UGPA - ECOLI - GREMLIN Contacts

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UGPA - sn-glycerol-3-phosphate transport system permease protein UgpA

UniProt:	P10905	Sequences: MSSSRPVFRSRWLPYLLVAPQLIITVIFFIWPAGEALWYSLQSVDPFGFSSQFVGLDNFVTLFHDSYYLDSFWTTIKFSTFVTVSGLLVSLFFAALVEYIVRGSRFYQTLMLLPYAVAPAVAAVLWIFLFNPGRGLITHFLAEFGYDWNHAQNSGQAMFLVVFASVWKQISYNFLFFYAALQSIPRSLIEAAAIDGAGPIRRFFKIALPLIAPVSFFLLVVNLVYAFFDTFPVIDAATSGGPVQATTTLIYKIYREGFTGLDLASSAAQSVVLMFLVIVLTVVQFRYVESKVRYQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11046
Length:	295 (255)
Sequences:	69641 (45297)
Seq/√Len:	2836.6

ECOLI - UGPA YCJO POTH YDCU PSTC MALG MALF YCJP THIP POTB PSTA YNJC UGPE CYSW POTI YDCV CYST POTC MODB TAUC SSUC YEHY PHNE YEHW PROW METI
BACSU - GANP AMYD YTEP YESP MDXF ARAP YURN LPLB GANQ MDXG YESQ YURM LPLC ARAQ YQGH AMYC YTCP YQGI YVGM YTLD SSUC OPUAB TCYB METP OPUCB TCYL OPUBB YXEN OPUCD OPUBD
HALSA - Q9HHQ7 Q9HMT4 Q9HP01 Q9HML6 Q9HR05 Q9HP02 Q9HHQ6 Q9HS11 Q9HPK3 Q9HNI9 Q9HS12
SULSO - Q97YY2 Q97UF3 Q97UZ0 Q97UF4 Q97YY3 Q97ZC2 Q97VC0 Q97UY9 Q97ZC1 Q97ZT7 Q97ZT6 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
201_R	205_K	3.901	1.00
73_W	77_K	3.236	1.00
193_A	202_R	3.093	1.00
178_Y	182_Q	3.023	1.00
70_D	73_W	2.643	1.00
71_S	252_K	2.583	1.00
180_A	214_V	2.518	1.00
85_S	166_V	2.502	1.00
99_Y	189_I	2.499	1.00
247_T	255_R	2.485	1.00
198_G	201_R	2.481	1.00
81_F	162_V	2.474	1.00
60_V	64_H	2.449	1.00
192_A	202_R	2.442	1.00
40_S	59_F	2.409	1.00
69_L	73_W	2.380	1.00
189_I	207_A	2.363	1.00
199_P	202_R	2.308	1.00
83_T	219_L	2.280	1.00
57_D	60_V	2.248	1.00
177_F	215_S	2.167	1.00
262_D	265_S	2.150	1.00
200_I	204_F	2.148	1.00
101_V	104_S	2.119	1.00
57_D	61_T	2.104	1.00
197_A	201_R	2.064	1.00
201_R	204_F	1.993	1.00
77_K	158_M	1.985	1.00
173_N	218_L	1.958	1.00
91_L	203_F	1.922	1.00
38_W	42_Q	1.916	1.00
188_L	210_L	1.900	1.00
98_E	182_Q	1.894	1.00
192_A	197_A	1.860	1.00
108_Q	178_Y	1.859	1.00
181_L	211_I	1.842	1.00
244_Q	247_T	1.810	1.00
91_L	211_I	1.802	1.00
87_L	219_L	1.760	1.00
34_G	38_W	1.739	1.00
70_D	74_T	1.718	1.00
193_A	199_P	1.693	1.00
82_V	226_A	1.679	1.00
189_I	202_R	1.675	1.00
282_V	286_R	1.638	1.00
90_S	173_N	1.625	1.00
77_K	81_F	1.621	1.00
79_S	223_L	1.612	1.00
91_L	177_F	1.591	1.00
189_I	193_A	1.590	1.00
93_F	174_F	1.583	1.00
61_T	265_S	1.567	1.00
