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OPENSEQ.org
D1_GI1
Genes: A B A+B
Length: 446 354 742
Sequences: 629 1852 89
Seq/Len: 1.41 5.23 0.12
MirrorTree (Pazo et al. 2001) 0.06
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 0.06 0.01 0.00
2 0.07 0.01 0.00
5 0.08 0.01 0.00
10 0.08 0.01 0.01
20 0.09 0.01 0.01
100 0.11 0.02 0.05
∞ 0.14 0.02 0.11
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
125_I 54_K 1.30 0.16 0.00
32_L 21_R 1.12 0.12 0.00
101_A 247_M 1.08 0.11 0.00
33_L 61_Y 1.08 0.11 0.00
75_V 24_R 1.04 0.10 0.00
62_F 146_Y 1.02 0.10 0.00
117_I 21_R 1.02 0.10 0.00
217_I 288_P 1.01 0.10 0.00
325_S 162_I 1.00 0.09 0.00
331_Y 278_I 0.99 0.09 0.00
152_V 155_Y 0.99 0.09 0.00
157_I 17_K 0.98 0.09 0.00
125_I 36_L 0.97 0.09 0.00
315_V 290_Y 0.95 0.09 0.00
179_L 107_L 0.94 0.08 0.00
278_M 278_I 0.92 0.08 0.00
200_V 56_I 0.91 0.08 0.00
33_L 54_K 0.91 0.08 0.00
264_F 162_I 0.90 0.08 0.00
296_P 333_Q 0.90 0.08 0.00
381_I 159_L 0.90 0.08 0.00
70_D 162_I 0.89 0.08 0.00
206_P 154_Y 0.88 0.07 0.00
215_T 264_I 0.88 0.07 0.00
338_R 156_L 0.88 0.07 0.00
62_F 84_I 0.87 0.07 0.00
345_L 334_F 0.87 0.07 0.00
319_F 150_D 0.87 0.07 0.00
72_L 256_N 0.87 0.07 0.00
290_I 159_L 0.86 0.07 0.00
331_Y 156_L 0.86 0.07 0.00
153_L 32_R 0.86 0.07 0.00
274_L 130_L 0.85 0.07 0.00
213_T 246_S 0.85 0.07 0.00
98_I 127_I 0.85 0.07 0.00
283_C 95_F 0.84 0.07 0.00
82_A 190_T 0.84 0.07 0.00
25_L 97_D 0.83 0.07 0.00
152_V 61_Y 0.83 0.07 0.00
276_V 77_T 0.83 0.07 0.00
149_T 290_Y 0.82 0.07 0.00
153_L 95_F 0.82 0.07 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
6053 0.12 D1_GI1 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) 0.00 Done
6051 0 D1_GI1 Δgene:(1, ∞) A:(1E-02, 2) B:(1E-02, 2) msa: HHblits (2015_06) Killed
6049 0 D1_GI1 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed
2527 0.1 D1_Gai1 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_06) Killed - Shared
2470 0.09 Set1_1 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_03) Killed
2461 0 Set1_1 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed
2459 0.03 Set1_1 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) Killed
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