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OPENSEQ.org
2yvj_A_B
Genes: A B A+B
Length: 401 108 497
Sequences: 10629 8870 1620
Seq/Len: 26.51 82.13 3.26
MirrorTree (Pazo et al. 2001) 0.67
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 0.02 2.33
2 0.04 0.10 2.53
5 0.05 0.11 2.83
10 0.06 0.13 3.04
20 0.07 0.14 3.18
100 0.11 0.19 4.04
∞ 0.21 0.26 6.14
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
323_I 5_A 0.87 0.52 0.00
216_D 70_C 0.86 0.50 0.00
230_I 13_P 0.83 0.47 0.00
336_V 97_V 0.82 0.45 0.00
252_V 49_L 0.78 0.40 0.00
173_P 95_R 0.77 0.38 0.00
135_A 72_R 0.76 0.38 0.00
126_T 88_Y 0.74 0.35 0.00
73_L 6_C 0.74 0.35 0.00
200_R 32_D 0.74 0.35 0.00
376_L 78_S 0.72 0.33 0.00
86_T 10_E 0.72 0.33 0.00
350_I 5_A 0.72 0.33 0.00
200_R 26_V 0.72 0.33 0.00
224_D 5_A 0.71 0.32 0.00
94_T 3_T 0.70 0.31 0.00
168_L 85_L 0.70 0.31 0.00
372_L 37_A 0.70 0.31 0.00
108_P 69_F 0.70 0.31 0.00
264_Y 93_E 0.70 0.30 0.00
144_L 72_R 0.70 0.30 0.00
357_I 61_E 0.69 0.30 0.00
180_A 29_F 0.68 0.28 0.00
269_V 10_E 0.67 0.28 0.00
216_D 99_V 0.67 0.28 0.00
77_A 98_L 0.67 0.28 0.00
295_A 98_L 0.66 0.27 0.00
250_I 10_E 0.66 0.27 0.00
349_L 36_F 0.66 0.26 0.00
208_S 70_C 0.66 0.26 0.00
178_R 67_G 0.65 0.26 0.00
230_I 12_P 0.64 0.25 0.00
311_L 71_V 0.64 0.25 0.00
306_P 28_I 0.64 0.25 0.00
163_G 30_N 0.64 0.24 0.00
148_G 11_V 0.64 0.24 0.00
90_S 5_A 0.63 0.23 0.00
255_Y 92_I 0.62 0.23 0.00
119_M 28_I 0.62 0.23 0.00
72_L 3_T 0.62 0.23 0.00
222_A 92_I 0.62 0.22 0.00
200_R 87_V 0.62 0.22 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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