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OPENSEQ.org
2D1P_BC
Genes: A B A+B
Length: 119 95 214
Sequences: 347 352 326
Seq/Len: 2.92 3.71 1.52
MirrorTree (Pazo et al. 2001) 0.72
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 0.00 1.52
2 0.00 0.00 1.52
5 0.00 0.00 1.52
10 0.00 0.00 1.52
20 0.00 0.00 1.52
100 0.00 0.00 1.52
∞ 0.00 0.00 1.52
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. 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
86_R 32_D 1.68 0.93 0.57
106_L 20_L 1.63 0.92 0.53
41_A 16_A 1.48 0.85 0.40
42_D 32_D 1.46 0.84 0.39
118_R 14_F 1.36 0.78 0.31
14_G 32_D 1.35 0.77 0.30
38_F 31_Q 1.25 0.70 0.23
21_G 1_M 1.24 0.68 0.22
67_L 92_Q 1.22 0.66 0.20
57_L 38_V 1.21 0.65 0.20
5_A 31_Q 1.18 0.63 0.18
60_D 61_L 1.18 0.63 0.18
45_F 25_D 1.16 0.61 0.17
45_F 54_V 1.12 0.57 0.15
60_D 75_I 1.12 0.56 0.15
86_R 8_S 1.11 0.56 0.15
46_Q 87_V 1.11 0.56 0.14
24_A 93_M 1.11 0.56 0.14
63_A 28_L 1.10 0.55 0.14
41_A 14_F 1.08 0.53 0.13
103_A 19_R 1.08 0.52 0.13
76_C 94_A 1.07 0.52 0.13
86_R 9_P 1.05 0.49 0.12
19_R 66_L 1.03 0.48 0.11
37_V 74_I 1.02 0.47 0.11
78_V 23_E 1.02 0.46 0.10
46_Q 85_L 1.01 0.45 0.10
31_L 13_D 1.00 0.45 0.10
97_E 47_L 0.99 0.43 0.09
52_K 62_I 0.98 0.43 0.09
104_D 22_S 0.98 0.42 0.09
62_I 56_A 0.98 0.42 0.09
87_G 79_Y 0.96 0.41 0.08
30_A 87_V 0.96 0.41 0.08
66_K 38_V 0.95 0.40 0.08
80_A 50_A 0.95 0.39 0.08
7_V 93_M 0.94 0.39 0.08
6_F 1_M 0.94 0.38 0.08
32_T 14_F 0.93 0.37 0.07
95_V 61_L 0.91 0.36 0.07
9_S 17_L 0.91 0.36 0.07
56_V 63_A 0.91 0.35 0.07
47_L 43_Y 0.91 0.35 0.07
44_V 27_L 0.90 0.34 0.07
15_T 77_I 0.90 0.34 0.06
7_V 37_A 0.88 0.33 0.06
42_D 10_W 0.88 0.33 0.06
86_R 10_W 0.88 0.32 0.06
9_S 3_H 0.88 0.32 0.06
79_C 31_Q 0.87 0.32 0.06
85_E 10_W 0.87 0.32 0.06
100_P 88_K 0.86 0.31 0.06
55_A 21_L 0.86 0.31 0.06
111_A 54_V 0.86 0.31 0.06
23_D 86_T 0.86 0.31 0.05
45_F 69_Q 0.85 0.30 0.05
74_E 29_L 0.85 0.30 0.05
34_D 78_D 0.84 0.29 0.05
29_S 65_G 0.84 0.29 0.05
109_E 21_L 0.84 0.29 0.05
7_V 51_P 0.83 0.29 0.05
16_A 31_Q 0.83 0.29 0.05
68_L 41_N 0.83 0.28 0.05
9_S 16_A 0.83 0.28 0.05
50_G 50_A 0.83 0.28 0.05
100_P 23_E 0.83 0.28 0.05
79_C 47_L 0.83 0.28 0.05
14_G 4_T 0.83 0.28 0.05
50_G 24_G 0.82 0.27 0.04
5_A 1_M 0.81 0.27 0.04
69_G 48_R 0.81 0.27 0.04
6_F 92_Q 0.81 0.27 0.04
104_D 58_N 0.81 0.26 0.04
91_Q 53_K 0.80 0.26 0.04
53_P 57_L 0.80 0.26 0.04
100_P 65_G 0.80 0.26 0.04
89_D 43_Y 0.79 0.25 0.04
111_A 86_T 0.79 0.25 0.04
17_A 17_L 0.79 0.25 0.04
27_A 6_H 0.78 0.24 0.04
29_S 93_M 0.78 0.24 0.04
66_K 9_P 0.78 0.24 0.04
56_V 19_R 0.78 0.24 0.04
86_R 79_Y 0.78 0.24 0.04
117_L 53_K 0.77 0.24 0.04
114_D 16_A 0.77 0.23 0.04
85_E 24_G 0.76 0.23 0.04
13_H 33_G 0.76 0.23 0.04
89_D 61_L 0.76 0.23 0.04
2_K 19_R 0.76 0.23 0.04
97_E 69_Q 0.76 0.23 0.04
40_I 54_V 0.76 0.23 0.04
20_E 57_L 0.76 0.23 0.03
5_A 6_H 0.76 0.23 0.03
7_V 77_I 0.76 0.23 0.03
28_T 91_S 0.75 0.22 0.03
37_V 25_D 0.75 0.22 0.03
36_A 6_H 0.75 0.22 0.03
20_E 64_R 0.75 0.22 0.03
95_V 27_L 0.75 0.22 0.03
61_Y 8_S 0.75 0.22 0.03
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
2d1pBEH:ADG:CIF:CIF:BEH:ADGContact Map
2hy5B:A:C:C:B:AContact Map
ID Seq/Len Name Options I_Prob Status
7254 2.18 2D1P_B_C Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 0.82 Done - Shared
0143 1.52 2D1P_BC Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2014_03) 0.57 Done - Shared
0142 0.48 2D1P_BC Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
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