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OPENSEQ.org
ntd p52_1_130
Genes: A B A+B
Length: 130 130 230
Sequences: 907 238 147
Seq/Len: 6.98 1.83 0.64
MirrorTree (Pazo et al. 2001) 0.74
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 0.51 0.02 0.57
2 0.56 0.02 0.57
5 0.58 0.02 0.58
10 0.58 0.02 0.58
20 0.59 0.02 0.58
100 0.59 0.02 0.58
∞ 0.60 0.02 0.61
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
76_T 126_G 1.74 0.79 0.03
22_V 66_L 1.65 0.74 0.03
39_R 23_L 1.62 0.72 0.03
29_F 33_R 1.59 0.71 0.02
42_H 42_L 1.52 0.66 0.02
87_K 56_V 1.47 0.62 0.02
24_K 90_L 1.46 0.61 0.02
86_I 35_Y 1.32 0.49 0.01
40_P 124_G 1.30 0.48 0.01
43_V 40_T 1.30 0.47 0.01
43_V 115_R 1.30 0.47 0.01
13_H 92_G 1.29 0.47 0.01
78_V 40_T 1.28 0.46 0.01
64_S 86_S 1.27 0.46 0.01
16_L 64_Q 1.26 0.45 0.01
39_R 22_F 1.25 0.43 0.01
55_A 122_L 1.24 0.43 0.01
81_G 42_L 1.24 0.43 0.01
77_G 40_T 1.24 0.43 0.01
66_I 75_V 1.23 0.42 0.01
78_V 124_G 1.23 0.42 0.01
26_A 87_T 1.22 0.41 0.01
69_Y 37_H 1.22 0.41 0.01
86_I 38_P 1.20 0.40 0.01
15_F 65_P 1.19 0.39 0.01
16_L 108_L 1.18 0.38 0.01
22_V 116_Q 1.17 0.37 0.01
28_D 48_L 1.16 0.37 0.01
109_S 93_L 1.16 0.36 0.01
46_Y 21_E 1.16 0.36 0.01
81_G 121_A 1.14 0.35 0.01
64_S 110_L 1.14 0.35 0.01
114_V 62_L 1.14 0.35 0.01
64_S 118_L 1.14 0.35 0.01
51_Y 93_L 1.12 0.34 0.01
45_E 58_R 1.09 0.31 0.01
56_A 51_L 1.09 0.31 0.01
41_T 118_L 1.08 0.31 0.01
118_L 115_R 1.08 0.31 0.01
20_S 60_L 1.07 0.30 0.01
38_C 72_A 1.07 0.30 0.01
76_T 30_V 1.07 0.30 0.01
24_K 65_P 1.05 0.29 0.01
27_Q 25_G 1.05 0.29 0.01
42_H 59_M 1.04 0.28 0.01
51_Y 86_S 1.03 0.27 0.01
41_T 58_R 1.02 0.27 0.01
64_S 12_V 1.02 0.27 0.01
87_K 78_E 1.01 0.26 0.00
103_N 124_G 1.01 0.26 0.00
81_G 72_A 1.01 0.26 0.00
69_Y 130_S 1.00 0.26 0.00
97_K 39_A 1.00 0.25 0.00
77_G 53_K 1.00 0.25 0.00
52_S 90_L 1.00 0.25 0.00
36_P 77_K 0.99 0.25 0.00
42_H 74_W 0.99 0.25 0.00
57_V 54_N 0.98 0.24 0.00
109_S 41_C 0.98 0.24 0.00
55_A 51_L 0.98 0.24 0.00
16_L 26_L 0.97 0.24 0.00
50_A 115_R 0.97 0.23 0.00
71_R 95_I 0.96 0.23 0.00
14_I 116_Q 0.96 0.23 0.00
93_Y 32_D 0.96 0.23 0.00
53_L 39_A 0.96 0.23 0.00
40_P 47_E 0.96 0.23 0.00
72_K 118_L 0.96 0.23 0.00
49_T 74_W 0.95 0.23 0.00
13_H 129_W 0.95 0.23 0.00
