YBGJ - ECOLI - GREMLIN Contacts

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YBGJ - Uncharacterized protein YbgJ

UniProt:	P0AAV4	Sequences: MQRARCYLIGETAVVLELEPPVTLASQKRIWRLAQRLVDMPNVVEAIPGMNNITVILRNPESLALDAIERLQRWWEESEALEPESRFIEIPVVYGGAGGPDLAVVAAHCGLSEKQVVELHSSVEYVVWFLGFQPGFPYLGSLPEQLHTPRRAEPRLLVPAGSVGIGGPQTGVYPLATPGGWQLIGHTSLSLFDPARDEPILLRPGDSVRFVPQKEGVC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13306
Length:	218 (211)
Sequences:	2917 (2025)
Seq/√Len:	139.4

ECOLI - YBGJ
BACSU - KIPI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
121_S	212_P	4.482	1.00
89_E	211_V	4.375	1.00
103_A	113_E	3.653	1.00
94_Y	120_H	3.268	1.00
151_R	182_Q	3.267	1.00
119_L	145_Q	3.209	1.00
118_E	122_S	3.047	1.00
124_E	207_S	3.002	1.00
86_R	206_D	2.891	1.00
157_L	176_A	2.789	1.00
115_Q	118_E	2.519	1.00
128_W	140_G	2.482	1.00
105_V	116_V	2.436	1.00
109_C	148_T	2.273	1.00
89_E	209_R	2.264	1.00
90_I	187_T	2.235	1.00
104_V	151_R	2.172	1.00
173_Y	179_G	2.106	1.00
127_V	202_L	2.068	1.00
114_K	118_E	2.043	1.00
40_M	43_V	1.972	1.00
124_E	209_R	1.961	1.00
112_S	115_Q	1.917	1.00
68_I	72_Q	1.906	1.00
91_P	189_L	1.873	1.00
193_D	196_R	1.813	1.00
87_F	124_E	1.778	1.00
93_V	98_G	1.766	1.00
57_L	64_A	1.747	1.00
191_L	202_L	1.688	1.00
10_G	13_A	1.681	1.00
103_A	107_A	1.672	1.00
119_L	146_L	1.605	1.00
136_F	171_G	1.585	1.00
95_G	99_G	1.569	1.00
120_H	170_T	1.549	1.00
93_V	186_H	1.543	1.00
34_A	38_V	1.534	1.00
15_V	54_T	1.527	1.00
18_L	33_L	1.521	1.00
164_G	173_Y	1.503	1.00
87_F	207_S	1.470	1.00
7_Y	17_E	1.468	1.00
119_L	143_P	1.467	1.00
106_A	113_E	1.422	1.00
164_G	179_G	1.395	1.00
190_S	193_D	1.383	1.00
34_A	46_A	1.364	1.00
139_L	208_V	1.358	1.00
109_C	116_V	1.346	1.00
58_R	61_E	1.332	1.00
47_I	56_I	1.329	1.00
13_A	54_T	1.321	1.00
147_H	168_P	1.317	1.00
188_S	213_Q	1.312	1.00
104_V	107_A	1.300	1.00
106_A	109_C	1.282	1.00
159_P	162_S	1.280	1.00
16_L	33_L	1.273	1.00
93_V	188_S	1.273	1.00
9_I	54_T	1.270	1.00
92_V	163_V	1.270	1.00
164_G	182_Q	1.264	1.00
172_V	191_L	1.263	1.00
64_A	68_I	1.259	1.00
164_G	171_G	1.254	1.00
5_R	17_E	1.240	1.00
105_V	148_T	1.231	1.00
133_Q	177_T	1.231	1.00
87_F	209_R	1.213	1.00
62_S	67_A	1.202	1.00
125_Y	170_T	1.200	1.00
91_P	211_V	1.191	1.00
50_M	169_Q	1.189	1.00
43_V	55_V	1.186	1.00
142_L	147_H	1.173	1.00
104_V	108_H	1.171	0.99
151_R	155_R	1.168	0.99
109_C	146_L	1.165	0.99
127_V	137_P	1.165	0.99
117_V	121_S	1.156	0.99
70_R	74_W	1.139	0.99
6_C	75_W	1.131	0.99
115_Q	119_L	1.130	0.99
18_L	75_W	1.129	0.99
33_L	53_I	1.129	0.99
114_K	212_P	1.125	0.99
18_L	30_I	1.125	0.99
165_I	184_I	1.119	0.99
102_L	106_A	1.111	0.99
198_E	203_R	1.110	0.99
40_M	70_R	1.097	0.99
85_S	207_S	1.096	0.99
104_V	182_Q	1.093	0.99
49_G	52_N	1.086	0.99
106_A	112_S	1.065	0.99
