WBBJ - ECOLI - GREMLIN Contacts

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WBBJ - Putative lipopolysaccharide biosynthesis O-acetyl transferase WbbJ

UniProt:	P37750	Sequences: MILKLAKRYGLCGFIRLVRDVLLTRVFYRNCRIIRFPCYIRNDGSINFGENFTSGVGLRLDAFGRGVIFFSDNVQVNDYVHIASIESVTIGRDTLIASKVFITDHNHGSFKHSDPMSSPNIPPDMRTLESSAVVIGQRVWLGENVTVLPGTIIGNGVVVGANSVVRGSIPENTVIAGVPAKIIKKYNHETKLWEKA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11984
Length:	196 (153)
Sequences:	3513 (2681)
Seq/√Len:	216.7

ECOLI - WBBJ WCAF THGA MAA WCAB YRDA CAIE PAAY YAIX LPXD
BACSU - MAA YVOF DAPH YTOA CYSE EPSM
HALSA - Q9HQ06 Q9HPT3 Q9HNN1
SULSO - Q980E1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
82_I	88_V	3.590	1.00
136_G	155_N	2.996	1.00
102_I	133_V	2.858	1.00
73_N	93_D	2.762	1.00
156_G	172_N	2.695	1.00
169_I	175_I	2.690	1.00
160_G	176_A	2.596	1.00
155_N	171_E	2.423	1.00
47_N	69_F	2.372	1.00
137_Q	155_N	2.336	1.00
79_Y	99_K	2.322	1.00
69_F	89_T	2.303	1.00
148_L	161_A	2.265	1.00
141_L	147_V	2.098	1.00
176_A	183_I	2.097	1.00
49_G	72_D	2.092	1.00
72_D	92_R	2.013	1.00
157_V	173_T	1.959	1.00
33_I	36_F	1.915	1.00
89_T	134_V	1.900	1.00
138_R	156_G	1.862	1.00
157_V	171_E	1.862	1.00
51_N	73_N	1.825	1.00
93_D	138_R	1.803	1.00
70_F	74_V	1.747	1.00
173_T	185_K	1.691	1.00
157_V	169_I	1.674	1.00
175_I	182_I	1.669	1.00
103_T	143_E	1.603	1.00
102_I	135_I	1.600	1.00
24_T	31_C	1.490	1.00
71_S	92_R	1.475	1.00
48_F	52_F	1.463	1.00
159_V	169_I	1.448	1.00
96_I	102_I	1.439	1.00
141_L	145_V	1.432	1.00
136_G	152_I	1.429	1.00
173_T	182_I	1.427	1.00
74_V	92_R	1.422	1.00
170_P	182_I	1.358	1.00
163_S	180_A	1.321	1.00
91_G	137_Q	1.317	1.00
85_I	130_S	1.315	1.00
50_E	72_D	1.314	1.00
69_F	87_S	1.302	1.00
92_R	137_Q	1.302	1.00
86_E	130_S	1.284	1.00
134_V	152_I	1.276	1.00
109_S	158_V	1.271	1.00
135_I	141_L	1.264	1.00
159_V	175_I	1.251	1.00
52_F	74_V	1.206	1.00
76_V	80_V	1.203	1.00
175_I	180_A	1.193	1.00
152_I	168_S	1.174	1.00
182_I	185_K	1.156	1.00
25_R	30_N	1.155	1.00
60_L	68_I	1.143	1.00
170_P	173_T	1.136	1.00
124_D	138_R	1.120	1.00
94_T	137_Q	1.114	1.00
24_T	28_Y	1.112	1.00
76_V	96_I	1.110	1.00
24_T	30_N	1.099	1.00
74_V	137_Q	1.099	1.00
109_S	174_V	1.096	1.00
38_C	42_N	1.091	1.00
151_T	168_S	1.076	1.00
100_V	145_V	1.065	1.00
101_F	144_N	1.062	1.00
153_I	169_I	1.059	1.00
163_S	178_V	1.043	1.00
90_I	96_I	1.040	1.00
131_S	150_G	1.036	1.00
70_F	76_V	1.030	1.00
99_K	144_N	1.024	1.00
81_H	99_K	1.010	1.00
80_V	100_V	1.005	1.00
123_P	126_R	1.003	1.00
101_F	146_T	1.002	1.00
139_V	157_V	1.001	1.00
94_T	155_N	1.001	1.00
52_F	70_F	0.995	1.00
36_F	39_Y	0.992	1.00
74_V	94_T	0.991	1.00
96_I	100_V	0.985	1.00
106_N	149_P	0.982	1.00
102_I	147_V	0.982	1.00
46_I	69_F	0.963	1.00
154_G	171_E	0.963	1.00
145_V	163_S	0.954	1.00
70_F	90_I	0.953	1.00
136_G	157_V	0.952	1.00
55_G	75_Q	0.931	0.99
170_P	175_I	0.930	0.99
91_G	136_G	0.892	0.99
57_G	79_Y	0.889	0.99
164_V	178_V	0.886	0.99
91_G	134_V	0.880	0.99
106_N	131_S	0.875	0.99
90_I	102_I	0.874	0.99
136_G	171_E	0.872	0.99
101_F	143_E	0.868	0.99
59_R	78_D	0.862	0.99
96_I	141_L	0.862	0.99
51_N	72_D	0.857	0.99
58_L	68_I	0.854	0.99
29_R	36_F	0.852	0.99
147_V	153_I	0.845	0.99
151_T	167_G	0.833	0.99
52_F	92_R	0.828	0.99
