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OPENSEQ.org
NUOJ NUOK
Genes: A B A+B
Length: 184 100 269
Sequences: 1371 2536 1009
Seq/Len: 7.45 25.36 3.75
MirrorTree (Pazo et al. 2001) 0.81
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 0.00 3.00
2 0.00 0.00 3.20
5 0.00 0.01 3.31
10 0.00 0.01 3.46
20 0.00 0.01 3.55
100 0.01 0.02 3.61
∞ 0.06 0.08 4.25
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
13_I 13_I 3.75 1.00 1.00
17_L 17_L 2.89 1.00 1.00
6_Y 6_H 2.64 1.00 1.00
16_T 14_L 2.17 1.00 0.99
19_V 33_I 1.93 1.00 0.98
20_I 21_G 1.82 0.99 0.97
39_I 44_L 1.78 0.99 0.97
147_L 75_I 1.77 0.99 0.97
132_T 56_T 1.75 0.99 0.96
29_L 33_I 1.74 0.99 0.96
42_V 10_L 1.66 0.99 0.95
129_V 60_V 1.65 0.99 0.95
55_E 40_N 1.62 0.98 0.94
144_A 67_S 1.61 0.98 0.94
159_G 81_L 1.60 0.98 0.94
16_T 17_L 1.45 0.96 0.90
73_M 32_L 1.42 0.96 0.89
44_F 98_M 1.36 0.94 0.86
43_F 40_N 1.32 0.93 0.84
58_V 92_I 1.31 0.93 0.83
144_A 66_I 1.29 0.92 0.82
51_A 89_N 1.21 0.88 0.76
4_A 98_M 1.20 0.88 0.75
82_E 42_S 1.20 0.88 0.75
142_E 9_I 1.16 0.85 0.72
35_S 37_I 1.16 0.85 0.72
39_I 10_L 1.15 0.85 0.71
40_S 11_A 1.14 0.84 0.70
62_A 76_G 1.12 0.82 0.68
43_F 62_Y 1.09 0.80 0.65
18_R 33_I 1.09 0.80 0.65
9_G 65_A 1.07 0.79 0.63
139_L 95_V 1.07 0.78 0.62
7_I 68_L 1.05 0.77 0.61
85_R 84_H 1.05 0.76 0.60
60_A 32_L 1.05 0.76 0.60
63_I 24_I 1.04 0.76 0.59
157_H 34_G 1.03 0.75 0.58
48_A 47_V 1.03 0.74 0.58
43_F 44_L 1.03 0.74 0.58
64_M 63_I 1.01 0.73 0.56
55_E 66_I 1.01 0.73 0.56
68_V 50_G 1.01 0.73 0.56
47_G 51_S 1.00 0.72 0.55
54_L 99_R 1.00 0.71 0.55
47_G 96_S 0.98 0.70 0.53
154_V 29_L 0.97 0.68 0.51
131_I 28_L 0.96 0.67 0.50
28_A 33_I 0.96 0.67 0.50
134_F 45_A 0.96 0.67 0.50
58_V 59_Q 0.96 0.67 0.50
29_L 49_A 0.96 0.67 0.50
154_V 99_R 0.96 0.67 0.49
20_I 20_T 0.95 0.66 0.48
149_L 74_S 0.95 0.66 0.48
72_M 59_Q 0.94 0.65 0.48
11_I 86_R 0.94 0.65 0.48
162_E 17_L 0.94 0.65 0.48
64_M 33_I 0.93 0.64 0.46
51_A 66_I 0.93 0.63 0.46
92_V 14_L 0.93 0.63 0.46
43_F 18_G 0.91 0.61 0.43
99_L 19_L 0.90 0.60 0.42
159_G 8_L 0.89 0.58 0.41
150_A 67_S 0.89 0.58 0.41
47_G 98_M 0.89 0.58 0.41
46_L 48_V 0.88 0.57 0.40
40_S 79_L 0.88 0.57 0.39
133_L 90_L 0.88 0.57 0.39
160_R 40_N 0.88 0.57 0.39
20_I 75_I 0.88 0.56 0.39
150_A 84_H 0.87 0.56 0.38
40_S 41_A 0.87 0.55 0.38
141_V 21_G 0.87 0.55 0.38
25_P 73_A 0.86 0.55 0.38
65_V 54_G 0.86 0.55 0.37
145_S 85_R 0.85 0.53 0.36
141_V 43_A 0.85 0.53 0.36
94_I 75_I 0.85 0.53 0.36
