May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
spP316342-135 trA0A088SGM1
Genes: A B A+B
Length: 134 887 975
Sequences: 3112 5863 2298
Seq/Len: 23.22 6.61 2.36
MirrorTree (Pazo et al. 2001) 0.80
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 0.03 0.00 0.01
2 0.03 0.00 0.09
5 0.03 0.00 0.35
10 0.03 0.00 2.25
20 0.03 0.00 2.25
100 0.03 0.00 2.25
∞ 0.03 0.00 2.25
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
112_G 745_I 1.27 0.82 0.10
65_P 37_N 1.24 0.81 0.09
33_V 780_L 1.20 0.77 0.08
57_Q 856_A 1.20 0.77 0.08
93_V 760_E 1.17 0.75 0.07
71_S 749_Q 1.13 0.71 0.07
57_Q 14_L 1.10 0.68 0.06
106_H 454_K 1.08 0.66 0.06
29_M 884_L 1.07 0.65 0.05
106_H 855_S 1.02 0.59 0.05
112_G 780_L 1.01 0.59 0.04
83_V 519_N 1.00 0.58 0.04
11_K 744_P 0.98 0.55 0.04
106_H 451_K 0.97 0.54 0.04
48_S 495_A 0.96 0.53 0.04
29_M 754_K 0.96 0.53 0.04
27_K 884_L 0.95 0.51 0.04
71_S 745_I 0.94 0.50 0.04
83_V 365_V 0.93 0.49 0.03
112_G 14_L 0.92 0.48 0.03
78_F 3_C 0.92 0.47 0.03
75_K 663_L 0.91 0.47 0.03
57_Q 774_I 0.91 0.47 0.03
108_V 18_L 0.91 0.47 0.03
45_L 744_P 0.90 0.46 0.03
85_W 746_H 0.90 0.46 0.03
45_L 827_E 0.90 0.46 0.03
78_F 876_R 0.90 0.45 0.03
33_V 747_K 0.89 0.45 0.03
8_S 15_V 0.89 0.45 0.03
111_T 13_L 0.89 0.45 0.03
94_K 744_P 0.89 0.44 0.03
78_F 365_V 0.89 0.44 0.03
83_V 694_S 0.89 0.44 0.03
74_L 604_I 0.88 0.44 0.03
78_F 378_K 0.88 0.44 0.03
71_S 780_L 0.88 0.43 0.03
129_G 208_K 0.88 0.43 0.03
71_S 14_L 0.88 0.43 0.03
33_V 745_I 0.88 0.43 0.03
45_L 764_R 0.88 0.43 0.03
57_Q 18_L 0.88 0.43 0.03
106_H 856_A 0.88 0.43 0.03
6_V 693_T 0.87 0.42 0.03
6_V 755_E 0.86 0.41 0.03
86_C 459_P 0.86 0.41 0.03
66_L 37_N 0.83 0.38 0.02
80_T 693_T 0.83 0.38 0.02
74_L 333_F 0.83 0.38 0.02
111_T 415_E 0.83 0.37 0.02
57_Q 454_K 0.83 0.37 0.02
89_A 4_L 0.82 0.37 0.02
106_H 220_Q 0.82 0.37 0.02
27_K 16_S 0.82 0.37 0.02
33_V 435_R 0.82 0.37 0.02
57_Q 744_P 0.82 0.36 0.02
83_V 846_W 0.82 0.36 0.02
8_S 884_L 0.82 0.36 0.02
59_I 590_T 0.81 0.36 0.02
129_G 468_N 0.81 0.36 0.02
41_D 546_T 0.81 0.35 0.02
128_S 16_S 0.81 0.35 0.02
24_G 690_F 0.81 0.35 0.02
19_R 496_Q 0.80 0.35 0.02
111_T 229_D 0.80 0.35 0.02
45_L 843_Q 0.80 0.34 0.02
111_T 754_K 0.79 0.34 0.02
130_R 114_N 0.79 0.34 0.02
30_L 760_E 0.79 0.34 0.02
74_L 344_Q 0.79 0.34 0.02
106_H 12_L 0.79 0.33 0.02
8_S 16_S 0.79 0.33 0.02
60_L 351_G 0.79 0.33 0.02
108_V 17_V 0.79 0.33 0.02
66_L 18_L 0.78 0.33 0.02
82_C 585_E 0.78 0.33 0.02
129_G 798_W 0.78 0.33 0.02
57_Q 37_N 0.78 0.33 0.02
6_V 349_F 0.78 0.32 0.02
68_P 876_R 0.78 0.32 0.02
14_E 849_A 0.78 0.32 0.02
14_E 847_R 0.78 0.32 0.02
19_R 219_I 0.77 0.32 0.02
33_V 799_L 0.77 0.32 0.02
45_L 331_L 0.77 0.32 0.02
66_L 333_F 0.77 0.31 0.02
75_K 318_G 0.77 0.31 0.02
71_S 770_W 0.77 0.31 0.02
14_E 780_L 0.77 0.31 0.02
41_D 475_I 0.77 0.31 0.02
68_P 475_I 0.76 0.31 0.02
92_K 755_E 0.76 0.31 0.02
61_T 855_S 0.76 0.30 0.02
27_K 174_F 0.75 0.30 0.02
61_T 15_V 0.75 0.29 0.02
45_L 774_I 0.75 0.29 0.02
111_T 227_Y 0.74 0.29 0.02
71_S 884_L 0.74 0.29 0.02
29_M 301_I 0.74 0.29 0.02
53_K 760_E 0.74 0.28 0.02
111_T 798_W 0.74 0.28 0.02
81_V 313_K 0.74 0.28 0.02
29_M 836_S 0.74 0.28 0.02
71_S 39_T 0.74 0.28 0.02
8_S 831_L 0.73 0.28 0.02
75_K 121_W 0.73 0.28 0.02
71_S 836_S 0.73 0.28 0.02
57_Q 392_T 0.73 0.28 0.02
14_E 509_E 0.73 0.28 0.02
60_L 638_P 0.73 0.28 0.02
83_V 446_I 0.73 0.28 0.02
58_K 863_T 0.73 0.27 0.02
60_L 187_Y 0.72 0.27 0.02
114_A 805_T 0.72 0.27 0.02
112_G 774_I 0.72 0.27 0.02
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 0.0859 seconds.