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OPENSEQ.org
cIV_B_6_cI_H_20_Pdenitr
Genes: A B A+B
Length: 252 345 552
Sequences: 4627 4758 2939
Seq/Len: 18.36 13.79 5.32
MirrorTree (Pazo et al. 2001) 0.74
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 0.14
2 0.00 0.00 0.30
5 0.00 0.00 1.84
10 0.01 0.01 3.44
20 0.01 0.01 3.59
100 0.02 0.02 3.77
∞ 0.04 0.04 4.92
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
143_A 100_V 1.11 0.89 0.11
222_I 196_L 1.00 0.81 0.08
164_V 257_L 0.92 0.72 0.06
180_I 147_S 0.91 0.71 0.06
23_A 131_V 0.90 0.69 0.05
195_V 133_M 0.87 0.66 0.05
212_Y 91_S 0.84 0.63 0.04
114_I 283_K 0.84 0.62 0.04
233_A 87_A 0.83 0.61 0.04
54_L 323_V 0.80 0.56 0.04
247_K 17_L 0.80 0.56 0.04
77_I 159_V 0.78 0.54 0.04
175_T 143_P 0.78 0.53 0.04
158_T 163_L 0.77 0.53 0.03
188_F 102_I 0.77 0.52 0.03
170_V 87_A 0.75 0.50 0.03
132_V 147_S 0.75 0.49 0.03
219_L 229_A 0.75 0.49 0.03
40_Y 180_I 0.74 0.48 0.03
225_A 225_S 0.73 0.46 0.03
88_I 16_L 0.72 0.45 0.03
36_H 225_S 0.72 0.45 0.03
57_I 323_V 0.71 0.44 0.03
44_A 133_M 0.71 0.44 0.03
243_L 242_L 0.71 0.44 0.03
117_I 181_V 0.71 0.43 0.03
212_Y 284_M 0.70 0.42 0.03
225_A 229_A 0.70 0.42 0.03
71_F 169_I 0.70 0.42 0.03
172_V 260_L 0.69 0.41 0.03
114_I 181_V 0.69 0.41 0.03
109_D 286_F 0.69 0.40 0.02
114_I 281_V 0.69 0.40 0.02
35_D 129_Y 0.68 0.40 0.02
103_S 324_L 0.68 0.40 0.02
164_V 123_A 0.68 0.39 0.02
133_A 195_W 0.68 0.39 0.02
245_G 137_A 0.67 0.38 0.02
162_V 144_F 0.67 0.38 0.02
202_L 131_V 0.67 0.38 0.02
49_V 152_A 0.67 0.38 0.02
188_F 162_G 0.67 0.38 0.02
116_A 261_L 0.67 0.38 0.02
90_V 25_F 0.67 0.38 0.02
81_W 306_L 0.67 0.37 0.02
143_A 330_R 0.66 0.37 0.02
80_I 86_L 0.66 0.37 0.02
235_S 319_L 0.66 0.37 0.02
20_F 150_S 0.66 0.36 0.02
102_R 116_G 0.66 0.36 0.02
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
3307 5.33 cIV_B_4_cI_H_20_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
3306 5.32 cIV_B_6_cI_H_20_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.11 Done - Shared
3305 5.31 cIV_B_6_cI_H_10_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3304 5.3 cIV_B_10_cI_H_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.03 Done - Shared
3303 5.34 cIV_B_20_cI_H_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.04 Done - Shared
3302 5.32 cIV_B_6_cI_H_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
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