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OPENSEQ.org
rf-gs-1
Genes: A B A+B
Length: 228 239 460
Sequences: 83932 992 997
Seq/Len: 368.12 4.15 2.17
MirrorTree (Pazo et al. 2001) 0.22
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 0.10 0.01 0.65
2 0.11 0.01 0.81
5 0.14 0.01 1.02
10 0.19 0.01 1.21
20 0.25 0.02 1.48
100 0.35 0.04 2.02
∞ 0.37 0.11 2.13
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
26_I 63_E 0.88 0.41 0.00
54_S 168_I 0.85 0.38 0.00
191_E 149_E 0.81 0.34 0.00
58_Y 156_G 0.79 0.32 0.00
32_E 218_L 0.77 0.30 0.00
222_F 168_I 0.77 0.29 0.00
30_I 125_Y 0.77 0.29 0.00
158_F 200_S 0.76 0.29 0.00
114_K 155_I 0.76 0.29 0.00
4_L 58_Q 0.75 0.28 0.00
198_I 17_V 0.74 0.27 0.00
64_I 67_I 0.71 0.25 0.00
47_T 231_R 0.71 0.25 0.00
26_I 64_W 0.69 0.23 0.00
26_I 194_R 0.69 0.23 0.00
187_T 128_T 0.68 0.22 0.00
35_F 23_L 0.68 0.21 0.00
87_I 199_S 0.67 0.21 0.00
55_S 205_Y 0.67 0.21 0.00
27_N 153_I 0.66 0.21 0.00
53_L 210_V 0.66 0.20 0.00
53_L 205_Y 0.66 0.20 0.00
217_K 79_R 0.65 0.20 0.00
134_L 106_R 0.65 0.20 0.00
13_Y 46_L 0.65 0.20 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
13435 0 rf-gs3 Δgene:(1, ∞) A:(1E-80, 8) B:(1E-60, 8) msa: HHblits (2015_06) Killed - Shared
13434 64.32 rf-gs-2 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06) 0.00 Done - Shared
13433 2.17 rf-gs-1 Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: HHblits (2015_06) 0.00 Done - Shared
13421 78.89 rf-gs Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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