
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
86_I 35_Y 2.11 0.96 0.81
39_R 23_L 1.82 0.89 0.62
69_Y 37_H 1.65 0.82 0.47
76_T 126_G 1.54 0.75 0.38
42_H 42_L 1.45 0.69 0.30
43_V 40_T 1.45 0.69 0.30
78_V 40_T 1.42 0.67 0.28
16_L 90_L 1.41 0.66 0.28
7_W 65_P 1.40 0.65 0.27
18_A 87_T 1.40 0.65 0.27
50_A 108_L 1.39 0.64 0.26
81_G 121_A 1.37 0.62 0.24
5_P 92_G 1.36 0.62 0.24
118_L 115_R 1.32 0.58 0.21
78_V 124_G 1.31 0.57 0.20
56_A 51_L 1.30 0.56 0.20
20_S 61_F 1.25 0.52 0.17
73_L 27_S 1.24 0.51 0.16
66_I 75_V 1.23 0.50 0.16
81_G 42_L 1.23 0.50 0.16
6_L 116_Q 1.22 0.49 0.15
14_I 66_L 1.21 0.48 0.14
8_V 64_Q 1.21 0.48 0.14
96_V 47_E 1.20 0.47 0.14
28_D 23_L 1.19 0.47 0.14
24_K 122_L 1.16 0.44 0.12
73_L 30_V 1.15 0.43 0.12
39_R 22_F 1.13 0.41 0.11
43_V 115_R 1.13 0.41 0.11
12_G 60_L 1.12 0.41 0.11
29_F 37_H 1.12 0.40 0.10
19_F 127_K 1.11 0.40 0.10
31_V 22_F 1.10 0.39 0.10
40_P 39_A 1.10 0.39 0.10
57_V 41_C 1.09 0.38 0.09
13_H 69_A 1.08 0.37 0.09
51_Y 93_L 1.08 0.37 0.09
7_W 59_M 1.06 0.36 0.09
87_K 125_G 1.06 0.36 0.09
31_V 82_A 1.06 0.35 0.08
48_L 96_W 1.05 0.35 0.08
94_G 31_L 1.04 0.34 0.08
10_P 27_S 1.04 0.34 0.08
48_L 55_W 1.03 0.33 0.07
40_P 93_L 1.03 0.33 0.07
57_V 54_N 1.02 0.33 0.07
51_Y 86_S 1.02 0.32 0.07
109_S 93_L 1.02 0.32 0.07
103_N 38_P 1.01 0.31 0.07
18_A 90_L 1.00 0.31 0.07
82_I 99_Q 1.00 0.31 0.07
86_I 93_L 1.00 0.31 0.07
87_K 93_L 1.00 0.31 0.07
96_V 41_C 0.99 0.30 0.06
4_R 27_S 0.99 0.30 0.06
40_P 47_E 0.99 0.30 0.06
3_S 50_S 0.98 0.30 0.06
7_W 25_G 0.98 0.30 0.06
69_Y 53_K 0.98 0.29 0.06
80_D 40_T 0.98 0.29 0.06
10_P 35_Y 0.98 0.29 0.06
14_I 97_H 0.97 0.29 0.06
52_S 74_W 0.97 0.29 0.06
106_F 113_I 0.97 0.29 0.06
63_T 115_R 0.97 0.29 0.06
12_G 92_G 0.97 0.29 0.06
72_K 112_P 0.96 0.28 0.06
65_D 93_L 0.96 0.28 0.06
6_L 64_Q 0.96 0.28 0.06
41_T 16_C 0.96 0.28 0.05
20_S 53_K 0.96 0.28 0.05
88_L 35_Y 0.95 0.27 0.05
23_Y 67_P 0.95 0.27 0.05
4_R 43_A 0.95 0.27 0.05
32_A 53_K 0.94 0.27 0.05
5_P 129_W 0.94 0.27 0.05
93_Y 32_D 0.94 0.27 0.05
79_P 90_L 0.94 0.26 0.05
40_P 124_G 0.94 0.26 0.05
69_Y 130_S 0.93 0.26 0.05
29_F 33_R 0.93 0.26 0.05
69_Y 84_E 0.93 0.26 0.05
94_G 25_G 0.93 0.26 0.05
115_I 19_L 0.93 0.26 0.05
67_T 94_R 0.92 0.25 0.05
77_G 40_T 0.92 0.25 0.05
51_Y 63_E 0.92 0.25 0.05
92_S 23_L 0.91 0.25 0.04
57_V 47_E 0.91 0.25 0.04
90_T 95_I 0.91 0.25 0.04
41_T 118_L 0.91 0.24 0.04
103_N 124_G 0.91 0.24 0.04
110_C 129_W 0.91 0.24 0.04
28_D 95_I 0.90 0.24 0.04
108_E 129_W 0.90 0.24 0.04
34_A 19_L 0.90 0.24 0.04
12_G 126_G 0.90 0.23 0.04
16_L 126_G 0.89 0.23 0.04
64_S 12_V 0.89 0.23 0.04
34_A 97_H 0.89 0.23 0.04
41_T 15_Q 0.89 0.23 0.04
7_W 57_M 0.89 0.23 0.04
