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OPENSEQ.org
D1_1B
Genes: A B A+B
Length: 100 125 207
Sequences: 1203 283 52
Seq/Len: 12.03 2.26 0.25
MirrorTree (Pazo et al. 2001) 0.21
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 0.04 0.05 0.00
2 0.04 0.05 0.00
5 0.04 0.05 0.00
10 0.04 0.05 0.00
20 0.04 0.05 0.00
100 0.06 0.05 0.04
∞ 0.10 0.05 0.23
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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
13_Y 4_V 1.90 0.62 0.01
48_G 72_D 1.41 0.32 0.00
47_I 26_E 1.26 0.24 0.00
37_L 73_L 1.26 0.24 0.00
55_K 111_Q 1.22 0.22 0.00
75_A 2_I 1.22 0.22 0.00
51_A 32_N 1.22 0.22 0.00
89_F 4_V 1.16 0.20 0.00
80_K 7_D 1.05 0.16 0.00
48_G 73_L 1.04 0.15 0.00
49_G 4_V 1.03 0.15 0.00
35_L 62_I 1.01 0.14 0.00
51_A 34_I 1.00 0.14 0.00
89_F 71_R 1.00 0.14 0.00
8_L 27_I 0.98 0.14 0.00
66_L 57_D 0.97 0.13 0.00
55_K 109_V 0.95 0.12 0.00
90_E 4_V 0.94 0.12 0.00
16_F 31_D 0.94 0.12 0.00
52_Q 87_R 0.91 0.12 0.00
26_S 37_T 0.91 0.12 0.00
92_K 71_R 0.90 0.11 0.00
23_P 30_L 0.90 0.11 0.00
50_L 51_M 0.90 0.11 0.00
21_G 89_A 0.90 0.11 0.00
81_Q 62_I 0.89 0.11 0.00
90_E 69_Q 0.86 0.10 0.00
41_Y 88_R 0.86 0.10 0.00
81_Q 92_Y 0.86 0.10 0.00
59_W 58_P 0.85 0.10 0.00
59_W 68_S 0.85 0.10 0.00
85_Y 94_Q 0.85 0.10 0.00
14_L 7_D 0.85 0.10 0.00
30_V 26_E 0.85 0.10 0.00
53_V 4_V 0.84 0.10 0.00
37_L 61_F 0.84 0.10 0.00
63_A 87_R 0.84 0.10 0.00
34_P 8_D 0.84 0.10 0.00
16_F 110_Q 0.83 0.10 0.00
88_A 85_E 0.82 0.09 0.00
32_K 16_S 0.82 0.09 0.00
38_F 2_I 0.81 0.09 0.00
86_L 4_V 0.81 0.09 0.00
24_V 28_A 0.79 0.09 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
6475 0.25 D1_1B Δgene:(0, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) 0.01 Done - Shared
6474 0 D1_1B Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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