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OPENSEQ.org
ParB_SMCNTH gremlin
Genes: A B A+B
Length: 282 166 433
Sequences: 2845 4671 944
Seq/Len: 10.09 28.14 2.18
MirrorTree (Pazo et al. 2001) 0.20
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 0.01 0.00
2 0.11 0.01 0.00
5 0.12 0.02 0.00
10 0.12 0.02 0.01
20 0.13 0.02 0.02
100 0.13 0.05 0.11
∞ 0.13 0.14 2.11
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
108_A 146_V 1.01 0.56 0.00
26_I 119_C 0.99 0.53 0.00
65_V 20_V 0.95 0.49 0.00
156_L 29_V 0.93 0.47 0.00
264_F 6_L 0.92 0.45 0.00
119_S 138_F 0.91 0.45 0.00
113_L 133_L 0.90 0.43 0.00
277_L 104_V 0.88 0.41 0.00
57_H 42_D 0.87 0.41 0.00
274_L 149_I 0.87 0.40 0.00
229_V 6_L 0.86 0.40 0.00
169_I 81_T 0.86 0.39 0.00
138_Q 103_R 0.86 0.39 0.00
41_H 124_I 0.84 0.37 0.00
162_P 79_E 0.82 0.35 0.00
120_P 64_I 0.82 0.34 0.00
40_K 48_L 0.81 0.34 0.00
204_N 67_A 0.81 0.34 0.00
213_Q 100_V 0.80 0.33 0.00
34_N 35_S 0.79 0.32 0.00
184_G 19_S 0.79 0.31 0.00
191_L 3_L 0.78 0.31 0.00
275_E 44_I 0.76 0.28 0.00
156_L 98_V 0.75 0.28 0.00
131_L 28_A 0.75 0.28 0.00
121_L 28_A 0.74 0.28 0.00
193_P 44_I 0.74 0.28 0.00
131_L 6_L 0.74 0.27 0.00
63_L 17_R 0.74 0.27 0.00
81_F 76_N 0.74 0.27 0.00
174_L 88_D 0.73 0.26 0.00
138_Q 48_L 0.73 0.26 0.00
13_F 142_S 0.72 0.26 0.00
109_L 95_F 0.72 0.26 0.00
72_Y 98_V 0.71 0.25 0.00
117_D 124_I 0.71 0.24 0.00
251_I 161_F 0.71 0.24 0.00
180_R 5_R 0.70 0.24 0.00
110_L 117_Q 0.69 0.23 0.00
153_A 109_E 0.69 0.23 0.00
63_L 145_K 0.69 0.23 0.00
109_L 132_G 0.69 0.23 0.00
31_L 77_L 0.69 0.22 0.00
180_R 150_L 0.68 0.22 0.00
44_D 16_E 0.68 0.22 0.00
59_I 109_E 0.68 0.22 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
6189 0.02 Spo0J w SMC NTH Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
5734 2.18 ParB_SMCNTH gremlin Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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