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OPENSEQ.org
4EB7
Genes: A B A+B
Length: 382 153 491
Sequences: 19192 1952 1708
Seq/Len: 50.24 12.76 3.48
MirrorTree (Pazo et al. 2001) 0.81
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.03 0.01 3.06
2 0.03 0.01 3.11
5 0.05 0.01 3.15
10 0.06 0.01 3.17
20 0.07 0.01 3.19
100 0.12 0.01 3.32
∞ 0.21 0.03 3.58
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
31_P 96_P 0.81 0.46 0.00
57_N 52_K 0.81 0.45 0.00
203_P 53_F 0.78 0.41 0.00
238_P 97_K 0.73 0.36 0.00
53_A 51_I 0.73 0.35 0.00
327_Q 32_V 0.70 0.32 0.00
357_E 42_K 0.69 0.31 0.00
17_L 68_A 0.65 0.27 0.00
22_P 43_V 0.64 0.26 0.00
302_E 34_G 0.64 0.26 0.00
52_V 14_R 0.63 0.25 0.00
322_S 68_A 0.62 0.24 0.00
317_T 26_G 0.62 0.24 0.00
70_T 43_V 0.62 0.23 0.00
300_E 34_G 0.61 0.23 0.00
99_M 30_N 0.61 0.23 0.00
34_V 66_S 0.60 0.22 0.00
35_H 81_L 0.60 0.22 0.00
4_F 45_D 0.59 0.21 0.00
114_E 83_I 0.59 0.21 0.00
369_V 10_F 0.59 0.21 0.00
337_L 32_V 0.59 0.21 0.00
7_T 63_A 0.58 0.20 0.00
252_M 82_K 0.58 0.20 0.00
203_P 13_P 0.58 0.20 0.00
129_S 82_K 0.57 0.20 0.00
332_L 52_K 0.57 0.19 0.00
359_V 42_K 0.57 0.19 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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