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OPENSEQ.org
m1_gnaq
Genes: A B A+B
Length: 460 359 752
Sequences: 558 2174 86
Seq/Len: 1.21 6.06 0.11
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 0.09 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 26_E 1.23 0.14 0.00
154_F 251_S 1.12 0.11 0.00
379_T 251_S 1.05 0.10 0.00
376_L 175_T 1.02 0.09 0.00
67_L 159_Y 1.01 0.09 0.00
178_C 188_G 1.01 0.09 0.00
130_P 179_V 0.98 0.09 0.00
126_S 100_P 0.94 0.08 0.00
162_L 62_I 0.94 0.08 0.00
72_L 27_R 0.93 0.08 0.00
374_F 61_I 0.92 0.08 0.00
67_L 58_Q 0.92 0.08 0.00
77_F 325_Y 0.91 0.08 0.00
67_L 277_D 0.90 0.07 0.00
376_L 26_E 0.89 0.07 0.00
406_L 268_S 0.89 0.07 0.00
120_S 338_R 0.88 0.07 0.00
386_L 261_Y 0.88 0.07 0.00
49_S 67_Y 0.88 0.07 0.00
49_S 337_I 0.88 0.07 0.00
40_V 179_V 0.87 0.07 0.00
67_L 45_L 0.87 0.07 0.00
67_L 46_G 0.87 0.07 0.00
67_L 51_G 0.87 0.07 0.00
67_L 54_T 0.87 0.07 0.00
112_S 309_I 0.86 0.07 0.00
43_N 155_D 0.85 0.07 0.00
374_F 294_E 0.85 0.07 0.00
424_A 254_L 0.85 0.07 0.00
414_N 277_D 0.85 0.07 0.00
370_I 32_D 0.84 0.07 0.00
112_S 206_V 0.84 0.07 0.00
54_T 137_N 0.83 0.07 0.00
154_F 87_M 0.83 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
7094 0.11 m1_gnaq Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (r132) 0.00 Done - Shared
6120 ACM1_GNAQ_HUMAN Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2016_06b) Running - Shared
6048 0.01 ACM1_GNAQ_HUMAN Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
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