YBGD - ECOLI - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

YBGD - Uncharacterized fimbrial-like protein YbgD

UniProt:	P37909	Sequences: MFKGQKTLAALAVSLLFTAPVYAADEGSGEIHFKGEVIEAPCEIHPEDIDKNIDLGQVTTTHINREHHSNKVAVDIRLINCDLPASDNGSGMPVSKVGVTFDSTAKTTGATPLLSNTSAGEATGVGVRLMDKNDGNIVLGSAAPDLDLDASSSEQTLNFFAWMEQIDNAVDVTAGEVTANATYVLDYK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12359
Length:	188 (165)
Sequences:	3315 (2637)
Seq/√Len:	205.3

ECOLI - YBGD FIMI YCBU YADN YGIL YCBV SFMA SFMF YRAH YDES FIMF YFCV FIMA1 YDER FIMG ELFA YFCP FIMH YDEQ

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
127_V	161_A	3.227	1.00
123_T	173_T	3.046	1.00
113_L	126_G	2.925	1.00
114_L	139_L	2.889	1.00
43_E	80_N	2.838	1.00
128_R	164_E	2.834	1.00
130_M	162_W	2.832	1.00
97_V	185_L	2.805	1.00
128_R	162_W	2.734	1.00
75_D	156_T	2.733	1.00
116_N	177_V	2.512	1.00
45_H	79_I	2.496	1.00
163_M	177_V	2.459	1.00
124_G	172_V	2.407	1.00
77_R	156_T	2.144	1.00
109_G	112_P	2.132	1.00
131_D	135_G	2.100	1.00
134_D	160_F	2.080	1.00
121_E	176_E	1.981	1.00
114_L	181_A	1.980	1.00
64_N	67_H	1.962	1.00
127_V	179_A	1.958	1.00
75_D	158_N	1.928	1.00
128_R	136_N	1.877	1.00
138_V	141_S	1.843	1.00
73_A	160_F	1.797	1.00
106_K	166_I	1.693	1.00
45_H	77_R	1.687	1.00
113_L	164_E	1.658	1.00
68_H	128_R	1.638	1.00
71_K	162_W	1.635	1.00
45_H	48_D	1.547	1.00
36_E	57_Q	1.537	1.00
63_I	165_Q	1.506	1.00
118_S	121_E	1.499	1.00
103_S	114_L	1.494	1.00
18_T	22_Y	1.469	1.00
58_V	69_S	1.467	1.00
48_D	77_R	1.437	1.00
68_H	162_W	1.428	1.00
16_L	19_A	1.424	1.00
25_D	28_S	1.422	1.00
102_D	184_V	1.418	1.00
56_G	72_V	1.414	1.00
21_V	25_D	1.396	1.00
102_D	140_G	1.390	1.00
55_L	163_M	1.380	1.00
73_A	158_N	1.362	1.00
74_V	129_L	1.352	1.00
51_K	76_I	1.352	1.00
99_V	157_L	1.344	1.00
112_P	138_V	1.339	1.00
63_I	172_V	1.330	1.00
98_G	186_D	1.310	1.00
48_D	51_K	1.273	1.00
113_L	128_R	1.264	1.00
56_G	70_N	1.248	1.00
14_S	17_F	1.193	1.00
103_S	106_K	1.187	1.00
55_L	177_V	1.179	1.00
68_H	130_M	1.151	1.00
96_K	147_D	1.146	1.00
32_H	180_N	1.142	1.00
132_K	158_N	1.141	1.00
15_L	18_T	1.119	1.00
68_H	164_E	1.106	1.00
97_V	155_Q	1.092	1.00
56_G	177_V	1.091	1.00
62_H	69_S	1.087	1.00
165_Q	172_V	1.083	1.00
43_E	79_I	1.079	1.00
