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OPENSEQ.org
cIV_B_10_cI_H_10_Pdenitr
Genes: A B A+B
Length: 252 345 551
Sequences: 4618 4774 2920
Seq/Len: 18.33 13.84 5.3
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 1.82
10 0.01 0.01 3.42
20 0.01 0.01 3.55
100 0.02 0.02 3.72
∞ 0.04 0.05 4.89
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 1.01 0.81 0.03
180_I 147_S 0.96 0.77 0.03
23_A 131_V 0.96 0.77 0.03
164_V 257_L 0.94 0.75 0.02
158_T 163_L 0.92 0.72 0.02
222_I 196_L 0.87 0.66 0.02
195_V 133_M 0.86 0.65 0.02
212_Y 91_S 0.84 0.62 0.02
233_A 87_A 0.84 0.62 0.02
77_I 159_V 0.83 0.61 0.02
90_V 292_A 0.79 0.55 0.01
188_F 102_I 0.76 0.51 0.01
20_F 150_S 0.76 0.51 0.01
132_V 147_S 0.76 0.51 0.01
172_V 260_L 0.75 0.50 0.01
241_A 16_L 0.75 0.49 0.01
54_L 323_V 0.74 0.48 0.01
114_I 283_K 0.74 0.48 0.01
170_V 87_A 0.74 0.48 0.01
175_T 143_P 0.73 0.47 0.01
225_A 229_A 0.73 0.47 0.01
44_A 133_M 0.73 0.46 0.01
243_L 242_L 0.73 0.46 0.01
225_A 225_S 0.71 0.43 0.01
103_S 324_L 0.70 0.43 0.01
114_I 181_V 0.70 0.42 0.01
71_F 169_I 0.70 0.42 0.01
40_Y 180_I 0.70 0.42 0.01
188_F 162_G 0.70 0.42 0.01
212_Y 134_G 0.70 0.42 0.01
184_T 123_A 0.69 0.41 0.01
127_Y 100_V 0.68 0.39 0.01
57_I 323_V 0.67 0.39 0.01
36_H 225_S 0.67 0.38 0.01
114_I 281_V 0.67 0.38 0.01
102_R 116_G 0.66 0.37 0.01
167_G 173_G 0.66 0.37 0.01
76_P 170_I 0.66 0.37 0.01
87_L 331_Y 0.66 0.37 0.01
35_D 129_Y 0.66 0.36 0.01
162_V 144_F 0.66 0.36 0.01
238_K 101_V 0.66 0.36 0.01
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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