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OPENSEQ.org
Nm33toNf5 t2
Genes: A B A+B
Length: 54 97 142
Sequences: 1136 9385 185
Seq/Len: 21.04 96.75 1.3
MirrorTree (Pazo et al. 2001) 0.15
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 0.09 0.07 0.09
2 0.10 0.08 0.17
5 0.10 0.09 0.23
10 0.10 0.10 0.33
20 0.10 0.11 0.47
100 0.13 0.13 0.85
∞ 0.16 0.16 1.23
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
45_W 58_L 1.31 0.70 0.01
29_K 62_V 1.21 0.60 0.01
42_V 61_L 1.14 0.54 0.01
44_Y 18_T 1.14 0.54 0.01
45_W 11_S 1.10 0.50 0.01
44_Y 81_R 1.08 0.48 0.00
53_R 64_G 1.08 0.48 0.00
35_R 75_V 1.03 0.43 0.00
26_C 71_Y 1.00 0.40 0.00
28_C 71_Y 1.00 0.40 0.00
37_C 71_Y 1.00 0.40 0.00
40_C 71_Y 1.00 0.40 0.00
23_N 92_G 0.99 0.39 0.00
20_D 52_N 0.93 0.34 0.00
29_K 16_R 0.93 0.33 0.00
32_V 96_E 0.90 0.31 0.00
8_S 23_S 0.89 0.31 0.00
29_K 61_L 0.89 0.30 0.00
3_C 71_Y 0.89 0.30 0.00
26_C 19_W 0.87 0.29 0.00
28_C 19_W 0.87 0.29 0.00
37_C 19_W 0.87 0.29 0.00
40_C 19_W 0.87 0.29 0.00
44_Y 63_T 0.87 0.29 0.00
36_R 45_P 0.87 0.28 0.00
48_G 23_S 0.86 0.28 0.00
51_G 53_A 0.85 0.27 0.00
3_C 69_T 0.85 0.27 0.00
45_W 39_R 0.83 0.26 0.00
21_P 17_I 0.83 0.25 0.00
17_T 24_L 0.82 0.25 0.00
33_A 15_I 0.82 0.25 0.00
7_G 19_W 0.81 0.24 0.00
54_P 55_A 0.80 0.24 0.00
53_R 45_P 0.80 0.23 0.00
3_C 94_T 0.80 0.23 0.00
36_R 24_L 0.80 0.23 0.00
29_K 21_D 0.80 0.23 0.00
7_G 84_S 0.79 0.22 0.00
20_D 18_T 0.78 0.22 0.00
33_A 62_V 0.78 0.22 0.00
8_S 51_K 0.77 0.21 0.00
19_C 94_T 0.75 0.20 0.00
29_K 25_P 0.75 0.20 0.00
54_P 13_D 0.75 0.20 0.00
8_S 77_V 0.74 0.20 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
6302 1.3 Nm33toNf5 t2 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.01 Done - Shared
6301 1.27 Nm33toNf5 t1 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) 0.01 Done - Shared
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