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OPENSEQ.org
cIp_1_4_cIV_C_4
Genes: A B A+B
Length: 438 274 695
Sequences: 2611 2893 403
Seq/Len: 5.96 10.56 0.58
MirrorTree (Pazo et al. 2001) 0.08
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 0.00
2 0.01 0.00 0.00
5 0.01 0.00 0.00
10 0.02 0.00 0.01
20 0.03 0.00 0.01
100 0.05 0.00 0.07
∞ 0.14 0.01 0.57
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
308_D 211_Y 0.97 0.22 0.00
235_A 57_V 0.96 0.22 0.00
51_D 56_L 0.90 0.18 0.00
339_D 191_A 0.89 0.18 0.00
11_P 206_Y 0.88 0.17 0.00
154_A 48_G 0.88 0.17 0.00
335_V 139_W 0.87 0.17 0.00
30_D 28_M 0.86 0.17 0.00
51_D 10_Q 0.86 0.17 0.00
30_D 184_V 0.83 0.15 0.00
134_V 20_F 0.83 0.15 0.00
227_V 161_H 0.83 0.15 0.00
53_V 230_V 0.82 0.15 0.00
236_D 57_V 0.81 0.14 0.00
276_I 223_I 0.80 0.14 0.00
138_Y 29_L 0.80 0.14 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
4034 0.43 cIp_1_4_cIV_C_4 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4033 0.58 cIp_1_4_cIV_C_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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