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OPENSEQ.org
cIV_cyoc_cI_M_Ecoli
Genes: A B A+B
Length: 204 509 688
Sequences: 4637 2110 1006
Seq/Len: 22.73 4.15 1.46
MirrorTree (Pazo et al. 2001) 0.29
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 0.01 0.02
2 0.03 0.01 0.05
5 0.03 0.01 0.13
10 0.04 0.02 0.24
20 0.04 0.02 0.31
100 0.05 0.03 0.45
∞ 0.08 0.06 1.41
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
33_L 411_L 1.19 0.62 0.00
30_W 83_I 0.95 0.38 0.00
103_A 15_F 0.92 0.35 0.00
94_N 429_L 0.92 0.35 0.00
94_N 171_A 0.90 0.34 0.00
115_M 338_Y 0.90 0.33 0.00
104_L 350_L 0.87 0.31 0.00
103_A 414_S 0.86 0.30 0.00
141_A 83_I 0.85 0.29 0.00
65_E 296_I 0.83 0.28 0.00
114_G 430_V 0.82 0.27 0.00
73_T 12_I 0.82 0.27 0.00
68_F 346_I 0.81 0.26 0.00
78_F 128_I 0.79 0.24 0.00
155_I 222_L 0.79 0.24 0.00
190_V 306_F 0.78 0.23 0.00
75_L 298_I 0.77 0.23 0.00
85_M 293_L 0.77 0.23 0.00
130_P 99_V 0.77 0.23 0.00
140_F 92_V 0.76 0.23 0.00
104_L 425_S 0.75 0.22 0.00
86_A 492_A 0.74 0.21 0.00
192_I 465_L 0.74 0.21 0.00
200_L 133_A 0.73 0.20 0.00
107_L 335_Q 0.73 0.20 0.00
64_F 414_S 0.73 0.20 0.00
77_L 143_W 0.73 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)
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