98_S	143_E	0.823	0.99
90_I	135_I	0.817	0.99
42_N	48_F	0.806	0.99
139_V	171_E	0.790	0.98
68_I	84_S	0.787	0.98
26_V	29_R	0.784	0.98
97_A	140_W	0.781	0.98
148_L	166_R	0.780	0.98
107_H	140_W	0.780	0.98
153_I	175_I	0.774	0.98
174_V	186_Y	0.773	0.98
104_D	149_P	0.768	0.98
37_P	56_V	0.763	0.98
82_I	102_I	0.762	0.98
41_R	45_S	0.761	0.98
29_R	37_P	0.758	0.98
86_E	104_D	0.757	0.98
155_N	172_N	0.754	0.98
165_V	180_A	0.751	0.98
156_G	171_E	0.751	0.98
106_N	129_E	0.750	0.98
184_K	187_N	0.749	0.98
48_F	70_F	0.742	0.97
94_T	139_V	0.731	0.97
87_S	132_A	0.730	0.97
61_D	85_I	0.721	0.97
30_N	33_I	0.720	0.97
25_R	28_Y	0.718	0.97
133_V	149_P	0.718	0.97
146_T	164_V	0.716	0.97
138_R	155_N	0.713	0.97
27_F	31_C	0.710	0.97
157_V	170_P	0.708	0.97
29_R	32_R	0.698	0.96
169_I	180_A	0.696	0.96
153_I	159_V	0.694	0.96
48_F	72_D	0.688	0.96
27_F	30_N	0.688	0.96
54_S	58_L	0.682	0.96
96_I	135_I	0.681	0.96
70_F	94_T	0.681	0.96
162_N	178_V	0.678	0.96
52_F	72_D	0.676	0.96
29_R	40_I	0.674	0.96
25_R	29_R	0.670	0.95
110_F	122_P	0.669	0.95
122_P	126_R	0.668	0.95
139_V	153_I	0.665	0.95
154_G	168_S	0.665	0.95
174_V	184_K	0.663	0.95
146_T	162_N	0.660	0.95
94_T	135_I	0.658	0.95
59_R	79_Y	0.657	0.95
158_V	174_V	0.654	0.95
74_V	90_I	0.651	0.95
154_G	170_P	0.644	0.94
80_V	96_I	0.644	0.94
76_V	82_I	0.639	0.94
87_S	134_V	0.631	0.94
153_I	168_S	0.622	0.93
122_P	125_M	0.621	0.93
139_V	155_N	0.620	0.93
168_S	175_I	0.617	0.93
100_V	141_L	0.617	0.93
169_I	173_T	0.617	0.93
28_Y	32_R	0.616	0.93
58_L	80_V	0.615	0.93
28_Y	31_C	0.611	0.93
26_V	41_R	0.604	0.92
29_R	33_I	0.600	0.92
111_K	156_G	0.597	0.92
34_I	38_C	0.596	0.92
177_G	180_A	0.596	0.92
85_I	105_H	0.595	0.92
89_T	132_A	0.593	0.91
154_G	175_I	0.584	0.91
109_S	186_Y	0.582	0.91
31_C	36_F	0.572	0.90
40_I	44_G	0.572	0.90
49_G	52_F	0.571	0.90
133_V	153_I	0.570	0.90
24_T	32_R	0.569	0.90
159_V	180_A	0.568	0.90
103_T	146_T	0.565	0.89
122_P	127_T	0.563	0.89
176_A	182_I	0.561	0.89
77_N	140_W	0.558	0.89
90_I	94_T	0.558	0.89
84_S	104_D	0.557	0.89
25_R	36_F	0.556	0.89
39_Y	43_D	0.556	0.89
77_N	97_A	0.554	0.88
139_V	159_V	0.553	0.88
83_A	105_H	0.546	0.88
169_I	176_A	0.545	0.88
30_N	34_I	0.538	0.87
97_A	105_H	0.536	0.87
178_V	181_K	0.535	0.87
157_V	175_I	0.534	0.87
88_V	133_V	0.534	0.87
49_G	71_S	0.528	0.86
24_T	29_R	0.525	0.86
101_F	133_V	0.524	0.86
93_D	137_Q	0.521	0.85
86_E	106_N	0.518	0.85
107_H	158_V	0.513	0.84
68_I	88_V	0.513	0.84
67_V	87_S	0.511	0.84
49_G	92_R	0.511	0.84
29_R	35_R	0.510	0.84
141_L	159_V	0.509	0.84
154_G	169_I	0.508	0.84
151_T	166_R	0.508	0.84
124_D	127_T	0.507	0.84
77_N	98_S	0.506	0.84
47_N	72_D	0.505	0.83
105_H	130_S	0.504	0.83
163_S	176_A	0.501	0.83
61_D	83_A	0.500	0.83

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
1krrA	3	0.9439	100	0.339	Contact Map
3srtA	3	0.9031	100	0.342	Contact Map
3fttA	3	0.9082	100	0.347	Contact Map
3nz2A	4	0.8929	100	0.354	Contact Map
2p2oA	3	0.898	100	0.357	Contact Map
3hjjA	3	0.9031	100	0.363	Contact Map
1ocxA	3	0.8776	100	0.393	Contact Map
3vbiA	3	0.9133	100	0.397	Contact Map
2wlgA	3	0.9439	100	0.428	Contact Map
3jqyB	3	0.9235	100	0.436	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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