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OPENSEQ.org
2D1P_B_C
Genes: A B A+B
Length: 119 95 214
Sequences: 508 505 466
Seq/Len: 4.27 5.32 2.18
MirrorTree (Pazo et al. 2001) 0.75
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 0.05 0.04 2.18
2 0.05 0.04 2.18
5 0.05 0.04 2.18
10 0.05 0.04 2.18
20 0.05 0.04 2.18
100 0.05 0.04 2.18
∞ 0.05 0.04 2.20
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
41_A 16_A 1.68 0.96 0.82
21_G 1_M 1.49 0.92 0.69
66_K 38_V 1.37 0.87 0.59
106_L 20_L 1.37 0.87 0.59
63_A 28_L 1.36 0.86 0.58
42_D 32_D 1.28 0.81 0.50
14_G 32_D 1.21 0.76 0.43
79_C 47_L 1.17 0.72 0.39
86_R 10_W 1.16 0.71 0.38
86_R 32_D 1.15 0.71 0.38
15_T 77_I 1.12 0.68 0.35
7_V 93_M 1.09 0.65 0.32
94_F 87_V 1.09 0.64 0.31
36_A 28_L 1.07 0.63 0.30
81_A 19_R 1.06 0.61 0.29
65_F 29_L 1.05 0.61 0.28
78_V 33_G 1.03 0.58 0.26
105_A 67_T 1.03 0.58 0.26
52_K 62_I 1.01 0.57 0.25
119_F 34_V 0.95 0.49 0.20
45_F 38_V 0.95 0.49 0.20
62_I 56_A 0.94 0.48 0.19
57_L 38_V 0.94 0.48 0.19
87_G 79_Y 0.93 0.47 0.19
38_F 31_Q 0.93 0.47 0.18
60_D 6_H 0.93 0.46 0.18
90_P 67_T 0.93 0.46 0.18
107_R 54_V 0.92 0.45 0.17
79_C 6_H 0.91 0.45 0.17
31_L 94_A 0.90 0.44 0.16
16_A 31_Q 0.90 0.43 0.16
60_D 61_L 0.89 0.42 0.16
91_Q 27_L 0.89 0.42 0.16
14_G 34_V 0.89 0.42 0.15
88_L 14_F 0.88 0.42 0.15
79_C 31_Q 0.88 0.41 0.15
78_V 23_E 0.88 0.41 0.15
20_E 81_D 0.88 0.41 0.15
86_R 8_S 0.87 0.41 0.15
46_Q 87_V 0.87 0.40 0.14
20_E 92_Q 0.87 0.40 0.14
56_V 63_A 0.87 0.40 0.14
43_G 78_D 0.87 0.40 0.14
40_I 20_L 0.87 0.40 0.14
36_A 7_R 0.86 0.39 0.14
11_A 30_L 0.85 0.38 0.13
114_D 33_G 0.84 0.38 0.13
42_D 8_S 0.84 0.38 0.13
97_E 4_T 0.84 0.37 0.13
98_A 95_W 0.84 0.37 0.13
24_A 93_M 0.84 0.37 0.13
13_H 82_F 0.84 0.37 0.13
23_D 25_D 0.84 0.37 0.13
116_I 28_L 0.84 0.36 0.12
10_T 87_V 0.83 0.36 0.12
86_R 9_P 0.83 0.36 0.12
115_V 74_I 0.83 0.36 0.12
32_T 92_Q 0.83 0.36 0.12
56_V 26_E 0.82 0.35 0.12
117_L 27_L 0.82 0.35 0.12
46_Q 85_L 0.82 0.35 0.12
100_P 65_G 0.82 0.35 0.12
103_A 19_R 0.81 0.34 0.11
43_G 10_W 0.81 0.34 0.11
37_V 3_H 0.81 0.34 0.11
34_D 78_D 0.81 0.34 0.11
7_V 19_R 0.81 0.34 0.11
97_E 22_S 0.81 0.34 0.11
89_D 28_L 0.81 0.34 0.11
111_A 54_V 0.81 0.34 0.11
100_P 27_L 0.81 0.33 0.11
31_L 31_Q 0.80 0.33 0.11
7_V 37_A 0.80 0.33 0.11
71_Y 33_G 0.80 0.32 0.10
50_G 77_I 0.79 0.32 0.10
37_V 79_Y 0.79 0.32 0.10
37_V 46_S 0.79 0.32 0.10
89_D 49_N 0.79 0.32 0.10
112_N 7_R 0.79 0.31 0.10
67_L 92_Q 0.78 0.31 0.10
115_V 91_S 0.78 0.31 0.10
9_S 16_A 0.78 0.31 0.10
95_V 27_L 0.78 0.31 0.10
26_L 35_T 0.78 0.31 0.10
6_F 92_Q 0.78 0.31 0.10
82_S 79_Y 0.78 0.30 0.10
39_F 2_L 0.77 0.30 0.09
68_L 41_N 0.77 0.30 0.09
99_T 15_A 0.77 0.30 0.09
57_L 92_Q 0.77 0.29 0.09
78_V 24_G 0.77 0.29 0.09
88_L 24_G 0.76 0.29 0.09
102_E 53_K 0.76 0.29 0.09
27_A 6_H 0.76 0.29 0.09
77_W 10_W 0.76 0.28 0.09
113_Y 28_L 0.76 0.28 0.09
29_S 65_G 0.76 0.28 0.09
50_G 24_G 0.75 0.28 0.09
42_D 10_W 0.75 0.28 0.09
54_D 23_E 0.75 0.28 0.08
57_L 1_M 0.75 0.28 0.08
79_C 56_A 0.75 0.28 0.08
118_R 7_R 0.74 0.27 0.08
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
7254 2.18 2D1P_B_C Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.82 Done - Shared
0143 1.52 2D1P_BC Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2014_03) 0.57 Done - Shared
0142 0.48 2D1P_BC Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
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