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OPENSEQ.org
1b6c
Genes: A B A+B
Length: 330 107 400
Sequences: 61125 5036 412
Seq/Len: 185.23 47.07 1.03
MirrorTree (Pazo et al. 2001) 0.19
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 0.19 0.10 0.16
2 0.20 0.10 0.27
5 0.23 0.10 0.52
10 0.26 0.11 0.94
20 0.28 0.12 1.59
100 0.32 0.13 3.49
∞ 0.34 0.20 5.21
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
185_A 73_K 1.07 0.41 0.00
243_R 34_K 1.07 0.41 0.00
37_L 63_V 1.01 0.36 0.00
35_I 63_V 0.92 0.28 0.00
241_I 102_E 0.91 0.28 0.00
284_I 53_Q 0.91 0.27 0.00
213_V 106_L 0.89 0.26 0.00
308_N 78_P 0.87 0.24 0.00
46_F 81_A 0.84 0.23 0.00
108_L 45_P 0.83 0.22 0.00
88_N 71_R 0.83 0.22 0.00
75_E 71_R 0.80 0.20 0.00
130_E 104_L 0.80 0.20 0.00
235_G 57_R 0.78 0.19 0.00
177_C 93_P 0.77 0.18 0.00
114_E 44_K 0.77 0.18 0.00
134_K 50_L 0.76 0.18 0.00
90_L 13_R 0.76 0.18 0.00
239_W 101_V 0.76 0.18 0.00
131_G 71_R 0.75 0.17 0.00
262_V 78_P 0.74 0.17 0.00
241_I 8_S 0.73 0.16 0.00
52_G 75_T 0.73 0.16 0.00
41_I 4_V 0.72 0.16 0.00
41_I 102_E 0.71 0.15 0.00
325_L 96_T 0.70 0.15 0.00
41_I 47_K 0.70 0.15 0.00
128_T 11_D 0.70 0.15 0.00
310_A 64_A 0.69 0.14 0.00
118_L 1_G 0.69 0.14 0.00
139_T 54_E 0.69 0.14 0.00
124_R 106_L 0.69 0.14 0.00
122_L 81_A 0.69 0.14 0.00
66_S 78_P 0.69 0.14 0.00
167_K 38_S 0.69 0.14 0.00
89_I 58_G 0.68 0.14 0.00
159_I 86_G 0.68 0.14 0.00
54_W 100_D 0.68 0.14 0.00
127_V 43_N 0.68 0.14 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
8696 0.88 16 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
4726 1.03 1b6c Δgene:(1, 10) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) 0.00 Done - Shared
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