UGPE - ECOLI - GREMLIN Contacts

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UGPE - sn-glycerol-3-phosphate transport system permease protein UgpE

UniProt:	P10906	Sequences: MIENRPWLTIFSHTMLILGIAVILFPLYVAFVAATLDKQAVYAAPMTLIPGTHLLENIHNIWVNGVGTNSAPFWRMLLNSFVMAFSITLGKITVSMLSAFAIVWFRFPLRNLFFWMIFITLMLPVEVRIFPTVEVIANLQMLDSYAGLTLPLMASATATFLFRQFFMTLPDELVEAARIDGASPMRFFCDIVFPLSKTNLAALFVITFIYGWNQYLWPLLIITDVDLGTTVAGIKGMIATGEGTTEWNSVMVAMLLTLIPPVVIVLVMQRAFVRGLVDSEK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11049
Length:	281 (248)
Sequences:	67408 (44223)
Seq/√Len:	2808.2

ECOLI - UGPE MALG YCJP POTH POTI UGPA YDCU YCJO YDCV POTB PSTC THIP POTC PSTA MALF YNJC CYST CYSW MODB SSUC TAUC PHNE YEHY YEHW METI PROW
BACSU - YTCP YESQ MDXG LPLC ARAQ GANQ AMYC YURM YURN GANP ARAP AMYD MDXF YTEP YESP LPLB YQGH YQGI YVGM SSUC YTLD OPUAB TCYB METP OPUCB TCYL YXEN OPUBB OPUCD OPUBD
HALSA - Q9HHQ6 Q9HML6 Q9HP02 Q9HMT4 Q9HHQ7 Q9HP01 Q9HS11 Q9HPK3 Q9HR05 Q9HNI9 Q9HS12
SULSO - Q97UF3 Q97UY9 Q97YY3 Q97ZC1 Q97YY2 Q97ZT6 Q97ZC2 Q97VC0 Q97UZ0 Q97ZT7 Q97UF4 Q97Z98

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
186_R	190_D	4.354	1.00
34_A	58_I	3.249	1.00
78_L	82_V	3.184	1.00
163_R	167_M	3.026	1.00
178_R	187_F	2.863	1.00
104_W	174_V	2.794	1.00
174_V	192_V	2.729	1.00
76_M	233_G	2.687	1.00
75_R	78_L	2.594	1.00
56_E	59_H	2.566	1.00
177_A	187_F	2.527	1.00
183_S	186_R	2.459	1.00
88_T	204_F	2.392	1.00
56_E	60_N	2.378	1.00
74_W	78_L	2.370	1.00
162_F	200_L	2.363	1.00
228_G	236_G	2.334	1.00
185_M	189_C	2.325	1.00
165_F	199_N	2.319	1.00
59_H	63_V	2.318	1.00
96_M	188_F	2.236	1.00
184_P	187_F	2.223	1.00
107_F	110_R	2.142	1.00
186_R	189_C	2.114	1.00
166_F	196_S	2.082	1.00
90_G	153_M	2.077	1.00
103_V	167_M	2.060	1.00
182_A	186_R	2.058	1.00
158_A	203_L	2.013	1.00
246_E	249_S	1.975	1.00
173_L	195_L	1.929	1.00
92_I	204_F	1.899	1.00
84_A	208_F	1.849	1.00
95_S	158_A	1.824	1.00
177_A	182_A	1.803	1.00
96_M	196_S	1.776	1.00
178_R	184_P	1.745	1.00
28_Y	32_V	1.712	1.00
102_I	159_T	1.701	1.00
75_R	79_N	1.694	1.00
114_F	163_R	1.687	1.00
174_V	187_F	1.684	1.00
32_V	36_L	1.658	1.00
96_M	162_F	1.639	1.00
82_V	86_S	1.638	1.00
233_G	237_M	1.616	1.00
225_V	228_G	1.598	1.00
98_S	159_T	1.593	1.00
87_I	211_G	1.588	1.00
54_L	57_N	1.567	1.00
86_S	149_T	1.565	1.00
215_Y	219_L	1.552	1.00
106_R	110_R	1.533	1.00
60_N	249_S	1.532	1.00
99_A	162_F	1.528	1.00
31_F	255_L	1.522	1.00
174_V	178_R	1.514	1.00
193_F	200_L	1.484	1.00
25_F	29_V	1.472	1.00
202_A	206_I	1.471	1.00
13_H	17_I	1.454	1.00
