YLAJ - BACSU - GREMLIN Contacts

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YLAJ - Uncharacterized lipoprotein YlaJ

UniProt:	O07634	Sequences: MRILFIIIQLTLILSACAYQQGKQGQNVEKESTRQQETKPIHVKDTTQETKDNGTRTDIAKHLVSVAEKNPDVKDATAVVLGGYAVVGIDVDDTLDRSKVETIKYSVAQALKNDRYGANAVVIADPDTVSRLREMSREISEGHPVTGILDELAAIVGRVLPEVPNDVIDNEDEPQTKQQNDQLNRKQQQEMEKEQNDQSDHHMKKNNND	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	209 (161)
Sequences:	292 (249)
Seq/√Len:	19.6

BACSU - YLAJ YHCN

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
72_D	106_S	3.543	1.00
86_V	156_V	3.241	1.00
104_K	124_A	3.230	1.00
63_L	111_L	2.694	0.98
81_L	84_Y	2.559	0.98
131_R	151_E	2.476	0.97
89_I	124_A	2.360	0.96
86_V	121_V	2.317	0.96
86_V	135_M	2.316	0.96
15_S	65_S	2.185	0.94
131_R	154_A	2.078	0.92
88_G	123_I	2.050	0.91
88_G	132_L	2.027	0.91
79_V	132_L	1.944	0.89
144_P	151_E	1.938	0.89
134_E	154_A	1.933	0.89
43_V	46_T	1.905	0.88
89_I	107_V	1.899	0.88
67_A	70_N	1.799	0.85
138_E	147_G	1.793	0.85
80_V	155_I	1.759	0.84
140_S	148_I	1.745	0.83
90_D	125_D	1.730	0.83
67_A	107_V	1.654	0.80
72_D	112_K	1.634	0.79
121_V	160_L	1.629	0.78
144_P	147_G	1.607	0.77
68_E	159_V	1.607	0.77
165_N	168_I	1.578	0.76
129_V	145_V	1.569	0.76
123_I	128_T	1.557	0.75
64_V	77_T	1.550	0.75
144_P	158_R	1.528	0.74
86_V	120_A	1.516	0.73
59_I	80_V	1.486	0.72
11_T	14_L	1.470	0.71
130_S	150_D	1.459	0.70
12_L	72_D	1.457	0.70
158_R	161_P	1.430	0.69
68_E	76_A	1.426	0.68
128_T	135_M	1.420	0.68
147_G	161_P	1.383	0.66
135_M	148_I	1.377	0.66
122_V	147_G	1.371	0.65
138_E	143_H	1.371	0.65
78_A	152_L	1.366	0.65
31_E	69_K	1.360	0.65
144_P	161_P	1.338	0.63
86_V	160_L	1.319	0.62
146_T	149_L	1.281	0.60
67_A	110_A	1.252	0.58
129_V	152_L	1.251	0.58
21_Q	150_D	1.224	0.56
25_G	30_K	1.214	0.56
80_V	117_G	1.208	0.55
60_A	79_V	1.204	0.55
8_I	15_S	1.185	0.54
86_V	123_I	1.167	0.53
67_A	73_V	1.162	0.52
100_V	157_G	1.159	0.52
79_V	136_S	1.158	0.52
86_V	128_T	1.152	0.52
106_S	109_Q	1.118	0.49
138_E	154_A	1.115	0.49
70_N	162_E	1.113	0.49
64_V	78_A	1.110	0.49
64_V	126_P	1.106	0.49
108_A	132_L	1.095	0.48
83_G	119_N	1.084	0.47
83_G	165_N	1.082	0.47
73_V	82_G	1.079	0.47
143_H	146_T	1.077	0.47
6_I	15_S	1.070	0.46
103_I	109_Q	1.070	0.46
58_D	61_K	1.065	0.46
78_A	81_L	1.061	0.46
117_G	120_A	1.046	0.45
18_A	21_Q	1.042	0.45
14_L	110_A	1.040	0.44
10_L	27_N	1.031	0.44
89_I	112_K	1.027	0.44
89_I	103_I	1.022	0.43
123_I	167_V	1.019	0.43
46_T	60_A	1.012	0.43
123_I	162_E	1.010	0.43
111_L	118_A	0.995	0.42
101_E	104_K	0.994	0.42
133_R	159_V	0.994	0.42
16_A	83_G	0.993	0.42
22_G	26_Q	0.993	0.42
21_Q	28_V	0.971	0.40
121_V	135_M	0.971	0.40
151_E	161_P	0.970	0.40
32_S	58_D	0.965	0.40
63_L	115_R	0.965	0.40
37_E	43_V	0.960	0.39
123_I	160_L	0.958	0.39
22_G	30_K	0.953	0.39
113_N	148_I	0.951	0.39
120_A	160_L	0.939	0.38
75_D	90_D	0.936	0.38
91_V	100_V	0.929	0.38
74_K	136_S	0.913	0.37
104_K	115_R	0.904	0.36
63_L	104_K	0.895	0.36
13_I	22_G	0.890	0.35
7_I	11_T	0.888	0.35
128_T	160_L	0.869	0.34
126_P	144_P	0.865	0.34
73_V	154_A	0.861	0.34
5_F	16_A	0.861	0.34
78_A	84_Y	0.861	0.34
42_H	69_K	0.858	0.33
125_D	163_V	0.857	0.33
58_D	75_D	0.856	0.33
122_V	161_P	0.845	0.33
99_K	103_I	0.839	0.32
12_L	16_A	0.836	0.32
14_L	127_D	0.833	0.32
96_D	151_E	0.829	0.32
