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OPENSEQ.org
pk-pdz (A, 100-450) (B, 1-103)
Genes: A B A+B
Length: 351 103 388
Sequences: 15436 1040 96
Seq/Len: 43.98 10.1 0.25
MirrorTree (Pazo et al. 2001) 0.14
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 0.08 0.29 0.02
2 0.09 0.29 0.03
5 0.10 0.29 0.08
10 0.11 0.29 0.12
20 0.14 0.30 0.21
100 0.21 0.30 0.55
∞ 0.28 0.32 0.89
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
321_K 49_I 1.42 0.33 0.00
149_L 34_K 1.39 0.31 0.00
202_A 23_I 1.37 0.30 0.00
110_V 62_G 1.29 0.26 0.00
222_L 73_V 1.13 0.18 0.00
271_W 55_G 1.11 0.18 0.00
147_S 73_V 1.08 0.17 0.00
149_L 70_L 1.08 0.17 0.00
231_V 27_K 1.05 0.16 0.00
103_G 75_K 1.04 0.15 0.00
220_N 32_G 1.04 0.15 0.00
233_D 32_G 1.04 0.15 0.00
236_L 64_L 1.01 0.14 0.00
125_I 71_V 1.01 0.14 0.00
300_V 88_S 1.01 0.14 0.00
145_R 75_K 1.00 0.14 0.00
277_L 65_K 0.99 0.14 0.00
327_D 66_P 0.98 0.13 0.00
113_G 70_L 0.98 0.13 0.00
125_I 56_G 0.97 0.13 0.00
213_H 62_G 0.96 0.13 0.00
88_G 54_P 0.95 0.13 0.00
121_A 67_G 0.94 0.12 0.00
331_R 32_G 0.93 0.12 0.00
168_E 27_K 0.93 0.12 0.00
333_S 77_S 0.93 0.12 0.00
300_V 33_L 0.93 0.12 0.00
80_A 33_L 0.91 0.12 0.00
183_G 65_K 0.91 0.12 0.00
174_S 55_G 0.91 0.12 0.00
235_G 32_G 0.91 0.11 0.00
180_R 60_K 0.91 0.11 0.00
123_K 32_G 0.90 0.11 0.00
150_V 25_I 0.90 0.11 0.00
141_M 56_G 0.90 0.11 0.00
210_N 75_K 0.90 0.11 0.00
220_N 68_D 0.90 0.11 0.00
233_D 68_D 0.90 0.11 0.00
225_E 51_E 0.90 0.11 0.00
189_G 30_G 0.88 0.11 0.00
218_A 75_K 0.88 0.11 0.00
225_E 72_S 0.87 0.11 0.00
267_K 25_I 0.87 0.10 0.00
102_I 53_I 0.86 0.10 0.00
339_E 24_T 0.86 0.10 0.00
213_H 32_G 0.86 0.10 0.00
142_T 49_I 0.86 0.10 0.00
324_W 23_I 0.86 0.10 0.00
122_V 69_Q 0.86 0.10 0.00
309_P 72_S 0.86 0.10 0.00
180_R 72_S 0.85 0.10 0.00
271_W 68_D 0.84 0.10 0.00
324_W 90_I 0.84 0.10 0.00
153_L 49_I 0.84 0.10 0.00
230_K 62_G 0.84 0.10 0.00
243_T 70_L 0.84 0.10 0.00
231_V 90_I 0.83 0.10 0.00
232_S 35_V 0.83 0.10 0.00
324_W 25_I 0.83 0.10 0.00
105_G 32_G 0.82 0.09 0.00
335_L 84_E 0.82 0.09 0.00
231_V 84_E 0.81 0.09 0.00
166_V 87_K 0.81 0.09 0.00
328_A 31_L 0.81 0.09 0.00
110_V 73_V 0.81 0.09 0.00
309_P 73_V 0.81 0.09 0.00
122_V 38_G 0.80 0.09 0.00
142_T 82_S 0.80 0.09 0.00
257_E 32_G 0.80 0.09 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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