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OPENSEQ.org
ParB ScpB
Genes: A B A+B
Length: 282 197 452
Sequences: 2845 2312 856
Seq/Len: 10.09 11.74 1.89
MirrorTree (Pazo et al. 2001) 0.69
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 0.01 0.02 0.00
2 0.11 0.02 0.00
5 0.12 0.02 0.00
10 0.12 0.02 0.01
20 0.13 0.02 0.01
100 0.13 0.02 0.02
∞ 0.13 0.02 1.79
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
204_N 115_I 1.40 0.85 0.17
250_N 61_I 1.09 0.60 0.07
169_I 97_V 1.06 0.57 0.06
94_A 95_L 1.03 0.54 0.05
164_N 107_I 1.01 0.52 0.05
264_F 142_P 1.01 0.52 0.05
175_S 90_L 0.99 0.49 0.05
92_V 29_L 0.97 0.47 0.04
152_I 40_L 0.96 0.47 0.04
132_K 60_L 0.95 0.45 0.04
182_L 141_G 0.94 0.44 0.04
166_Q 107_I 0.92 0.42 0.04
33_P 162_T 0.91 0.41 0.04
269_D 69_L 0.89 0.39 0.03
1_M 130_K 0.89 0.39 0.03
147_K 158_F 0.88 0.38 0.03
252_K 73_K 0.88 0.38 0.03
165_I 115_I 0.87 0.37 0.03
57_H 113_E 0.87 0.37 0.03
121_L 88_K 0.83 0.33 0.03
43_D 84_E 0.83 0.33 0.03
72_Y 169_L 0.82 0.32 0.03
74_I 75_F 0.82 0.32 0.03
76_A 142_P 0.82 0.32 0.03
13_F 78_Y 0.82 0.32 0.03
233_V 110_A 0.81 0.31 0.02
64_I 88_K 0.81 0.31 0.02
260_I 29_L 0.81 0.31 0.02
260_I 107_I 0.80 0.29 0.02
144_R 132_L 0.79 0.29 0.02
127_Y 100_I 0.79 0.29 0.02
138_Q 138_R 0.79 0.29 0.02
92_V 41_N 0.79 0.29 0.02
26_I 95_L 0.79 0.29 0.02
241_L 49_D 0.79 0.29 0.02
133_H 92_Q 0.78 0.28 0.02
59_I 152_P 0.77 0.28 0.02
110_L 144_R 0.77 0.27 0.02
262_I 115_I 0.77 0.27 0.02
272_R 121_E 0.77 0.27 0.02
251_I 112_I 0.77 0.27 0.02
74_I 37_E 0.77 0.27 0.02
233_V 132_L 0.77 0.27 0.02
52_E 65_D 0.76 0.26 0.02
85_K 104_K 0.76 0.26 0.02
57_H 90_L 0.76 0.26 0.02
9_I 62_E 0.75 0.26 0.02
34_N 132_L 0.75 0.26 0.02
239_S 151_T 0.75 0.25 0.02
184_G 21_D 0.75 0.25 0.02
264_F 141_G 0.75 0.25 0.02
181_T 148_Y 0.75 0.25 0.02
207_Q 31_T 0.75 0.25 0.02
179_G 82_L 0.74 0.25 0.02
125_Q 101_V 0.74 0.25 0.02
74_I 97_V 0.74 0.24 0.02
150_P 94_S 0.74 0.24 0.02
141_L 69_L 0.74 0.24 0.02
239_S 148_Y 0.73 0.24 0.02
75_V 47_V 0.73 0.24 0.02
60_L 15_L 0.73 0.24 0.02
156_L 10_A 0.73 0.24 0.02
92_V 170_P 0.73 0.24 0.02
34_N 90_L 0.73 0.23 0.02
147_K 120_S 0.72 0.23 0.02
270_L 25_T 0.72 0.23 0.02
245_F 101_V 0.72 0.23 0.02
13_F 66_T 0.72 0.23 0.02
142_A 120_S 0.72 0.23 0.02
68_S 23_G 0.72 0.23 0.02
180_R 92_Q 0.71 0.23 0.02
162_P 94_S 0.71 0.23 0.02
227_E 31_T 0.71 0.23 0.02
36_Y 163_L 0.71 0.23 0.02
119_S 131_A 0.71 0.22 0.02
75_V 16_L 0.71 0.22 0.02
133_H 108_T 0.71 0.22 0.01
202_Q 97_V 0.70 0.22 0.01
131_L 128_V 0.70 0.22 0.01
169_I 8_W 0.70 0.21 0.01
59_I 71_T 0.70 0.21 0.01
217_Q 29_L 0.70 0.21 0.01
114_Q 113_E 0.70 0.21 0.01
37_Q 174_E 0.69 0.21 0.01
208_L 51_Y 0.69 0.21 0.01
64_I 126_S 0.69 0.20 0.01
247_T 40_L 0.69 0.20 0.01
138_Q 92_Q 0.69 0.20 0.01
15_Q 47_V 0.68 0.20 0.01
116_E 146_I 0.68 0.20 0.01
127_Y 94_S 0.68 0.20 0.01
71_G 95_L 0.68 0.20 0.01
261_E 68_M 0.68 0.20 0.01
269_D 164_D 0.68 0.20 0.01
120_P 99_A 0.68 0.20 0.01
21_E 107_I 0.67 0.20 0.01
179_G 142_P 0.67 0.20 0.01
150_P 159_G 0.67 0.19 0.01
103_L 40_L 0.67 0.19 0.01
176_M 125_H 0.67 0.19 0.01
180_R 67_Y 0.67 0.19 0.01
151_H 56_R 0.67 0.19 0.01
114_Q 145_A 0.66 0.19 0.01
247_T 76_A 0.66 0.19 0.01
175_S 132_L 0.66 0.19 0.01
81_F 142_P 0.66 0.19 0.01
60_L 12_V 0.66 0.19 0.01
26_I 46_D 0.66 0.19 0.01
140_Q 33_L 0.66 0.19 0.01
200_A 45_A 0.66 0.19 0.01
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
5779 1.89 ParB ScpB Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.17 Done - Shared
4322 1.9 ParB_ScpB Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
2866 0.07 ParB-ScpB coevolution Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) Killed
2865 0.06 ParB-ScpB coevolution Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed
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