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OPENSEQ.org
4EB7-2
Genes: A B A+B
Length: 377 138 489
Sequences: 19536 2240 1975
Seq/Len: 51.82 16.23 4.04
MirrorTree (Pazo et al. 2001) 0.79
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 3.68
2 0.03 0.01 3.76
5 0.05 0.01 3.79
10 0.06 0.01 3.80
20 0.07 0.01 3.83
100 0.13 0.01 3.96
∞ 0.21 0.04 4.28
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
237_P 96_K 0.72 0.37 0.00
16_L 67_A 0.70 0.36 0.00
30_P 95_P 0.70 0.36 0.00
17_E 78_E 0.70 0.35 0.00
154_Q 91_L 0.69 0.34 0.00
299_E 33_G 0.68 0.33 0.00
301_E 33_G 0.67 0.32 0.00
247_E 47_I 0.66 0.31 0.00
202_P 52_F 0.66 0.31 0.00
179_Q 67_A 0.62 0.26 0.00
57_G 96_K 0.62 0.26 0.00
336_L 31_V 0.61 0.25 0.00
49_E 8_H 0.61 0.25 0.00
251_M 81_K 0.61 0.25 0.00
145_H 71_A 0.60 0.24 0.00
321_S 67_A 0.60 0.24 0.00
326_Q 31_V 0.58 0.23 0.00
356_E 41_K 0.58 0.23 0.00
157_E 48_E 0.58 0.22 0.00
301_E 95_P 0.58 0.22 0.00
91_L 115_D 0.57 0.22 0.00
357_D 75_T 0.57 0.21 0.00
21_P 42_V 0.57 0.21 0.00
363_E 43_K 0.56 0.20 0.00
33_V 65_S 0.56 0.20 0.00
263_L 50_I 0.55 0.20 0.00
300_G 67_A 0.55 0.20 0.00
70_E 28_G 0.55 0.20 0.00
98_M 33_G 0.55 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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