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OPENSEQ.org
k8
Genes: A B A+B
Length: 329 412 738
Sequences: 5959 1583 81
Seq/Len: 18.11 3.84 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 HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.05 0.06 0.01
2 0.06 0.07 0.01
5 0.06 0.07 0.04
10 0.07 0.07 0.07
20 0.08 0.07 0.11
100 0.13 0.12 0.34
∞ 0.20 0.16 0.78
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
61_V 93_D 1.51 0.22 0.00
277_I 232_L 1.26 0.14 0.00
324_A 110_V 1.22 0.13 0.00
325_K 39_V 1.18 0.12 0.00
3_M 88_I 1.08 0.10 0.00
189_H 173_C 1.07 0.10 0.00
173_E 364_L 1.07 0.10 0.00
229_I 10_Q 1.06 0.10 0.00
126_S 163_T 1.06 0.10 0.00
112_L 304_A 1.04 0.10 0.00
159_V 347_A 1.03 0.10 0.00
134_V 356_A 1.01 0.09 0.00
297_Q 134_Y 1.00 0.09 0.00
206_I 163_T 1.00 0.09 0.00
248_V 196_T 0.98 0.09 0.00
112_L 248_V 0.97 0.09 0.00
169_P 163_T 0.97 0.09 0.00
92_T 144_I 0.96 0.08 0.00
70_L 364_L 0.96 0.08 0.00
206_I 304_A 0.95 0.08 0.00
297_Q 127_M 0.94 0.08 0.00
281_N 205_G 0.93 0.08 0.00
241_G 357_I 0.93 0.08 0.00
112_L 275_M 0.91 0.07 0.00
281_N 143_S 0.90 0.07 0.00
59_M 205_G 0.89 0.07 0.00
125_C 39_V 0.89 0.07 0.00
116_I 92_L 0.89 0.07 0.00
168_Q 126_L 0.89 0.07 0.00
145_N 352_S 0.89 0.07 0.00
80_T 273_N 0.89 0.07 0.00
277_I 205_G 0.88 0.07 0.00
93_H 41_V 0.88 0.07 0.00
68_P 163_T 0.88 0.07 0.00
152_R 124_S 0.88 0.07 0.00
206_I 360_A 0.87 0.07 0.00
85_G 42_D 0.87 0.07 0.00
85_G 79_G 0.87 0.07 0.00
90_G 42_D 0.87 0.07 0.00
90_G 79_G 0.87 0.07 0.00
91_K 42_D 0.87 0.07 0.00
91_K 79_G 0.87 0.07 0.00
230_D 42_D 0.87 0.07 0.00
230_D 79_G 0.87 0.07 0.00
314_T 345_Q 0.87 0.07 0.00
61_V 401_L 0.87 0.07 0.00
305_S 95_I 0.87 0.07 0.00
263_V 39_V 0.87 0.07 0.00
82_F 378_V 0.86 0.07 0.00
267_L 225_L 0.85 0.07 0.00
52_F 15_I 0.85 0.07 0.00
295_N 113_S 0.85 0.07 0.00
289_K 387_E 0.85 0.07 0.00
93_H 15_I 0.85 0.07 0.00
51_V 93_D 0.84 0.07 0.00
5_V 134_Y 0.84 0.07 0.00
127_T 48_I 0.84 0.07 0.00
279_Y 185_I 0.82 0.06 0.00
266_A 56_Y 0.82 0.06 0.00
9_V 60_F 0.82 0.06 0.00
137_E 124_S 0.82 0.06 0.00
189_H 174_A 0.81 0.06 0.00
288_L 121_G 0.81 0.06 0.00
269_N 6_I 0.81 0.06 0.00
193_V 196_T 0.81 0.06 0.00
103_G 216_R 0.81 0.06 0.00
289_K 48_I 0.81 0.06 0.00
209_R 144_I 0.81 0.06 0.00
289_K 144_I 0.81 0.06 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
5585 0.11 k8 Δgene:(1, 20) A:(1E-04, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
5584 0.11 k8 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.00 Done - Shared
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