59_I	63_L	0.827	0.32
142_G	161_P	0.827	0.32
62_H	105_Y	0.820	0.31
21_Q	41_I	0.819	0.31
28_V	47_T	0.818	0.31
18_A	25_G	0.817	0.31
92_D	110_A	0.813	0.31
84_Y	121_V	0.808	0.31
142_G	158_R	0.803	0.30
42_H	46_T	0.798	0.30
23_K	143_H	0.796	0.30
5_F	8_I	0.787	0.29
64_V	135_M	0.786	0.29
138_E	146_T	0.784	0.29
11_T	65_S	0.778	0.29
6_I	10_L	0.776	0.29
150_D	154_A	0.773	0.29
111_L	117_G	0.766	0.28
138_E	159_V	0.763	0.28
112_K	162_E	0.761	0.28
70_N	141_E	0.755	0.28
70_N	138_E	0.753	0.28
121_V	133_R	0.752	0.28
4_L	11_T	0.751	0.28
16_A	20_Q	0.746	0.27
82_G	155_I	0.743	0.27
152_L	160_L	0.743	0.27
78_A	123_I	0.743	0.27
66_V	152_L	0.743	0.27
130_S	154_A	0.742	0.27
38_T	41_I	0.740	0.27
52_D	148_I	0.732	0.27
111_L	120_A	0.731	0.27
10_L	16_A	0.730	0.27
58_D	65_S	0.724	0.26
102_T	105_Y	0.721	0.26
107_V	160_L	0.720	0.26
63_L	132_L	0.719	0.26
64_V	128_T	0.706	0.25
86_V	125_D	0.704	0.25
100_V	105_Y	0.699	0.25
9_Q	65_S	0.699	0.25
88_G	106_S	0.699	0.25
4_L	22_G	0.699	0.25
77_T	112_K	0.698	0.25
70_N	145_V	0.697	0.25
32_S	41_I	0.691	0.25
12_L	94_T	0.685	0.24
105_Y	125_D	0.684	0.24
60_A	138_E	0.681	0.24
43_V	47_T	0.679	0.24
5_F	39_K	0.676	0.24
9_Q	146_T	0.671	0.24
22_G	65_S	0.668	0.24
96_D	139_I	0.664	0.23
61_K	119_N	0.663	0.23
91_V	96_D	0.661	0.23
151_E	158_R	0.661	0.23
57_T	135_M	0.661	0.23
76_A	139_I	0.659	0.23
13_I	32_S	0.658	0.23
122_V	158_R	0.658	0.23
135_M	160_L	0.657	0.23
20_Q	162_E	0.657	0.23
22_G	116_Y	0.645	0.22
82_G	104_K	0.638	0.22
4_L	7_I	0.636	0.22
59_I	162_E	0.636	0.22
97_R	105_Y	0.628	0.22
87_V	119_N	0.627	0.22
55_T	61_K	0.626	0.22
122_V	140_S	0.624	0.22
78_A	148_I	0.621	0.21
83_G	146_T	0.617	0.21
26_Q	150_D	0.613	0.21
66_V	120_A	0.613	0.21
83_G	118_A	0.612	0.21
126_P	141_E	0.610	0.21
82_G	117_G	0.605	0.21
104_K	142_G	0.599	0.20
22_G	29_E	0.599	0.20
19_Y	65_S	0.596	0.20
56_R	110_A	0.595	0.20
70_N	119_N	0.584	0.20
14_L	25_G	0.580	0.20
78_A	126_P	0.577	0.20
5_F	24_Q	0.575	0.19
7_I	10_L	0.574	0.19
24_Q	38_T	0.572	0.19
134_E	138_E	0.571	0.19
131_R	161_P	0.569	0.19
127_D	158_R	0.569	0.19
154_A	163_V	0.568	0.19
88_G	125_D	0.566	0.19
72_D	92_D	0.562	0.19
70_N	168_I	0.562	0.19
9_Q	113_N	0.561	0.19
121_V	128_T	0.559	0.19
163_V	166_D	0.556	0.19
140_S	147_G	0.556	0.19
15_S	167_V	0.553	0.19
23_K	30_K	0.552	0.19
149_L	159_V	0.551	0.19
43_V	67_A	0.549	0.18
124_A	131_R	0.546	0.18
23_K	94_T	0.544	0.18
157_G	164_P	0.543	0.18
57_T	64_V	0.541	0.18
57_T	131_R	0.540	0.18
66_V	117_G	0.536	0.18
72_D	126_P	0.534	0.18
53_N	79_V	0.532	0.18
86_V	95_L	0.527	0.18
11_T	23_K	0.523	0.17
79_V	100_V	0.521	0.17
55_T	84_Y	0.519	0.17
60_A	64_V	0.517	0.17
11_T	32_S	0.514	0.17
97_R	107_V	0.512	0.17
8_I	61_K	0.508	0.17
20_Q	167_V	0.501	0.17
116_Y	160_L	0.500	0.17

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
3zbiC	1	0.134	70.2	0.935	Contact Map
4q2lA	1	0.3062	61.1	0.938	Contact Map
2ru9A	1	0.3349	38.9	0.946	Contact Map
3ne5A	3	0.9617	31.1	0.949	Contact Map
2jliA	1	0.4593	29.5	0.949	Contact Map
4mt1A	3	0.7703	28.3	0.95	Contact Map
4pj0U	1	0.4354	26.4	0.95	Contact Map
3ucpA	1	0.5502	26.3	0.95	Contact Map
3pmqA	1	0.4689	24.2	0.951	Contact Map
2qgmA	1	0.7033	20.3	0.953	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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