125_Y	142_L	1.063	0.99
90_I	189_L	1.058	0.99
63_L	66_D	1.057	0.99
111_L	119_L	1.056	0.99
66_D	70_R	1.055	0.99
49_G	129_F	1.055	0.99
123_V	143_P	1.048	0.99
9_I	15_V	1.015	0.99
91_P	188_S	1.010	0.99
94_Y	121_S	1.009	0.98
126_V	207_S	1.005	0.98
173_Y	177_T	1.002	0.98
94_Y	170_T	0.990	0.98
35_Q	38_V	0.989	0.98
88_I	206_D	0.988	0.98
50_M	128_W	0.980	0.98
90_I	172_V	0.976	0.98
27_Q	31_W	0.975	0.98
102_L	113_E	0.972	0.98
137_P	202_L	0.967	0.98
189_L	201_L	0.965	0.98
14_V	67_A	0.962	0.98
148_T	182_Q	0.954	0.98
119_L	122_S	0.953	0.98
162_S	186_H	0.952	0.98
92_V	185_G	0.950	0.98
120_H	184_I	0.944	0.98
203_R	206_D	0.943	0.98
15_V	49_G	0.942	0.98
106_A	116_V	0.941	0.98
96_G	99_G	0.934	0.98
36_R	39_D	0.934	0.98
174_P	183_L	0.928	0.97
141_S	171_G	0.923	0.97
162_S	183_L	0.917	0.97
99_G	102_L	0.910	0.97
36_R	74_W	0.899	0.97
122_S	143_P	0.898	0.97
73_R	77_E	0.892	0.97
162_S	176_A	0.887	0.97
105_V	109_C	0.884	0.97
19_E	26_S	0.882	0.96
42_N	58_R	0.880	0.96
14_V	68_I	0.877	0.96
132_F	173_Y	0.874	0.96
36_R	77_E	0.863	0.96
140_G	169_Q	0.862	0.96
164_G	183_L	0.859	0.96
43_V	67_A	0.859	0.96
99_G	183_L	0.857	0.96
105_V	184_I	0.851	0.96
123_V	141_S	0.838	0.95
7_Y	15_V	0.833	0.95
17_E	51_N	0.830	0.95
142_L	166_G	0.829	0.95
106_A	115_Q	0.827	0.95
90_I	202_L	0.812	0.94
70_R	73_R	0.812	0.94
196_R	201_L	0.809	0.94
160_A	190_S	0.809	0.94
30_I	48_P	0.806	0.94
93_V	214_K	0.801	0.94
144_E	168_P	0.800	0.94
24_L	126_V	0.797	0.94
177_T	183_L	0.796	0.94
139_L	210_F	0.795	0.94
43_V	46_A	0.795	0.94
142_L	146_L	0.792	0.94
132_F	179_G	0.791	0.94
102_L	117_V	0.790	0.94
167_G	171_G	0.786	0.93
31_W	34_A	0.779	0.93
34_A	53_I	0.776	0.93
129_F	204_P	0.775	0.93
143_P	146_L	0.769	0.93
95_G	98_G	0.762	0.92
64_A	67_A	0.755	0.92
111_L	116_V	0.753	0.92
38_V	46_A	0.752	0.92
46_A	55_V	0.752	0.92
173_Y	183_L	0.751	0.92
94_Y	125_Y	0.748	0.92
67_A	71_L	0.748	0.92
159_P	183_L	0.746	0.92
35_Q	39_D	0.745	0.91
94_Y	117_V	0.745	0.91
46_A	53_I	0.736	0.91
167_G	182_Q	0.732	0.91
105_V	108_H	0.728	0.91
9_I	13_A	0.720	0.90
93_V	213_Q	0.720	0.90
44_V	58_R	0.719	0.90
66_D	69_E	0.715	0.90
127_V	208_V	0.704	0.89
108_H	182_Q	0.704	0.89
108_H	149_P	0.703	0.89
124_E	142_L	0.699	0.89
41_P	61_E	0.696	0.88
170_T	184_I	0.691	0.88
37_L	55_V	0.691	0.88
65_L	68_I	0.687	0.88
8_L	64_A	0.684	0.88
45_E	56_I	0.684	0.88
133_Q	175_L	0.680	0.87
6_C	68_I	0.679	0.87
179_G	183_L	0.678	0.87
174_P	177_T	0.673	0.87
95_G	113_E	0.672	0.87
151_R	156_L	0.670	0.87
128_W	169_Q	0.669	0.86
109_C	142_L	0.668	0.86
106_A	111_L	0.668	0.86
159_P	176_A	0.666	0.86
172_V	210_F	0.659	0.86
88_I	91_P	0.658	0.86
57_L	60_P	0.656	0.85
192_F	200_I	0.654	0.85
117_V	212_P	0.653	0.85
125_Y	136_F	0.653	0.85
26_S	30_I	0.647	0.85
120_H	210_F	0.646	0.84
