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OPENSEQ.org
cIV_B_4_cI_K_6_Pdenitr
Genes: A B A+B
Length: 252 101 328
Sequences: 4637 4661 2733
Seq/Len: 18.4 46.15 8.33
MirrorTree (Pazo et al. 2001) 0.59
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 0.15
2 0.00 0.00 0.26
5 0.00 0.01 2.45
10 0.01 0.01 4.68
20 0.01 0.01 4.84
100 0.02 0.03 5.25
∞ 0.04 0.07 7.74
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
195_V 43_V 1.05 0.93 0.07
176_A 93_V 0.88 0.80 0.04
169_K 47_F 0.86 0.78 0.04
73_H 14_L 0.83 0.75 0.03
202_L 64_M 0.83 0.74 0.03
131_G 45_I 0.82 0.73 0.03
236_Q 30_I 0.79 0.69 0.03
239_Y 74_A 0.77 0.65 0.03
212_Y 25_N 0.76 0.65 0.03
147_A 65_F 0.76 0.65 0.03
16_G 69_V 0.73 0.59 0.02
71_F 18_G 0.73 0.59 0.02
59_R 22_I 0.72 0.59 0.02
147_A 74_A 0.72 0.58 0.02
60_F 31_V 0.71 0.56 0.02
212_Y 94_E 0.70 0.56 0.02
48_F 25_N 0.70 0.55 0.02
159_D 89_G 0.70 0.55 0.02
233_A 47_F 0.68 0.52 0.02
20_F 17_T 0.67 0.50 0.02
39_L 70_A 0.67 0.50 0.02
52_L 75_A 0.66 0.48 0.02
170_V 95_D 0.65 0.47 0.02
185_I 97_N 0.65 0.47 0.02
103_S 99_M 0.65 0.47 0.02
172_V 65_F 0.65 0.47 0.02
103_S 39_M 0.64 0.46 0.02
180_I 51_S 0.64 0.46 0.02
205_S 25_N 0.64 0.46 0.02
209_E 97_N 0.63 0.44 0.01
195_V 71_A 0.63 0.44 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
3301 8.31 cIV_B_10_cI_K_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.10 Done - Shared
3300 8.28 cIV_B_6_cI_K_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.17 Done - Shared
3299 2.61 cIV_B_6_cI_K_20_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3297 7.24 cIV_B_6_cI_K_10_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3296 7.26 cIV_B_4_cI_K_10_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3295 8.33 cIV_B_4_cI_K_6_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3294 8.64 cIV_B_4_cI_K_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
3239 0.62 cIV_B_40_cI_K_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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