28_A 28_L 0.85 0.53 0.36
129_V 82_Q 0.85 0.53 0.36
88_L 13_I 0.85 0.53 0.36
56_I 86_R 0.84 0.52 0.35
39_I 66_I 0.84 0.52 0.35
146_M 11_A 0.84 0.52 0.35
96_P 46_F 0.84 0.52 0.34
139_L 41_A 0.84 0.52 0.34
67_F 25_R 0.83 0.51 0.34
28_A 27_N 0.83 0.50 0.34
71_V 89_N 0.83 0.50 0.33
135_G 60_V 0.83 0.50 0.33
155_A 32_L 0.83 0.50 0.33
58_V 23_V 0.83 0.50 0.33
16_T 37_I 0.83 0.50 0.33
39_I 14_L 0.82 0.49 0.33
48_A 48_V 0.82 0.49 0.33
41_G 10_L 0.82 0.49 0.33
39_I 40_N 0.82 0.48 0.32
126_A 59_Q 0.81 0.48 0.32
73_M 66_I 0.81 0.48 0.32
26_V 42_S 0.81 0.48 0.32
64_M 25_R 0.81 0.48 0.31
140_A 64_L 0.81 0.48 0.31
156_F 21_G 0.81 0.48 0.31
62_A 87_R 0.81 0.47 0.31
139_L 82_Q 0.81 0.47 0.31
132_T 57_D 0.81 0.47 0.31
8_C 41_A 0.81 0.47 0.31
141_V 30_F 0.80 0.46 0.30
42_V 7_G 0.79 0.46 0.29
20_I 34_G 0.79 0.45 0.29
36_L 22_L 0.79 0.45 0.29
76_L 62_Y 0.79 0.45 0.29
83_Q 46_F 0.79 0.45 0.29
154_V 18_G 0.79 0.45 0.28
30_L 98_M 0.79 0.45 0.28
142_E 40_N 0.78 0.44 0.28
74_L 75_I 0.78 0.44 0.28
56_I 31_M 0.78 0.44 0.28
161_E 48_V 0.78 0.44 0.28
144_A 78_A 0.78 0.43 0.27
20_I 24_I 0.78 0.43 0.27
148_L 45_A 0.78 0.43 0.27
55_E 84_H 0.78 0.43 0.27
38_A 83_L 0.78 0.43 0.27
95_G 25_R 0.78 0.43 0.27
128_A 8_L 0.77 0.43 0.27
71_V 19_L 0.77 0.43 0.27
54_L 35_L 0.77 0.42 0.27
67_F 33_I 0.77 0.42 0.26
42_V 2_I 0.77 0.42 0.26
140_A 63_I 0.76 0.41 0.26
159_G 65_A 0.76 0.41 0.26
106_V 87_R 0.76 0.41 0.26
16_T 48_V 0.76 0.41 0.25
130_G 18_G 0.76 0.41 0.25
53_A 40_N 0.75 0.40 0.25
8_C 46_F 0.75 0.40 0.24
41_G 29_L 0.75 0.40 0.24
137_Y 64_L 0.75 0.40 0.24
71_V 67_S 0.75 0.40 0.24
165_G 17_L 0.75 0.39 0.24
32_L 35_L 0.74 0.39 0.24
22_H 37_I 0.74 0.39 0.24
127_K 88_Q 0.74 0.39 0.23
130_G 73_A 0.74 0.39 0.23
130_G 69_A 0.74 0.39 0.23
145_S 57_D 0.74 0.38 0.23
123_P 11_A 0.74 0.38 0.23
155_A 29_L 0.74 0.38 0.23
26_V 67_S 0.73 0.38 0.23
129_V 29_L 0.73 0.38 0.23
122_T 75_I 0.73 0.38 0.23
165_G 42_S 0.73 0.38 0.23
158_V 82_Q 0.73 0.38 0.23
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
3rkoJF:KGContact Map
4he8JD:KEContact Map
ID Seq/Len Name Options I_Prob Status
14274 6.75 a Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) 1.00 Done - Shared
2308 5.91 cI_F_G Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 1.00 Done - Shared
0001 3.75 NUOJ NUOK Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) (2013_03) 1.00 Done - Shared
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