95_G	100_P	0.644	0.84
16_L	71_L	0.643	0.84
74_W	77_E	0.639	0.84
58_R	62_S	0.638	0.84
155_R	183_L	0.637	0.84
127_V	206_D	0.636	0.84
12_T	56_I	0.635	0.83
140_G	168_P	0.635	0.83
16_L	37_L	0.634	0.83
68_I	71_L	0.633	0.83
19_E	29_R	0.632	0.83
101_D	136_F	0.629	0.83
55_V	71_L	0.629	0.83
136_F	139_L	0.626	0.83
57_L	67_A	0.625	0.82
139_L	171_G	0.624	0.82
144_E	147_H	0.624	0.82
155_R	173_Y	0.621	0.82
164_G	177_T	0.618	0.82
134_P	138_Y	0.617	0.82
130_L	204_P	0.608	0.81
91_P	187_T	0.603	0.80
117_V	120_H	0.602	0.80
63_L	67_A	0.595	0.79
69_E	107_A	0.594	0.79
171_G	174_P	0.594	0.79
150_R	181_W	0.593	0.79
34_A	48_P	0.588	0.79
147_H	166_G	0.587	0.78
202_L	208_V	0.586	0.78
113_E	117_V	0.586	0.78
155_R	164_G	0.586	0.78
9_I	12_T	0.582	0.78
96_G	113_E	0.581	0.78
15_V	52_N	0.580	0.78
138_Y	161_G	0.580	0.78
50_M	129_F	0.578	0.77
166_G	177_T	0.578	0.77
69_E	77_E	0.577	0.77
129_F	174_P	0.577	0.77
136_F	174_P	0.576	0.77
101_D	155_R	0.572	0.77
137_P	191_L	0.571	0.76
86_R	203_R	0.571	0.76
57_L	62_S	0.569	0.76
125_Y	165_I	0.569	0.76
127_V	171_G	0.569	0.76
125_Y	146_L	0.566	0.76
32_R	78_S	0.565	0.76
155_R	179_G	0.565	0.76
137_P	206_D	0.564	0.76
13_A	156_L	0.561	0.75
25_A	46_A	0.557	0.75
15_V	129_F	0.555	0.74
158_V	175_L	0.554	0.74
6_C	16_L	0.552	0.74
175_L	200_I	0.551	0.74
111_L	115_Q	0.551	0.74
59_N	62_S	0.548	0.74
67_A	70_R	0.547	0.73
66_D	74_W	0.546	0.73
23_T	26_S	0.545	0.73
19_E	22_V	0.543	0.73
141_S	146_L	0.541	0.73
83_P	107_A	0.540	0.72
25_A	107_A	0.536	0.72
132_F	174_P	0.535	0.72
120_H	125_Y	0.534	0.72
25_A	97_A	0.534	0.72
77_E	82_E	0.532	0.71
71_L	75_W	0.532	0.71
174_P	179_G	0.530	0.71
64_A	71_L	0.529	0.71
51_N	129_F	0.529	0.71
28_K	80_A	0.526	0.71
50_M	138_Y	0.524	0.70
63_L	78_S	0.523	0.70
31_W	35_Q	0.522	0.70
27_Q	129_F	0.520	0.70
196_R	199_P	0.520	0.70
8_L	16_L	0.519	0.70
111_L	145_Q	0.519	0.70
138_Y	166_G	0.518	0.69
78_S	83_P	0.518	0.69
31_W	204_P	0.517	0.69
6_C	14_V	0.515	0.69
20_P	51_N	0.514	0.69
122_S	209_R	0.514	0.69
83_P	86_R	0.513	0.69
118_E	190_S	0.512	0.68
169_Q	192_F	0.512	0.68
49_G	128_W	0.510	0.68
164_G	174_P	0.509	0.68
69_E	72_Q	0.509	0.68
30_I	33_L	0.504	0.67
51_N	133_Q	0.503	0.67
111_L	146_L	0.503	0.67
129_F	177_T	0.501	0.67
88_I	189_L	0.500	0.67

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
2phcB	1	0.9771	100	0.056	Contact Map
3mmlB	1	0.9358	100	0.125	Contact Map
3oepA	1	0.8945	100	0.133	Contact Map
3va7A	1	0.9771	100	0.159	Contact Map
2zp2A	1	0.5734	100	0.295	Contact Map
2kwaA	1	0.3945	99.6	0.78	Contact Map
4q2lA	1	0.2844	80.3	0.941	Contact Map
2ru9A	1	0.3119	39	0.955	Contact Map
3cjkB	1	0.3349	37.5	0.955	Contact Map
2g9oA	1	0.3165	29.4	0.958	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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