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OPENSEQ.org
2g38
Genes: A B A+B
Length: 99 198 287
Sequences: 405 650 202
Seq/Len: 4.09 3.28 0.7
MirrorTree (Pazo et al. 2001) 0.38
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 0.15 0.35
2 0.10 0.18 0.38
5 0.13 0.19 0.46
10 0.15 0.22 0.59
20 0.18 0.25 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
42_P 158_S 1.62 0.75 0.01
6_T 61_V 1.62 0.75 0.01
38_A 109_I 1.58 0.72 0.01
90_A 108_Q 1.33 0.53 0.01
59_A 37_E 1.22 0.43 0.01
72_V 125_L 1.20 0.42 0.00
59_A 190_S 1.19 0.41 0.00
76_F 61_V 1.18 0.40 0.00
25_A 21_P 1.17 0.39 0.00
22_R 71_F 1.13 0.36 0.00
13_V 62_M 1.12 0.36 0.00
42_P 23_S 1.10 0.34 0.00
68_A 61_V 1.06 0.31 0.00
86_K 10_V 1.06 0.31 0.00
35_M 35_D 1.03 0.29 0.00
16_T 93_V 1.03 0.29 0.00
36_T 60_V 1.02 0.28 0.00
51_A 92_I 1.01 0.27 0.00
71_V 94_R 1.00 0.27 0.00
60_R 35_D 0.99 0.27 0.00
2_S 185_P 0.99 0.26 0.00
58_Y 19_P 0.98 0.26 0.00
62_Y 65_M 0.98 0.26 0.00
69_A 27_A 0.98 0.25 0.00
66_I 90_H 0.97 0.25 0.00
39_V 36_V 0.97 0.25 0.00
76_F 41_V 0.97 0.25 0.00
29_D 14_N 0.95 0.24 0.00
62_Y 78_L 0.94 0.23 0.00
88_A 31_W 0.94 0.23 0.00
66_I 157_V 0.94 0.23 0.00
61_K 85_V 0.93 0.23 0.00
11_L 13_A 0.93 0.22 0.00
26_I 155_L 0.93 0.22 0.00
82_T 50_L 0.92 0.22 0.00
25_A 41_V 0.92 0.22 0.00
30_A 49_L 0.92 0.22 0.00
56_V 96_Y 0.91 0.21 0.00
64_Q 40_A 0.91 0.21 0.00
78_H 152_D 0.90 0.21 0.00
26_I 83_S 0.90 0.20 0.00
89_T 183_V 0.90 0.20 0.00
32_V 155_L 0.89 0.20 0.00
95_I 40_A 0.89 0.20 0.00
58_Y 96_Y 0.89 0.20 0.00
38_A 47_R 0.89 0.20 0.00
40_R 138_E 0.89 0.20 0.00
76_F 40_A 0.88 0.20 0.00
61_K 125_L 0.87 0.19 0.00
58_Y 40_A 0.87 0.19 0.00
47_V 140_D 0.87 0.19 0.00
46_L 14_N 0.87 0.19 0.00
54_F 19_P 0.86 0.19 0.00
23_D 81_Q 0.86 0.19 0.00
32_V 128_F 0.86 0.19 0.00
24_R 65_M 0.84 0.18 0.00
46_L 1_M 0.84 0.17 0.00
11_L 35_D 0.83 0.17 0.00
51_A 2_A 0.83 0.17 0.00
29_D 188_A 0.83 0.17 0.00
66_I 64_L 0.82 0.17 0.00
85_D 17_A 0.82 0.17 0.00
56_V 47_R 0.82 0.17 0.00
16_T 117_Q 0.82 0.17 0.00
19_R 24_M 0.82 0.17 0.00
16_T 23_S 0.81 0.16 0.00
5_I 40_A 0.81 0.16 0.00
82_T 10_V 0.81 0.16 0.00
60_R 120_I 0.81 0.16 0.00
27_Q 24_M 0.81 0.16 0.00
71_V 66_E 0.81 0.16 0.00
29_D 134_D 0.80 0.16 0.00
33_A 136_D 0.80 0.16 0.00
62_Y 34_L 0.79 0.15 0.00
74_E 179_L 0.79 0.15 0.00
66_I 130_A 0.79 0.15 0.00
59_A 32_R 0.79 0.15 0.00
6_T 47_R 0.79 0.15 0.00
3_F 170_P 0.79 0.15 0.00
73_L 115_E 0.79 0.15 0.00
57_E 159_D 0.79 0.15 0.00
75_E 94_R 0.79 0.15 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)
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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