ApoO - PFAM28P - GREMLIN Contacts

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ApoO - Apolipoprotein O

PFAM:	PF09769	Sequences: SLYSVRSPPEEPPGRLEEQISSARLFLEPYTAWCEDAVNSVKDKIIDLEQSGTDTYASLANPPEGLLPGLGYIGVAGLAGSILARNRSIFKRLVYPLGLGGLAASVCYPQTAKNTGDLLYDYEQQKYPAV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	130 (121)
Sequences:	598 (394)
Seq/√Len:	35.9
META:	0.125

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
21_S	25_L	4.420	1.00
47_D	51_S	3.963	1.00
59_L	115_T	2.828	1.00
79_A	82_I	2.726	1.00
87_R	91_K	2.703	1.00
77_G	100_G	2.657	1.00
113_K	117_D	2.526	1.00
85_R	96_P	2.478	1.00
123_E	128_P	2.161	0.99
78_L	103_A	2.089	0.99
48_L	51_S	1.926	0.98
78_L	82_I	1.898	0.98
88_S	93_L	1.788	0.97
75_V	79_A	1.781	0.97
72_Y	76_A	1.745	0.96
121_D	124_Q	1.740	0.96
45_I	53_T	1.728	0.96
84_A	95_Y	1.719	0.96
119_L	124_Q	1.661	0.95
116_G	127_Y	1.648	0.95
76_A	103_A	1.643	0.95
88_S	91_K	1.556	0.93
104_A	112_A	1.547	0.93
42_K	45_I	1.531	0.92
70_L	73_I	1.487	0.91
73_I	108_Y	1.484	0.91
73_I	80_G	1.432	0.89
18_E	40_S	1.389	0.88
37_A	40_S	1.383	0.88
122_Y	126_K	1.365	0.87
32_A	56_Y	1.364	0.87
22_S	30_Y	1.358	0.87
75_V	82_I	1.347	0.86
90_F	94_V	1.345	0.86
48_L	53_T	1.275	0.83
39_N	45_I	1.271	0.83
114_N	118_L	1.263	0.82
72_Y	123_E	1.258	0.82
80_G	84_A	1.252	0.82
26_F	37_A	1.223	0.80
80_G	99_L	1.213	0.80
91_K	95_Y	1.206	0.79
37_A	41_V	1.195	0.79
84_A	87_R	1.177	0.78
112_A	116_G	1.161	0.77
50_Q	99_L	1.131	0.75
20_I	46_I	1.117	0.74
47_D	50_Q	1.115	0.74
74_G	81_S	1.106	0.73
71_G	106_V	1.096	0.72
21_S	119_L	1.087	0.72
64_E	114_N	1.079	0.71
27_L	92_R	1.060	0.70
59_L	86_N	1.058	0.70
53_T	57_A	1.058	0.70
44_K	48_L	1.046	0.69
108_Y	111_T	1.044	0.69
69_G	107_C	1.023	0.67
61_N	69_G	1.012	0.66
76_A	107_C	0.992	0.65
26_F	30_Y	0.989	0.64
51_S	92_R	0.976	0.63
68_P	75_V	0.973	0.63
45_I	67_L	0.961	0.62
24_R	109_P	0.959	0.62
34_C	84_A	0.953	0.61
76_A	99_L	0.944	0.61
54_D	58_S	0.939	0.60
76_A	85_R	0.935	0.60
118_L	123_E	0.929	0.59
67_L	95_Y	0.928	0.59
103_A	107_C	0.923	0.59
49_E	64_E	0.922	0.59
20_I	102_L	0.921	0.59
35_E	112_A	0.916	0.58
63_P	110_Q	0.913	0.58
83_L	117_D	0.897	0.57
66_L	70_L	0.896	0.57
39_N	53_T	0.887	0.56
46_I	53_T	0.870	0.54
79_A	83_L	0.868	0.54
61_N	73_I	0.866	0.54
55_T	114_N	0.864	0.54
41_V	94_V	0.864	0.54
101_G	110_Q	0.864	0.54
26_F	120_Y	0.863	0.54
17_E	29_P	0.857	0.53
110_Q	126_K	0.839	0.52
105_S	112_A	0.836	0.51
34_C	111_T	0.812	0.49
98_G	110_Q	0.803	0.49
121_D	127_Y	0.792	0.48
124_Q	128_P	0.792	0.48
