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OPENSEQ.org
1CL0_A Thioredoxin reductse FAD 2TIR_A Thioredoxin 1
Genes: A B A+B
Length: 320 108 413
Sequences: 46975 9156 1522
Seq/Len: 146.8 84.78 3.69
MirrorTree (Pazo et al. 2001) 0.37
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 0.08 0.02 1.60
2 0.10 0.02 1.80
5 0.12 0.03 2.22
10 0.14 0.03 2.70
20 0.17 0.04 3.56
100 0.23 0.06 7.30
∞ 0.27 0.13 12.05
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
230_N 103_L 0.85 0.53 0.00
313_L 41_I 0.73 0.38 0.00
11_L 99_L 0.71 0.34 0.00
237_A 59_N 0.70 0.33 0.00
122_P 97_G 0.69 0.32 0.00
103_Y 36_E 0.68 0.31 0.00
201_L 20_D 0.68 0.30 0.00
239_L 56_A 0.67 0.30 0.00
100_N 89_T 0.66 0.28 0.00
220_V 78_L 0.65 0.28 0.00
234_L 103_L 0.65 0.27 0.00
80_I 58_L 0.62 0.25 0.00
49_V 16_V 0.62 0.24 0.00
113_G 76_P 0.60 0.23 0.00
252_F 72_I 0.60 0.23 0.00
232_E 39_A 0.60 0.23 0.00
63_L 99_L 0.59 0.22 0.00
7_K 25_V 0.58 0.21 0.00
171_V 42_L 0.58 0.21 0.00
284_A 83_N 0.57 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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