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OPENSEQ.org
3PNLA
Genes: A B A+B
Length: 357 211 529
Sequences: 1718 2044 848
Seq/Len: 4.81 9.69 1.6
MirrorTree (Pazo et al. 2001) 0.71
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 0.01 0.02 1.44
2 0.07 0.05 1.47
5 0.09 0.05 1.49
10 0.10 0.05 1.49
20 0.10 0.05 1.49
100 0.11 0.06 1.50
∞ 0.14 0.09 1.51
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
120_L 90_I 1.39 0.82 0.07
123_D 90_I 1.35 0.79 0.07
115_E 121_R 1.13 0.60 0.04
119_E 91_R 1.11 0.57 0.03
84_P 39_H 1.04 0.50 0.03
108_T 182_Y 1.00 0.46 0.02
80_T 80_A 1.00 0.46 0.02
202_K 29_G 0.98 0.44 0.02
98_E 118_V 0.97 0.42 0.02
204_S 32_R 0.96 0.42 0.02
212_M 43_M 0.95 0.41 0.02
80_T 73_L 0.95 0.40 0.02
152_A 37_A 0.93 0.38 0.02
80_T 34_I 0.92 0.37 0.02
127_K 165_S 0.91 0.37 0.02
119_E 121_R 0.90 0.35 0.02
115_E 123_K 0.89 0.35 0.02
77_E 73_L 0.89 0.34 0.01
84_P 197_S 0.88 0.34 0.01
138_A 193_P 0.85 0.31 0.01
123_D 94_Q 0.85 0.31 0.01
73_A 81_S 0.84 0.31 0.01
297_V 200_F 0.84 0.30 0.01
58_E 79_G 0.83 0.29 0.01
11_D 140_E 0.81 0.28 0.01
84_P 131_M 0.81 0.28 0.01
236_V 207_L 0.81 0.28 0.01
61_H 182_Y 0.80 0.27 0.01
80_T 45_R 0.79 0.26 0.01
204_S 135_W 0.78 0.25 0.01
58_E 78_G 0.78 0.25 0.01
64_Y 81_S 0.78 0.25 0.01
35_Y 13_L 0.78 0.25 0.01
58_E 39_H 0.77 0.25 0.01
80_T 77_V 0.77 0.24 0.01
80_T 42_N 0.77 0.24 0.01
155_V 13_L 0.77 0.24 0.01
71_S 163_A 0.77 0.24 0.01
61_H 81_S 0.76 0.24 0.01
115_E 80_A 0.76 0.24 0.01
105_K 81_S 0.76 0.24 0.01
105_K 182_Y 0.76 0.23 0.01
292_S 39_H 0.75 0.23 0.01
112_L 61_D 0.75 0.23 0.01
72_G 92_A 0.75 0.23 0.01
147_G 182_Y 0.75 0.23 0.01
85_D 75_S 0.74 0.22 0.01
292_S 83_P 0.73 0.21 0.01
101_L 9_I 0.73 0.21 0.01
233_D 56_A 0.73 0.21 0.01
58_E 83_P 0.72 0.21 0.01
321_C 71_M 0.72 0.21 0.01
352_A 79_G 0.72 0.21 0.01
112_L 142_L 0.72 0.21 0.01
77_E 45_R 0.71 0.20 0.01
229_F 9_I 0.71 0.20 0.01
154_T 182_Y 0.71 0.20 0.01
22_K 18_D 0.71 0.20 0.01
331_I 49_K 0.71 0.20 0.01
89_E 125_E 0.71 0.20 0.01
80_T 198_V 0.70 0.20 0.01
236_V 92_A 0.70 0.20 0.01
120_L 75_S 0.70 0.19 0.01
50_L 72_T 0.70 0.19 0.01
105_K 177_K 0.70 0.19 0.01
158_E 42_N 0.70 0.19 0.01
129_T 70_G 0.69 0.19 0.01
80_T 197_S 0.69 0.19 0.01
58_E 81_S 0.69 0.19 0.01
105_K 42_N 0.69 0.19 0.01
231_S 187_S 0.68 0.18 0.01
307_Q 105_E 0.68 0.18 0.01
147_G 181_S 0.68 0.18 0.01
281_A 142_L 0.68 0.18 0.01
154_T 79_G 0.68 0.18 0.01
327_T 202_M 0.68 0.18 0.01
74_C 37_A 0.68 0.18 0.01
112_L 32_R 0.67 0.18 0.01
8_D 109_Q 0.67 0.17 0.01
154_T 81_S 0.67 0.17 0.01
222_P 87_T 0.67 0.17 0.01
240_F 29_G 0.67 0.17 0.01
114_F 122_G 0.67 0.17 0.01
324_L 181_S 0.67 0.17 0.01
187_S 33_E 0.66 0.17 0.01
23_A 93_A 0.66 0.17 0.01
95_D 56_A 0.66 0.17 0.01
70_L 182_Y 0.65 0.17 0.01
197_V 180_A 0.65 0.16 0.01
51_S 180_A 0.65 0.16 0.01
240_F 103_T 0.65 0.16 0.01
72_G 20_F 0.65 0.16 0.01
336_V 28_T 0.65 0.16 0.01
125_G 94_Q 0.64 0.16 0.01
81_S 42_N 0.64 0.16 0.01
138_A 73_L 0.64 0.16 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)
ID Seq/Len Name Options I_Prob Status
7278 1.5 3PNLA Δgene:(0, 0) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.03 Done - Shared
7269 3.06 3PNLA Δgene:(0, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.11 Done - Shared
7244 1.6 3PNLA Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.07 Done - Shared
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