May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cIm_K_2_cytb_2_human
Genes: A B A+B
Length: 98 378 473
Sequences: 7223 4500 3515
Seq/Len: 73.7 11.9 7.43
MirrorTree (Pazo et al. 2001) 0.66
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 0.00 0.39
2 0.00 0.00 2.92
5 0.00 0.00 5.27
10 0.00 0.00 5.57
20 0.00 0.00 5.71
100 0.01 0.00 5.95
∞ 0.04 0.00 7.38
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
66_F 322_Q 1.16 0.95 0.20
29_S 322_Q 0.83 0.70 0.07
96_L 222_P 0.81 0.68 0.07
71_A 180_T 0.80 0.67 0.06
35_G 236_I 0.78 0.64 0.06
31_L 274_F 0.73 0.57 0.05
67_A 212_T 0.73 0.56 0.05
15_S 202_E 0.72 0.55 0.05
29_S 180_T 0.71 0.54 0.04
33_L 232_L 0.70 0.52 0.04
98_C 56_S 0.70 0.52 0.04
36_M 364_I 0.70 0.52 0.04
61_I 225_T 0.69 0.51 0.04
9_M 365_L 0.69 0.49 0.04
20_L 30_W 0.68 0.49 0.04
91_H 254_D 0.67 0.46 0.04
67_A 251_G 0.67 0.46 0.04
76_A 232_L 0.66 0.46 0.04
29_S 10_L 0.66 0.45 0.04
61_I 313_Q 0.66 0.45 0.04
97_Q 129_M 0.66 0.45 0.04
77_L 338_I 0.66 0.45 0.04
76_A 164_I 0.65 0.44 0.03
45_T 361_T 0.65 0.44 0.03
61_I 254_D 0.65 0.43 0.03
61_I 80_R 0.64 0.43 0.03
85_Y 176_T 0.64 0.43 0.03
66_F 164_I 0.64 0.42 0.03
72_A 350_I 0.64 0.42 0.03
49_L 169_S 0.64 0.42 0.03
82_S 55_Y 0.63 0.41 0.03
89_Y 197_L 0.63 0.41 0.03
8_I 329_A 0.63 0.40 0.03
38_L 257_T 0.62 0.40 0.03
67_A 307_L 0.62 0.40 0.03
23_R 71_R 0.62 0.40 0.03
58_I 156_I 0.62 0.40 0.03
86_G 347_F 0.62 0.39 0.03
26_L 89_M 0.62 0.39 0.03
10_L 295_L 0.62 0.39 0.03
82_S 180_T 0.61 0.38 0.03
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
5753 7.43 cIm_K_2_cytb_2_human Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.20 Done - Shared
5751 7.22 cIm_K_4_cytb_4_human Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b) 0.04 Done - Shared
5750 0.26 cIm_K_40_cytb_40_human Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b) 0.01 Done - Shared
Page generated in 0.2393 seconds.