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OPENSEQ.org
FliH_FliM_second_attempt
Genes: A B A+B
Length: 235 334 549
Sequences: 617 1468 386
Seq/Len: 2.63 4.4 0.7
MirrorTree (Pazo et al. 2001) 0.77
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 0.26 0.00
2 0.00 0.26 0.01
5 0.00 0.27 0.45
10 0.00 0.27 0.56
20 0.00 0.27 0.60
100 0.00 0.31 0.63
∞ 0.04 0.32 0.68
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
201_L 91_E 1.43 0.61 0.00
223_W 165_Y 1.35 0.55 0.00
195_L 308_T 1.26 0.47 0.00
128_M 51_L 1.25 0.46 0.00
74_G 194_S 1.22 0.43 0.00
65_A 286_I 1.20 0.42 0.00
95_Q 286_I 1.19 0.41 0.00
132_L 84_I 1.19 0.41 0.00
157_L 52_Q 1.18 0.40 0.00
119_L 39_D 1.16 0.38 0.00
138_V 280_P 1.15 0.38 0.00
138_V 127_V 1.15 0.38 0.00
222_R 300_P 1.15 0.38 0.00
123_I 294_A 1.13 0.36 0.00
173_H 230_L 1.12 0.35 0.00
162_P 285_P 1.11 0.35 0.00
161_E 185_Q 1.11 0.35 0.00
92_A 321_I 1.10 0.34 0.00
206_C 128_D 1.10 0.34 0.00
194_R 275_I 1.09 0.34 0.00
83_L 35_I 1.09 0.33 0.00
231_A 11_I 1.09 0.33 0.00
175_D 224_I 1.09 0.33 0.00
228_R 130_L 1.08 0.33 0.00
203_H 154_I 1.08 0.32 0.00
222_R 152_R 1.07 0.32 0.00
155_Q 137_F 1.06 0.31 0.00
204_G 132_G 1.06 0.31 0.00
193_W 177_V 1.06 0.31 0.00
72_Q 142_E 1.06 0.31 0.00
198_D 298_G 1.05 0.30 0.00
205_G 128_D 1.04 0.30 0.00
218_S 75_R 1.04 0.30 0.00
13_D 92_F 1.04 0.29 0.00
60_E 91_E 1.04 0.29 0.00
79_Y 9_A 1.03 0.29 0.00
142_T 186_V 1.03 0.29 0.00
171_R 308_T 1.03 0.29 0.00
132_L 57_I 1.03 0.29 0.00
15_L 138_P 1.02 0.28 0.00
205_G 69_L 1.01 0.28 0.00
224_Q 292_I 1.01 0.28 0.00
157_L 185_Q 1.01 0.27 0.00
44_E 315_L 1.00 0.27 0.00
186_A 286_I 1.00 0.27 0.00
127_L 136_R 1.00 0.27 0.00
49_Q 286_I 0.99 0.27 0.00
218_S 123_V 0.99 0.27 0.00
222_R 60_R 0.99 0.26 0.00
203_H 301_V 0.99 0.26 0.00
118_A 302_L 0.99 0.26 0.00
120_D 296_V 0.99 0.26 0.00
161_E 78_D 0.98 0.26 0.00
36_T 279_K 0.98 0.26 0.00
112_F 127_V 0.98 0.26 0.00
210_A 178_E 0.98 0.26 0.00
117_D 269_P 0.97 0.25 0.00
222_R 66_R 0.97 0.25 0.00
197_G 275_I 0.96 0.25 0.00
201_L 273_S 0.95 0.24 0.00
215_L 310_N 0.95 0.24 0.00
157_L 97_P 0.95 0.24 0.00
204_G 133_G 0.95 0.24 0.00
170_L 153_V 0.95 0.24 0.00
81_E 276_L 0.95 0.24 0.00
47_L 162_L 0.95 0.24 0.00
59_H 117_V 0.95 0.23 0.00
157_L 186_V 0.94 0.23 0.00
98_Q 39_D 0.94 0.23 0.00
36_T 37_P 0.94 0.23 0.00
86_G 55_E 0.94 0.23 0.00
213_G 185_Q 0.94 0.23 0.00
112_F 56_I 0.93 0.23 0.00
81_E 317_V 0.93 0.23 0.00
223_W 92_F 0.93 0.23 0.00
128_M 257_S 0.93 0.23 0.00
173_H 262_V 0.93 0.23 0.00
12_P 296_V 0.93 0.22 0.00
14_D 322_N 0.93 0.22 0.00
223_W 151_Q 0.93 0.22 0.00
186_A 292_I 0.93 0.22 0.00
85_Q 154_I 0.92 0.22 0.00
139_I 289_P 0.92 0.22 0.00
158_L 308_T 0.92 0.22 0.00
137_Q 81_V 0.92 0.22 0.00
128_M 284_L 0.92 0.22 0.00
223_W 181_R 0.92 0.22 0.00
147_N 36_R 0.91 0.21 0.00
133_E 213_G 0.91 0.21 0.00
215_L 250_L 0.91 0.21 0.00
18_P 254_V 0.91 0.21 0.00
222_R 169_W 0.91 0.21 0.00
222_R 45_R 0.90 0.21 0.00
214_D 254_V 0.90 0.21 0.00
205_G 199_V 0.90 0.21 0.00
157_L 187_K 0.90 0.21 0.00
82_G 131_F 0.90 0.21 0.00
26_E 287_E 0.90 0.21 0.00
