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OPENSEQ.org
RodA vs MreD
Genes: A B A+B
Length: 370 162 490
Sequences: 4939 1716 1143
Seq/Len: 13.35 10.59 2.33
MirrorTree (Pazo et al. 2001) 0.47
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 0.00 0.03
2 0.01 0.00 0.79
5 0.01 0.00 1.08
10 0.02 0.00 1.11
20 0.02 0.00 1.16
100 0.05 0.00 1.42
∞ 0.18 0.00 2.15
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
211_V 154_K 1.23 0.79 0.06
266_A 56_V 1.18 0.75 0.05
344_S 78_V 1.14 0.72 0.05
269_A 142_G 1.10 0.68 0.04
82_C 141_N 1.05 0.63 0.04
298_A 119_F 1.03 0.60 0.03
227_H 119_F 1.02 0.59 0.03
171_L 79_L 1.01 0.58 0.03
177_S 13_W 0.95 0.52 0.03
173_V 139_V 0.95 0.52 0.03
155_A 147_W 0.95 0.51 0.03
355_I 58_T 0.95 0.51 0.03
31_S 118_V 0.94 0.50 0.03
264_I 101_W 0.94 0.50 0.03
103_L 18_I 0.93 0.49 0.02
31_S 63_G 0.93 0.49 0.02
181_W 84_I 0.93 0.48 0.02
275_V 57_G 0.91 0.47 0.02
90_D 21_L 0.91 0.47 0.02
148_F 18_I 0.90 0.46 0.02
141_G 41_L 0.90 0.45 0.02
110_F 113_V 0.90 0.45 0.02
268_L 76_V 0.90 0.45 0.02
113_S 139_V 0.90 0.45 0.02
332_V 51_P 0.90 0.45 0.02
339_V 13_W 0.89 0.44 0.02
164_I 126_I 0.89 0.44 0.02
118_I 107_V 0.89 0.44 0.02
334_V 83_I 0.89 0.44 0.02
201_F 18_I 0.88 0.43 0.02
21_L 160_A 0.87 0.42 0.02
240_L 44_L 0.87 0.42 0.02
355_I 125_V 0.86 0.41 0.02
332_V 103_Q 0.86 0.41 0.02
294_I 79_L 0.85 0.40 0.02
274_L 125_V 0.85 0.40 0.02
275_V 21_L 0.84 0.39 0.02
47_E 148_I 0.84 0.39 0.02
29_V 22_L 0.84 0.39 0.02
283_L 69_I 0.84 0.39 0.02
167_A 124_L 0.84 0.38 0.02
247_H 21_L 0.84 0.38 0.02
179_L 99_A 0.83 0.37 0.02
73_G 40_L 0.82 0.37 0.02
125_A 78_V 0.82 0.37 0.02
50_I 86_Y 0.82 0.36 0.02
50_I 61_V 0.82 0.36 0.02
74_W 69_I 0.82 0.36 0.02
294_I 136_W 0.81 0.35 0.02
17_D 55_N 0.81 0.35 0.01
149_M 140_V 0.80 0.35 0.01
317_Y 46_W 0.80 0.34 0.01
97_K 60_F 0.80 0.34 0.01
22_L 27_W 0.80 0.34 0.01
174_L 31_L 0.80 0.34 0.01
252_Q 23_Q 0.79 0.34 0.01
274_L 30_N 0.79 0.34 0.01
145_V 148_I 0.79 0.33 0.01
47_E 18_I 0.79 0.33 0.01
31_S 52_H 0.79 0.33 0.01
132_V 87_L 0.79 0.33 0.01
30_Y 59_G 0.79 0.33 0.01
278_L 120_W 0.79 0.33 0.01
84_I 139_V 0.79 0.33 0.01
305_V 119_F 0.79 0.33 0.01
239_G 105_L 0.79 0.33 0.01
282_A 40_L 0.79 0.33 0.01
38_A 58_T 0.78 0.32 0.01
266_A 140_V 0.78 0.32 0.01
253_L 46_W 0.78 0.32 0.01
209_Q 42_I 0.77 0.31 0.01
84_I 22_L 0.77 0.31 0.01
125_A 74_L 0.77 0.31 0.01
155_A 95_F 0.77 0.31 0.01
322_I 121_A 0.77 0.31 0.01
128_I 71_G 0.76 0.30 0.01
121_P 98_L 0.76 0.30 0.01
260_H 41_L 0.76 0.30 0.01
171_L 17_L 0.76 0.30 0.01
295_A 131_R 0.76 0.30 0.01
245_W 145_W 0.75 0.29 0.01
132_V 88_V 0.75 0.29 0.01
115_I 144_L 0.75 0.29 0.01
345_A 100_L 0.74 0.28 0.01
224_A 57_G 0.74 0.28 0.01
152_L 140_V 0.74 0.28 0.01
141_G 129_S 0.74 0.28 0.01
57_L 109_L 0.74 0.28 0.01
326_S 20_L 0.74 0.28 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
13612 roda-mred Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) Running - Shared
13611 0.4 roda-mred Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
10916 2.33 RodA vs MreD Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.06 Done
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