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OPENSEQ.org
1GRN
Genes: A B A+B
Length: 191 242 389
Sequences: 11230 3049 315
Seq/Len: 58.8 12.6 0.81
MirrorTree (Pazo et al. 2001) 0.23
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 0.03 0.05
2 0.05 0.03 0.13
5 0.07 0.03 0.29
10 0.09 0.06 0.46
20 0.11 0.09 0.73
100 0.20 0.12 1.80
∞ 0.26 0.17 2.74
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
84_V 204_L 1.17 0.43 0.00
84_V 160_L 1.12 0.39 0.00
82_F 117_P 1.01 0.30 0.00
91_E 148_D 0.94 0.26 0.00
84_V 136_D 0.93 0.25 0.00
90_F 62_I 0.93 0.25 0.00
93_V 125_L 0.90 0.23 0.00
140_E 223_T 0.88 0.22 0.00
8_V 203_L 0.88 0.21 0.00
139_P 73_L 0.84 0.20 0.00
91_E 150_S 0.82 0.18 0.00
48_G 70_V 0.81 0.18 0.00
107_K 49_L 0.80 0.17 0.00
67_L 222_F 0.79 0.17 0.00
64_Y 109_D 0.79 0.17 0.00
23_Y 182_S 0.78 0.16 0.00
14_V 124_F 0.78 0.16 0.00
94_K 192_N 0.78 0.16 0.00
84_V 95_E 0.78 0.16 0.00
89_S 46_G 0.77 0.16 0.00
40_Y 49_L 0.77 0.16 0.00
78_F 193_T 0.76 0.15 0.00
28_F 156_T 0.75 0.15 0.00
110_F 127_E 0.75 0.15 0.00
50_P 227_L 0.75 0.15 0.00
169_F 198_V 0.74 0.15 0.00
138_T 227_L 0.74 0.14 0.00
84_V 97_Q 0.74 0.14 0.00
91_E 222_F 0.74 0.14 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
9111 0.81 1GRN Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
4113 0.89 1A4R_A CDC42 GTPase GDP 1RGP_ CDC42 GAP Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4076 1.51 1A4R_A CDC42 GTPase GDP 1RGP_ CDC42 GAP Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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