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OPENSEQ.org
cIV_A_4_cI_K_6_Pdenitr
Genes: A B A+B
Length: 538 101 612
Sequences: 4477 4661 2096
Seq/Len: 8.32 46.15 3.42
MirrorTree (Pazo et al. 2001) 0.15
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 0.01 0.00 0.03
2 0.01 0.00 0.07
5 0.02 0.01 0.25
10 0.03 0.01 1.31
20 0.03 0.01 1.41
100 0.05 0.03 1.76
∞ 0.08 0.07 3.28
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
196_M 34_M 1.12 0.80 0.05
21_F 81_L 0.96 0.64 0.03
273_I 34_M 0.93 0.61 0.03
435_M 13_I 0.92 0.60 0.03
354_K 23_F 0.86 0.52 0.02
438_I 29_V 0.84 0.49 0.02
186_T 75_A 0.82 0.46 0.02
282_A 18_G 0.80 0.44 0.02
408_I 38_L 0.79 0.43 0.02
308_A 69_V 0.79 0.43 0.02
507_W 60_Q 0.79 0.42 0.02
22_T 42_A 0.78 0.42 0.02
5_R 70_A 0.78 0.41 0.02
33_F 48_V 0.77 0.41 0.02
42_Q 29_V 0.77 0.40 0.02
466_F 21_G 0.75 0.38 0.02
224_G 13_I 0.75 0.38 0.02
157_T 74_A 0.74 0.37 0.02
29_I 30_I 0.73 0.36 0.02
469_W 45_I 0.73 0.35 0.01
251_Y 55_G 0.73 0.35 0.01
278_I 36_I 0.72 0.34 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
3364 2.98 cIV_A_6_cI_K_10_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3362 2.97 cIV_A_10_cI_K_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3359 3.4 cIV_A_6_cI_K_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3358 3.42 cIV_A_4_cI_K_6_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.05 Done - Shared
3356 0.36 cIV_A_40_cI_K_40_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3355 3.6 cIV_A_4_cI_K_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.02 Done - Shared
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