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OPENSEQ.org
cI_1_4_cI_6_4_tt
Genes: A B A+B
Length: 438 181 584
Sequences: 2611 1709 916
Seq/Len: 5.96 9.44 1.57
MirrorTree (Pazo et al. 2001) 0.58
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 0.00
2 0.01 0.01 0.05
5 0.01 0.02 0.95
10 0.02 0.02 1.01
20 0.03 0.03 1.02
100 0.05 0.04 1.09
∞ 0.14 0.10 1.48
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
227_V 130_V 0.95 0.40 0.00
115_I 161_Q 0.95 0.40 0.00
252_Y 105_V 0.93 0.38 0.00
314_E 110_A 0.86 0.32 0.00
275_L 78_M 0.86 0.31 0.00
355_K 119_N 0.82 0.28 0.00
223_T 13_E 0.82 0.28 0.00
29_L 34_N 0.82 0.28 0.00
237_W 137_V 0.82 0.28 0.00
96_S 85_S 0.81 0.27 0.00
272_F 21_F 0.80 0.27 0.00
236_D 53_S 0.80 0.26 0.00
336_S 19_I 0.79 0.26 0.00
57_V 13_E 0.79 0.25 0.00
390_L 103_K 0.78 0.25 0.00
106_I 75_A 0.74 0.22 0.00
290_I 25_E 0.74 0.22 0.00
223_T 106_I 0.72 0.21 0.00
56_E 95_V 0.72 0.20 0.00
276_I 56_A 0.71 0.20 0.00
258_V 101_D 0.70 0.19 0.00
318_A 130_V 0.70 0.19 0.00
127_A 20_L 0.70 0.19 0.00
410_V 145_E 0.69 0.19 0.00
53_V 95_V 0.69 0.19 0.00
410_V 95_V 0.68 0.18 0.00
44_V 29_A 0.67 0.17 0.00
290_I 86_K 0.67 0.17 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
4926 1.42 cI_1_20_cI_6_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4922 1.57 cI_1_4_cI_6_4_tt Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4921 1.4 cI_1_40_cI_6_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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