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OPENSEQ.org
motA fliG salty jh
Genes: A B A+B
Length: 295 331 610
Sequences: 4099 2592 1472
Seq/Len: 13.89 7.83 2.41
MirrorTree (Pazo et al. 2001) 0.49
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.00 0.03
2 0.00 0.00 0.05
5 0.00 0.00 0.34
10 0.00 0.00 1.18
20 0.01 0.00 1.58
100 0.01 0.01 2.35
∞ 0.05 0.02 3.10
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
253_A 289_D 1.38 0.89 0.32
196_A 47_I 1.22 0.79 0.21
38_G 266_A 1.17 0.75 0.18
146_L 154_R 1.12 0.71 0.16
88_K 317_E 1.02 0.60 0.11
99_R 280_Q 0.99 0.57 0.10
35_V 209_Q 0.97 0.54 0.09
95_F 277_N 0.97 0.54 0.09
47_V 175_L 0.95 0.52 0.09
220_I 124_D 0.95 0.52 0.09
185_V 120_D 0.93 0.50 0.08
85_L 303_N 0.91 0.47 0.07
185_V 42_A 0.90 0.46 0.07
109_I 164_F 0.90 0.46 0.07
260_F 20_D 0.90 0.46 0.07
191_A 139_R 0.90 0.46 0.07
41_G 149_F 0.89 0.45 0.07
263_K 323_I 0.89 0.45 0.07
91_Q 244_D 0.86 0.42 0.06
59_K 17_I 0.86 0.42 0.06
96_S 86_G 0.86 0.41 0.06
254_P 122_I 0.85 0.41 0.06
38_G 240_V 0.85 0.41 0.06
169_G 4_L 0.84 0.39 0.06
256_I 230_I 0.84 0.39 0.06
147_M 97_I 0.83 0.39 0.06
167_M 158_M 0.83 0.39 0.06
228_R 94_L 0.83 0.38 0.06
92_Q 266_A 0.83 0.38 0.05
41_G 80_V 0.82 0.38 0.05
10_V 94_L 0.82 0.38 0.05
126_I 291_A 0.82 0.37 0.05
61_I 150_D 0.81 0.36 0.05
16_G 328_D 0.81 0.36 0.05
34_L 321_M 0.81 0.36 0.05
246_L 149_F 0.80 0.35 0.05
43_G 171_A 0.80 0.35 0.05
213_I 276_R 0.80 0.35 0.05
151_I 51_Q 0.80 0.35 0.05
12_G 50_K 0.80 0.35 0.05
46_I 212_E 0.80 0.35 0.05
150_E 27_K 0.79 0.34 0.05
236_K 15_M 0.79 0.34 0.05
224_A 25_V 0.79 0.34 0.05
204_H 49_N 0.79 0.34 0.05
102_E 280_Q 0.79 0.34 0.05
147_M 63_A 0.79 0.33 0.04
96_S 55_V 0.78 0.33 0.04
148_D 14_L 0.78 0.33 0.04
213_I 256_S 0.78 0.32 0.04
57_T 118_A 0.77 0.32 0.04
23_G 177_E 0.77 0.32 0.04
210_F 118_A 0.77 0.32 0.04
8_L 318_T 0.77 0.32 0.04
5_L 47_I 0.77 0.32 0.04
223_L 61_Q 0.76 0.31 0.04
268_S 122_I 0.76 0.31 0.04
132_L 176_T 0.76 0.31 0.04
59_K 317_E 0.76 0.31 0.04
203_A 272_E 0.76 0.31 0.04
183_G 234_F 0.76 0.31 0.04
102_E 12_I 0.76 0.30 0.04
125_F 47_I 0.76 0.30 0.04
37_I 182_L 0.75 0.30 0.04
151_I 87_E 0.75 0.30 0.04
27_A 22_A 0.75 0.30 0.04
256_I 317_E 0.75 0.30 0.04
97_L 249_R 0.75 0.29 0.04
265_L 324_G 0.74 0.29 0.04
197_E 134_L 0.74 0.29 0.04
239_Q 261_I 0.74 0.29 0.04
91_Q 291_A 0.74 0.29 0.04
64_L 51_Q 0.74 0.29 0.04
198_L 290_L 0.74 0.29 0.04
127_V 139_R 0.74 0.29 0.04
241_V 20_D 0.73 0.28 0.04
97_L 252_Q 0.73 0.28 0.04
5_L 116_Q 0.73 0.28 0.04
59_K 219_R 0.73 0.28 0.04
165_L 118_A 0.72 0.28 0.04
168_V 83_K 0.72 0.27 0.04
245_L 219_R 0.72 0.27 0.04
17_G 280_Q 0.72 0.27 0.04
164_S 13_L 0.72 0.27 0.04
17_G 229_I 0.72 0.27 0.04
223_L 5_S 0.72 0.27 0.04
93_G 86_G 0.72 0.27 0.03
188_L 111_N 0.72 0.27 0.03
45_F 69_L 0.72 0.27 0.03
169_G 215_I 0.72 0.27 0.03
65_F 122_I 0.71 0.27 0.03
204_H 230_I 0.71 0.27 0.03
146_L 14_L 0.71 0.27 0.03
5_L 77_L 0.71 0.27 0.03
169_G 33_E 0.71 0.26 0.03
7_Y 100_T 0.71 0.26 0.03
269_E 229_I 0.71 0.26 0.03
219_F 229_I 0.71 0.26 0.03
131_R 286_L 0.71 0.26 0.03
32_A 317_E 0.71 0.26 0.03
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
10914 1.56 1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.28 Done - Shared
9357 2.41 motA fliG salty jh Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) 0.32 Done
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