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OPENSEQ.org
3jwn_K_I
Genes: A B A+B
Length: 154 205 357
Sequences: 2976 2071 1484
Seq/Len: 19.32 10.1 4.16
MirrorTree (Pazo et al. 2001) 0.44
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 0.31 0.01 3.35
2 0.31 0.03 3.97
5 0.52 0.14 4.11
10 0.53 0.15 4.12
20 0.53 0.16 4.13
100 0.55 0.20 4.16
∞ 0.56 0.26 4.21
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
154_Q 165_A 1.22 0.90 0.24
154_Q 151_T 1.19 0.89 0.23
69_G 54_L 1.05 0.80 0.15
151_L 131_L 1.05 0.79 0.15
18_V 107_I 1.02 0.76 0.14
12_R 151_T 0.98 0.73 0.12
125_L 37_V 0.92 0.66 0.10
149_F 105_L 0.92 0.66 0.10
149_F 62_E 0.89 0.61 0.09
103_I 22_V 0.86 0.57 0.08
92_G 10_I 0.86 0.57 0.08
13_D 6_A 0.86 0.57 0.08
125_L 104_Q 0.85 0.56 0.07
10_Y 193_Y 0.84 0.55 0.07
26_T 81_S 0.82 0.52 0.07
92_G 147_P 0.80 0.49 0.06
100_Q 172_E 0.80 0.49 0.06
93_I 103_L 0.79 0.48 0.06
15_G 109_S 0.78 0.46 0.06
78_L 93_M 0.77 0.46 0.06
3_S 87_V 0.77 0.45 0.06
38_N 174_T 0.76 0.44 0.05
151_L 114_Y 0.76 0.44 0.05
108_P 150_L 0.76 0.43 0.05
110_S 140_L 0.76 0.43 0.05
150_T 111_I 0.75 0.43 0.05
34_A 90_I 0.75 0.43 0.05
103_I 77_Q 0.75 0.43 0.05
149_F 21_A 0.75 0.42 0.05
51_I 53_P 0.75 0.42 0.05
18_V 3_A 0.74 0.41 0.05
113_S 10_I 0.73 0.39 0.05
6_T 115_Y 0.72 0.39 0.04
138_V 92_S 0.72 0.38 0.04
45_P 22_V 0.71 0.38 0.04
12_R 164_N 0.71 0.37 0.04
154_Q 152_V 0.70 0.37 0.04
5_I 98_L 0.70 0.37 0.04
64_K 81_S 0.70 0.36 0.04
7_I 151_T 0.70 0.36 0.04
93_I 14_G 0.69 0.35 0.04
108_P 90_I 0.69 0.35 0.04
48_P 93_M 0.68 0.34 0.04
24_N 172_E 0.68 0.34 0.04
125_L 106_A 0.68 0.33 0.04
14_N 6_A 0.67 0.33 0.04
87_A 39_N 0.67 0.33 0.04
66_G 150_L 0.67 0.33 0.04
59_A 171_G 0.67 0.32 0.04
93_I 102_T 0.67 0.32 0.04
42_A 76_P 0.67 0.32 0.04
72_D 111_I 0.67 0.32 0.04
154_Q 153_T 0.67 0.32 0.04
73_S 118_A 0.66 0.32 0.04
15_G 26_D 0.65 0.30 0.03
127_F 151_T 0.65 0.30 0.03
124_T 14_G 0.65 0.30 0.03
26_T 93_M 0.64 0.29 0.03
29_L 58_K 0.64 0.29 0.03
149_F 63_N 0.64 0.29 0.03
94_Q 11_Y 0.64 0.29 0.03
66_G 49_I 0.64 0.29 0.03
15_G 63_N 0.64 0.28 0.03
146_T 77_Q 0.64 0.28 0.03
153_Y 7_T 0.63 0.28 0.03
24_N 99_T 0.63 0.28 0.03
145_A 20_L 0.63 0.28 0.03
154_Q 190_I 0.63 0.28 0.03
12_R 166_L 0.63 0.27 0.03
21_E 148_Y 0.62 0.27 0.03
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)
WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.53 > 0.4) of paralogs.
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