May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
Ftype_a_c_trunc
Genes: A B A+B
Length: 226 31 253
Sequences: 5369 95 206
Seq/Len: 23.76 3.06 0.81
MirrorTree (Pazo et al. 2001) 0.59
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.01 0.12
2 0.00 0.01 0.21
5 0.00 0.01 0.42
10 0.00 0.01 0.69
20 0.00 0.01 0.80
100 0.00 0.01 0.88
∞ 0.00 0.01 0.88
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
79_I 25_V 1.43 0.66 0.00
169_L 22_C 1.42 0.65 0.00
121_T 22_C 1.36 0.60 0.00
176_G 31_F 1.22 0.48 0.00
196_L 1_K 1.21 0.46 0.00
155_A 8_A 1.19 0.45 0.00
60_I 31_F 1.17 0.43 0.00
215_T 26_A 1.14 0.41 0.00
147_I 26_A 1.13 0.40 0.00
105_A 18_M 1.10 0.38 0.00
17_L 25_V 1.09 0.36 0.00
43_V 31_F 1.08 0.36 0.00
152_Q 1_K 1.08 0.36 0.00
223_H 15_S 1.08 0.36 0.00
16_G 31_F 1.08 0.36 0.00
59_S 3_Q 1.05 0.33 0.00
181_L 25_V 1.03 0.32 0.00
190_L 26_A 1.03 0.32 0.00
222_L 31_F 1.02 0.32 0.00
220_L 18_M 1.01 0.30 0.00
198_L 6_S 1.00 0.29 0.00
215_T 25_V 0.96 0.27 0.00
129_L 31_F 0.96 0.27 0.00
111_G 14_L 0.93 0.25 0.00
116_G 25_V 0.93 0.25 0.00
204_F 3_Q 0.91 0.23 0.00
136_P 1_K 0.90 0.23 0.00
212_Y 14_L 0.90 0.23 0.00
85_L 19_G 0.89 0.22 0.00
94_P 25_V 0.89 0.22 0.00
113_V 18_M 0.89 0.22 0.00
173_L 3_Q 0.88 0.22 0.00
223_H 29_I 0.84 0.19 0.00
90_H 21_F 0.83 0.19 0.00
219_S 15_S 0.83 0.19 0.00
112_A 7_Y 0.82 0.18 0.00
137_L 8_A 0.82 0.18 0.00
197_I 8_A 0.82 0.18 0.00
98_L 12_F 0.81 0.18 0.00
19_L 1_K 0.81 0.18 0.00
98_L 14_L 0.81 0.18 0.00
11_T 22_C 0.81 0.18 0.00
101_N 26_A 0.81 0.18 0.00
173_L 7_Y 0.81 0.17 0.00
52_L 1_K 0.80 0.17 0.00
73_M 18_M 0.80 0.17 0.00
35_N 1_K 0.79 0.17 0.00
18_P 26_A 0.79 0.17 0.00
170_L 24_M 0.77 0.16 0.00
95_T 29_I 0.77 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)
Page generated in 1.1011 seconds.