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OPENSEQ.org
cIV_B_6_cI_N_10_1_Pdenitr
Genes: A B A+B
Length: 252 499 709
Sequences: 4627 3881 1168
Seq/Len: 18.36 7.78 1.65
MirrorTree (Pazo et al. 2001) 0.18
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 0.16 0.01
2 0.00 0.27 0.04
5 0.00 0.29 0.07
10 0.01 0.29 0.14
20 0.01 0.30 0.22
100 0.02 0.31 0.38
∞ 0.04 0.34 1.56
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
118_G 408_V 0.91 0.37 0.00
114_I 442_G 0.88 0.35 0.00
80_I 175_A 0.87 0.34 0.00
239_Y 399_V 0.82 0.29 0.00
87_L 252_A 0.81 0.28 0.00
114_I 284_G 0.76 0.24 0.00
212_Y 234_S 0.76 0.24 0.00
170_V 182_A 0.75 0.23 0.00
176_A 267_G 0.74 0.23 0.00
20_F 192_S 0.74 0.23 0.00
25_S 52_M 0.74 0.23 0.00
88_I 389_F 0.73 0.22 0.00
167_G 449_L 0.73 0.22 0.00
57_I 362_A 0.72 0.21 0.00
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
3315 1.12 cIV_B_2_cI_N_40_1_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.26 Done - Shared
3314 1.11 cIV_B_4_cI_N_40_1_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.27 Done - Shared
3313 0.83 cIV_B_6_cI_N_60_1_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-60, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3312 1.12 cIV_B_6_cI_N_40_1_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.18 Done - Shared
3311 1.65 cIV_B_6_cI_N_10_1_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3308 1.24 cIV_B_6_cI_N_20_1_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.01 Done - Shared
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