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OPENSEQ.org
hht1 hhf1
Genes: A B A+B
Length: 136 103 239
Sequences: 712 758 71
Seq/Len: 5.24 7.36 0.3
MirrorTree (Pazo et al. 2001) -0.10
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.05 0.05 0.12
2 0.06 0.05 0.13
5 0.07 0.06 0.13
10 0.08 0.06 0.14
20 0.08 0.07 0.13
100 0.09 0.12 0.17
∞ 0.12 0.16 0.30
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
54_R 51_I 1.31 0.30 0.00
96_S 49_G 1.07 0.18 0.00
91_G 35_I 1.04 0.17 0.00
39_P 2_S 1.02 0.17 0.00
78_D 70_S 1.01 0.16 0.00
60_E 87_V 0.94 0.14 0.00
54_R 1_M 0.93 0.13 0.00
47_V 101_F 0.91 0.13 0.00
75_I 57_A 0.90 0.12 0.00
130_R 62_F 0.89 0.12 0.00
108_T 60_K 0.89 0.12 0.00
42_Y 62_F 0.87 0.12 0.00
25_A 51_I 0.86 0.11 0.00
36_V 3_G 0.86 0.11 0.00
96_S 84_S 0.85 0.11 0.00
93_L 56_R 0.84 0.11 0.00
115_A 60_K 0.83 0.11 0.00
83_L 101_F 0.82 0.10 0.00
123_K 49_G 0.82 0.10 0.00
120_I 58_V 0.81 0.10 0.00
43_K 90_A 0.77 0.09 0.00
96_S 2_S 0.77 0.09 0.00
102_V 62_F 0.77 0.09 0.00
55_F 40_R 0.77 0.09 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
9643 0.3 hht1 hhf1 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
0698 0.1 hist Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
0697 0.09 hist Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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