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pengfei

Genes: A B A+B
Length: 317 153 464
Sequences: 2593 1996 192
Seq/Len: 8.18 13.05 0.41
MirrorTree (Pazo et al. 2001) 0.29
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 0.11 0.33 0.08
2 0.13 0.35 0.11
5 0.15 0.39 0.14
10 0.16 0.40 0.18
20 0.16 0.41 0.21
100 0.17 0.43 0.31
0.21 0.48 0.41
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
304_L 48_S 1.50 0.50 0.00
48_V 45_A 1.43 0.45 0.00
15_Y 37_L 1.32 0.37 0.00
15_Y 22_A 1.21 0.30 0.00
18_L 139_L 1.20 0.29 0.00
148_V 107_A 1.20 0.29 0.00
48_V 89_A 1.17 0.28 0.00
240_I 139_L 1.15 0.27 0.00
162_V 6_I 1.14 0.26 0.00
240_I 131_Q 1.11 0.24 0.00
55_L 54_K 1.09 0.23 0.00
22_V 52_T 1.08 0.23 0.00
25_A 82_A 1.03 0.21 0.00
18_L 105_A 1.03 0.20 0.00
130_Y 111_G 1.03 0.20 0.00
67_I 89_A 1.03 0.20 0.00
240_I 18_L 1.02 0.20 0.00
35_I 22_A 1.01 0.20 0.00
230_V 121_G 0.99 0.19 0.00
143_Y 93_L 0.99 0.18 0.00
228_R 149_L 0.97 0.18 0.00
62_M 59_L 0.96 0.17 0.00
186_R 38_G 0.95 0.17 0.00
230_V 101_L 0.93 0.16 0.00
181_V 35_K 0.93 0.16 0.00
66_T 16_P 0.93 0.16 0.00
234_S 22_A 0.93 0.16 0.00
20_E 130_H 0.91 0.15 0.00
202_I 102_N 0.91 0.15 0.00
155_I 71_R 0.91 0.15 0.00
55_L 152_G 0.90 0.15 0.00
237_G 92_F 0.89 0.15 0.00
20_E 89_A 0.89 0.14 0.00
181_V 82_A 0.87 0.14 0.00
48_V 91_Q 0.86 0.14 0.00
25_A 30_A 0.85 0.13 0.00
67_I 73_E 0.85 0.13 0.00
17_T 83_I 0.85 0.13 0.00
228_R 118_S 0.85 0.13 0.00
168_L 78_N 0.84 0.13 0.00
251_D 59_L 0.84 0.13 0.00
269_A 57_A 0.84 0.13 0.00
156_F 139_L 0.84 0.13 0.00
234_S 58_S 0.83 0.13 0.00
249_D 83_I 0.83 0.13 0.00
143_Y 148_N 0.83 0.12 0.00
85_L 136_L 0.83 0.12 0.00
229_T 32_K 0.83 0.12 0.00
181_V 42_I 0.83 0.12 0.00
55_L 26_D 0.83 0.12 0.00
184_Q 105_A 0.81 0.12 0.00
240_I 45_A 0.81 0.12 0.00
143_Y 58_S 0.81 0.12 0.00
28_K 54_K 0.81 0.12 0.00
17_T 88_Q 0.81 0.12 0.00
50_S 6_I 0.80 0.12 0.00
48_V 90_K 0.80 0.12 0.00
258_Y 143_V 0.79 0.11 0.00
181_V 135_K 0.79 0.11 0.00
37_V 148_N 0.79 0.11 0.00
229_T 108_A 0.79 0.11 0.00
163_F 97_D 0.79 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)

WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.48 > 0.4) of paralogs.

ID Seq/Len Name Options I_Prob Status
8229 0.41 pengfei Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
8081 0.24 pengfei Δgene:(1, 20) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (r132) 0.00 Done
8066 0.21 tt Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done
8065 0.27 tt Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
8064 0.22 test Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done
8063 0.26 ss Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (r132) 0.00 Done - Shared

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