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OPENSEQ.org
flhAflhB
Genes: A B A+B
Length: 335 211 524
Sequences: 1331 1992 1316
Seq/Len: 3.97 9.44 2.51
MirrorTree (Pazo et al. 2001) 0.69
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 1.77
2 0.01 0.00 1.99
5 0.01 0.01 2.04
10 0.01 0.01 2.25
20 0.02 0.02 2.41
100 0.03 0.03 2.59
∞ 0.07 0.07 2.77
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
232_S 13_T 1.43 0.92 0.47
263_I 5_D 1.22 0.81 0.30
150_T 5_D 1.14 0.73 0.23
152_V 185_R 1.10 0.70 0.21
217_I 92_A 1.03 0.63 0.17
242_A 126_I 0.99 0.58 0.14
281_N 117_K 0.98 0.57 0.14
323_L 200_L 0.97 0.56 0.13
261_G 155_F 0.97 0.56 0.13
35_I 8_K 0.96 0.55 0.13
94_I 180_Q 0.96 0.55 0.13
261_G 209_L 0.96 0.54 0.13
132_I 10_E 0.95 0.54 0.13
234_Q 143_E 0.94 0.52 0.12
150_T 11_E 0.94 0.52 0.12
323_L 59_L 0.94 0.52 0.12
129_I 208_F 0.94 0.52 0.12
139_L 162_L 0.94 0.52 0.12
135_C 13_T 0.92 0.50 0.11
82_I 136_F 0.92 0.50 0.11
188_R 108_M 0.92 0.50 0.11
214_V 14_S 0.92 0.49 0.11
210_K 16_K 0.91 0.48 0.11
186_R 14_S 0.91 0.48 0.11
221_I 204_V 0.91 0.48 0.11
94_I 179_T 0.90 0.47 0.10
78_F 10_E 0.89 0.47 0.10
123_V 46_L 0.89 0.46 0.10
40_I 210_V 0.89 0.46 0.10
71_K 35_I 0.88 0.45 0.10
226_G 169_L 0.87 0.44 0.09
217_I 36_V 0.86 0.43 0.09
210_K 30_Q 0.86 0.43 0.09
303_V 95_V 0.86 0.42 0.09
152_V 19_D 0.86 0.42 0.09
219_I 136_F 0.85 0.42 0.09
181_D 196_I 0.85 0.42 0.09
267_A 84_I 0.85 0.42 0.09
311_P 192_A 0.85 0.42 0.09
150_T 31_D 0.85 0.42 0.09
65_I 84_I 0.85 0.42 0.08
272_I 134_N 0.85 0.41 0.08
36_L 31_D 0.84 0.41 0.08
328_L 145_I 0.84 0.41 0.08
324_V 103_V 0.83 0.40 0.08
91_S 157_I 0.83 0.40 0.08
182_E 64_Q 0.83 0.40 0.08
85_I 140_K 0.83 0.40 0.08
182_E 15_K 0.83 0.40 0.08
179_L 198_A 0.83 0.39 0.08
290_L 80_M 0.83 0.39 0.08
216_G 170_P 0.83 0.39 0.08
222_I 58_N 0.83 0.39 0.08
199_Y 111_G 0.82 0.39 0.07
190_Q 108_M 0.82 0.38 0.07
84_I 140_K 0.82 0.38 0.07
38_I 187_R 0.82 0.38 0.07
64_L 185_R 0.82 0.38 0.07
284_E 200_L 0.81 0.38 0.07
278_D 38_L 0.81 0.37 0.07
150_T 140_K 0.81 0.37 0.07
213_A 131_G 0.81 0.37 0.07
239_L 71_F 0.81 0.36 0.07
145_V 165_F 0.80 0.36 0.07
319_G 96_L 0.80 0.36 0.07
254_G 31_D 0.80 0.36 0.07
222_I 163_L 0.80 0.36 0.07
192_V 209_L 0.80 0.36 0.07
286_T 41_G 0.80 0.35 0.07
57_A 204_V 0.79 0.35 0.07
94_I 189_I 0.79 0.35 0.07
270_I 145_I 0.79 0.35 0.07
53_A 208_F 0.79 0.35 0.07