105_A	112_P	1.079	1.00
29_G	33_F	1.069	1.00
71_K	160_F	1.050	1.00
148_L	155_Q	1.046	1.00
63_I	125_V	1.037	1.00
106_K	109_G	1.033	1.00
17_F	20_P	1.029	1.00
122_A	125_V	1.015	1.00
126_G	166_I	1.008	1.00
46_P	51_K	1.007	1.00
63_I	166_I	1.000	1.00
64_N	165_Q	0.999	1.00
29_G	183_Y	0.993	1.00
53_I	74_V	0.987	1.00
20_P	23_A	0.983	1.00
16_L	20_P	0.974	1.00
22_Y	25_D	0.966	1.00
30_E	50_D	0.949	0.99
165_Q	171_D	0.949	0.99
98_G	145_D	0.948	0.99
114_L	179_A	0.948	0.99
58_V	163_M	0.938	0.99
99_V	185_L	0.931	0.99
100_T	142_A	0.925	0.99
58_V	63_I	0.917	0.99
14_S	18_T	0.912	0.99
58_V	177_V	0.909	0.99
101_F	129_L	0.904	0.99
100_T	186_D	0.900	0.99
39_E	60_T	0.892	0.99
67_H	165_Q	0.882	0.99
55_L	127_V	0.877	0.99
129_L	181_A	0.863	0.99
149_D	155_Q	0.861	0.99
13_V	16_L	0.859	0.99
137_I	143_A	0.848	0.99
59_T	62_H	0.842	0.99
65_R	165_Q	0.840	0.99
34_K	54_D	0.840	0.99
34_K	52_N	0.838	0.99
63_I	67_H	0.837	0.99
23_A	27_G	0.836	0.99
125_V	163_M	0.833	0.99
37_V	172_V	0.831	0.99
51_K	183_Y	0.827	0.98
139_L	159_F	0.818	0.98
19_A	23_A	0.805	0.98
96_K	145_D	0.798	0.98
106_K	126_G	0.797	0.98
166_I	170_V	0.794	0.98
105_A	139_L	0.792	0.98
39_E	82_D	0.790	0.98
130_M	136_N	0.789	0.98
55_L	161_A	0.783	0.98
127_V	177_V	0.781	0.98
78_L	155_Q	0.779	0.98
141_S	144_P	0.772	0.98
8_L	12_A	0.767	0.98
15_L	20_P	0.764	0.97
130_M	160_F	0.762	0.97
76_I	183_Y	0.759	0.97
60_T	174_A	0.752	0.97
149_D	152_S	0.747	0.97
146_L	149_D	0.741	0.97
41_P	163_M	0.731	0.97
68_H	71_K	0.729	0.97
55_L	72_V	0.725	0.97
139_L	179_A	0.724	0.97
19_A	22_Y	0.722	0.96
10_A	17_F	0.722	0.96
167_D	171_D	0.720	0.96
32_H	52_N	0.718	0.96
29_G	35_G	0.713	0.96
9_A	19_A	0.712	0.96
32_H	50_D	0.709	0.96
143_A	159_F	0.708	0.96
11_L	14_S	0.707	0.96
118_S	178_T	0.706	0.96
116_N	178_T	0.701	0.96
120_G	176_E	0.697	0.96
101_F	159_F	0.694	0.96
116_N	120_G	0.691	0.95
8_L	15_L	0.687	0.95
15_L	22_Y	0.687	0.95
8_L	14_S	0.679	0.95
9_A	12_A	0.670	0.95
15_L	19_A	0.664	0.94
124_G	167_D	0.660	0.94
82_D	85_A	0.659	0.94
12_A	16_L	0.657	0.94
104_T	115_S	0.657	0.94
46_P	49_I	0.655	0.94
8_L	11_L	0.654	0.94
62_H	70_N	0.651	0.94
12_A	15_L	0.650	0.94
9_A	13_V	0.649	0.94
71_K	130_M	0.644	0.93
11_L	19_A	0.640	0.93
108_T	126_G	0.640	0.93
98_G	142_A	0.640	0.93
