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Problem 51

Genes: A B A+B
Length: 306 252 555
Sequences: 3031 2626 2378
Seq/Len: 9.91 10.42 4.28
MirrorTree (Pazo et al. 2001) 0.90
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 0.01 4.21
2 0.01 0.01 4.23
5 0.01 0.01 4.25
10 0.01 0.01 4.26
20 0.02 0.02 4.26
100 0.03 0.03 4.27
0.09 0.08 4.30
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
174_S 171_A 4.12 1.00 1.00
103_L 137_A 3.33 1.00 1.00
99_R 137_A 2.96 1.00 1.00
135_K 220_E 2.67 1.00 1.00
305_K 240_D 2.14 1.00 0.99
105_D 103_K 2.02 1.00 0.99
273_V 242_L 1.89 1.00 0.98
108_V 130_A 1.78 0.99 0.97
122_E 225_R 1.73 0.99 0.97
178_D 168_Q 1.70 0.99 0.96
133_V 223_S 1.69 0.99 0.96
102_A 134_M 1.67 0.99 0.96
99_R 143_Q 1.66 0.99 0.96
177_A 169_T 1.51 0.98 0.93
172_L 140_G 1.50 0.98 0.92
305_K 243_V 1.47 0.98 0.91
68_A 143_Q 1.32 0.94 0.85
289_Y 242_L 1.30 0.94 0.84
172_L 142_A 1.28 0.93 0.82
176_V 169_T 1.23 0.91 0.79
102_A 138_I 1.16 0.88 0.73
107_M 97_E 1.15 0.87 0.73
176_V 171_A 1.11 0.84 0.69
173_S 170_I 1.07 0.81 0.64
73_A 140_G 1.01 0.76 0.58
130_A 224_V 1.00 0.75 0.56
95_N 143_Q 1.00 0.75 0.56
291_L 239_V 0.98 0.72 0.54
130_A 19_V 0.95 0.70 0.51
135_K 222_V 0.95 0.69 0.50
103_L 140_G 0.94 0.69 0.50
110_S 128_M 0.93 0.67 0.47
98_P 129_N 0.92 0.66 0.46
302_L 243_V 0.92 0.66 0.46
110_S 130_A 0.91 0.65 0.46
271_V 249_A 0.91 0.65 0.46
200_G 58_I 0.89 0.63 0.43
105_D 138_I 0.89 0.62 0.43
293_G 116_L 0.86 0.58 0.39
126_Y 25_G 0.85 0.57 0.38
137_K 220_E 0.85 0.56 0.37
95_N 145_T 0.82 0.53 0.34
176_V 158_K 0.81 0.52 0.33
210_I 17_A 0.80 0.50 0.32
98_P 36_N 0.80 0.50 0.32
172_L 173_S 0.80 0.50 0.32
120_T 222_V 0.79 0.48 0.30
291_L 236_V 0.78 0.48 0.30
193_R 211_Y 0.78 0.47 0.29
131_I 225_R 0.77 0.47 0.29
179_E 169_T 0.77 0.46 0.28
270_K 249_A 0.75 0.44 0.27
224_S 195_I 0.75 0.43 0.26
174_S 173_S 0.75 0.43 0.26
194_V 131_T 0.74 0.42 0.25
98_P 144_A 0.74 0.42 0.25
108_V 128_M 0.73 0.41 0.24
144_T 24_S 0.73 0.41 0.24
290_G 198_A 0.73 0.40 0.23
72_A 137_A 0.72 0.40 0.23
92_D 170_I 0.72 0.39 0.23
146_R 36_N 0.71 0.39 0.22
68_A 170_I 0.71 0.38 0.22
270_K 202_P 0.71 0.38 0.22
278_D 199_K 0.71 0.38 0.22
242_T 180_A 0.70 0.37 0.21
228_V 127_D 0.70 0.37 0.21
107_M 219_L 0.70 0.37 0.21
169_D 142_A 0.70 0.36 0.21
151_D 251_V 0.70 0.36 0.21
232_Y 6_P 0.69 0.36 0.20
272_I 230_R 0.69 0.35 0.20
279_E 168_Q 0.68 0.34 0.19
194_V 118_I 0.67 0.34 0.18
229_D 188_R 0.67 0.33 0.18
273_V 160_T 0.67 0.33 0.18
263_L 77_A 0.67 0.33 0.18
105_D 99_L 0.66 0.32 0.17
133_V 222_V 0.65 0.31 0.17
132_Q 221_V 0.64 0.30 0.16
93_A 42_A 0.64 0.30 0.16
107_M 218_R 0.64 0.30 0.16
306_L 247_K 0.63 0.29 0.15
242_T 14_N 0.63 0.29 0.15
123_R 127_D 0.63 0.29 0.15
124_P 127_D 0.63 0.28 0.15
277_K 199_K 0.63 0.28 0.15
94_K 146_F 0.63 0.28 0.15
304_G 178_V 0.62 0.27 0.14
133_V 225_R 0.62 0.27 0.14
299_V 105_L 0.61 0.27 0.14
98_P 130_A 0.61 0.27 0.14
132_Q 224_V 0.61 0.27 0.14
179_E 158_K 0.61 0.26 0.13
254_V 192_L 0.61 0.26 0.13
179_E 160_T 0.60 0.26 0.13
112_V 101_V 0.60 0.26 0.13
275_I 222_V 0.60 0.25 0.13
239_V 182_L 0.60 0.25 0.13
143_F 4_L 0.60 0.25 0.13
20_A 88_A 0.60 0.25 0.12
298_V 157_A 0.60 0.25 0.12
61_A 247_K 0.60 0.25 0.12
17_T 47_I 0.59 0.25 0.12
279_E 118_I 0.59 0.24 0.12
100_V 220_E 0.59 0.24 0.12
63_Y 139_L 0.59 0.24 0.12
150_F 162_E 0.59 0.24 0.12
241_Q 124_I 0.59 0.24 0.12
89_A 28_L 0.58 0.24 0.12
148_A 224_V 0.58 0.24 0.12
68_A 137_A 0.58 0.23 0.12
126_Y 126_N 0.58 0.23 0.12
89_A 127_D 0.58 0.23 0.11
52_V 101_V 0.58 0.23 0.11
209_I 71_T 0.58 0.23 0.11
216_K 243_V 0.58 0.23 0.11
144_T 130_A 0.58 0.23 0.11
179_E 163_V 0.58 0.23 0.11
222_G 109_A 0.57 0.23 0.11
194_V 244_G 0.57 0.23 0.11
225_R 44_E 0.57 0.22 0.11
145_I 6_P 0.57 0.22 0.11
130_A 37_P 0.57 0.22 0.11
285_Q 190_A 0.57 0.22 0.10
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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