103_V	163_R	1.452	1.00
109_L	112_L	1.434	1.00
55_L	59_H	1.426	1.00
158_A	207_T	1.415	1.00
60_N	63_V	1.389	1.00
83_M	229_T	1.376	1.00
171_D	174_V	1.372	1.00
162_F	203_L	1.356	1.00
166_F	192_V	1.353	1.00
217_W	221_I	1.342	1.00
177_A	191_I	1.322	1.00
145_Y	227_L	1.316	1.00
91_K	207_T	1.315	1.00
104_W	171_D	1.308	1.00
215_Y	235_K	1.301	1.00
58_I	255_L	1.276	1.00
93_T	97_L	1.274	1.00
29_V	33_A	1.268	1.00
96_M	200_L	1.261	1.00
171_D	175_E	1.255	1.00
72_P	75_R	1.245	1.00
169_L	195_L	1.238	1.00
82_V	145_Y	1.234	1.00
266_L	270_R	1.231	1.00
222_I	227_L	1.227	1.00
224_D	227_L	1.198	1.00
86_S	89_L	1.191	1.00
100_F	166_F	1.183	1.00
183_S	187_F	1.166	1.00
261_P	265_V	1.151	1.00
161_L	203_L	1.146	1.00
89_L	93_T	1.140	1.00
162_F	199_N	1.130	1.00
172_E	175_E	1.126	1.00
155_S	159_T	1.120	1.00
30_A	255_L	1.120	1.00
228_G	233_G	1.116	1.00
17_I	21_A	1.106	1.00
237_M	246_E	1.098	1.00
40_A	52_T	1.097	1.00
37_D	40_A	1.091	1.00
229_T	232_A	1.090	1.00
195_L	198_T	1.087	1.00
62_W	74_W	1.087	1.00
214_Q	218_P	1.083	1.00
100_F	188_F	1.080	1.00
197_K	201_A	1.077	1.00
112_L	115_W	1.066	1.00
8_L	12_S	1.060	1.00
92_I	200_L	1.059	1.00
86_S	90_G	1.058	1.00
174_V	184_P	1.056	1.00
80_S	230_T	1.054	1.00
112_L	116_M	1.053	1.00
110_R	167_M	1.040	1.00
79_N	82_V	1.037	1.00
97_L	101_A	1.022	1.00
87_I	91_K	1.021	1.00
267_V	271_A	1.021	1.00
100_F	184_P	1.016	1.00
136_I	147_G	1.009	1.00
57_N	248_N	1.005	1.00
182_A	187_F	0.992	1.00
77_L	230_T	0.991	1.00
228_G	232_A	0.991	1.00
143_D	224_D	0.981	1.00
81_F	85_F	0.977	1.00
103_V	166_F	0.976	1.00
10_I	14_T	0.971	1.00
12_S	16_L	0.970	1.00
214_Q	217_W	0.965	1.00
147_G	151_P	0.960	1.00
118_F	160_F	0.959	1.00
108_P	111_N	0.956	1.00
187_F	190_D	0.955	1.00
218_P	229_T	0.954	1.00
35_T	53_H	0.945	1.00
141_M	146_A	0.945	1.00
151_P	221_I	0.939	1.00
129_I	220_L	0.937	1.00
10_I	13_H	0.931	1.00
188_F	193_F	0.926	1.00
165_F	196_S	0.924	1.00
77_L	81_F	0.920	1.00
73_F	253_A	0.915	1.00
36_L	40_A	0.911	1.00
87_I	152_L	0.909	1.00
132_T	221_I	0.906	1.00
33_A	251_M	0.905	1.00
197_K	200_L	0.886	1.00
196_S	199_N	0.885	1.00
85_F	89_L	0.883	1.00
20_I	24_L	0.880	1.00
9_T	13_H	0.878	1.00
70_S	74_W	0.875	1.00
162_F	196_S	0.874	1.00
35_T	54_L	0.873	1.00
134_E	138_N	0.873	1.00
90_G	93_T	0.871	1.00
158_A	162_F	0.871	1.00
222_I	228_G	0.866	1.00
189_C	193_F	0.866	1.00
102_I	114_F	0.865	1.00
99_A	103_V	0.863	1.00
34_A	38_K	0.861	1.00
111_N	114_F	0.861	1.00
148_L	152_L	0.860	1.00
29_V	32_V	0.856	1.00
242_E	245_T	0.852	1.00
162_F	166_F	0.852	1.00
63_V	70_S	0.850	1.00
99_A	159_T	0.849	1.00
