May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cI_2_10_cI_9_10_tt
Genes: A B A+B
Length: 181 182 332
Sequences: 2578 961 784
Seq/Len: 14.24 5.28 2.36
MirrorTree (Pazo et al. 2001) 0.67
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 0.01
2 0.00 0.05 0.02
5 0.01 0.05 1.60
10 0.01 0.06 1.75
20 0.02 0.06 1.79
100 0.04 0.07 1.86
∞ 0.10 0.11 2.16
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
150_L 17_L 1.27 0.82 0.10
9_D 19_S 1.06 0.64 0.05
11_L 10_L 0.94 0.51 0.04
12_E 103_L 0.93 0.49 0.04
25_A 67_A 0.92 0.48 0.03
137_N 129_L 0.89 0.45 0.03
63_V 11_G 0.88 0.43 0.03
122_V 112_A 0.87 0.42 0.03
104_L 9_S 0.85 0.40 0.03
34_V 19_S 0.84 0.39 0.03
81_Q 112_A 0.82 0.36 0.02
77_K 12_I 0.82 0.36 0.02
59_E 60_A 0.81 0.35 0.02
104_L 13_T 0.79 0.34 0.02
158_R 20_K 0.79 0.34 0.02
26_A 58_L 0.78 0.33 0.02
82_V 7_A 0.78 0.32 0.02
135_Q 112_A 0.77 0.31 0.02
55_T 15_K 0.77 0.31 0.02
61_M 91_Y 0.77 0.31 0.02
19_P 41_H 0.76 0.30 0.02
102_E 18_F 0.76 0.30 0.02
22_G 2_T 0.76 0.30 0.02
42_R 125_E 0.75 0.30 0.02
121_K 52_K 0.74 0.28 0.02
130_T 100_F 0.74 0.28 0.02
36_Q 122_A 0.74 0.28 0.02
36_Q 153_T 0.74 0.28 0.02
60_V 8_Q 0.73 0.28 0.02
138_D 127_S 0.73 0.28 0.02
127_S 17_L 0.73 0.28 0.02
144_C 120_E 0.73 0.28 0.02
112_T 134_E 0.73 0.27 0.02
85_T 95_M 0.72 0.27 0.02
93_A 73_A 0.72 0.27 0.02
119_V 13_T 0.72 0.27 0.02
172_C 7_A 0.72 0.27 0.02
21_E 134_E 0.72 0.27 0.02
5_D 7_A 0.72 0.26 0.01
57_P 12_I 0.71 0.26 0.01
96_L 135_D 0.71 0.26 0.01
24_R 153_T 0.71 0.26 0.01
79_H 70_V 0.70 0.25 0.01
134_I 24_V 0.70 0.25 0.01
6_D 17_L 0.69 0.24 0.01
75_T 133_K 0.68 0.23 0.01
156_G 152_R 0.68 0.23 0.01
101_T 22_V 0.68 0.23 0.01
86_L 129_L 0.68 0.23 0.01
28_M 131_Y 0.68 0.23 0.01
30_L 95_M 0.68 0.23 0.01
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
4944 2.24 cI_2_40_cI_9_40_tt Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
4943 2.36 cI_2_10_cI_9_10_tt Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) 0.10 Done - Shared
4938 2.49 cI_2_20_cI_9_20_tt Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.17 Done - Shared
Page generated in 0.2546 seconds.