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OPENSEQ.org
cIp_1_40_cIV_A_40
Genes: A B A+B
Length: 438 558 950
Sequences: 2611 4375 1101
Seq/Len: 5.96 7.84 1.16
MirrorTree (Pazo et al. 2001) 0.05
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 0.01 0.00
2 0.01 0.01 0.00
5 0.01 0.02 0.00
10 0.02 0.03 0.02
20 0.03 0.03 0.04
100 0.05 0.05 0.25
∞ 0.14 0.08 1.11
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
145_L 494_Y 0.86 0.26 0.00
84_G 45_I 0.84 0.24 0.00
154_A 184_F 0.84 0.24 0.00
260_R 454_I 0.81 0.22 0.00
134_V 398_L 0.80 0.22 0.00
186_T 309_V 0.76 0.19 0.00
223_T 392_V 0.76 0.19 0.00
30_D 99_M 0.76 0.19 0.00
278_E 493_A 0.75 0.18 0.00
171_L 143_A 0.75 0.18 0.00
143_D 41_I 0.75 0.18 0.00
423_A 491_I 0.74 0.18 0.00
308_D 204_F 0.72 0.17 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
4031 1.16 cIp_1_40_cIV_A_40 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4030 0.79 cIp_1_40_cIV_A_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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