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1ggr_B_A

Genes: A B A+B
Length: 85 168 235
Sequences: 3242 2920 293
Seq/Len: 38.14 17.38 1.25
MirrorTree (Pazo et al. 2001) 0.66
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 0.41
2 0.01 0.01 0.81
5 0.01 0.02 1.02
10 0.01 0.04 1.08
20 0.01 0.05 1.16
100 0.06 0.10 1.56
0.14 0.18 3.24
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
58_G 123_D 1.35 0.72 0.01
33_I 136_T 1.23 0.62 0.01
60_V 29_E 1.20 0.58 0.01
35_V 105_R 1.10 0.49 0.01
76_H 139_V 1.08 0.47 0.01
62_T 26_L 1.07 0.46 0.01
9_T 40_V 1.07 0.46 0.01
62_T 30_I 1.03 0.42 0.00
71_Q 129_E 1.02 0.41 0.00
70_E 59_M 1.00 0.39 0.00
74_V 139_V 0.95 0.35 0.00
75_E 70_I 0.95 0.35 0.00
22_F 69_K 0.95 0.34 0.00
66_E 19_T 0.94 0.34 0.00
27_K 79_I 0.93 0.33 0.00
33_I 32_N 0.93 0.33 0.00
71_Q 147_K 0.90 0.31 0.00
25_E 61_A 0.90 0.30 0.00
35_V 24_A 0.89 0.29 0.00
16_T 88_F 0.89 0.29 0.00
11_P 97_E 0.89 0.29 0.00
43_S 46_V 0.88 0.29 0.00
57_Q 87_L 0.87 0.28 0.00
59_T 42_A 0.87 0.28 0.00
53_L 66_T 0.87 0.28 0.00
3_Q 85_V 0.84 0.26 0.00
16_T 140_I 0.82 0.24 0.00
83_E 70_I 0.82 0.24 0.00
33_I 19_T 0.82 0.24 0.00
7_T 66_T 0.81 0.23 0.00
49_K 69_K 0.81 0.23 0.00
36_T 84_G 0.81 0.23 0.00
51_Q 88_F 0.81 0.23 0.00
48_F 46_V 0.80 0.23 0.00
48_F 105_R 0.80 0.23 0.00
48_F 78_S 0.80 0.23 0.00
3_Q 134_T 0.80 0.23 0.00
51_Q 46_V 0.80 0.22 0.00
21_Q 66_T 0.79 0.22 0.00
14_L 145_E 0.79 0.22 0.00
40_K 59_M 0.77 0.21 0.00
56_T 63_V 0.77 0.21 0.00
55_L 86_E 0.77 0.21 0.00
59_T 138_V 0.77 0.21 0.00
64_S 130_K 0.77 0.20 0.00
28_G 32_N 0.77 0.20 0.00
63_I 112_R 0.76 0.20 0.00
50_L 84_G 0.76 0.20 0.00
33_I 42_A 0.76 0.20 0.00
36_T 91_F 0.75 0.20 0.00
65_A 133_S 0.75 0.20 0.00
2_F 127_L 0.75 0.20 0.00
29_F 73_T 0.75 0.20 0.00
5_E 127_L 0.75 0.19 0.00
31_S 94_D 0.75 0.19 0.00
50_L 68_G 0.74 0.19 0.00
58_G 135_L 0.74 0.19 0.00
31_S 63_V 0.74 0.19 0.00
51_Q 73_T 0.74 0.19 0.00
65_A 56_G 0.73 0.19 0.00
42_A 72_E 0.73 0.19 0.00
7_T 42_A 0.73 0.18 0.00
22_F 32_N 0.73 0.18 0.00
11_P 114_K 0.73 0.18 0.00
79_K 121_E 0.73 0.18 0.00
50_L 111_Q 0.73 0.18 0.00
64_S 29_E 0.72 0.18 0.00
16_T 78_S 0.72 0.18 0.00
27_K 89_V 0.72 0.18 0.00
34_T 153_S 0.71 0.17 0.00
39_G 138_V 0.71 0.17 0.00
81_M 23_I 0.70 0.17 0.00
47_L 72_E 0.70 0.16 0.00
53_L 79_I 0.70 0.16 0.00
50_L 67_I 0.70 0.16 0.00
46_S 133_S 0.69 0.16 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)

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