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OPENSEQ.org
HK_RR
Genes: A B A+B
Length: 592 235 814
Sequences: 4439 33549 1995
Seq/Len: 7.5 142.76 2.45
MirrorTree (Pazo et al. 2001) 0.62
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 0.01 2.01
2 0.01 0.02 2.05
5 0.01 0.04 2.12
10 0.01 0.06 2.22
20 0.01 0.09 2.41
100 0.03 0.19 3.22
∞ 0.13 0.25 4.24
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
384_T 15_I 1.88 0.99 0.95
391_E 109_S 1.88 0.99 0.95
388_G 18_L 1.82 0.98 0.94
392_T 22_N 1.53 0.95 0.84
406_R 17_E 1.49 0.94 0.82
413_D 14_N 1.48 0.93 0.81
407_F 21_F 1.41 0.91 0.77
389_Y 18_L 1.22 0.80 0.60
549_R 12_E 1.17 0.76 0.55
414_E 14_N 1.16 0.75 0.54
410_V 18_L 1.15 0.74 0.52
373_S 86_K 1.01 0.60 0.38
389_Y 201_V 0.97 0.55 0.33
410_V 14_N 0.97 0.55 0.33
386_I 179_T 0.94 0.52 0.30
508_I 94_L 0.93 0.51 0.29
395_D 25_K 0.93 0.51 0.29
450_E 157_V 0.90 0.47 0.26
178_V 157_V 0.90 0.47 0.26
498_K 48_I 0.90 0.47 0.26
389_Y 17_E 0.89 0.45 0.25
430_Q 87_E 0.84 0.40 0.20
391_E 89_E 0.83 0.39 0.20
385_S 14_N 0.83 0.39 0.20
123_G 10_D 0.83 0.39 0.19
565_L 10_D 0.81 0.37 0.18
183_I 8_V 0.81 0.36 0.18
187_L 203_I 0.80 0.36 0.17
508_I 77_D 0.80 0.35 0.17
88_I 221_I 0.80 0.35 0.17
489_Y 135_C 0.80 0.35 0.17
584_F 55_L 0.79 0.34 0.16
385_S 12_E 0.77 0.32 0.15
397_R 22_N 0.77 0.32 0.15
522_I 41_D 0.75 0.30 0.14
417_R 10_D 0.75 0.30 0.14
385_S 15_I 0.74 0.29 0.13
185_L 8_V 0.73 0.28 0.12
430_Q 157_V 0.72 0.28 0.12
380_R 105_T 0.72 0.28 0.12
537_F 15_I 0.72 0.28 0.12
422_I 63_L 0.72 0.28 0.12
506_V 42_K 0.72 0.27 0.12
87_I 88_K 0.72 0.27 0.12
57_Q 19_V 0.71 0.27 0.12
415_T 18_L 0.71 0.26 0.11
49_T 10_D 0.71 0.26 0.11
380_R 92_R 0.70 0.26 0.11
480_G 181_N 0.70 0.26 0.11
283_E 80_I 0.70 0.25 0.11
167_F 179_T 0.70 0.25 0.10
421_L 166_L 0.70 0.25 0.10
56_L 28_Y 0.70 0.25 0.10
226_L 150_V 0.69 0.25 0.10
236_M 97_E 0.69 0.24 0.10
371_F 87_E 0.69 0.24 0.10
404_R 160_T 0.68 0.24 0.10
492_L 203_I 0.68 0.24 0.10
418_L 230_R 0.68 0.24 0.10
478_I 51_L 0.68 0.24 0.10
570_G 10_D 0.68 0.23 0.09
424_D 225_R 0.67 0.23 0.09
547_R 56_M 0.67 0.23 0.09
179_V 19_V 0.67 0.23 0.09
383_L 139_G 0.67 0.23 0.09
424_D 205_R 0.67 0.23 0.09
193_K 30_V 0.67 0.23 0.09
521_I 142_V 0.67 0.23 0.09
96_G 162_K 0.67 0.23 0.09
367_I 162_K 0.66 0.22 0.09
395_D 110_P 0.66 0.22 0.09
131_T 6_I 0.66 0.22 0.09
531_E 154_D 0.66 0.22 0.09
430_Q 19_V 0.66 0.22 0.09
186_I 137_K 0.66 0.22 0.09
572_I 201_V 0.66 0.22 0.09
410_V 17_E 0.66 0.22 0.09
74_V 119_A 0.65 0.22 0.08
561_V 18_L 0.65 0.21 0.08
226_L 17_E 0.65 0.21 0.08
534_P 37_Q 0.65 0.21 0.08
43_E 6_I 0.65 0.21 0.08
569_N 203_I 0.65 0.21 0.08
519_S 164_F 0.65 0.21 0.08
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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