91_K	95_S	0.844	1.00
129_I	216_L	0.844	1.00
82_V	85_F	0.843	1.00
89_L	204_F	0.843	1.00
173_L	191_I	0.838	1.00
238_I	250_V	0.838	1.00
233_G	236_G	0.833	1.00
237_M	244_T	0.831	1.00
219_L	232_A	0.830	1.00
233_G	253_A	0.828	1.00
30_A	251_M	0.828	1.00
249_S	253_A	0.824	1.00
95_S	159_T	0.820	1.00
61_I	256_L	0.818	1.00
25_F	28_Y	0.816	1.00
99_A	166_F	0.816	1.00
188_F	192_V	0.812	1.00
60_N	70_S	0.811	1.00
152_L	211_G	0.804	1.00
90_G	149_T	0.797	1.00
37_D	51_G	0.794	1.00
207_T	211_G	0.793	1.00
151_P	217_W	0.792	1.00
148_L	218_P	0.789	1.00
149_T	153_M	0.788	1.00
101_A	107_F	0.786	1.00
60_N	246_E	0.784	1.00
33_A	36_L	0.779	1.00
78_L	81_F	0.778	1.00
84_A	88_T	0.771	1.00
197_K	271_A	0.770	1.00
133_V	137_A	0.768	1.00
118_F	121_L	0.765	1.00
251_M	255_L	0.754	1.00
92_I	162_F	0.746	1.00
102_I	113_F	0.745	1.00
145_Y	149_T	0.744	1.00
171_D	178_R	0.744	1.00
187_F	192_V	0.743	1.00
237_M	253_A	0.743	1.00
14_T	17_I	0.741	1.00
54_L	58_I	0.741	1.00
76_M	79_N	0.740	1.00
59_H	62_W	0.735	1.00
169_L	196_S	0.734	1.00
91_K	158_A	0.733	1.00
40_A	51_G	0.728	1.00
184_P	188_F	0.728	1.00
88_T	208_F	0.726	1.00
200_L	203_L	0.724	1.00
146_A	150_L	0.721	1.00
11_F	15_M	0.720	1.00
257_T	261_P	0.720	1.00
61_I	249_S	0.716	1.00
88_T	92_I	0.715	1.00
263_V	267_V	0.712	1.00
80_S	231_V	0.702	1.00
232_A	236_G	0.702	1.00
102_I	163_R	0.700	1.00
268_M	271_A	0.691	1.00
137_A	142_L	0.688	1.00
192_V	195_L	0.687	1.00
144_S	227_L	0.684	1.00
86_S	153_M	0.684	1.00
125_V	216_L	0.683	1.00
95_S	162_F	0.682	1.00
55_L	58_I	0.682	1.00
33_A	37_D	0.676	1.00
139_L	142_L	0.674	1.00
53_H	56_E	0.673	1.00
98_S	155_S	0.667	1.00
74_W	77_L	0.665	1.00
58_I	252_V	0.665	1.00
265_V	269_Q	0.663	1.00
136_I	142_L	0.662	1.00
15_M	19_G	0.661	1.00
121_L	156_A	0.654	1.00
36_L	52_T	0.653	1.00
57_N	60_N	0.652	1.00
87_I	149_T	0.652	1.00
30_A	254_M	0.646	1.00
37_D	52_T	0.645	1.00
19_G	23_I	0.642	1.00
182_A	190_D	0.641	1.00
176_A	180_D	0.639	1.00
243_G	246_E	0.638	1.00
114_F	160_F	0.636	1.00
20_I	23_I	0.636	1.00
83_M	152_L	0.635	1.00
200_L	204_F	0.632	1.00
199_N	203_L	0.632	1.00
106_R	111_N	0.631	1.00
209_I	213_N	0.631	1.00
61_I	253_A	0.630	1.00
121_L	157_T	0.630	1.00
149_T	152_L	0.627	1.00
214_Q	229_T	0.626	1.00
147_G	221_I	0.623	1.00
147_G	152_L	0.622	1.00
49_I	52_T	0.622	1.00
36_L	50_P	0.619	1.00
161_L	199_N	0.618	1.00
107_F	113_F	0.615	1.00
135_V	142_L	0.611	1.00
72_P	225_V	0.610	1.00
183_S	189_C	0.609	1.00
237_M	249_S	0.608	1.00
88_T	211_G	0.606	1.00
91_K	211_G	0.605	1.00
101_A	105_F	0.605	1.00
83_M	145_Y	0.604	1.00
