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OPENSEQ.org
pbp1a_lpoa_Jackhmmer
Genes: A B A+B
Length: 480 425 826
Sequences: 5722 3310 923
Seq/Len: 11.92 7.79 1.12
MirrorTree (Pazo et al. 2001) 0.41
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 0.00 0.00 0.01
2 0.00 0.00 0.01
5 0.00 0.00 0.01
10 0.00 0.01 0.02
20 0.00 0.01 0.06
100 0.00 0.01 0.20
∞ 0.03 0.04 1.02
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
444_N 400_T 0.91 0.29 0.00
59_Y 214_Q 0.80 0.21 0.00
118_F 5_K 0.79 0.20 0.00
188_A 353_Q 0.78 0.20 0.00
451_V 285_V 0.73 0.17 0.00
249_D 285_V 0.73 0.17 0.00
416_I 333_E 0.72 0.17 0.00
298_T 118_I 0.72 0.17 0.00
201_L 418_Q 0.72 0.17 0.00
440_I 105_L 0.72 0.16 0.00
149_I 20_G 0.71 0.16 0.00
433_V 220_T 0.71 0.16 0.00
28_G 12_L 0.71 0.16 0.00
365_A 417_Q 0.70 0.15 0.00
79_L 6_I 0.69 0.15 0.00
152_V 222_L 0.69 0.15 0.00
280_M 335_L 0.69 0.15 0.00
475_I 220_T 0.69 0.15 0.00
433_V 396_T 0.68 0.15 0.00
238_L 371_G 0.68 0.15 0.00
60_S 193_L 0.68 0.15 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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