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OPENSEQ.org
Vladimir
Genes: A B A+B
Length: 96 26 119
Sequences: 1446 514 90
Seq/Len: 15.06 19.77 0.76
MirrorTree (Pazo et al. 2001) 0.09
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 0.06 0.06 0.01
2 0.06 0.06 0.01
5 0.06 0.06 0.02
10 0.06 0.06 0.04
20 0.06 0.07 0.07
100 0.07 0.09 0.18
∞ 0.10 0.10 0.74
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
32_F 18_T 1.32 0.55 0.00
28_T 25_E 1.32 0.55 0.00
95_I 25_E 1.28 0.51 0.00
9_I 21_D 1.21 0.45 0.00
50_F 12_R 1.16 0.41 0.00
27_D 5_R 1.16 0.41 0.00
30_I 20_E 1.16 0.41 0.00
21_P 25_E 1.14 0.39 0.00
49_S 2_D 1.09 0.35 0.00
26_N 22_L 1.01 0.29 0.00
44_T 9_D 1.01 0.29 0.00
75_D 8_Y 0.97 0.27 0.00
14_R 9_D 0.95 0.25 0.00
60_Y 5_R 0.94 0.24 0.00
83_P 10_G 0.94 0.24 0.00
86_L 8_Y 0.93 0.24 0.00
76_K 9_D 0.92 0.23 0.00
72_T 2_D 0.91 0.23 0.00
76_K 24_M 0.91 0.22 0.00
85_N 15_A 0.90 0.22 0.00
63_V 21_D 0.89 0.21 0.00
81_F 20_E 0.88 0.21 0.00
54_N 25_E 0.88 0.21 0.00
18_T 5_R 0.86 0.20 0.00
40_S 23_D 0.86 0.19 0.00
73_Q 16_D 0.85 0.19 0.00
34_M 1_M 0.85 0.19 0.00
49_S 26_D 0.84 0.19 0.00
13_V 3_S 0.84 0.19 0.00
8_N 26_D 0.84 0.18 0.00
63_V 23_D 0.82 0.18 0.00
65_R 13_I 0.81 0.17 0.00
54_N 23_D 0.79 0.16 0.00
68_K 4_L 0.79 0.16 0.00
24_W 24_M 0.79 0.16 0.00
9_I 12_R 0.77 0.15 0.00
14_R 22_L 0.77 0.15 0.00
73_Q 17_Q 0.76 0.15 0.00
14_R 26_D 0.76 0.15 0.00
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
6391 0.76 Vladimir Δgene:(1, ∞) A:(1E-06, 2) B:(1E-06, 2) msa: HHblits (2015_06) 0.00 Done - Shared
6390 0.18 Vladimir Δgene:(1, 100) A:(1E-06, 2) B:(1E-06, 2) msa: HHblits (2015_06) Killed - Shared
6389 0.05 Ulp1_425_520 and smt3_61_86 Δgene:(1, 20) A:(1E-10, 2) B:(1E-10, 2) msa: HHblits (2015_06) Killed - Shared
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