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OPENSEQ.org
CCparA-parB
Genes: A B A+B
Length: 267 304 547
Sequences: 14413 3653 2590
Seq/Len: 53.98 12.02 4.73
MirrorTree (Pazo et al. 2001) 0.87
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 0.03 4.35
2 0.04 0.09 4.46
5 0.05 0.10 4.50
10 0.07 0.10 4.52
20 0.08 0.10 4.54
100 0.12 0.11 4.66
∞ 0.17 0.12 4.97
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
224_R 17_G 1.77 1.00 0.96
247_A 289_T 1.04 0.81 0.55
201_Q 17_G 0.98 0.76 0.49
101_E 24_A 0.92 0.69 0.42
156_C 133_I 0.92 0.68 0.41
47_G 216_A 0.89 0.66 0.38
178_L 26_L 0.84 0.58 0.32
43_A 169_I 0.80 0.54 0.28
41_I 267_V 0.79 0.51 0.26
24_A 300_L 0.78 0.51 0.26
174_V 26_L 0.77 0.49 0.25
29_T 180_M 0.73 0.44 0.21
78_A 296_L 0.72 0.41 0.20
124_P 156_E 0.71 0.41 0.19
91_A 211_D 0.70 0.40 0.18
226_S 155_M 0.69 0.38 0.18
152_V 46_E 0.68 0.37 0.17
147_A 225_S 0.68 0.37 0.17
9_L 232_L 0.68 0.37 0.17
28_G 290_L 0.67 0.35 0.16
173_R 23_S 0.67 0.35 0.16
128_V 191_S 0.66 0.34 0.15
211_G 87_R 0.66 0.34 0.15
38_V 266_S 0.66 0.34 0.15
47_G 118_I 0.66 0.34 0.15
28_G 300_L 0.65 0.33 0.14
141_V 25_L 0.65 0.33 0.14
173_R 27_G 0.64 0.32 0.14
209_H 23_S 0.64 0.31 0.13
138_V 96_Y 0.64 0.31 0.13
28_G 157_K 0.63 0.30 0.13
8_V 31_A 0.62 0.30 0.12
105_T 66_E 0.62 0.29 0.12
88_V 22_L 0.61 0.28 0.12
51_T 179_T 0.61 0.28 0.12
23_T 22_L 0.61 0.28 0.12
83_L 165_I 0.61 0.28 0.12
197_S 284_T 0.61 0.28 0.12
245_S 298_N 0.61 0.28 0.12
224_R 16_R 0.60 0.27 0.11
38_V 127_A 0.60 0.27 0.11
168_M 152_K 0.60 0.27 0.11
245_S 144_V 0.60 0.27 0.11
76_D 248_R 0.60 0.27 0.11
208_A 69_E 0.59 0.26 0.11
198_L 181_R 0.59 0.26 0.10
89_I 64_R 0.59 0.26 0.10
97_G 21_G 0.59 0.26 0.10
201_Q 16_R 0.59 0.26 0.10
244_G 201_G 0.59 0.26 0.10
131_D 101_G 0.59 0.25 0.10
131_D 104_R 0.59 0.25 0.10
171_I 126_L 0.59 0.25 0.10
251_L 130_E 0.58 0.25 0.10
175_R 237_P 0.58 0.25 0.10
106_A 241_A 0.58 0.25 0.10
47_G 192_Y 0.58 0.25 0.10
87_D 300_L 0.58 0.25 0.10
164_L 133_I 0.58 0.25 0.10
133_P 147_E 0.58 0.25 0.10
9_L 268_L 0.58 0.25 0.10
68_L 209_A 0.58 0.25 0.10
152_V 75_I 0.58 0.25 0.10
79_V 242_G 0.58 0.24 0.10
197_S 16_R 0.58 0.24 0.10
196_N 168_T 0.58 0.24 0.10
208_A 122_E 0.57 0.24 0.09
184_I 85_L 0.56 0.23 0.09
67_V 98_I 0.56 0.23 0.09
154_L 158_F 0.56 0.23 0.09
80_K 238_N 0.56 0.23 0.09
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
8225 3.95 ParA-ParB Δgene:(1, 5) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.58 Done
6897 3.96 AB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.67 Done - Shared
4212 4.73 CCparA-parB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.96 Done - Shared
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