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OPENSEQ.org
MreB - RodZ
Genes: A B A+B
Length: 347 337 655
Sequences: 6348 563 413
Seq/Len: 18.29 1.67 0.63
MirrorTree (Pazo et al. 2001) 0.40
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 0.00 0.00
2 0.02 0.00 0.00
5 0.02 0.00 0.02
10 0.03 0.00 0.16
20 0.04 0.00 0.20
100 0.11 0.00 0.30
∞ 0.22 0.00 0.60
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
266_G 267_V 1.28 0.46 0.00
175_V 96_P 1.24 0.42 0.00
215_A 62_R 1.21 0.40 0.00
286_I 296_L 1.17 0.36 0.00
213_A 72_V 1.07 0.30 0.00
208_S 75_P 1.04 0.27 0.00
327_R 263_C 1.03 0.27 0.00
275_L 61_L 1.02 0.27 0.00
202_V 44_V 1.01 0.26 0.00
129_S 278_G 0.99 0.25 0.00
271_V 304_V 0.98 0.24 0.00
149_I 304_V 0.97 0.23 0.00
291_M 250_A 0.96 0.23 0.00
264_L 68_Y 0.95 0.22 0.00
284_S 70_R 0.94 0.22 0.00
26_V 218_V 0.92 0.21 0.00
318_A 40_K 0.91 0.20 0.00
241_L 312_P 0.90 0.20 0.00
244_G 126_G 0.90 0.19 0.00
251_L 249_V 0.90 0.19 0.00
175_V 32_A 0.89 0.19 0.00
96_K 255_L 0.88 0.19 0.00
256_I 28_L 0.88 0.18 0.00
272_M 47_I 0.88 0.18 0.00
311_T 70_R 0.87 0.18 0.00
92_Q 327_L 0.87 0.18 0.00
327_R 284_G 0.87 0.18 0.00
44_D 39_L 0.86 0.17 0.00
25_Y 133_W 0.86 0.17 0.00
21_N 32_A 0.86 0.17 0.00
170_T 63_G 0.85 0.17 0.00
298_A 26_L 0.85 0.17 0.00
120_Q 298_I 0.85 0.17 0.00
120_Q 33_V 0.85 0.17 0.00
82_A 76_E 0.85 0.17 0.00
68_G 123_V 0.84 0.17 0.00
215_A 126_G 0.84 0.17 0.00
194_F 59_T 0.84 0.17 0.00
265_T 120_V 0.84 0.17 0.00
82_A 100_F 0.84 0.16 0.00
44_D 265_L 0.84 0.16 0.00
82_A 56_L 0.84 0.16 0.00
189_I 267_V 0.84 0.16 0.00
197_A 124_V 0.83 0.16 0.00
323_T 44_V 0.82 0.16 0.00
39_V 24_E 0.82 0.16 0.00
198_I 255_L 0.82 0.16 0.00
34_N 323_Q 0.82 0.15 0.00
249_F 28_L 0.82 0.15 0.00
320_D 266_E 0.81 0.15 0.00
198_I 201_P 0.81 0.15 0.00
98_V 116_F 0.81 0.15 0.00
26_V 28_L 0.81 0.15 0.00
136_R 75_P 0.81 0.15 0.00
34_N 266_E 0.80 0.15 0.00
201_Y 20_R 0.80 0.15 0.00
309_E 119_L 0.80 0.15 0.00
266_G 38_C 0.79 0.15 0.00
53_A 265_L 0.79 0.14 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
0562 0.63 MreB - RodZ Δgene:(1, ∞) A:(1E-20, 8) B:(1E-04, 8) msa: HHblits (2013_03) 0.00 Done - Shared
0561 0.32 MreB - RodZ Δgene:(1, 100) A:(1E-20, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
0560 0.21 MreB - RodZ Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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