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OPENSEQ.org
cI_H_cIII_ISP_Ecoli
Genes: A B A+B
Length: 325 183 491
Sequences: 4760 2509 679
Seq/Len: 14.65 13.71 1.38
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 0.00 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.01
10 0.01 0.01 0.02
20 0.01 0.02 0.03
100 0.02 0.03 0.16
∞ 0.05 0.08 1.34
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
116_I 149_T 1.04 0.46 0.00
118_F 29_A 1.04 0.45 0.00
310_L 147_F 0.97 0.39 0.00
20_V 39_V 0.96 0.38 0.00
26_V 15_R 0.95 0.37 0.00
101_V 121_Y 0.94 0.36 0.00
132_F 36_W 0.89 0.32 0.00
163_S 42_L 0.87 0.30 0.00
160_L 150_S 0.87 0.30 0.00
169_A 136_L 0.87 0.29 0.00
154_L 35_V 0.86 0.29 0.00
16_L 104_D 0.86 0.29 0.00
101_V 93_T 0.86 0.29 0.00
125_L 38_L 0.84 0.28 0.00
317_A 81_H 0.84 0.28 0.00
193_F 34_A 0.84 0.28 0.00
193_F 162_L 0.84 0.27 0.00
217_A 147_F 0.83 0.27 0.00
101_V 30_G 0.83 0.26 0.00
80_R 39_V 0.80 0.25 0.00
269_I 114_Q 0.80 0.24 0.00
99_A 15_R 0.79 0.23 0.00
278_F 28_A 0.77 0.22 0.00
171_A 156_G 0.77 0.22 0.00
78_S 29_A 0.77 0.22 0.00
283_I 28_A 0.77 0.22 0.00
23_L 125_A 0.77 0.22 0.00
78_S 77_I 0.76 0.22 0.00
173_S 18_C 0.76 0.22 0.00
315_V 36_W 0.76 0.21 0.00
20_V 133_P 0.76 0.21 0.00
201_I 70_R 0.76 0.21 0.00
11_I 66_Q 0.75 0.21 0.00
14_T 32_A 0.75 0.21 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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