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OPENSEQ.org
stbAB
Genes: A B A+B
Length: 196 112 301
Sequences: 2258 2806 216
Seq/Len: 11.52 25.05 0.72
MirrorTree (Pazo et al. 2001) 0.34
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 0.00 0.03 0.06
2 0.00 0.04 0.08
5 0.00 0.04 0.09
10 0.00 0.04 0.13
20 0.00 0.04 0.20
100 0.00 0.05 0.70
∞ 0.01 0.18 3.52
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
161_T 19_A 1.24 0.46 0.00
72_V 76_K 1.16 0.39 0.00
7_V 96_V 1.16 0.39 0.00
178_Q 7_I 1.14 0.38 0.00
152_I 102_I 1.14 0.38 0.00
21_Y 99_V 1.11 0.36 0.00
165_M 108_D 1.08 0.33 0.00
89_N 102_I 1.08 0.33 0.00
72_V 7_I 1.07 0.32 0.00
95_I 108_D 1.06 0.32 0.00
26_D 63_I 1.06 0.32 0.00
172_D 7_I 1.05 0.31 0.00
177_G 95_P 1.03 0.29 0.00
61_G 27_G 1.02 0.29 0.00
39_E 74_I 1.02 0.29 0.00
168_Q 4_V 1.02 0.28 0.00
88_G 4_V 1.00 0.28 0.00
83_Y 29_T 0.96 0.25 0.00
92_Q 97_D 0.93 0.23 0.00
26_D 100_I 0.91 0.22 0.00
97_R 102_I 0.91 0.22 0.00
64_A 16_V 0.90 0.21 0.00
77_N 95_P 0.90 0.21 0.00
112_F 95_P 0.89 0.20 0.00
60_L 27_G 0.87 0.20 0.00
156_P 65_V 0.86 0.19 0.00
64_A 14_D 0.86 0.19 0.00
9_T 63_I 0.85 0.18 0.00
177_G 71_E 0.85 0.18 0.00
133_C 96_V 0.84 0.18 0.00
187_L 93_V 0.84 0.18 0.00
144_T 4_V 0.84 0.18 0.00
87_Y 64_V 0.84 0.18 0.00
182_L 91_I 0.83 0.17 0.00
117_A 95_P 0.83 0.17 0.00
47_E 45_R 0.82 0.17 0.00
115_A 81_A 0.81 0.17 0.00
39_E 100_I 0.81 0.17 0.00
64_A 29_T 0.81 0.16 0.00
137_I 85_E 0.81 0.16 0.00
108_R 25_I 0.80 0.16 0.00
12_P 40_K 0.80 0.16 0.00
114_C 31_S 0.80 0.16 0.00
43_E 52_T 0.79 0.16 0.00
82_L 16_V 0.79 0.16 0.00
8_A 24_G 0.78 0.15 0.00
10_G 68_H 0.78 0.15 0.00
127_L 110_E 0.78 0.15 0.00
31_L 79_A 0.77 0.15 0.00
162_F 54_E 0.77 0.15 0.00
126_A 102_I 0.77 0.15 0.00
53_A 2_K 0.76 0.14 0.00
73_V 93_V 0.76 0.14 0.00
123_G 85_E 0.75 0.14 0.00
30_Q 73_V 0.75 0.14 0.00
115_A 75_E 0.75 0.14 0.00
159_R 80_A 0.74 0.14 0.00
102_L 46_Y 0.74 0.14 0.00
60_L 96_V 0.74 0.14 0.00
16_Q 25_I 0.74 0.14 0.00
43_E 73_V 0.74 0.13 0.00
165_M 99_V 0.74 0.13 0.00
37_D 8_I 0.74 0.13 0.00
56_V 18_I 0.73 0.13 0.00
97_R 112_I 0.73 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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