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OPENSEQ.org
ParB_ScpB
Genes: A B A+B
Length: 282 197 461
Sequences: 3280 1974 878
Seq/Len: 11.63 10.02 1.9
MirrorTree (Pazo et al. 2001) 0.55
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 0.03 0.00 0.00
2 0.11 0.00 0.00
5 0.12 0.00 0.00
10 0.12 0.00 0.00
20 0.12 0.00 0.00
100 0.13 0.00 0.03
∞ 0.14 0.00 1.83
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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 1.18 0.70 0.01
250_N 61_I 1.00 0.51 0.01
132_K 60_L 0.98 0.49 0.01
92_V 170_P 0.98 0.49 0.01
164_N 107_I 0.96 0.46 0.01
152_I 152_P 0.95 0.45 0.01
236_E 112_I 0.94 0.45 0.01
33_P 162_T 0.93 0.43 0.01
72_Y 169_L 0.93 0.43 0.01
182_L 141_G 0.93 0.43 0.01
210_Q 133_L 0.93 0.43 0.01
12_L 14_A 0.92 0.42 0.01
94_A 95_L 0.92 0.42 0.01
9_I 62_E 0.92 0.42 0.01
169_I 97_V 0.90 0.40 0.01
232_A 111_E 0.89 0.39 0.01
76_A 142_P 0.87 0.37 0.01
3_K 80_K 0.87 0.36 0.01
273_I 107_I 0.86 0.36 0.01
254_Q 24_L 0.86 0.36 0.01
235_K 133_L 0.86 0.35 0.01
160_T 133_L 0.85 0.35 0.01
156_L 10_A 0.85 0.34 0.01
18_L 165_E 0.84 0.34 0.01
142_A 151_T 0.84 0.34 0.01
184_G 122_R 0.84 0.34 0.01
165_I 97_V 0.84 0.34 0.00
144_R 132_L 0.84 0.34 0.00
233_V 110_A 0.84 0.33 0.00
207_Q 158_F 0.84 0.33 0.00
175_S 90_L 0.83 0.33 0.00
36_Y 163_L 0.83 0.33 0.00
166_Q 107_I 0.83 0.33 0.00
133_H 92_Q 0.82 0.32 0.00
264_F 142_P 0.82 0.32 0.00
127_Y 94_S 0.82 0.32 0.00
217_Q 29_L 0.82 0.32 0.00
260_I 29_L 0.81 0.31 0.00
181_T 148_Y 0.81 0.31 0.00
239_S 151_T 0.81 0.31 0.00
233_V 139_A 0.81 0.31 0.00
233_V 132_L 0.80 0.30 0.00
150_P 94_S 0.80 0.30 0.00
264_F 159_G 0.80 0.30 0.00
141_L 157_Q 0.79 0.29 0.00
15_Q 47_V 0.79 0.29 0.00
121_L 80_K 0.78 0.28 0.00
260_I 146_I 0.78 0.28 0.00
116_E 146_I 0.78 0.28 0.00
273_I 43_I 0.78 0.28 0.00
92_V 41_N 0.78 0.28 0.00
120_P 55_T 0.77 0.28 0.00
147_K 158_F 0.77 0.27 0.00
57_H 113_E 0.77 0.27 0.00
109_L 89_G 0.77 0.27 0.00
13_F 78_Y 0.76 0.27 0.00
127_Y 100_I 0.76 0.26 0.00
198_V 27_K 0.76 0.26 0.00
139_E 177_V 0.75 0.26 0.00
233_V 69_L 0.75 0.26 0.00
133_H 108_T 0.75 0.26 0.00
208_L 100_I 0.75 0.26 0.00
52_E 65_D 0.75 0.26 0.00
57_H 90_L 0.75 0.25 0.00
96_V 67_Y 0.75 0.25 0.00
152_I 40_L 0.74 0.25 0.00
155_H 142_P 0.74 0.25 0.00
103_L 40_L 0.74 0.25 0.00
213_Q 169_L 0.74 0.25 0.00
4_G 58_I 0.74 0.24 0.00
204_N 12_V 0.74 0.24 0.00
225_K 24_L 0.74 0.24 0.00
40_K 101_V 0.73 0.24 0.00
252_K 29_L 0.73 0.24 0.00
122_E 29_L 0.73 0.24 0.00
33_P 142_P 0.73 0.24 0.00
26_I 46_D 0.73 0.24 0.00
269_D 132_L 0.73 0.24 0.00
131_L 128_V 0.72 0.23 0.00
127_Y 83_I 0.72 0.23 0.00
167_Q 46_D 0.72 0.23 0.00
270_L 25_T 0.72 0.23 0.00
208_L 62_E 0.71 0.23 0.00
207_Q 147_L 0.71 0.23 0.00
59_I 152_P 0.71 0.23 0.00
76_A 145_A 0.71 0.23 0.00
244_Y 169_L 0.71 0.23 0.00
67_K 162_T 0.71 0.22 0.00
240_Y 170_P 0.71 0.22 0.00
252_K 12_V 0.71 0.22 0.00
208_L 8_W 0.70 0.22 0.00
180_R 92_Q 0.70 0.22 0.00
89_L 60_L 0.70 0.22 0.00
245_F 101_V 0.70 0.22 0.00
100_S 7_N 0.70 0.22 0.00
135_D 57_G 0.70 0.21 0.00
129_S 20_G 0.70 0.21 0.00
26_I 95_L 0.70 0.21 0.00
147_K 171_E 0.70 0.21 0.00
141_L 69_L 0.70 0.21 0.00
86_L 101_V 0.70 0.21 0.00
81_F 23_G 0.70 0.21 0.00
190_K 133_L 0.70 0.21 0.00
192_E 112_I 0.70 0.21 0.00
261_E 68_M 0.69 0.21 0.00
114_Q 145_A 0.69 0.21 0.00
7_K 45_A 0.69 0.21 0.00
2_A 65_D 0.69 0.21 0.00
64_I 126_S 0.69 0.21 0.00
252_K 73_K 0.69 0.21 0.00
264_F 158_F 0.69 0.21 0.00
144_R 15_L 0.69 0.20 0.00
123_E 16_L 0.69 0.20 0.00
142_A 68_M 0.68 0.20 0.00
130_L 151_T 0.68 0.20 0.00
113_L 92_Q 0.68 0.20 0.00
11_A 112_I 0.68 0.20 0.00
142_A 173_A 0.68 0.20 0.00
192_E 12_V 0.68 0.20 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
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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