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OPENSEQ.org
rodA-pbp2a-tp
Genes: A B A+B
Length: 393 330 657
Sequences: 3826 7322 2308
Seq/Len: 9.74 22.19 3.51
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 0.02 0.03 1.41
2 0.02 0.03 1.46
5 0.02 0.03 2.98
10 0.02 0.05 3.14
20 0.02 0.07 3.19
100 0.07 0.17 3.54
∞ 0.24 0.26 4.13
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
47_Q 298_N 1.09 0.79 0.04
259_S 173_Q 0.84 0.50 0.02
354_I 323_E 0.79 0.43 0.02
185_S 294_A 0.78 0.41 0.02
233_W 155_G 0.77 0.40 0.02
274_V 169_F 0.76 0.40 0.01
73_L 12_V 0.74 0.37 0.01
268_S 101_N 0.74 0.37 0.01
347_G 155_G 0.74 0.37 0.01
116_S 264_A 0.73 0.36 0.01
286_I 101_N 0.73 0.36 0.01
310_V 238_V 0.73 0.36 0.01
320_N 303_I 0.73 0.35 0.01
274_V 318_Y 0.71 0.33 0.01
315_K 301_I 0.71 0.33 0.01
197_G 111_V 0.70 0.33 0.01
61_V 12_V 0.69 0.31 0.01
325_F 307_V 0.69 0.31 0.01
333_L 24_N 0.69 0.31 0.01
226_Q 103_F 0.69 0.31 0.01
83_L 12_V 0.68 0.30 0.01
17_I 91_G 0.67 0.29 0.01
226_Q 155_G 0.67 0.29 0.01
365_S 272_F 0.67 0.28 0.01
180_V 246_A 0.66 0.28 0.01
340_Q 139_F 0.66 0.28 0.01
189_W 143_V 0.65 0.27 0.01
187_I 16_A 0.65 0.27 0.01
248_W 74_I 0.64 0.26 0.01
55_G 256_A 0.64 0.26 0.01
310_V 170_A 0.64 0.26 0.01
73_L 307_V 0.64 0.26 0.01
226_Q 235_I 0.64 0.26 0.01
300_I 50_A 0.64 0.26 0.01
255_M 101_N 0.64 0.26 0.01
199_G 9_N 0.64 0.26 0.01
351_V 105_F 0.64 0.26 0.01
369_T 136_F 0.64 0.26 0.01
26_I 64_N 0.63 0.25 0.01
339_F 3_V 0.63 0.25 0.01
82_I 107_T 0.62 0.24 0.01
233_W 75_G 0.62 0.24 0.01
368_S 102_V 0.62 0.24 0.01
23_F 91_G 0.62 0.24 0.01
302_F 55_G 0.61 0.23 0.01
354_I 263_A 0.61 0.23 0.01
227_I 318_Y 0.61 0.23 0.01
82_I 197_K 0.61 0.23 0.01
104_S 174_Y 0.61 0.23 0.01
253_A 180_L 0.61 0.23 0.01
226_Q 105_F 0.61 0.23 0.01
236_A 22_R 0.61 0.23 0.01
230_V 176_T 0.61 0.23 0.01
108_I 3_V 0.61 0.23 0.01
131_I 101_N 0.60 0.22 0.01
304_F 22_R 0.60 0.22 0.01
305_L 327_E 0.60 0.22 0.01
61_V 138_Q 0.60 0.22 0.01
351_V 155_G 0.59 0.22 0.01
169_G 24_N 0.59 0.21 0.01
115_P 70_E 0.59 0.21 0.01
236_A 19_Q 0.59 0.21 0.01
154_G 318_Y 0.59 0.21 0.01
18_F 170_A 0.59 0.21 0.01
83_L 138_Q 0.59 0.21 0.01
274_V 175_D 0.58 0.21 0.01
361_Y 288_T 0.58 0.21 0.01
183_F 292_A 0.58 0.21 0.01
322_F 179_P 0.58 0.21 0.01
352_T 166_L 0.58 0.21 0.01
118_F 307_V 0.58 0.21 0.01
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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