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OPENSEQ.org
cIp_9_4_cIV_C_4
Genes: A B A+B
Length: 163 274 427
Sequences: 2843 2893 434
Seq/Len: 17.44 10.56 1.02
MirrorTree (Pazo et al. 2001) 0.11
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 0.01
2 0.03 0.00 0.01
5 0.04 0.00 0.01
10 0.04 0.00 0.02
20 0.05 0.00 0.03
100 0.07 0.00 0.12
∞ 0.16 0.01 0.99
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
35_L 237_K 1.10 0.43 0.00
73_V 15_S 1.06 0.40 0.00
35_L 185_C 0.96 0.31 0.00
73_V 243_K 0.95 0.30 0.00
157_Q 154_V 0.91 0.27 0.00
139_Q 232_L 0.89 0.26 0.00
157_Q 108_A 0.86 0.24 0.00
35_L 200_G 0.85 0.23 0.00
89_G 170_K 0.83 0.22 0.00
82_D 179_A 0.82 0.21 0.00
51_E 229_F 0.80 0.20 0.00
150_A 180_V 0.80 0.20 0.00
157_Q 177_I 0.80 0.20 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
3871 0.41 cIp_9_40_1_cIV_C_40_1 Δgene:(1, ∞) A:(1E-40, 1) B:(1E-40, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3687 1.02 cIp_9_4_cIV_C_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3686 0.57 cIp_9_40_cIV_C_40 Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.01 Done - Shared
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