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OPENSEQ.org
iscuiscs
Genes: A B A+B
Length: 128 404 509
Sequences: 1994 53003 1755
Seq/Len: 15.58 131.2 3.45
MirrorTree (Pazo et al. 2001) 0.76
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 0.04 3.02
2 0.00 0.07 3.08
5 0.00 0.09 3.14
10 0.00 0.11 3.18
20 0.00 0.15 3.30
100 0.00 0.28 3.67
∞ 0.03 0.32 4.07
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
52_I 18_R 0.69 0.31 0.00
84_E 21_E 0.65 0.26 0.00
98_E 351_S 0.63 0.24 0.00
34_A 346_D 0.60 0.22 0.00
100_P 36_P 0.60 0.22 0.00
86_Q 7_L 0.60 0.22 0.00
87_A 135_K 0.59 0.21 0.00
83_D 283_D 0.59 0.21 0.00
15_R 366_I 0.58 0.20 0.00
38_G 309_E 0.58 0.20 0.00
42_K 7_L 0.57 0.19 0.00
42_K 388_E 0.56 0.19 0.00
88_I 120_E 0.56 0.19 0.00
33_G 77_E 0.56 0.18 0.00
51_G 373_V 0.56 0.18 0.00
77_V 81_L 0.55 0.18 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)
ID Seq/Len Name Options I_Prob Status
2042 3.61 IscUIscSmaxdist2 Δgene:(1, 2) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
1966 1.65 iscuiscs Δgene:(1, 2) A:(1E-20, 2) B:(1E-20, 2) msa: Jackhmmer (2015_03) 0.00 Done - Shared
1493 3.64 iscuiscs Δgene:(1, 5) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
1474 3.72 iscuiscs Δgene:(1, ∞) A:(1E-10, 4) B:(1E-20, 4) msa: Jackhmmer (2014_03) 0.00 Done - Shared
1460 2.84 iscuiscs Δgene:(1, 1) A:(1E-20, 4) B:(1E-20, 4) msa: Jackhmmer (2014_03) 0.00 Done - Shared
1448 3.45 iscuiscs Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2014_03) 0.00 Done - Shared
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