May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
140-276
Genes: A B A+B
Length: 300 137 421
Sequences: 7484 2559 119
Seq/Len: 24.95 18.68 0.28
MirrorTree (Pazo et al. 2001) 0.12
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 0.08 0.01
2 0.04 0.09 0.02
5 0.05 0.10 0.03
10 0.06 0.11 0.04
20 0.07 0.12 0.05
100 0.13 0.13 0.14
∞ 0.22 0.16 0.27
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
189_L 109_L 1.48 0.39 0.00
30_T 65_S 1.47 0.38 0.00
144_L 119_N 1.40 0.34 0.00
55_L 58_R 1.28 0.27 0.00
63_K 53_I 1.24 0.25 0.00
19_L 65_S 1.24 0.25 0.00
78_L 94_I 1.17 0.22 0.00
74_V 83_S 1.14 0.20 0.00
55_L 62_V 1.13 0.20 0.00
232_Q 53_I 1.12 0.19 0.00
167_L 114_V 1.10 0.19 0.00
123_C 3_D 1.09 0.18 0.00
38_L 7_C 1.07 0.17 0.00
27_E 49_A 1.06 0.17 0.00
147_L 19_M 1.06 0.17 0.00
160_A 64_V 1.05 0.17 0.00
269_S 16_V 1.04 0.16 0.00
174_E 65_S 1.04 0.16 0.00
284_L 68_Y 1.04 0.16 0.00
103_Y 11_S 1.03 0.16 0.00
144_L 43_T 1.01 0.15 0.00
78_L 54_E 1.01 0.15 0.00
235_G 23_L 1.00 0.15 0.00
65_R 65_S 1.00 0.15 0.00
277_S 63_V 0.99 0.15 0.00
102_L 106_P 0.98 0.14 0.00
38_L 116_D 0.97 0.14 0.00
161_C 63_V 0.96 0.14 0.00
70_L 90_Q 0.96 0.14 0.00
248_L 70_Q 0.95 0.13 0.00
258_I 63_V 0.95 0.13 0.00
116_C 16_V 0.94 0.13 0.00
189_L 62_V 0.94 0.13 0.00
56_G 68_Y 0.93 0.13 0.00
186_V 65_S 0.93 0.13 0.00
264_L 6_I 0.93 0.13 0.00
167_L 107_S 0.93 0.13 0.00
227_N 11_S 0.91 0.12 0.00
80_H 102_K 0.91 0.12 0.00
263_S 4_A 0.91 0.12 0.00
19_L 7_C 0.90 0.12 0.00
108_T 110_R 0.90 0.12 0.00
280_A 5_F 0.90 0.12 0.00
119_A 7_C 0.89 0.12 0.00
211_G 112_I 0.89 0.12 0.00
72_R 61_V 0.89 0.12 0.00
31_R 65_S 0.89 0.12 0.00
19_L 71_S 0.89 0.12 0.00
102_L 48_I 0.89 0.12 0.00
148_A 46_W 0.89 0.12 0.00
252_T 96_I 0.89 0.12 0.00
268_V 65_S 0.89 0.12 0.00
107_R 95_P 0.88 0.12 0.00
286_L 107_S 0.88 0.11 0.00
60_N 61_V 0.88 0.11 0.00
60_N 8_Y 0.87 0.11 0.00
55_L 9_C 0.87 0.11 0.00
164_V 87_G 0.86 0.11 0.00
26_P 61_V 0.86 0.11 0.00
286_L 3_D 0.86 0.11 0.00
111_A 116_D 0.85 0.11 0.00
283_A 70_Q 0.85 0.11 0.00
207_D 65_S 0.85 0.11 0.00
144_L 113_T 0.85 0.11 0.00
78_L 23_L 0.85 0.11 0.00
74_V 3_D 0.84 0.10 0.00
37_L 61_V 0.84 0.10 0.00
223_L 63_V 0.84 0.10 0.00
43_V 7_C 0.84 0.10 0.00
58_I 121_C 0.84 0.10 0.00
72_R 110_R 0.84 0.10 0.00
213_G 82_L 0.83 0.10 0.00
192_S 6_I 0.83 0.10 0.00
198_F 96_I 0.83 0.10 0.00
81_M 61_V 0.83 0.10 0.00
19_L 5_F 0.83 0.10 0.00
260_A 68_Y 0.83 0.10 0.00
102_L 62_V 0.83 0.10 0.00
144_L 63_V 0.83 0.10 0.00
65_R 113_T 0.83 0.10 0.00
103_Y 64_V 0.82 0.10 0.00
106_R 10_P 0.82 0.10 0.00
152_E 51_E 0.82 0.10 0.00
276_K 63_V 0.81 0.10 0.00
83_K 20_I 0.81 0.10 0.00
164_V 116_D 0.80 0.10 0.00
43_V 51_E 0.80 0.09 0.00
120_L 33_C 0.80 0.09 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
7549 0.3 140-276 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
7540 0.28 140-276 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-02, 8) msa: HHblits (2015_06) 0.00 Done - Shared
Page generated in 0.6015 seconds.