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OPENSEQ.org
FtsZ_MreB
Genes: A B A+B
Length: 383 347 646
Sequences: 2098 9308 1380
Seq/Len: 5.48 26.82 2.14
MirrorTree (Pazo et al. 2001) 0.02
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 0.02 0.06 0.02
2 0.02 0.06 0.02
5 0.02 0.07 0.02
10 0.02 0.07 0.04
20 0.02 0.08 0.10
100 0.03 0.11 0.48
∞ 0.05 0.19 1.89
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
88_L 76_M 0.97 0.51 0.00
227_S 245_V 0.96 0.50 0.00
162_T 129_S 0.91 0.44 0.00
80_A 305_R 0.86 0.38 0.00
104_M 194_F 0.85 0.38 0.00
272_L 92_Q 0.85 0.37 0.00
129_A 153_L 0.84 0.37 0.00
112_A 71_A 0.84 0.36 0.00
78_R 121_V 0.80 0.32 0.00
224_M 324_C 0.76 0.29 0.00
154_S 201_Y 0.76 0.28 0.00
130_V 305_R 0.76 0.28 0.00
310_V 283_A 0.76 0.28 0.00
270_L 24_I 0.76 0.28 0.00
104_M 166_I 0.76 0.28 0.00
162_T 307_L 0.75 0.28 0.00
86_D 196_E 0.73 0.26 0.00
297_S 294_T 0.73 0.26 0.00
272_L 173_V 0.73 0.26 0.00
48_A 39_V 0.73 0.26 0.00
301_D 303_L 0.72 0.25 0.00
234_D 180_G 0.72 0.25 0.00
125_I 38_V 0.72 0.25 0.00
38_E 266_G 0.71 0.24 0.00
129_A 156_S 0.71 0.24 0.00
38_E 155_V 0.71 0.24 0.00
21_G 237_R 0.71 0.24 0.00
123_L 309_E 0.70 0.24 0.00
264_I 257_L 0.70 0.24 0.00
167_K 114_V 0.70 0.24 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
14326 FtsZ_MreB Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) Running - Shared
14305 2.14 FtsZ_MreB Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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