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OPENSEQ.org
ParB ScpA
Genes: A B A+B
Length: 282 251 517
Sequences: 2845 2308 841
Seq/Len: 10.09 9.2 1.63
MirrorTree (Pazo et al. 2001) 0.71
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 0.00
20 0.13 0.02 0.01
100 0.13 0.02 0.03
∞ 0.13 0.02 1.58
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
59_I 203_D 1.50 0.88 0.24
169_I 188_I 1.41 0.83 0.19
202_Q 29_I 1.22 0.69 0.11
84_A 203_D 1.18 0.65 0.10
140_Q 238_S 1.15 0.62 0.09
162_P 127_K 1.14 0.61 0.09
76_A 40_Q 1.14 0.60 0.08
260_I 55_I 1.14 0.60 0.08
47_L 56_A 1.10 0.57 0.07
184_G 231_I 1.09 0.55 0.07
119_S 24_R 1.08 0.55 0.07
254_Q 188_I 1.05 0.52 0.06
75_V 213_L 1.03 0.50 0.06
247_T 201_F 1.02 0.49 0.06
60_L 26_E 1.02 0.49 0.06
261_E 37_I 1.01 0.48 0.06
72_Y 229_V 1.01 0.48 0.06
84_A 160_V 1.01 0.48 0.05
274_L 58_E 1.01 0.47 0.05
141_L 15_L 1.00 0.47 0.05
176_M 174_I 1.00 0.46 0.05
113_L 241_Y 0.98 0.45 0.05
52_E 159_K 0.97 0.44 0.05
10_N 214_V 0.96 0.42 0.04
96_V 146_L 0.96 0.42 0.04
75_V 191_S 0.95 0.41 0.04
280_R 109_D 0.94 0.40 0.04
271_D 160_V 0.94 0.40 0.04
15_Q 245_S 0.92 0.39 0.04
208_L 83_F 0.92 0.38 0.04
28_I 227_Q 0.92 0.38 0.04
245_F 56_A 0.91 0.37 0.04
218_N 242_I 0.90 0.36 0.04
159_L 32_I 0.90 0.36 0.04
76_A 41_Y 0.90 0.36 0.04
145_L 225_K 0.89 0.35 0.03
246_G 92_D 0.89 0.35 0.03
270_L 215_V 0.89 0.35 0.03
63_L 215_V 0.88 0.35 0.03
34_N 127_K 0.88 0.35 0.03
70_K 72_R 0.88 0.34 0.03
40_K 229_V 0.88 0.34 0.03
251_I 183_A 0.88 0.34 0.03
74_I 102_I 0.88 0.34 0.03
110_L 240_I 0.88 0.34 0.03
185_L 28_D 0.88 0.34 0.03
73_D 149_T 0.87 0.34 0.03
76_A 21_L 0.87 0.33 0.03
260_I 41_Y 0.87 0.33 0.03
279_E 229_V 0.87 0.33 0.03
273_I 27_I 0.86 0.33 0.03
120_P 32_I 0.85 0.32 0.03
273_I 79_E 0.85 0.32 0.03
144_R 45_V 0.85 0.32 0.03
193_P 238_S 0.85 0.32 0.03
82_R 22_I 0.85 0.32 0.03
160_T 225_K 0.85 0.31 0.03
152_I 149_T 0.85 0.31 0.03
102_A 45_V 0.85 0.31 0.03
142_A 235_H 0.84 0.31 0.03
277_L 245_S 0.84 0.31 0.03
264_F 205_F 0.84 0.30 0.03
85_K 195_R 0.84 0.30 0.03
156_L 35_A 0.84 0.30 0.03
207_Q 45_V 0.84 0.30 0.03
34_N 20_H 0.84 0.30 0.03
144_R 55_I 0.83 0.30 0.03
144_R 6_V 0.83 0.29 0.03
104_M 105_R 0.83 0.29 0.03
109_L 98_I 0.83 0.29 0.03
277_L 114_L 0.82 0.29 0.03
240_Y 234_E 0.82 0.29 0.03
123_E 233_Q 0.82 0.29 0.03
60_L 231_I 0.82 0.29 0.03
96_V 246_E 0.82 0.28 0.03
171_E 242_I 0.82 0.28 0.03
132_K 231_I 0.81 0.28 0.03
94_A 121_R 0.81 0.28 0.03
10_N 27_I 0.81 0.28 0.02
269_D 229_V 0.81 0.28 0.02
174_L 195_R 0.81 0.28 0.02
3_K 98_I 0.80 0.27 0.02
174_L 2_E 0.80 0.27 0.02
81_F 209_Q 0.80 0.27 0.02
60_L 54_D 0.80 0.27 0.02
270_L 12_E 0.79 0.27 0.02
