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OPENSEQ.org
LamBfirstJH
Genes: A B A+B
Length: 421 166 579
Sequences: 575 193 66
Seq/Len: 1.37 1.16 0.11
MirrorTree (Pazo et al. 2001) 0.07
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 0.00
2 0.00 0.00 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.00
20 0.00 0.01 0.01
100 0.04 0.01 0.03
∞ 0.08 0.05 0.11
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
93_E 31_I 1.17 0.12 0.00
322_T 30_D 0.99 0.09 0.00
375_K 11_T 0.93 0.08 0.00
280_M 8_S 0.93 0.08 0.00
409_D 4_S 0.92 0.08 0.00
269_M 9_N 0.91 0.08 0.00
238_S 125_G 0.91 0.07 0.00
91_L 70_V 0.91 0.07 0.00
232_V 15_N 0.91 0.07 0.00
6_Y 20_G 0.89 0.07 0.00
6_Y 24_A 0.89 0.07 0.00
6_Y 29_G 0.89 0.07 0.00
8_R 20_G 0.89 0.07 0.00
8_R 24_A 0.89 0.07 0.00
8_R 29_G 0.89 0.07 0.00
10_G 20_G 0.89 0.07 0.00
10_G 24_A 0.89 0.07 0.00
10_G 29_G 0.89 0.07 0.00
101_W 20_G 0.89 0.07 0.00
101_W 24_A 0.89 0.07 0.00
101_W 29_G 0.89 0.07 0.00
103_G 20_G 0.89 0.07 0.00
103_G 24_A 0.89 0.07 0.00
103_G 29_G 0.89 0.07 0.00
126_G 20_G 0.89 0.07 0.00
126_G 24_A 0.89 0.07 0.00
126_G 29_G 0.89 0.07 0.00
128_G 20_G 0.89 0.07 0.00
128_G 24_A 0.89 0.07 0.00
128_G 29_G 0.89 0.07 0.00
276_G 20_G 0.89 0.07 0.00
276_G 24_A 0.89 0.07 0.00
276_G 29_G 0.89 0.07 0.00
360_R 20_G 0.89 0.07 0.00
360_R 24_A 0.89 0.07 0.00
360_R 29_G 0.89 0.07 0.00
414_G 20_G 0.89 0.07 0.00
414_G 24_A 0.89 0.07 0.00
414_G 29_G 0.89 0.07 0.00
418_E 20_G 0.89 0.07 0.00
418_E 24_A 0.89 0.07 0.00
418_E 29_G 0.89 0.07 0.00
420_W 20_G 0.89 0.07 0.00
420_W 24_A 0.89 0.07 0.00
420_W 29_G 0.89 0.07 0.00
266_N 31_I 0.84 0.07 0.00
361_P 20_G 0.83 0.07 0.00
361_P 24_A 0.83 0.07 0.00
361_P 29_G 0.83 0.07 0.00
31_K 1_N 0.83 0.07 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
5665 0.06 LamBfirstJH Δgene:(1, ∞) A:(1E-60, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) Killed - Shared
5664 0.11 LamBfirstJH Δgene:(1, ∞) A:(1E-40, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5663 0.11 LamBfirstJH Δgene:(1, ∞) A:(1E-20, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done - Shared
5662 0.04 LamBfirstJH Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) Killed - Shared
5661 0.02 LamBfirst Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
5660 0.02 LamBfirst Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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