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OPENSEQ.org
2NS1(amtB-glnK)
Genes: A B A+B
Length: 428 112 526
Sequences: 5820 3798 2187
Seq/Len: 13.6 33.91 4.16
MirrorTree (Pazo et al. 2001) 0.26
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 0.01 0.01 3.93
2 0.01 0.01 4.00
5 0.01 0.02 4.01
10 0.01 0.02 4.03
20 0.01 0.02 4.05
100 0.02 0.02 4.16
∞ 0.05 0.07 4.69
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
410_E 85_K 1.29 0.93 0.42
43_L 38_R 0.72 0.39 0.07
76_L 72_E 0.68 0.34 0.06
96_F 79_K 0.66 0.31 0.05
353_I 77_V 0.63 0.28 0.04
152_I 65_I 0.62 0.27 0.04
264_I 8_I 0.59 0.24 0.04
261_A 61_I 0.58 0.23 0.04
354_F 82_Y 0.58 0.23 0.03
47_I 4_V 0.58 0.22 0.03
382_A 97_Q 0.57 0.22 0.03
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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