18_T	21_V	0.633	0.93
84_P	95_S	0.626	0.92
159_F	183_Y	0.626	0.92
37_V	58_V	0.625	0.92
11_L	15_L	0.625	0.92
165_Q	170_V	0.623	0.92
129_L	139_L	0.619	0.92
124_G	170_V	0.616	0.92
118_S	176_E	0.613	0.92
8_L	22_Y	0.611	0.92
54_D	163_M	0.611	0.92
16_L	22_Y	0.611	0.92
8_L	20_P	0.610	0.91
98_G	143_A	0.606	0.91
31_I	74_V	0.605	0.91
106_K	115_S	0.604	0.91
116_N	121_E	0.604	0.91
97_V	143_A	0.602	0.91
18_T	24_A	0.602	0.91
76_I	139_L	0.596	0.90
125_V	172_V	0.596	0.90
124_G	166_I	0.593	0.90
112_P	126_G	0.592	0.90
10_A	14_S	0.590	0.90
116_N	163_M	0.590	0.90
8_L	16_L	0.589	0.90
69_S	163_M	0.587	0.90
56_G	178_T	0.585	0.90
75_D	105_A	0.585	0.90
135_G	144_P	0.584	0.90
27_G	30_E	0.584	0.90
29_G	36_E	0.576	0.89
134_D	144_P	0.575	0.89
100_T	103_S	0.575	0.89
60_T	125_V	0.574	0.89
54_D	72_V	0.573	0.89
27_G	33_F	0.572	0.89
53_I	161_A	0.568	0.88
83_L	152_S	0.567	0.88
48_D	129_L	0.566	0.88
8_L	21_V	0.559	0.88
10_A	18_T	0.559	0.88
114_L	137_I	0.554	0.87
9_A	17_F	0.549	0.87
31_I	47_E	0.548	0.86
8_L	13_V	0.546	0.86
77_R	154_E	0.546	0.86
13_V	22_Y	0.544	0.86
14_S	19_A	0.543	0.86
11_L	18_T	0.543	0.86
60_T	172_V	0.542	0.86
73_A	132_K	0.540	0.86
109_G	113_L	0.538	0.85
22_Y	27_G	0.536	0.85
41_P	83_L	0.534	0.85
102_D	182_T	0.534	0.85
100_T	141_S	0.532	0.85
79_I	154_E	0.531	0.85
55_L	162_W	0.531	0.85
12_A	17_F	0.530	0.85
63_I	170_V	0.529	0.85
82_D	130_M	0.529	0.85
12_A	20_P	0.527	0.84
10_A	16_L	0.526	0.84
24_A	27_G	0.524	0.84
96_K	152_S	0.522	0.84
9_A	16_L	0.519	0.83
38_I	82_D	0.517	0.83
141_S	145_D	0.517	0.83
37_V	116_N	0.516	0.83
21_V	28_S	0.514	0.83
78_L	97_V	0.509	0.82
39_E	85_A	0.508	0.82
133_N	160_F	0.507	0.82
55_L	69_S	0.505	0.82
8_L	17_F	0.502	0.81
20_P	25_D	0.500	0.81

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
2jmrA	1	0.7979	100	0.299	Contact Map
2xg5B	1	0.7819	100	0.302	Contact Map
2uy6B	2	0.8191	100	0.312	Contact Map
2jtyA	1	0.8138	100	0.317	Contact Map
1pdkB	1	0.7447	100	0.342	Contact Map
3bwuF	1	0.6543	100	0.389	Contact Map
2w07B	1	0.6277	100	0.394	Contact Map
5afoA	1	0.9096	99.9	0.419	Contact Map
4dwhB	1	0.7021	99.9	0.419	Contact Map
3bfqG	1	0.6968	99.9	0.421	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.

Page generated in 0.0076 seconds.