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OPENSEQ.org
stbAB
Genes: A B A+B
Length: 196 112 302
Sequences: 2910 2226 203
Seq/Len: 14.85 19.88 0.67
MirrorTree (Pazo et al. 2001) 0.48
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 0.00 0.02 0.07
2 0.00 0.03 0.08
5 0.00 0.03 0.08
10 0.00 0.03 0.14
20 0.00 0.03 0.18
100 0.00 0.04 0.66
∞ 0.01 0.11 3.20
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
21_Y 99_V 1.57 0.70 0.01
92_Q 63_I 1.34 0.52 0.00
88_G 4_V 1.31 0.50 0.00
9_T 22_N 1.13 0.35 0.00
152_I 102_I 1.10 0.33 0.00
88_G 7_I 1.10 0.33 0.00
82_L 4_V 1.07 0.31 0.00
97_R 102_I 1.06 0.30 0.00
57_A 86_I 1.06 0.30 0.00
139_T 65_V 1.04 0.29 0.00
95_I 108_D 1.04 0.29 0.00
83_Y 93_V 1.03 0.28 0.00
109_Q 25_I 0.99 0.26 0.00
39_E 100_I 0.98 0.25 0.00
16_Q 97_D 0.97 0.24 0.00
100_N 96_V 0.96 0.24 0.00
137_I 85_E 0.96 0.23 0.00
97_R 112_I 0.95 0.23 0.00
22_L 15_E 0.95 0.23 0.00
47_E 15_E 0.94 0.23 0.00
165_M 108_D 0.93 0.22 0.00
123_G 17_K 0.93 0.22 0.00
113_V 8_I 0.93 0.22 0.00
63_W 85_E 0.93 0.22 0.00
127_L 100_I 0.92 0.21 0.00
166_T 97_D 0.90 0.20 0.00
133_C 102_I 0.89 0.20 0.00
116_I 17_K 0.88 0.19 0.00
141_P 13_L 0.87 0.19 0.00
50_C 65_V 0.87 0.19 0.00
44_T 62_E 0.85 0.18 0.00
5_L 80_A 0.85 0.18 0.00
178_Q 99_V 0.85 0.18 0.00
182_L 100_I 0.85 0.18 0.00
115_A 8_I 0.84 0.17 0.00
177_G 99_V 0.84 0.17 0.00
13_G 10_P 0.84 0.17 0.00
51_L 34_R 0.83 0.17 0.00
25_S 98_Q 0.83 0.17 0.00
138_L 96_V 0.82 0.17 0.00
47_E 55_F 0.82 0.16 0.00
37_D 65_V 0.82 0.16 0.00
10_G 68_H 0.82 0.16 0.00
103_G 25_I 0.81 0.16 0.00
183_L 44_E 0.81 0.16 0.00
178_Q 7_I 0.81 0.16 0.00
58_K 63_I 0.80 0.15 0.00
38_I 9_R 0.80 0.15 0.00
168_Q 75_E 0.80 0.15 0.00
25_S 4_V 0.80 0.15 0.00
31_L 5_E 0.80 0.15 0.00
82_L 76_K 0.79 0.15 0.00
142_Q 61_V 0.79 0.15 0.00
45_F 41_G 0.79 0.15 0.00
97_R 108_D 0.78 0.14 0.00
104_N 68_H 0.78 0.14 0.00
24_E 112_I 0.77 0.14 0.00
3_Q 93_V 0.77 0.14 0.00
90_T 112_I 0.77 0.14 0.00
115_A 25_I 0.77 0.14 0.00
76_L 40_K 0.77 0.14 0.00
102_L 85_E 0.77 0.14 0.00
126_A 17_K 0.77 0.14 0.00
177_G 64_V 0.77 0.14 0.00
61_G 24_G 0.77 0.14 0.00
131_G 81_A 0.77 0.14 0.00
88_G 60_K 0.76 0.14 0.00
130_E 107_S 0.76 0.14 0.00
180_F 54_E 0.76 0.14 0.00
26_D 98_Q 0.76 0.14 0.00
59_G 99_V 0.75 0.13 0.00
87_Y 36_F 0.75 0.13 0.00
24_E 110_E 0.75 0.13 0.00
71_L 96_V 0.75 0.13 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
0350 0.2 stbAB Δgene:(1, 20) A:(1E-04, 4) B:(1E-04, 4) msa: HHblits (2013_03) Killed
0349 0.67 stbAB Δgene:(1, 100) A:(1E-04, 4) B:(1E-04, 4) msa: Jackhmmer (2014_03) 0.01 Done
0348 0.62 stbAB Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.00 Done - Shared
0347 0.72 stbAB Δgene:(1, 100) A:(1E-04, 4) B:(1E-04, 4) msa: HHblits (2013_03) 0.00 Done
0346 0.53 stbAB Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed
0345 3.16 stbAB Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.00 Done - Shared
0344 2.81 stbAB Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.00 Done - Shared
0343 0.14 stbAB Δgene:(1, 20) A:(1E-40, 8) B:(1E-10, 8) msa: HHblits (2013_03) Killed - Shared
0342 0.15 stbAB Δgene:(1, 20) A:(1E-20, 8) B:(1E-10, 8) msa: HHblits (2013_03) Killed - Shared
0341 0.15 stbAB Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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