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OPENSEQ.org
cIV_cyoc_cI_K2_2_Ecoli
Genes: A B A+B
Length: 204 100 292
Sequences: 4744 5077 2880
Seq/Len: 23.25 50.77 9.86
MirrorTree (Pazo et al. 2001) 0.48
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 0.03 0.00 0.11
2 0.03 0.00 2.14
5 0.03 0.01 5.13
10 0.04 0.01 5.70
20 0.04 0.02 5.95
100 0.05 0.03 6.56
∞ 0.08 0.07 9.47
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
75_L 73_A 1.15 0.97 0.20
64_F 65_A 1.01 0.93 0.13
26_I 92_I 0.90 0.86 0.09
135_F 67_S 0.89 0.85 0.09
74_F 44_L 0.83 0.79 0.07
62_D 44_L 0.79 0.74 0.06
23_G 44_L 0.79 0.74 0.06
167_R 43_A 0.79 0.74 0.06
96_S 73_A 0.79 0.74 0.06
78_F 30_F 0.75 0.68 0.05
118_Y 74_S 0.75 0.68 0.05
64_F 73_A 0.75 0.68 0.05
100_S 68_L 0.73 0.65 0.05
64_F 70_A 0.73 0.65 0.05
86_A 18_G 0.73 0.64 0.05
37_C 41_A 0.72 0.64 0.05
198_V 67_S 0.71 0.62 0.04
117_I 33_I 0.69 0.59 0.04
52_N 88_Q 0.69 0.58 0.04
74_F 68_L 0.68 0.57 0.04
68_F 94_S 0.68 0.56 0.04
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)
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