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OPENSEQ.org
1vs5_H_Q
Genes: A B A+B
Length: 130 84 211
Sequences: 2935 2442 1947
Seq/Len: 22.58 29.07 9.23
MirrorTree (Pazo et al. 2001) 0.82
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 0.09 0.08 0.01
2 0.09 0.08 0.01
5 0.09 0.08 8.21
10 0.09 0.08 9.00
20 0.09 0.08 9.10
100 0.09 0.08 9.32
∞ 0.09 0.09 9.74
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
121_L 63_E 1.11 0.96 0.13
70_A 37_F 1.02 0.92 0.10
35_A 40_R 0.77 0.70 0.04
49_F 4_K 0.72 0.61 0.03
34_V 25_I 0.69 0.56 0.03
107_S 75_L 0.67 0.53 0.03
61_L 4_K 0.67 0.53 0.03
20_A 73_W 0.67 0.53 0.03
110_V 24_A 0.66 0.52 0.03
127_C 40_R 0.64 0.48 0.02
22_K 45_H 0.64 0.47 0.02
88_R 35_G 0.62 0.44 0.02
124_E 31_H 0.61 0.44 0.02
127_C 53_C 0.61 0.44 0.02
87_K 72_S 0.61 0.43 0.02
128_Y 35_G 0.60 0.41 0.02
6_P 11_R 0.58 0.39 0.02
74_S 33_I 0.58 0.39 0.02
31_K 80_E 0.57 0.38 0.02
16_N 66_P 0.57 0.37 0.02
97_A 8_L 0.57 0.37 0.02
109_G 56_G 0.57 0.37 0.02
118_Q 62_R 0.57 0.37 0.02
63_L 70_T 0.56 0.36 0.02
73_E 42_T 0.56 0.36 0.02
97_A 5_I 0.56 0.36 0.02
130_A 72_S 0.56 0.35 0.02
30_S 20_S 0.55 0.34 0.02
15_R 48_D 0.55 0.33 0.02
118_Q 69_K 0.55 0.33 0.02
62_T 40_R 0.54 0.33 0.02
20_A 34_Y 0.54 0.32 0.01
20_A 42_T 0.54 0.32 0.01
103_V 8_L 0.54 0.32 0.01
28_P 63_E 0.53 0.31 0.01
102_A 21_I 0.53 0.31 0.01
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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