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OPENSEQ.org
2g38
Genes: A B A+B
Length: 99 198 289
Sequences: 405 580 295
Seq/Len: 4.09 2.93 1.02
MirrorTree (Pazo et al. 2001) 0.21
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 0.16 0.35
2 0.10 0.19 0.38
5 0.13 0.20 0.46
10 0.15 0.23 0.59
20 0.18 0.26 0.68
100 0.25 0.32 0.97
∞ 0.27 0.37 0.99
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. Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on HHsearch results which uses the overall probability and per-site alignment confidence. Inter-chain contacts in the pdb are in shades of red. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
38_A 109_I 1.61 0.83 0.08
42_P 158_S 1.55 0.80 0.07
25_A 21_P 1.44 0.73 0.05
90_A 108_Q 1.31 0.63 0.04
36_T 60_V 1.28 0.60 0.03
16_T 23_S 1.21 0.53 0.03
56_V 47_R 1.17 0.50 0.02
16_T 93_V 1.14 0.47 0.02
23_D 81_Q 1.13 0.46 0.02
66_I 90_H 1.05 0.39 0.01
46_L 71_F 1.04 0.38 0.01
74_E 179_L 1.00 0.35 0.01
6_T 61_V 1.00 0.34 0.01
78_H 152_D 0.99 0.34 0.01
62_Y 134_D 0.98 0.33 0.01
60_R 46_N 0.98 0.33 0.01
17_E 29_R 0.98 0.33 0.01
29_D 166_P 0.97 0.32 0.01
82_T 10_V 0.96 0.31 0.01
79_A 50_L 0.96 0.31 0.01
43_A 10_V 0.95 0.30 0.01
21_I 60_V 0.94 0.30 0.01
3_F 157_V 0.94 0.30 0.01
40_R 138_E 0.94 0.29 0.01
94_N 160_A 0.94 0.29 0.01
62_Y 78_L 0.92 0.28 0.01
11_L 79_C 0.92 0.28 0.01
60_R 109_I 0.91 0.27 0.01
35_M 35_D 0.91 0.27 0.01
76_F 61_V 0.90 0.26 0.01
41_P 130_A 0.89 0.26 0.01
73_L 14_N 0.89 0.26 0.01
16_T 61_V 0.88 0.25 0.01
4_V 160_A 0.88 0.25 0.01
62_Y 65_M 0.88 0.25 0.01
67_A 69_K 0.88 0.25 0.01
59_A 155_L 0.87 0.24 0.01
16_T 117_Q 0.85 0.23 0.01
61_K 125_L 0.85 0.23 0.01
53_T 76_T 0.85 0.23 0.01
54_F 19_P 0.84 0.23 0.01
22_R 71_F 0.84 0.22 0.01
39_V 179_L 0.84 0.22 0.01
39_V 46_N 0.84 0.22 0.01
24_R 33_S 0.84 0.22 0.01
2_S 185_P 0.83 0.22 0.01
42_P 111_N 0.83 0.22 0.01
42_P 23_S 0.83 0.21 0.01
81_T 191_R 0.82 0.21 0.01
88_A 83_S 0.82 0.21 0.01
59_A 167_W 0.82 0.21 0.01
42_P 66_E 0.82 0.21 0.01
58_Y 40_A 0.81 0.21 0.01
47_V 104_V 0.81 0.21 0.01
76_F 41_V 0.81 0.20 0.01
71_V 66_E 0.81 0.20 0.01
47_V 140_D 0.81 0.20 0.01
77_A 37_E 0.81 0.20 0.01
6_T 140_D 0.80 0.20 0.01
10_A 162_S 0.80 0.20 0.01
6_T 129_T 0.79 0.20 0.01
39_V 57_A 0.79 0.20 0.01
24_R 65_M 0.79 0.19 0.01
64_Q 138_E 0.79 0.19 0.01
5_I 152_D 0.78 0.19 0.01
59_A 21_P 0.78 0.19 0.01
81_T 98_W 0.77 0.18 0.01
56_V 165_T 0.77 0.18 0.01
78_H 14_N 0.77 0.18 0.01
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)
HHsearch results
2g38BD:ACContact Map
4i0xAKEIGC:BJHDFL:BJHDFLContact Map
ID Seq/Len Name Options I_Prob Status
0177 0.7 2g38 Δgene:(1, 20) A:(1E-10, 4) B:(1E-10, 4) msa: Jackhmmer (2014_03) 0.01 Done
0176 1.02 2g38 Δgene:(0, ∞) A:(1E-10, 4) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.08 Done
0175 0.7 2g38 Δgene:(1, 20) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.03 Done
0174 0.7 2g38 Δgene:(1, 20) A:(1E-10, 4) B:(1E-20, 8) msa: Jackhmmer (2014_03) 0.06 Done - Shared
0173 0 2g38 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
0172 0.49 2g38 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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