GREMLIN.BAKERLAB.org
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TLE

Genes: A B A+B
Length: 253 221 409
Sequences: 81371 1051 176
Seq/Len: 321.62 4.76 0.43
MirrorTree (Pazo et al. 2001) 0.58
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 0.04 0.00 0.00
2 0.07 0.00 0.01
5 0.10 0.00 0.06
10 0.14 0.00 0.23
20 0.18 0.00 0.37
100 0.27 0.00 1.26
0.31 0.00 1.99
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
156_A 15_A 1.38 0.43 0.00
108_R 16_L 1.31 0.38 0.00
176_V 170_K 1.27 0.35 0.00
157_V 46_L 1.22 0.32 0.00
200_P 39_I 1.22 0.32 0.00
204_A 159_T 1.20 0.30 0.00
160_I 53_R 1.19 0.30 0.00
175_T 130_I 1.19 0.30 0.00
77_L 146_G 1.10 0.25 0.00
153_S 40_A 1.09 0.24 0.00
108_R 25_S 1.08 0.24 0.00
54_M 10_E 1.07 0.23 0.00
108_R 73_S 1.07 0.23 0.00
95_S 107_E 1.05 0.22 0.00
199_R 29_L 1.02 0.21 0.00
190_D 130_I 1.02 0.21 0.00
133_F 24_L 1.02 0.20 0.00
129_A 104_T 1.01 0.20 0.00
157_V 108_I 1.01 0.20 0.00
189_A 121_I 1.01 0.20 0.00
62_D 9_V 0.99 0.19 0.00
93_I 121_I 0.99 0.19 0.00
203_L 21_A 0.99 0.19 0.00
249_A 6_P 0.98 0.19 0.00
60_C 167_A 0.97 0.18 0.00
249_A 85_R 0.97 0.18 0.00
176_V 47_R 0.97 0.18 0.00
225_L 160_L 0.97 0.18 0.00
206_L 17_L 0.96 0.18 0.00
167_A 53_R 0.96 0.18 0.00
225_L 29_L 0.95 0.17 0.00
67_A 111_V 0.95 0.17 0.00
220_V 76_M 0.94 0.17 0.00
138_P 35_E 0.94 0.17 0.00
61_H 140_G 0.93 0.16 0.00
98_R 72_L 0.92 0.16 0.00
210_P 87_S 0.92 0.16 0.00
176_V 40_A 0.91 0.16 0.00
141_D 97_V 0.91 0.16 0.00
167_A 42_G 0.91 0.16 0.00
226_N 60_V 0.89 0.15 0.00
249_A 157_L 0.89 0.15 0.00
203_L 130_I 0.89 0.15 0.00
183_G 49_R 0.89 0.15 0.00
55_L 76_M 0.88 0.14 0.00
125_L 108_I 0.87 0.14 0.00
57_A 74_F 0.87 0.14 0.00
163_I 152_M 0.87 0.14 0.00
221_Q 152_M 0.87 0.14 0.00
233_G 61_A 0.86 0.14 0.00
60_C 157_L 0.86 0.14 0.00
225_L 31_K 0.86 0.14 0.00
152_P 162_D 0.86 0.14 0.00
189_A 24_L 0.85 0.14 0.00
174_A 27_V 0.85 0.14 0.00
60_C 110_A 0.85 0.13 0.00
128_L 115_Q 0.84 0.13 0.00
77_L 23_P 0.84 0.13 0.00
171_G 17_L 0.84 0.13 0.00
99_K 29_L 0.84 0.13 0.00
139_T 19_A 0.84 0.13 0.00
85_M 61_A 0.84 0.13 0.00
130_Q 107_E 0.84 0.13 0.00
164_A 157_L 0.84 0.13 0.00
209_E 70_A 0.84 0.13 0.00
90_M 130_I 0.83 0.13 0.00
55_L 59_C 0.83 0.13 0.00
95_S 110_A 0.83 0.13 0.00
177_K 26_D 0.82 0.13 0.00
178_G 111_V 0.82 0.12 0.00
210_P 162_D 0.82 0.12 0.00
59_L 160_L 0.82 0.12 0.00
223_A 131_R 0.82 0.12 0.00
200_P 168_E 0.82 0.12 0.00
160_I 46_L 0.81 0.12 0.00
236_I 30_A 0.81 0.12 0.00
140_L 88_K 0.81 0.12 0.00
234_G 124_L 0.81 0.12 0.00
230_R 103_V 0.81 0.12 0.00
156_A 131_R 0.81 0.12 0.00
189_A 61_A 0.80 0.12 0.00
60_C 29_L 0.80 0.12 0.00
174_A 165_G 0.80 0.12 0.00
130_Q 159_T 0.80 0.12 0.00
234_G 159_T 0.80 0.12 0.00
244_R 151_F 0.80 0.12 0.00
75_D 17_L 0.79 0.12 0.00
165_A 128_G 0.79 0.12 0.00
70_I 56_E 0.79 0.12 0.00
96_S 107_E 0.79 0.12 0.00
90_M 145_F 0.79 0.12 0.00
223_A 87_S 0.79 0.12 0.00
70_I 97_V 0.79 0.12 0.00
70_I 145_F 0.79 0.12 0.00
79_D 47_R 0.79 0.12 0.00
102_D 56_E 0.79 0.12 0.00
229_V 111_V 0.78 0.11 0.00
65_S 13_I 0.78 0.11 0.00
216_G 103_V 0.78 0.11 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)

ID Seq/Len Name Options I_Prob Status
6884 0 TLE Δgene:(1, 20) A:(1E-10, 1) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
6883 0 TLE Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
6872 0.43 TLE Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.00 Done - Shared

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