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OPENSEQ.org
MotA-FliL_K12
Genes: A B A+B
Length: 295 154 412
Sequences: 1664 693 449
Seq/Len: 5.64 4.5 1.09
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 0.00 0.01 0.01
2 0.00 0.01 0.12
5 0.00 0.01 0.14
10 0.01 0.01 0.14
20 0.01 0.01 0.45
100 0.02 0.01 0.69
∞ 0.11 0.03 1.00
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
42_I 115_T 1.25 0.59 0.00
188_L 74_Y 1.21 0.56 0.00
92_M 120_K 1.19 0.53 0.00
245_L 62_F 1.14 0.49 0.00
42_I 30_A 1.10 0.46 0.00
89_S 153_L 1.08 0.43 0.00
188_L 63_T 1.07 0.43 0.00
140_T 99_S 1.07 0.42 0.00
169_G 73_L 1.03 0.38 0.00
150_E 116_E 1.01 0.37 0.00
54_I 102_L 0.97 0.34 0.00
82_L 109_D 0.97 0.33 0.00
188_L 84_E 0.95 0.32 0.00
143_I 56_F 0.95 0.32 0.00
245_L 122_L 0.94 0.31 0.00
220_I 134_L 0.94 0.31 0.00
151_I 146_V 0.94 0.31 0.00
267_S 77_I 0.92 0.29 0.00
92_M 115_T 0.91 0.28 0.00
132_L 79_L 0.90 0.28 0.00
218_G 90_L 0.90 0.27 0.00
227_L 61_T 0.89 0.27 0.00
43_G 60_D 0.89 0.27 0.00
101_I 54_P 0.89 0.27 0.00
91_Q 108_Q 0.88 0.26 0.00
46_I 128_T 0.88 0.26 0.00
34_L 141_Q 0.88 0.26 0.00
123_L 72_V 0.88 0.26 0.00
52_K 151_F 0.87 0.26 0.00
245_L 97_V 0.87 0.26 0.00
188_L 29_S 0.86 0.25 0.00
152_E 149_T 0.86 0.25 0.00
124_D 32_Y 0.86 0.25 0.00
204_H 62_F 0.85 0.24 0.00
126_I 30_A 0.85 0.24 0.00
52_K 76_G 0.84 0.24 0.00
227_L 57_Y 0.84 0.24 0.00
219_F 84_E 0.84 0.24 0.00
69_K 57_Y 0.84 0.24 0.00
101_I 34_Y 0.84 0.23 0.00
206_M 154_R 0.84 0.23 0.00
82_L 143_V 0.84 0.23 0.00
268_S 29_S 0.83 0.23 0.00
102_E 111_A 0.83 0.23 0.00
252_Y 54_P 0.83 0.23 0.00
132_L 148_Y 0.83 0.23 0.00
72_K 76_G 0.83 0.23 0.00
245_L 126_I 0.83 0.23 0.00
106_E 101_L 0.83 0.23 0.00
134_I 148_Y 0.83 0.23 0.00
219_F 143_V 0.82 0.22 0.00
64_L 71_R 0.82 0.22 0.00
25_L 93_Y 0.82 0.22 0.00
94_M 98_R 0.81 0.22 0.00
134_I 121_N 0.81 0.21 0.00
102_E 109_D 0.81 0.21 0.00
38_A 138_Q 0.81 0.21 0.00
223_L 105_F 0.80 0.21 0.00
207_V 117_E 0.80 0.20 0.00
151_I 54_P 0.79 0.20 0.00
228_R 113_L 0.79 0.20 0.00
241_V 80_R 0.79 0.20 0.00
131_R 99_S 0.79 0.20 0.00
164_S 70_D 0.79 0.20 0.00
25_L 79_L 0.78 0.20 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)
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