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OPENSEQ.org
Caulobacter ParD-ParE
Genes: A B A+B
Length: 88 96 177
Sequences: 898 2803 649
Seq/Len: 10.2 29.2 3.67
MirrorTree (Pazo et al. 2001) 0.56
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 3.53
2 0.00 0.00 3.53
5 0.00 0.01 3.58
10 0.01 0.02 3.60
20 0.01 0.03 3.64
100 0.02 0.05 3.74
∞ 0.07 0.10 4.07
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
75_E 11_K 2.53 1.00 1.00
75_E 15_D 2.40 1.00 1.00
59_E 61_Y 2.14 1.00 0.99
57_E 9_R 2.00 1.00 0.98
58_G 83_R 1.91 1.00 0.98
55_L 61_Y 1.77 0.99 0.97
73_I 35_R 1.72 0.99 0.96
55_L 72_F 1.69 0.99 0.95
77_S 31_A 1.68 0.99 0.95
56_I 58_R 1.56 0.98 0.93
58_G 82_I 1.43 0.96 0.89
65_E 11_K 1.35 0.94 0.85
79_A 19_T 1.30 0.92 0.82
52_R 57_L 1.17 0.85 0.72
73_I 31_A 1.07 0.78 0.62
59_E 74_R 1.06 0.77 0.61
76_R 19_T 1.03 0.74 0.57
16_A 19_T 1.02 0.72 0.56
54_A 83_R 1.00 0.71 0.54
7_S 91_A 0.96 0.66 0.48
79_A 15_D 0.92 0.61 0.43
69_F 41_I 0.91 0.60 0.42
77_S 38_Q 0.91 0.59 0.42
67_F 18_W 0.90 0.59 0.41
66_D 8_R 0.88 0.56 0.38
42_E 83_R 0.85 0.52 0.34
61_S 73_Y 0.84 0.51 0.34
54_A 89_M 0.83 0.49 0.32
8_V 58_R 0.82 0.48 0.31
64_I 7_S 0.81 0.48 0.31
16_A 79_V 0.81 0.47 0.30
73_I 38_Q 0.80 0.46 0.29
21_Q 25_W 0.80 0.46 0.29
52_R 60_G 0.79 0.45 0.28
44_N 37_L 0.78 0.44 0.27
7_S 18_W 0.78 0.43 0.27
72_F 14_L 0.77 0.42 0.26
68_D 79_V 0.77 0.42 0.26
22_V 51_G 0.76 0.40 0.25
76_R 15_D 0.76 0.40 0.25
70_D 38_Q 0.75 0.40 0.24
5_N 25_W 0.75 0.39 0.23
58_G 13_D 0.74 0.39 0.23
78_R 19_T 0.73 0.37 0.22
38_L 51_G 0.73 0.37 0.22
21_Q 90_N 0.73 0.36 0.21
44_N 70_V 0.72 0.36 0.21
7_S 7_S 0.72 0.36 0.21
7_S 87_Q 0.72 0.36 0.21
22_V 5_R 0.71 0.34 0.20
10_L 81_I 0.71 0.34 0.20
73_I 34_A 0.71 0.34 0.20
69_F 34_A 0.70 0.34 0.19
55_L 66_S 0.70 0.34 0.19
62_G 7_S 0.70 0.34 0.19
61_S 83_R 0.69 0.32 0.18
34_I 24_R 0.69 0.32 0.18
14_F 72_F 0.69 0.32 0.18
23_A 34_A 0.69 0.32 0.18
5_N 56_N 0.68 0.31 0.17
76_R 18_W 0.68 0.31 0.17
56_I 68_S 0.68 0.30 0.17
17_F 51_G 0.67 0.30 0.17
70_D 11_K 0.67 0.30 0.17
69_F 6_L 0.67 0.30 0.16
77_S 30_A 0.67 0.29 0.16
14_F 20_Y 0.66 0.29 0.16
10_L 14_L 0.66 0.29 0.16
43_E 68_S 0.66 0.28 0.15
34_I 64_C 0.66 0.28 0.15
29_S 56_N 0.65 0.28 0.15
52_R 56_N 0.65 0.28 0.15
38_L 44_I 0.64 0.27 0.14
80_S 18_W 0.64 0.27 0.14
18_I 87_Q 0.64 0.27 0.14
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
1175 0.67 TT Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.91 Done - Shared
0718 3.72 3KXE Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2014_03) 1.00 Done - Shared
0663 3.67 Caulobacter ParD-ParE Δgene:(1, 1) A:(1E-04, 4) B:(1E-04, 4) msa: Jackhmmer (2014_03) 1.00 Done - Shared
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