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OPENSEQ.org
cI_B_20_cIV_B_20_Pdenitr
Genes: A B A+B
Length: 175 252 400
Sequences: 1183 4606 741
Seq/Len: 6.76 18.28 1.85
MirrorTree (Pazo et al. 2001) 0.24
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 0.01
10 0.02 0.01 0.02
20 0.02 0.01 0.08
100 0.03 0.02 0.24
∞ 0.08 0.04 1.74
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
157_L 177_T 0.91 0.40 0.00
114_I 242_W 0.82 0.31 0.00
111_R 28_A 0.81 0.30 0.00
133_V 114_I 0.77 0.27 0.00
161_L 168_K 0.75 0.25 0.00
109_E 174_V 0.75 0.25 0.00
65_P 225_A 0.75 0.25 0.00
38_N 243_L 0.74 0.24 0.00
38_N 240_E 0.74 0.24 0.00
60_M 130_D 0.73 0.23 0.00
85_L 192_Q 0.73 0.23 0.00
131_S 54_L 0.72 0.23 0.00
30_L 182_A 0.71 0.22 0.00
137_D 85_P 0.71 0.22 0.00
97_A 170_V 0.70 0.22 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
3491 1.97 cI_B_6_cIV_B_6_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
3490 1.85 cI_B_20_cIV_B_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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