60_A	116_G	0.783	0.47
63_P	126_K	0.782	0.47
27_L	77_G	0.782	0.47
82_I	100_G	0.781	0.47
125_Q	129_A	0.779	0.47
31_T	35_E	0.774	0.46
11_E	17_E	0.770	0.46
47_D	119_L	0.767	0.45
97_L	112_A	0.759	0.45
25_L	28_E	0.754	0.44
91_K	94_V	0.752	0.44
55_T	118_L	0.749	0.44
72_Y	81_S	0.747	0.44
9_P	97_L	0.745	0.44
19_Q	47_D	0.741	0.43
121_D	125_Q	0.741	0.43
102_L	106_V	0.734	0.43
104_A	115_T	0.732	0.43
38_V	42_K	0.726	0.42
20_I	24_R	0.724	0.42
13_P	55_T	0.723	0.42
77_G	83_L	0.719	0.41
70_L	110_Q	0.716	0.41
77_G	108_Y	0.714	0.41
53_T	78_L	0.713	0.41
38_V	116_G	0.709	0.41
49_E	75_V	0.705	0.40
61_N	79_A	0.702	0.40
91_K	111_T	0.700	0.40
60_A	127_Y	0.692	0.39
82_I	91_K	0.686	0.39
62_P	110_Q	0.686	0.39
60_A	104_A	0.684	0.38
36_D	39_N	0.677	0.38
70_L	77_G	0.673	0.38
72_Y	82_I	0.673	0.38
39_N	51_S	0.671	0.37
55_T	64_E	0.665	0.37
111_T	114_N	0.663	0.37
114_N	128_P	0.660	0.37
94_V	111_T	0.652	0.36
67_L	71_G	0.637	0.35
103_A	116_G	0.634	0.34
13_P	17_E	0.632	0.34
11_E	27_L	0.628	0.34
26_F	76_A	0.626	0.34
72_Y	85_R	0.626	0.34
74_G	102_L	0.622	0.34
43_D	50_Q	0.612	0.33
92_R	111_T	0.609	0.33
39_N	42_K	0.606	0.32
9_P	71_G	0.598	0.32
10_E	82_I	0.595	0.31
124_Q	129_A	0.594	0.31
93_L	97_L	0.591	0.31
73_I	104_A	0.590	0.31
69_G	81_S	0.588	0.31
45_I	54_D	0.583	0.31
87_R	95_Y	0.578	0.30
31_T	59_L	0.573	0.30
88_S	94_V	0.571	0.30
27_L	34_C	0.571	0.30
49_E	52_G	0.570	0.30
40_S	43_D	0.569	0.30
17_E	107_C	0.555	0.29
72_Y	103_A	0.554	0.28
49_E	54_D	0.553	0.28
88_S	101_G	0.549	0.28
16_L	81_S	0.546	0.28
115_T	120_Y	0.542	0.28
63_P	117_D	0.536	0.27
68_P	110_Q	0.534	0.27
79_A	100_G	0.527	0.27
71_G	74_G	0.527	0.27
17_E	78_L	0.526	0.27
88_S	96_P	0.521	0.26
31_T	38_V	0.520	0.26
43_D	67_L	0.518	0.26
19_Q	22_S	0.517	0.26
84_A	89_I	0.515	0.26
21_S	44_K	0.513	0.26
75_V	78_L	0.513	0.26
101_G	119_L	0.511	0.26
85_R	91_K	0.509	0.25
100_G	128_P	0.507	0.25
28_E	97_L	0.507	0.25
29_P	83_L	0.506	0.25
64_E	89_I	0.501	0.25
16_L	57_A	0.500	0.25

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
4qjvB	1	0.3846	13.5	0.922	Contact Map
4c2mK	1	0.4	12.4	0.923	Contact Map
2j69A	1	0.9154	11.7	0.924	Contact Map
2pa8L	1	0.3846	11.4	0.924	Contact Map
3sjrA	2	0.5	11.2	0.925	Contact Map
1twfK	1	0.4154	8.7	0.928	Contact Map
2bvfA	1	0.3769	7.3	0.93	Contact Map
1oefA	1	0.1846	7.2	0.93	Contact Map
4a01A	2	0.8462	5.5	0.934	Contact Map
1vimA	4	0.7846	5	0.936	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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