May 4, 2021 - We are working on upgrading the webserver, some pages may not work.
OPENSEQ.org
cIV_A_4_cI_A_6_Pdenitr
Genes: A B A+B
Length: 538 121 630
Sequences: 4477 4993 2208
Seq/Len: 8.32 41.26 3.5
MirrorTree (Pazo et al. 2001) 0.30
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 0.01 0.00 0.14
2 0.01 0.00 0.29
5 0.02 0.00 1.53
10 0.03 0.00 1.88
20 0.03 0.00 2.04
100 0.05 0.01 2.27
∞ 0.08 0.02 3.35
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
235_F 115_K 1.16 0.83 0.09
175_A 33_A 1.06 0.75 0.07
28_L 77_V 1.04 0.73 0.07
27_G 84_A 0.99 0.68 0.06
293_V 45_Y 0.98 0.67 0.05
289_Y 83_W 0.96 0.65 0.05
526_T 111_Y 0.93 0.61 0.05
313_T 113_W 0.90 0.57 0.04
104_I 80_L 0.90 0.57 0.04
522_P 66_V 0.89 0.56 0.04
369_V 15_L 0.88 0.55 0.04
483_S 79_F 0.87 0.53 0.04
29_I 78_A 0.85 0.51 0.04
523_P 80_L 0.85 0.51 0.04
293_V 75_L 0.84 0.50 0.04
281_F 75_L 0.83 0.48 0.03
526_T 67_S 0.83 0.48 0.03
70_L 109_F 0.82 0.47 0.03
382_L 117_A 0.81 0.46 0.03
432_H 62_R 0.80 0.44 0.03
526_T 84_A 0.79 0.43 0.03
365_F 86_S 0.78 0.42 0.03
7_F 94_A 0.77 0.41 0.03
274_I 24_V 0.77 0.41 0.03
134_L 72_I 0.77 0.41 0.03
240_F 77_V 0.77 0.40 0.03
358_L 68_I 0.77 0.40 0.03
298_A 61_V 0.76 0.39 0.03
106_A 26_I 0.76 0.39 0.03
480_S 81_F 0.76 0.39 0.03
347_W 64_Y 0.74 0.37 0.02
426_E 20_A 0.74 0.37 0.02
472_I 13_V 0.74 0.37 0.02
337_I 71_I 0.74 0.36 0.02
24_G 96_W 0.73 0.36 0.02
128_L 51_A 0.73 0.36 0.02
131_A 26_I 0.73 0.36 0.02
102_L 80_L 0.73 0.36 0.02
378_S 38_D 0.73 0.36 0.02
431_L 77_V 0.73 0.36 0.02
32_C 80_L 0.73 0.36 0.02
160_G 45_Y 0.73 0.36 0.02
36_Y 69_L 0.73 0.36 0.02
494_T 103_A 0.72 0.35 0.02
12_H 120_W 0.72 0.34 0.02
24_G 42_V 0.72 0.34 0.02
117_L 13_V 0.71 0.34 0.02
222_L 26_I 0.71 0.34 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
3350 3.54 cIV_A_2_cI_A_2_Pdenitr Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.06 Done - Shared
3349 3.53 cIV_A_6_cI_A_4_Pdenitr Δgene:(1, ∞) A:(1E-06, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.07 Done - Shared
3346 3.5 cIV_A_4_cI_A_6_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_06) 0.09 Done - Shared
3345 3.52 cIV_A_4_cI_A_4_Pdenitr Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) 0.12 Done - Shared
3344 0.52 cIV_A_4_cI_A_20_1_Pdenitr Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
Page generated in 2.4356 seconds.