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OPENSEQ.org
ParB_ScpA
Genes: A B A+B
Length: 282 251 522
Sequences: 3280 2020 870
Seq/Len: 11.63 8.05 1.67
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 0.01
20 0.12 0.00 0.01
100 0.13 0.00 0.04
∞ 0.14 0.00 1.63
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 1.35 0.80 0.05
47_L 56_A 1.32 0.78 0.05
169_I 188_I 1.27 0.74 0.04
270_L 215_V 1.10 0.58 0.03
202_Q 29_I 1.09 0.57 0.03
76_A 40_Q 1.09 0.57 0.03
260_I 55_I 1.09 0.57 0.03
277_L 42_L 1.06 0.54 0.02
123_E 233_Q 1.05 0.53 0.02
119_S 24_R 1.04 0.52 0.02
113_L 241_Y 1.04 0.51 0.02
274_L 58_E 1.01 0.48 0.02
261_E 37_I 1.00 0.47 0.02
75_V 213_L 1.00 0.47 0.02
223_T 210_K 0.99 0.46 0.02
230_K 59_Y 0.97 0.44 0.02
76_A 41_Y 0.97 0.44 0.02
52_E 159_K 0.97 0.44 0.02
60_L 26_E 0.95 0.42 0.02
76_A 21_L 0.94 0.41 0.02
7_K 37_I 0.94 0.40 0.01
32_R 45_V 0.94 0.40 0.01
141_L 15_L 0.93 0.40 0.01
84_A 203_D 0.92 0.39 0.01
247_T 201_F 0.92 0.39 0.01
57_H 4_Y 0.91 0.37 0.01
247_T 104_Y 0.90 0.37 0.01
28_I 227_Q 0.89 0.36 0.01
105_R 61_V 0.89 0.35 0.01
187_N 188_I 0.88 0.35 0.01
264_F 42_L 0.88 0.35 0.01
109_L 98_I 0.88 0.35 0.01
10_N 214_V 0.88 0.34 0.01
141_L 125_F 0.87 0.34 0.01
126_A 157_F 0.86 0.33 0.01
63_L 215_V 0.86 0.33 0.01
159_L 32_I 0.86 0.33 0.01
140_Q 238_S 0.86 0.33 0.01
185_L 28_D 0.86 0.33 0.01
269_D 229_V 0.85 0.32 0.01
94_A 121_R 0.85 0.32 0.01
34_N 20_H 0.85 0.32 0.01
74_I 102_I 0.85 0.32 0.01
123_E 21_L 0.85 0.32 0.01
9_I 219_A 0.85 0.32 0.01
222_E 6_V 0.84 0.31 0.01
196_Q 114_L 0.84 0.31 0.01
85_K 67_L 0.84 0.31 0.01
110_L 240_I 0.83 0.30 0.01
72_Y 156_A 0.83 0.30 0.01
145_L 215_V 0.83 0.30 0.01
240_Y 234_E 0.83 0.30 0.01
218_N 242_I 0.83 0.30 0.01
116_E 32_I 0.82 0.30 0.01
130_L 64_A 0.82 0.30 0.01
31_L 123_K 0.82 0.29 0.01
153_A 34_V 0.82 0.29 0.01
127_Y 7_K 0.82 0.29 0.01
184_G 231_I 0.81 0.29 0.01
169_I 124_S 0.81 0.28 0.01
247_T 220_V 0.81 0.28 0.01
162_P 127_K 0.81 0.28 0.01
194_L 107_Y 0.81 0.28 0.01
222_E 64_A 0.81 0.28 0.01
95_I 21_L 0.80 0.28 0.01
3_K 111_A 0.80 0.27 0.01
191_L 59_Y 0.80 0.27 0.01
166_Q 112_K 0.80 0.27 0.01
144_R 45_V 0.79 0.27 0.01
98_E 230_L 0.79 0.27 0.01
183_L 21_L 0.79 0.27 0.01
203_L 85_D 0.79 0.26 0.01
264_F 61_V 0.78 0.26 0.01
117_D 87_L 0.78 0.26 0.01
28_I 190_H 0.78 0.26 0.01
186_K 220_V 0.78 0.26 0.01
169_I 242_I 0.78 0.26 0.01
94_A 216_T 0.78 0.26 0.01
245_F 56_A 0.78 0.26 0.01
257_K 217_F 0.78 0.26 0.01
207_Q 145_K 0.77 0.25 0.01
170_A 153_M 0.77 0.25 0.01
74_I 45_V 0.77 0.25 0.01
126_A 181_I 0.77 0.25 0.01
242_Q 33_P 0.77 0.25 0.01
156_L 35_A 0.77 0.25 0.01
120_P 111_A 0.76 0.24 0.01
141_L 181_I 0.76 0.24 0.01
255_K 192_L 0.76 0.24 0.01
18_L 116_E 0.76 0.24 0.01
142_A 235_H 0.76 0.24 0.01
145_L 225_K 0.76 0.24 0.01
44_D 181_I 0.75 0.24 0.01
106_E 37_I 0.75 0.24 0.01
269_D 181_I 0.75 0.23 0.01
202_Q 107_Y 0.75 0.23 0.01
91_T 213_L 0.75 0.23 0.01
116_E 69_I 0.75 0.23 0.01
102_A 42_L 0.75 0.23 0.01
178_H 100_K 0.74 0.23 0.01
29_A 133_S 0.74 0.23 0.01
208_L 177_Q 0.74 0.23 0.01
36_Y 59_Y 0.74 0.23 0.01
170_A 240_I 0.74 0.23 0.01
156_L 191_S 0.74 0.23 0.01
204_N 95_E 0.74 0.23 0.01
71_G 32_I 0.74 0.22 0.01
31_L 220_V 0.73 0.22 0.01
120_P 31_D 0.73 0.22 0.01
26_I 188_I 0.73 0.22 0.01
11_A 45_V 0.73 0.22 0.01
43_D 203_D 0.73 0.22 0.01
140_Q 166_I 0.73 0.22 0.01
147_K 125_F 0.73 0.22 0.01
160_T 225_K 0.73 0.22 0.01
126_A 225_K 0.73 0.22 0.01
179_G 4_Y 0.73 0.22 0.01
44_D 229_V 0.73 0.22 0.01
198_V 155_G 0.73 0.22 0.01
264_F 205_F 0.73 0.22 0.01
137_T 4_Y 0.72 0.21 0.01
146_G 22_I 0.72 0.21 0.01
73_D 149_T 0.72 0.21 0.01
227_E 235_H 0.72 0.21 0.01
34_N 127_K 0.72 0.21 0.01
176_M 179_I 0.72 0.21 0.01
97_R 39_E 0.72 0.21 0.01
223_T 153_M 0.72 0.21 0.01
260_I 105_R 0.71 0.21 0.01
270_L 12_E 0.71 0.21 0.01
174_L 137_K 0.71 0.21 0.01
134_L 38_T 0.71 0.21 0.01
277_L 114_L 0.71 0.21 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
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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