246_Y 104_L 0.79 0.35 0.07
240_S 58_N 0.79 0.35 0.07
250_T 182_A 0.79 0.34 0.06
233_F 19_D 0.79 0.34 0.06
243_A 88_L 0.79 0.34 0.06
69_I 38_L 0.78 0.34 0.06
290_L 157_I 0.78 0.34 0.06
291_L 137_S 0.78 0.34 0.06
186_R 193_A 0.78 0.34 0.06
77_T 80_M 0.78 0.34 0.06
141_N 127_N 0.78 0.34 0.06
236_D 90_I 0.78 0.34 0.06
56_I 188_A 0.78 0.34 0.06
302_F 22_K 0.78 0.33 0.06
85_I 143_E 0.77 0.33 0.06
153_S 35_I 0.77 0.33 0.06
233_F 89_I 0.77 0.33 0.06
186_R 90_I 0.77 0.33 0.06
201_A 74_R 0.77 0.32 0.06
143_M 19_D 0.77 0.32 0.06
81_L 49_M 0.77 0.32 0.06
325_F 16_K 0.76 0.32 0.06
80_T 123_L 0.76 0.32 0.06
184_T 204_V 0.76 0.32 0.06
246_Y 43_T 0.76 0.32 0.06
104_G 162_L 0.76 0.32 0.06
270_I 196_I 0.76 0.32 0.06
197_N 200_L 0.76 0.32 0.06
258_Q 143_E 0.76 0.31 0.06
243_A 93_P 0.76 0.31 0.06
32_L 19_D 0.76 0.31 0.06
182_E 23_E 0.76 0.31 0.06
143_M 92_A 0.75 0.31 0.06
250_T 121_P 0.75 0.31 0.06
232_S 52_M 0.75 0.31 0.06
229_L 78_A 0.75 0.31 0.06
222_I 61_R 0.75 0.31 0.06
251_I 52_M 0.75 0.30 0.05
214_V 99_M 0.74 0.30 0.05
309_L 56_I 0.74 0.30 0.05
265_S 91_L 0.74 0.30 0.05
242_A 16_K 0.74 0.30 0.05
250_T 11_E 0.74 0.30 0.05
278_D 104_L 0.74 0.30 0.05
82_I 13_T 0.74 0.29 0.05
143_M 84_I 0.73 0.29 0.05
133_V 121_P 0.73 0.29 0.05
53_A 202_I 0.73 0.29 0.05
217_I 145_I 0.73 0.29 0.05
72_P 161_V 0.73 0.29 0.05
224_I 142_V 0.73 0.29 0.05
222_I 137_S 0.73 0.29 0.05
36_L 20_A 0.73 0.29 0.05
217_I 134_N 0.73 0.29 0.05
225_I 152_G 0.73 0.29 0.05
62_I 37_T 0.73 0.29 0.05
247_T 100_I 0.73 0.28 0.05
322_A 114_F 0.73 0.28 0.05
295_R 129_L 0.73 0.28 0.05
220_T 149_L 0.73 0.28 0.05
315_T 153_I 0.72 0.28 0.05
174_D 8_K 0.72 0.28 0.05
41_V 169_L 0.72 0.28 0.05
129_I 26_V 0.72 0.28 0.05
55_S 199_F 0.72 0.28 0.05
54_L 87_V 0.72 0.28 0.05
150_T 27_P 0.72 0.28 0.05
62_I 147_I 0.72 0.27 0.05
147_K 120_M 0.72 0.27 0.05
30_G 127_N 0.71 0.27 0.05
244_S 32_A 0.71 0.27 0.05
35_I 47_F 0.71 0.27 0.05
311_P 172_V 0.71 0.27 0.05
120_E 169_L 0.71 0.27 0.05
64_L 32_A 0.71 0.27 0.05
310_V 178_V 0.71 0.27 0.05
32_L 35_I 0.71 0.27 0.05
322_A 144_S 0.71 0.27 0.05
69_I 31_D 0.71 0.27 0.04
201_A 129_L 0.71 0.27 0.04
229_L 195_V 0.71 0.26 0.04
228_F 18_E 0.71 0.26 0.04
301_G 167_Q 0.70 0.26 0.04
139_L 43_T 0.70 0.26 0.04
66_S 4_E 0.70 0.26 0.04
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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