36_L	51_G	0.604	1.00
231_V	257_T	0.602	1.00
234_I	253_A	0.601	1.00
71_A	75_R	0.600	1.00
33_A	38_K	0.599	1.00
91_K	155_S	0.596	1.00
176_A	179_I	0.594	1.00
248_N	251_M	0.594	1.00
109_L	113_F	0.594	1.00
11_F	14_T	0.593	1.00
216_L	220_L	0.593	1.00
230_T	257_T	0.592	1.00
249_S	252_V	0.592	1.00
79_N	145_Y	0.591	1.00
132_T	135_V	0.586	1.00
267_V	270_R	0.586	1.00
245_T	249_S	0.582	1.00
34_A	252_V	0.580	1.00
151_P	154_A	0.580	1.00
99_A	163_R	0.577	1.00
247_W	250_V	0.576	1.00
126_E	220_L	0.576	1.00
71_A	74_W	0.575	1.00
52_T	56_E	0.573	1.00
34_A	255_L	0.572	1.00
251_M	254_M	0.572	1.00
80_S	212_W	0.571	1.00
84_A	211_G	0.571	1.00
224_D	228_G	0.569	1.00
76_M	230_T	0.569	1.00
113_F	117_I	0.567	1.00
13_H	16_L	0.565	1.00
125_V	129_I	0.563	1.00
134_E	137_A	0.563	1.00
236_G	243_G	0.563	1.00
16_L	20_I	0.562	1.00
102_I	107_F	0.561	1.00
98_S	117_I	0.561	1.00
216_L	219_L	0.560	1.00
187_F	191_I	0.559	1.00
232_A	235_K	0.558	1.00
169_L	174_V	0.556	1.00
105_F	184_P	0.553	1.00
70_S	249_S	0.552	1.00
94_V	155_S	0.551	1.00
210_Y	213_N	0.551	1.00
31_F	35_T	0.551	1.00
83_M	87_I	0.548	1.00
62_W	256_L	0.548	1.00
52_T	55_L	0.547	1.00
234_I	254_M	0.546	1.00
106_R	171_D	0.545	1.00
92_I	97_L	0.544	1.00
123_L	127_V	0.544	1.00
38_K	50_P	0.541	1.00
160_F	164_Q	0.541	1.00
207_T	210_Y	0.539	1.00
82_V	146_A	0.538	1.00
120_T	156_A	0.534	1.00
117_I	156_A	0.533	1.00
218_P	232_A	0.530	1.00
247_W	251_M	0.530	1.00
9_T	12_S	0.527	1.00
92_I	96_M	0.526	1.00
201_A	204_F	0.525	1.00
111_N	115_W	0.524	1.00
260_P	263_V	0.521	1.00
96_M	193_F	0.518	1.00
142_L	146_A	0.518	1.00
37_D	54_L	0.516	1.00
196_S	200_L	0.515	1.00
115_W	119_I	0.513	1.00
203_L	207_T	0.511	1.00
129_I	217_W	0.510	1.00
108_P	112_L	0.510	1.00
254_M	257_T	0.509	1.00
227_L	238_I	0.507	1.00
175_E	178_R	0.507	1.00
233_G	238_I	0.506	1.00
204_F	207_T	0.506	1.00
21_A	25_F	0.505	1.00
248_N	252_V	0.504	1.00
192_V	196_S	0.503	1.00
262_V	266_L	0.503	1.00
32_V	53_H	0.503	1.00
63_V	71_A	0.501	1.00
238_I	242_E	0.500	1.00
190_D	195_L	0.500	1.00

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
4tquN	1	0.9431	100	0.285	Contact Map
3rlfG	1	0.9609	100	0.306	Contact Map
2onkC	2	0.8541	100	0.333	Contact Map
3d31C	2	0.8363	100	0.359	Contact Map
4tquM	1	0.8932	100	0.36	Contact Map
3rlfF	1	0.911	100	0.391	Contact Map
4ymuD	2	0.7544	99.9	0.502	Contact Map
3tuiA	2	0.7331	99.9	0.541	Contact Map
4hfiA	3	0.4448	6.2	0.954	Contact Map
3hd7A	1	0.1174	6	0.954	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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