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OPENSEQ.org
cIV_B_20_cI_J_20_Pdenitr
Genes: A B A+B
Length: 252 200 438
Sequences: 4606 2148 1009
Seq/Len: 18.28 10.74 2.3
MirrorTree (Pazo et al. 2001) 0.40
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 0.06
2 0.00 0.00 0.12
5 0.00 0.01 0.25
10 0.01 0.01 0.43
20 0.01 0.01 0.53
100 0.02 0.02 0.68
∞ 0.04 0.03 2.23
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
239_Y 64_V 1.30 0.84 0.12
77_I 151_G 1.22 0.78 0.10
114_I 149_L 1.10 0.68 0.07
112_L 88_R 1.07 0.65 0.06
54_L 95_V 1.04 0.61 0.06
82_T 21_V 1.03 0.60 0.06
119_H 55_L 0.96 0.52 0.04
188_F 151_G 0.89 0.44 0.04
21_Q 30_V 0.89 0.43 0.03
108_N 64_V 0.86 0.41 0.03
119_H 151_G 0.86 0.40 0.03
113_V 57_V 0.84 0.39 0.03
212_Y 9_F 0.84 0.38 0.03
47_I 59_V 0.84 0.38 0.03
57_I 59_V 0.84 0.38 0.03
24_S 76_D 0.84 0.38 0.03
44_A 108_F 0.83 0.37 0.03
131_G 10_A 0.83 0.37 0.03
170_V 159_I 0.82 0.37 0.03
51_L 10_A 0.82 0.36 0.03
97_L 32_W 0.82 0.36 0.03
231_V 128_A 0.81 0.35 0.03
37_F 53_A 0.79 0.33 0.02
176_A 34_I 0.79 0.33 0.02
237_E 20_V 0.79 0.32 0.02
212_Y 159_I 0.78 0.32 0.02
138_M 74_M 0.78 0.32 0.02
80_I 135_L 0.76 0.30 0.02
182_A 167_R 0.76 0.30 0.02
192_Q 151_G 0.76 0.29 0.02
195_V 97_G 0.75 0.29 0.02
234_V 53_A 0.75 0.29 0.02
88_I 94_L 0.75 0.29 0.02
114_I 29_S 0.75 0.29 0.02
103_S 28_H 0.74 0.28 0.02
239_Y 53_A 0.74 0.28 0.02
58_V 102_A 0.73 0.28 0.02
25_S 79_F 0.73 0.27 0.02
225_A 99_V 0.72 0.26 0.02
47_I 143_Y 0.72 0.26 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
3238 0.58 cIV_B_40_cI_J_60_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-60, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3237 0.92 cIV_B_40_cI_J_40_Pdenitr Δgene:(1, ∞) A:(1E-60, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.04 Done - Shared
3236 0.99 cIV_B_40_cI_J_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.31 Done - Shared
3235 2.02 cIV_B_40_cI_J_10_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.13 Done - Shared
3234 2 cIV_B_40_cI_J_20_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.14 Done - Shared
3233 1.1 cIV_B_20_cI_J_40_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3232 2.3 cIV_B_20_cI_J_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.12 Done - Shared
3231 2.3 cIV_B_4_cI_J_20_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
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