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OPENSEQ.org
m1
Genes: A B A+B
Length: 460 355 754
Sequences: 558 2171 87
Seq/Len: 1.21 6.12 0.12
MirrorTree (Pazo et al. 2001) 0.10
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 0.07 0.10 0.00
2 0.07 0.10 0.00
5 0.08 0.11 0.01
10 0.09 0.11 0.01
20 0.09 0.12 0.01
100 0.10 0.14 0.03
∞ 0.13 0.17 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
35_L 20_D 1.15 0.12 0.00
154_F 247_S 1.12 0.12 0.00
379_T 247_S 1.05 0.10 0.00
376_L 171_T 1.01 0.10 0.00
178_C 184_G 1.00 0.09 0.00
67_L 155_Y 1.00 0.09 0.00
203_V 98_P 0.97 0.09 0.00
49_S 333_V 0.94 0.08 0.00
130_P 175_V 0.94 0.08 0.00
162_L 56_I 0.93 0.08 0.00
370_I 26_D 0.93 0.08 0.00
374_F 55_I 0.92 0.08 0.00
338_G 291_Y 0.91 0.08 0.00
67_L 52_Q 0.90 0.08 0.00
386_L 257_N 0.90 0.08 0.00
77_F 321_Y 0.89 0.08 0.00
67_L 273_D 0.89 0.07 0.00
120_S 334_Q 0.88 0.07 0.00
49_S 61_Y 0.87 0.07 0.00
57_K 22_N 0.87 0.07 0.00
374_F 290_E 0.86 0.07 0.00
406_L 264_S 0.86 0.07 0.00
433_L 26_D 0.85 0.07 0.00
67_L 39_L 0.85 0.07 0.00
67_L 40_G 0.85 0.07 0.00
67_L 45_G 0.85 0.07 0.00
67_L 48_T 0.85 0.07 0.00
414_N 273_D 0.85 0.07 0.00
161_I 120_L 0.85 0.07 0.00
40_V 175_V 0.85 0.07 0.00
424_A 250_L 0.84 0.07 0.00
112_S 202_V 0.84 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
7092 0.12 m1 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
6452 ACM1_GNAI_2_HUMAN_2 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b) Running - Shared
6451 0.05 ACM1_GNAI_2_HUMAN_2 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
6122 ACM1_GNAI_2_HUMAN Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) Running - Shared
6046 0.01 ACM1_GNAI_2_HUMAN Δgene:(1, 20) A:(1E-02, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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