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OPENSEQ.org
METN - METQ
Genes: A B A+B
Length: 343 271 605
Sequences: 3685 1563 872
Seq/Len: 10.74 5.77 1.44
MirrorTree (Pazo et al. 2001) 0.40
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 0.05 0.39
2 0.00 0.06 1.29
5 0.01 0.06 1.36
10 0.01 0.07 1.37
20 0.02 0.07 1.42
100 0.07 0.10 1.57
∞ 0.56 0.59 2.27
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
28_V 124_L 1.00 0.43 0.00
191_G 34_K 0.91 0.34 0.00
194_I 170_V 0.88 0.32 0.00
208_C 266_G 0.88 0.32 0.00
240_F 219_F 0.87 0.31 0.00
104_A 139_P 0.86 0.30 0.00
206_R 135_V 0.85 0.29 0.00
103_V 79_G 0.83 0.27 0.00
125_L 141_N 0.81 0.26 0.00
215_S 71_L 0.81 0.26 0.00
64_V 126_E 0.80 0.25 0.00
196_L 80_D 0.77 0.23 0.00
33_I 81_I 0.77 0.23 0.00
181_E 261_K 0.77 0.23 0.00
99_V 117_Y 0.77 0.23 0.00
192_L 121_I 0.76 0.22 0.00
164_C 23_C 0.75 0.21 0.00
140_N 37_V 0.75 0.21 0.00
161_V 91_Y 0.74 0.21 0.00
150_A 54_K 0.74 0.20 0.00
116_E 179_I 0.73 0.20 0.00
111_N 100_G 0.73 0.20 0.00
95_S 138_D 0.73 0.20 0.00
95_S 141_N 0.71 0.19 0.00
33_I 49_A 0.71 0.19 0.00
161_V 65_T 0.71 0.19 0.00
121_V 188_P 0.70 0.18 0.00
11_F 79_G 0.70 0.18 0.00
37_I 176_N 0.70 0.18 0.00
69_L 64_V 0.70 0.18 0.00
273_F 188_P 0.70 0.18 0.00
125_L 136_P 0.69 0.17 0.00
273_F 97_K 0.69 0.17 0.00
330_L 246_F 0.69 0.17 0.00
64_V 118_S 0.68 0.17 0.00
235_P 50_Q 0.68 0.17 0.00
118_K 239_D 0.68 0.17 0.00
250_P 40_G 0.68 0.17 0.00
218_E 34_K 0.68 0.17 0.00
312_M 232_V 0.67 0.17 0.00
125_L 138_D 0.67 0.16 0.00
236_L 80_D 0.67 0.16 0.00
11_F 38_I 0.67 0.16 0.00
200_E 86_F 0.67 0.16 0.00
125_L 145_S 0.66 0.16 0.00
62_V 150_Q 0.66 0.16 0.00
8_T 54_K 0.66 0.16 0.00
1_M 23_C 0.66 0.16 0.00
209_D 199_A 0.65 0.15 0.00
301_M 114_I 0.65 0.15 0.00
228_V 127_L 0.65 0.15 0.00
307_V 79_G 0.65 0.15 0.00
204_V 113_P 0.65 0.15 0.00
7_I 58_G 0.65 0.15 0.00
299_A 182_L 0.64 0.15 0.00
240_F 203_T 0.64 0.15 0.00
297_I 128_Q 0.64 0.15 0.00
50_C 251_Q 0.64 0.15 0.00
271_L 248_Q 0.64 0.15 0.00
114_K 60_D 0.64 0.15 0.00
125_L 196_I 0.63 0.14 0.00
139_S 172_E 0.63 0.14 0.00
321_Q 140_T 0.63 0.14 0.00
188_R 197_A 0.63 0.14 0.00
69_L 79_G 0.63 0.14 0.00
70_T 185_P 0.63 0.14 0.00
213_V 30_P 0.63 0.14 0.00
105_L 69_Y 0.63 0.14 0.00
188_R 125_D 0.62 0.14 0.00
164_C 49_A 0.62 0.14 0.00
114_K 177_L 0.62 0.14 0.00
25_S 80_D 0.62 0.14 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
0012 1.44 METN - METQ Δgene:(1, 20) A:(1E-60, 8) B:(1E-60, 8) (2013_03) 0.00 Done - Shared
0011 1.45 METN - METQ Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) (2013_03) 0.00 Done - Shared
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