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OPENSEQ.org
PcrD - Pcr1 (B, 6-75)
Genes: A B A+B
Length: 456 70 489
Sequences: 1584 84 69
Seq/Len: 3.47 1.2 0.14
MirrorTree (Pazo et al. 2001) 0.68
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 0.01 0.01 0.00
2 0.01 0.01 0.03
5 0.01 0.01 0.10
10 0.01 0.01 0.11
20 0.01 0.01 0.12
100 0.01 0.01 0.13
∞ 0.08 0.01 0.13
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
373_G 25_L 1.81 0.40 0.00
282_G 64_L 1.65 0.32 0.00
166_L 16_V 1.43 0.23 0.00
263_D 69_Q 1.28 0.17 0.00
254_S 64_L 1.27 0.17 0.00
340_S 10_L 1.25 0.16 0.00
253_L 10_L 1.24 0.16 0.00
326_Q 55_F 1.24 0.16 0.00
448_I 39_F 1.24 0.16 0.00
390_T 17_G 1.23 0.16 0.00
297_M 7_V 1.22 0.15 0.00
176_E 4_T 1.21 0.15 0.00
374_I 3_L 1.19 0.15 0.00
43_L 43_L 1.18 0.14 0.00
422_Y 37_I 1.16 0.14 0.00
294_L 40_F 1.16 0.14 0.00
412_V 39_F 1.12 0.13 0.00
184_V 54_V 1.12 0.13 0.00
37_G 64_L 1.12 0.13 0.00
175_G 41_R 1.12 0.13 0.00
196_L 45_R 1.12 0.13 0.00
64_G 10_L 1.11 0.12 0.00
36_I 50_L 1.11 0.12 0.00
210_V 50_L 1.10 0.12 0.00
56_L 4_T 1.10 0.12 0.00
370_I 59_E 1.10 0.12 0.00
317_I 25_L 1.09 0.12 0.00
286_K 15_W 1.09 0.12 0.00
361_L 24_L 1.09 0.12 0.00
13_S 55_F 1.08 0.12 0.00
333_Q 30_L 1.08 0.12 0.00
119_F 11_L 1.07 0.12 0.00
300_I 39_F 1.06 0.12 0.00
166_L 59_E 1.06 0.11 0.00
343_K 54_V 1.05 0.11 0.00
231_H 46_L 1.04 0.11 0.00
1_A 14_R 1.03 0.11 0.00
194_G 10_L 1.03 0.11 0.00
295_Q 8_I 1.01 0.10 0.00
141_S 22_Q 1.00 0.10 0.00
111_G 8_I 0.99 0.10 0.00
397_V 63_N 0.99 0.10 0.00
327_K 37_I 0.99 0.10 0.00
301_L 57_D 0.99 0.10 0.00
118_E 7_V 0.98 0.10 0.00
286_K 57_D 0.98 0.10 0.00
417_M 61_R 0.98 0.10 0.00
426_L 50_L 0.97 0.10 0.00
179_V 65_L 0.97 0.10 0.00
61_L 7_V 0.96 0.09 0.00
423_V 17_G 0.95 0.09 0.00
361_L 50_L 0.95 0.09 0.00
405_A 70_M 0.95 0.09 0.00
55_F 15_W 0.95 0.09 0.00
298_T 67_A 0.94 0.09 0.00
374_I 10_L 0.93 0.09 0.00
233_D 50_L 0.93 0.09 0.00
427_V 65_L 0.93 0.09 0.00
450_P 54_V 0.93 0.09 0.00
135_E 8_I 0.93 0.09 0.00
270_T 65_L 0.93 0.09 0.00
401_V 38_H 0.92 0.09 0.00
311_I 8_I 0.92 0.09 0.00
120_A 25_L 0.92 0.09 0.00
184_V 15_W 0.92 0.09 0.00
179_V 35_R 0.92 0.09 0.00
45_G 25_L 0.92 0.09 0.00
65_G 12_E 0.92 0.09 0.00
63_G 12_E 0.91 0.09 0.00
18_D 5_G 0.91 0.09 0.00
281_Y 15_W 0.91 0.09 0.00
272_Y 63_N 0.91 0.08 0.00
288_A 5_G 0.91 0.08 0.00
125_L 15_W 0.91 0.08 0.00
424_R 67_A 0.91 0.08 0.00
249_L 34_A 0.90 0.08 0.00
281_Y 60_Q 0.90 0.08 0.00
13_S 54_V 0.90 0.08 0.00
454_I 7_V 0.90 0.08 0.00
65_G 16_V 0.90 0.08 0.00
281_Y 33_V 0.90 0.08 0.00
75_A 16_V 0.90 0.08 0.00
182_Q 54_V 0.89 0.08 0.00
426_L 65_L 0.89 0.08 0.00
213_E 4_T 0.89 0.08 0.00
59_A 46_L 0.89 0.08 0.00
159_V 39_F 0.88 0.08 0.00
327_K 38_H 0.88 0.08 0.00
384_A 10_L 0.88 0.08 0.00
299_E 12_E 0.88 0.08 0.00
174_D 48_R 0.88 0.08 0.00
115_E 8_I 0.88 0.08 0.00
426_L 10_L 0.88 0.08 0.00
68_F 8_I 0.88 0.08 0.00
413_L 67_A 0.88 0.08 0.00
299_E 50_L 0.87 0.08 0.00
253_L 65_L 0.87 0.08 0.00
327_K 30_L 0.87 0.08 0.00
132_S 35_R 0.86 0.08 0.00
394_L 52_V 0.86 0.08 0.00
332_V 68_C 0.86 0.08 0.00
301_L 15_W 0.86 0.08 0.00
255_H 55_F 0.86 0.08 0.00
114_A 34_A 0.86 0.08 0.00
186_V 36_Q 0.85 0.08 0.00
298_T 28_L 0.85 0.08 0.00
329_K 51_P 0.85 0.08 0.00
298_T 19_A 0.85 0.07 0.00
282_G 9_A 0.85 0.07 0.00
413_L 5_G 0.85 0.07 0.00
350_Y 8_I 0.85 0.07 0.00
1_A 69_Q 0.85 0.07 0.00
4_A 57_D 0.85 0.07 0.00
292_V 41_R 0.84 0.07 0.00
431_Y 40_F 0.84 0.07 0.00
451_L 12_E 0.84 0.07 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)
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