May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cI_A_10_cIII_isp_20_Pdenitr
Genes: A B A+B
Length: 147 190 303
Sequences: 3460 1043 300
Seq/Len: 23.54 5.49 0.99
MirrorTree (Pazo et al. 2001) 0.38
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 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.00
10 0.01 0.01 0.01
20 0.01 0.01 0.02
100 0.01 0.01 0.09
∞ 0.02 0.02 0.89
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
33_G 176_I 1.87 0.93 0.54
20_L 58_V 1.52 0.78 0.28
16_F 131_V 1.35 0.65 0.17
24_I 58_V 1.35 0.65 0.17
124_D 19_L 1.29 0.60 0.14
98_V 38_L 1.24 0.56 0.12
29_L 31_A 1.22 0.53 0.11
124_D 33_A 1.20 0.52 0.10
23_A 125_W 1.18 0.50 0.10
24_I 124_E 1.18 0.50 0.10
94_E 22_A 1.13 0.45 0.08
108_F 32_G 1.11 0.44 0.08
25_G 31_A 1.10 0.43 0.07
22_V 92_V 1.09 0.42 0.07
16_F 42_M 1.09 0.41 0.07
71_V 59_S 1.07 0.40 0.07
108_F 48_V 1.06 0.39 0.06
18_I 42_M 1.05 0.38 0.06
117_L 156_G 1.05 0.38 0.06
47_N 55_Q 1.04 0.38 0.06
115_V 35_A 1.03 0.36 0.06
35_W 41_Q 1.02 0.35 0.05
100_F 78_I 1.01 0.34 0.05
47_N 172_Q 1.00 0.34 0.05
115_V 18_F 0.98 0.33 0.05
14_W 79_R 0.97 0.31 0.04
92_I 141_G 0.97 0.31 0.04
58_G 78_I 0.97 0.31 0.04
26_L 131_V 0.96 0.31 0.04
91_S 38_L 0.96 0.31 0.04
90_T 159_Y 0.96 0.30 0.04
115_V 105_S 0.95 0.30 0.04
38_G 168_G 0.95 0.29 0.04
32_V 101_S 0.94 0.29 0.04
33_G 36_W 0.94 0.29 0.04
90_T 187_I 0.94 0.29 0.04
112_A 86_I 0.93 0.28 0.04
124_D 62_E 0.93 0.28 0.04
29_L 41_Q 0.91 0.27 0.03
34_G 47_D 0.90 0.26 0.03
33_G 29_V 0.89 0.26 0.03
115_V 83_E 0.89 0.25 0.03
17_A 142_D 0.88 0.25 0.03
77_I 30_A 0.88 0.25 0.03
50_F 166_R 0.88 0.24 0.03
44_R 22_A 0.88 0.24 0.03
23_A 159_Y 0.87 0.24 0.03
105_I 162_S 0.87 0.24 0.03
21_I 87_Q 0.87 0.24 0.03
37_L 140_I 0.87 0.24 0.03
56_S 185_T 0.86 0.23 0.03
39_G 98_I 0.86 0.23 0.03
88_W 71_W 0.86 0.23 0.03
29_L 47_D 0.86 0.23 0.03
44_R 59_S 0.86 0.23 0.03
40_R 19_L 0.85 0.23 0.03
37_L 112_A 0.84 0.22 0.03
95_S 34_A 0.84 0.22 0.02
35_W 72_L 0.83 0.21 0.02
117_L 50_A 0.83 0.21 0.02
82_A 23_T 0.82 0.21 0.02
72_A 53_S 0.82 0.21 0.02
34_G 45_S 0.82 0.21 0.02
82_A 52_A 0.82 0.21 0.02
77_I 150_W 0.82 0.20 0.02
119_R 40_N 0.81 0.20 0.02
112_A 140_I 0.81 0.20 0.02
17_A 48_V 0.81 0.20 0.02
23_A 181_F 0.81 0.20 0.02
72_A 176_I 0.81 0.20 0.02
72_A 39_V 0.81 0.20 0.02
90_T 98_I 0.81 0.20 0.02
12_H 47_D 0.81 0.20 0.02
85_L 87_Q 0.80 0.20 0.02
28_C 35_A 0.80 0.20 0.02
100_F 114_D 0.80 0.20 0.02
80_V 179_A 0.80 0.20 0.02
23_A 47_D 0.80 0.19 0.02
90_T 23_T 0.80 0.19 0.02
118_V 77_F 0.79 0.19 0.02
23_A 23_T 0.79 0.19 0.02
98_V 59_S 0.79 0.19 0.02
30_M 41_Q 0.79 0.19 0.02
60_A 186_T 0.79 0.19 0.02
33_G 131_V 0.78 0.19 0.02
101_V 80_R 0.77 0.18 0.02
124_D 65_T 0.77 0.18 0.02
103_A 15_R 0.77 0.18 0.02
56_S 114_D 0.77 0.18 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)
ID Seq/Len Name Options I_Prob Status
2955 1.6 cI_A_10_cIII_isp_6_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.94 Done - Shared
2954 1.55 cI_A_6_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.97 Done - Shared
2953 1.53 cI_A_10_cIII_isp_10_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.98 Done - Shared
2952 0.99 cI_A_10_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.54 Done - Shared
2951 0.1 cI_A_40_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
2950 0.99 cI_A_20_cIII_isp_20_Pdenitr Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.35 Done - Shared
2434 1.48 cI_E_cIII_isp_6 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-06, 8) msa: Jackhmmer (2015_03) 0.97 Done - Shared
Page generated in 0.3461 seconds.