224_Q 254_V 0.90 0.21 0.00
205_G 146_F 0.90 0.20 0.00
222_R 50_R 0.90 0.20 0.00
172_V 104_L 0.89 0.20 0.00
199_P 163_E 0.89 0.20 0.00
155_Q 126_A 0.89 0.20 0.00
219_V 269_P 0.89 0.20 0.00
211_D 248_D 0.89 0.20 0.00
223_W 218_C 0.89 0.20 0.00
150_L 206_V 0.89 0.20 0.00
62_G 119_S 0.89 0.20 0.00
199_P 78_D 0.89 0.20 0.00
164_F 261_L 0.89 0.20 0.00
201_L 277_K 0.88 0.20 0.00
210_A 177_V 0.88 0.20 0.00
150_L 137_F 0.88 0.20 0.00
146_D 256_H 0.88 0.20 0.00
115_T 209_G 0.88 0.19 0.00
177_L 172_I 0.87 0.19 0.00
97_Q 224_I 0.87 0.19 0.00
213_G 296_V 0.87 0.19 0.00
115_T 52_Q 0.87 0.19 0.00
215_L 306_Y 0.87 0.19 0.00
204_G 220_P 0.87 0.19 0.00
134_A 93_A 0.87 0.19 0.00
117_D 275_I 0.87 0.19 0.00
222_R 228_R 0.87 0.19 0.00
184_L 160_L 0.86 0.19 0.00
202_H 292_I 0.86 0.19 0.00
138_V 278_L 0.86 0.19 0.00
154_I 189_T 0.86 0.19 0.00
183_M 69_L 0.86 0.19 0.00
222_R 46_V 0.86 0.18 0.00
112_F 101_N 0.86 0.18 0.00
68_A 311_G 0.86 0.18 0.00
208_V 31_S 0.85 0.18 0.00
52_A 235_P 0.85 0.18 0.00
85_Q 155_N 0.85 0.18 0.00
195_L 242_E 0.85 0.18 0.00
100_P 34_D 0.85 0.18 0.00
61_Q 284_L 0.85 0.18 0.00
222_R 70_F 0.85 0.18 0.00
110_S 272_L 0.85 0.18 0.00
149_A 296_V 0.85 0.18 0.00
216_D 89_Y 0.85 0.18 0.00
208_V 24_E 0.85 0.18 0.00
146_D 126_A 0.85 0.18 0.00
217_A 188_F 0.85 0.18 0.00
198_D 84_I 0.85 0.18 0.00
18_P 33_S 0.85 0.18 0.00
146_D 41_N 0.85 0.18 0.00
97_Q 283_V 0.85 0.18 0.00
215_L 236_L 0.85 0.18 0.00
186_A 280_P 0.84 0.18 0.00
17_P 269_P 0.84 0.18 0.00
102_H 215_F 0.84 0.18 0.00
213_G 210_N 0.84 0.18 0.00
198_D 263_A 0.84 0.18 0.00
13_D 201_N 0.84 0.18 0.00
136_R 260_E 0.84 0.18 0.00
103_A 206_V 0.84 0.18 0.00
194_R 311_G 0.84 0.18 0.00
82_G 179_Y 0.84 0.18 0.00
201_L 19_S 0.84 0.17 0.00
193_W 315_L 0.84 0.17 0.00
14_D 203_P 0.84 0.17 0.00
188_L 297_D 0.83 0.17 0.00
105_M 155_N 0.83 0.17 0.00
168_P 127_V 0.83 0.17 0.00
222_R 146_F 0.83 0.17 0.00
154_I 187_K 0.83 0.17 0.00
222_R 131_F 0.83 0.17 0.00
184_L 284_L 0.83 0.17 0.00
213_G 97_P 0.83 0.17 0.00
27_A 295_H 0.83 0.17 0.00
180_V 302_L 0.83 0.17 0.00
90_G 159_K 0.82 0.17 0.00
158_L 252_R 0.82 0.17 0.00
142_T 141_V 0.82 0.17 0.00
28_D 254_V 0.82 0.17 0.00
103_A 274_Q 0.82 0.17 0.00
225_E 258_E 0.82 0.17 0.00
226_L 258_E 0.82 0.17 0.00
6_P 175_L 0.82 0.17 0.00
13_D 209_G 0.82 0.17 0.00
46_Q 316_R 0.82 0.17 0.00
111_E 271_R 0.82 0.17 0.00
193_W 158_L 0.82 0.17 0.00
170_L 141_V 0.82 0.17 0.00
12_P 196_N 0.81 0.16 0.00
213_G 320_L 0.81 0.16 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
6088 0.7 FliH_FliM_second_attempt Δgene:(0, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
6005 0.62 FliH_FliM_fourth_attempt Δgene:(1, 20) A:(1E-20, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
6003 0.55 FliH_FliM_third_attempt Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
6001 0.45 FliH_FliM_second_attempt Δgene:(1, 20) A:(1E-10, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
6000 0.62 FliH_FliM_first_attempt Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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