28_D 40_T 0.94 0.22 0.00
15_F 55_W 0.94 0.22 0.00
90_T 90_L 0.94 0.22 0.00
94_G 31_L 0.94 0.22 0.00
64_S 50_S 0.94 0.22 0.00
62_Q 65_P 0.94 0.22 0.00
71_R 19_L 0.93 0.21 0.00
106_F 65_P 0.93 0.21 0.00
20_S 92_G 0.93 0.21 0.00
79_P 90_L 0.93 0.21 0.00
78_V 42_L 0.93 0.21 0.00
97_K 75_V 0.92 0.21 0.00
40_P 39_A 0.92 0.21 0.00
48_L 96_W 0.92 0.20 0.00
94_G 53_K 0.91 0.20 0.00
36_P 71_V 0.91 0.20 0.00
54_Y 26_L 0.91 0.20 0.00
11_D 66_L 0.91 0.20 0.00
108_E 129_W 0.91 0.20 0.00
28_D 21_E 0.90 0.20 0.00
76_T 125_G 0.90 0.20 0.00
90_T 54_N 0.90 0.20 0.00
12_G 49_P 0.90 0.20 0.00
104_R 103_G 0.89 0.19 0.00
31_V 118_L 0.89 0.19 0.00
51_Y 26_L 0.89 0.19 0.00
57_V 47_E 0.89 0.19 0.00
39_R 30_V 0.89 0.19 0.00
71_R 94_R 0.89 0.19 0.00
69_Y 53_K 0.89 0.19 0.00
15_F 86_S 0.89 0.19 0.00
20_S 55_W 0.88 0.19 0.00
104_R 44_V 0.88 0.19 0.00
31_V 22_F 0.88 0.19 0.00
54_Y 22_F 0.88 0.18 0.00
44_H 39_A 0.88 0.18 0.00
40_P 93_L 0.88 0.18 0.00
92_S 19_L 0.87 0.18 0.00
12_G 125_G 0.87 0.18 0.00
90_T 53_K 0.87 0.18 0.00
77_G 55_W 0.87 0.18 0.00
11_D 50_S 0.86 0.18 0.00
57_V 111_N 0.86 0.18 0.00
81_G 124_G 0.86 0.18 0.00
69_Y 26_L 0.86 0.18 0.00
84_Q 38_P 0.86 0.18 0.00
110_C 129_W 0.86 0.18 0.00
50_A 108_L 0.86 0.18 0.00
19_F 93_L 0.85 0.17 0.00
67_T 94_R 0.85 0.17 0.00
28_D 53_K 0.85 0.17 0.00
105_Y 33_R 0.85 0.17 0.00
68_E 130_S 0.84 0.17 0.00
80_D 40_T 0.84 0.17 0.00
53_L 62_L 0.84 0.17 0.00
73_L 87_T 0.84 0.17 0.00
64_S 123_L 0.84 0.17 0.00
68_E 117_N 0.83 0.16 0.00
113_D 109_I 0.83 0.16 0.00
90_T 95_I 0.83 0.16 0.00
34_A 112_P 0.83 0.16 0.00
118_L 53_K 0.83 0.16 0.00
86_I 59_M 0.83 0.16 0.00
47_K 50_S 0.82 0.16 0.00
58_S 112_P 0.82 0.16 0.00
82_I 97_H 0.82 0.16 0.00
51_Y 112_P 0.82 0.16 0.00
34_A 19_L 0.82 0.16 0.00
106_F 41_C 0.82 0.16 0.00
103_N 110_L 0.82 0.16 0.00
116_Q 127_K 0.81 0.16 0.00
107_V 115_R 0.81 0.15 0.00
14_I 67_P 0.81 0.15 0.00
43_V 120_I 0.81 0.15 0.00
94_G 25_G 0.81 0.15 0.00
77_G 58_R 0.81 0.15 0.00
41_T 15_Q 0.81 0.15 0.00
90_T 72_A 0.81 0.15 0.00
20_S 73_L 0.80 0.15 0.00
43_V 108_L 0.80 0.15 0.00
22_V 51_L 0.80 0.15 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
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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