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OPENSEQ.org
1F6M
Genes: A B A+B
Length: 320 108 416
Sequences: 30502 18214 2052
Seq/Len: 95.32 168.65 4.93
MirrorTree (Pazo et al. 2001) 0.32
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 0.02 0.02 1.54
2 0.03 0.03 1.82
5 0.04 0.03 2.48
10 0.06 0.04 3.38
20 0.09 0.05 4.79
100 0.17 0.10 11.10
∞ 0.23 0.20 19.41
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
122_P 97_G 0.72 0.44 0.00
276_T 84_G 0.68 0.38 0.00
178_D 98_Q 0.61 0.29 0.00
208_E 24_L 0.59 0.27 0.00
205_R 72_I 0.58 0.25 0.00
283_A 83_N 0.57 0.25 0.00
281_V 89_T 0.56 0.23 0.00
252_F 20_D 0.56 0.23 0.00
220_V 105_A 0.56 0.23 0.00
257_E 47_D 0.55 0.23 0.00
239_L 79_L 0.55 0.23 0.00
205_R 71_G 0.55 0.23 0.00
63_L 61_D 0.54 0.21 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
13399 5.73 1F6M Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) 0.00 Done - Shared
9132 4.93 1F6M Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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