16_L 31_L 0.89 0.23 0.04
23_Y 105_L 0.89 0.23 0.04
42_H 59_M 0.88 0.23 0.04
104_R 119_R 0.88 0.22 0.04
90_T 54_N 0.88 0.22 0.04
84_Q 93_L 0.88 0.22 0.04
75_K 38_P 0.87 0.22 0.04
55_A 122_L 0.87 0.22 0.04
35_E 68_Q 0.87 0.22 0.04
116_Q 45_F 0.87 0.22 0.04
52_S 122_L 0.87 0.22 0.04
78_V 130_S 0.87 0.22 0.04
71_R 19_L 0.87 0.22 0.04
21_P 33_R 0.86 0.22 0.04
108_E 71_V 0.86 0.21 0.04
62_Q 22_F 0.86 0.21 0.03
90_T 41_C 0.86 0.21 0.03
50_A 23_L 0.85 0.21 0.03
81_G 47_E 0.85 0.21 0.03
71_R 129_W 0.85 0.21 0.03
67_T 46_R 0.85 0.21 0.03
84_Q 38_P 0.85 0.21 0.03
3_S 63_E 0.85 0.21 0.03
5_P 61_F 0.85 0.21 0.03
39_R 30_V 0.85 0.21 0.03
53_L 108_L 0.85 0.20 0.03
43_V 120_I 0.84 0.20 0.03
7_W 79_F 0.84 0.20 0.03
112_P 67_P 0.83 0.20 0.03
41_T 108_L 0.83 0.20 0.03
63_T 109_I 0.83 0.20 0.03
57_V 111_N 0.83 0.20 0.03
78_V 39_A 0.83 0.20 0.03
54_Y 129_W 0.83 0.20 0.03
48_L 80_S 0.83 0.20 0.03
51_Y 91_S 0.83 0.20 0.03
19_F 66_L 0.83 0.19 0.03
48_L 36_G 0.83 0.19 0.03
36_P 77_K 0.83 0.19 0.03
45_E 24_G 0.82 0.19 0.03
29_F 36_G 0.82 0.19 0.03
88_L 93_L 0.82 0.19 0.03
20_S 108_L 0.82 0.19 0.03
94_G 41_C 0.82 0.19 0.03
20_S 21_E 0.82 0.19 0.03
93_Y 50_S 0.81 0.19 0.03
20_S 52_A 0.81 0.19 0.03
20_S 40_T 0.81 0.19 0.03
50_A 115_R 0.81 0.19 0.03
77_G 77_K 0.81 0.18 0.03
45_E 70_A 0.81 0.18 0.03
24_K 49_P 0.81 0.18 0.03
50_A 20_Q 0.81 0.18 0.03
20_S 55_W 0.80 0.18 0.03
8_V 108_L 0.80 0.18 0.03
28_D 94_R 0.80 0.18 0.03
82_I 74_W 0.80 0.18 0.03
14_I 50_S 0.80 0.18 0.03
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
2247 0.86 ntd p52_1_130 Δgene:(0, 0) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_03) 0.81 Done
2241 0.64 ntd p52_1_130 Δgene:(0, 0) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_03) 0.03 Done
2239 0.02 ntd p52_1_130 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_03) Killed
2238 0.02 ntd p52_1_130 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_03) Killed
2237 0.06 ntd p52_1_130 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_03) Killed
2236 0.06 ntd p52_1_130 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_03) Killed
2235 0.09 ntd p52_1_130 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_03) Killed
2234 0.09 ntd p52_1_130 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_03) Killed
2233 0 ntd p52_1_130 Δgene:(0, 0) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) Killed - Shared
2232 0 ntd p52_1_130 Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) Killed - Shared
2227 0 ntd p52_1_130 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) Killed - Shared
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