127_Y 7_K 0.79 0.27 0.02
244_Y 31_D 0.79 0.27 0.02
270_L 118_E 0.79 0.27 0.02
123_E 225_K 0.79 0.26 0.02
70_K 32_I 0.79 0.26 0.02
9_I 219_A 0.79 0.26 0.02
136_L 218_L 0.79 0.26 0.02
135_D 203_D 0.79 0.26 0.02
145_L 215_V 0.79 0.26 0.02
142_A 245_S 0.78 0.26 0.02
223_T 213_L 0.78 0.26 0.02
72_Y 156_A 0.78 0.26 0.02
123_E 21_L 0.78 0.25 0.02
242_Q 4_Y 0.78 0.25 0.02
196_Q 114_L 0.78 0.25 0.02
185_L 27_I 0.78 0.25 0.02
241_L 56_A 0.77 0.25 0.02
251_I 62_M 0.77 0.25 0.02
140_Q 235_H 0.77 0.24 0.02
101_E 188_I 0.77 0.24 0.02
52_E 173_T 0.77 0.24 0.02
236_E 117_R 0.77 0.24 0.02
186_K 220_V 0.76 0.24 0.02
13_F 211_E 0.76 0.24 0.02
128_D 100_K 0.76 0.24 0.02
72_Y 23_N 0.76 0.24 0.02
232_A 58_E 0.76 0.24 0.02
198_V 44_Y 0.76 0.24 0.02
171_E 240_I 0.76 0.24 0.02
27_K 27_I 0.76 0.23 0.02
119_S 242_I 0.75 0.23 0.02
164_N 107_Y 0.75 0.23 0.02
151_H 124_S 0.75 0.23 0.02
150_P 37_I 0.75 0.23 0.02
119_S 220_V 0.75 0.23 0.02
247_T 104_Y 0.75 0.23 0.02
35_P 15_L 0.75 0.23 0.02
31_L 123_K 0.75 0.23 0.02
16_V 213_L 0.75 0.23 0.02
31_L 220_V 0.74 0.23 0.02
46_A 58_E 0.74 0.23 0.02
145_L 12_E 0.74 0.23 0.02
139_E 82_L 0.74 0.23 0.02
264_F 37_I 0.74 0.22 0.02
113_L 189_V 0.74 0.22 0.02
189_N 54_D 0.74 0.22 0.02
172_G 163_R 0.74 0.22 0.02
131_L 36_K 0.74 0.22 0.02
95_I 246_E 0.74 0.22 0.02
140_Q 166_I 0.74 0.22 0.02
241_L 61_V 0.74 0.22 0.02
180_R 160_V 0.74 0.22 0.02
26_I 235_H 0.74 0.22 0.02
86_L 81_E 0.74 0.22 0.02
248_T 64_A 0.73 0.22 0.02
74_I 227_Q 0.73 0.22 0.02
182_L 238_S 0.73 0.22 0.02
156_L 191_S 0.73 0.22 0.02
74_I 231_I 0.73 0.22 0.02
174_L 8_I 0.73 0.22 0.02
85_K 190_H 0.73 0.22 0.02
25_E 224_M 0.73 0.22 0.02
225_K 190_H 0.73 0.22 0.02
264_F 42_L 0.73 0.22 0.02
214_Q 43_L 0.73 0.21 0.02
140_Q 154_I 0.73 0.21 0.02
182_L 46_H 0.73 0.21 0.02
52_E 242_I 0.73 0.21 0.02
105_R 61_V 0.72 0.21 0.02
105_R 102_I 0.72 0.21 0.02
170_A 153_M 0.72 0.21 0.02
4_G 225_K 0.72 0.21 0.02
193_P 128_P 0.72 0.21 0.02
2_A 229_V 0.72 0.21 0.02
151_H 214_V 0.72 0.21 0.02
36_Y 92_D 0.72 0.21 0.02
277_L 12_E 0.72 0.21 0.02
174_L 124_S 0.72 0.21 0.02
266_S 37_I 0.72 0.21 0.02
31_L 160_V 0.72 0.21 0.02
138_Q 27_I 0.72 0.21 0.02
91_T 213_L 0.72 0.21 0.02
264_F 34_V 0.72 0.21 0.02
277_L 42_L 0.72 0.21 0.02
117_D 6_V 0.71 0.21 0.02
24_E 229_V 0.71 0.20 0.02
194_L 107_Y 0.71 0.20 0.02
187_N 188_I 0.71 0.20 0.02
187_N 43_L 0.71 0.20 0.02
187_N 64_A 0.71 0.20 0.02
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
5760 1.63 ParB ScpA Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.24 Done - Shared
4323 1.67 ParB_ScpA Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
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