252_K	256_E	1.561	1.00
158_M	246_T	1.544	1.00
97_V	174_F	1.530	1.00
186_R	189_I	1.525	1.00
19_A	23_I	1.496	1.00
67_Y	70_D	1.448	1.00
240_G	245_A	1.432	1.00
61_T	64_H	1.422	1.00
31_W	35_E	1.418	1.00
103_G	106_F	1.407	1.00
56_L	60_V	1.399	1.00
35_E	39_Y	1.388	1.00
173_N	222_N	1.380	1.00
100_I	104_S	1.372	1.00
37_L	271_V	1.371	1.00
256_E	260_G	1.371	1.00
98_E	178_Y	1.360	1.00
86_G	222_N	1.329	1.00
55_G	58_N	1.326	1.00
181_L	207_A	1.324	1.00
94_A	177_F	1.319	1.00
88_L	92_F	1.316	1.00
208_L	215_S	1.316	1.00
247_T	252_K	1.314	1.00
78_F	248_T	1.302	1.00
217_F	221_V	1.297	1.00
177_F	218_L	1.286	1.00
186_R	190_E	1.286	1.00
231_F	235_D	1.284	1.00
187_S	190_E	1.259	1.00
91_L	215_S	1.253	1.00
106_F	109_T	1.228	1.00
95_A	181_L	1.224	1.00
99_Y	186_R	1.215	1.00
231_F	254_Y	1.213	1.00
238_T	246_T	1.211	1.00
156_Q	159_F	1.209	1.00
130_F	160_L	1.205	1.00
233_V	237_A	1.198	1.00
87_L	215_S	1.196	1.00
12_W	16_L	1.190	1.00
84_V	88_L	1.188	1.00
192_A	206_I	1.182	1.00
75_T	249_L	1.171	1.00
256_E	262_D	1.171	1.00
255_R	259_T	1.159	1.00
46_P	53_F	1.156	1.00
13_L	17_L	1.155	1.00
81_F	84_V	1.151	1.00
212_A	216_F	1.149	1.00
74_T	77_K	1.146	1.00
184_I	210_L	1.138	1.00
157_A	246_T	1.125	1.00
23_I	27_I	1.125	1.00
164_A	237_A	1.119	1.00
198_G	202_R	1.117	1.00
161_V	234_I	1.110	1.00
162_V	166_V	1.109	1.00
43_S	46_P	1.105	1.00
35_E	38_W	1.097	1.00
286_R	289_E	1.095	1.00
131_N	134_R	1.091	1.00
14_P	18_V	1.091	1.00
106_F	110_L	1.082	1.00
128_F	132_P	1.080	1.00
85_S	162_V	1.061	1.00
177_F	214_V	1.039	1.00
248_T	251_Y	1.038	1.00
16_L	20_P	1.034	1.00
98_E	181_L	1.030	1.00
36_A	271_V	1.022	1.00
189_I	199_P	1.020	1.00
82_V	86_G	1.017	1.00
170_I	174_F	1.013	1.00
247_T	251_Y	1.012	1.00
230_T	233_V	1.010	1.00
67_Y	244_Q	1.009	1.00
158_M	162_V	1.006	1.00
81_F	85_S	1.002	1.00
16_L	19_A	1.002	1.00
15_Y	19_A	0.999	1.00
63_F	69_L	0.992	1.00
176_F	218_L	0.980	1.00
13_L	16_L	0.976	1.00
76_I	80_T	0.974	1.00
95_A	199_P	0.973	1.00
92_F	96_L	0.972	1.00
95_A	203_F	0.971	1.00
159_F	163_F	0.967	1.00
210_L	213_P	0.965	1.00
82_V	165_S	0.964	1.00
197_A	202_R	0.963	1.00
84_V	219_L	0.961	1.00
283_V	287_Y	0.951	1.00
61_T	65_D	0.950	1.00
257_G	266_S	0.944	1.00
234_I	248_T	0.942	1.00
202_R	205_K	0.934	1.00
77_K	159_F	0.932	1.00
252_K	269_Q	0.919	1.00
39_Y	42_Q	0.919	1.00
252_K	255_R	0.918	1.00
18_V	22_L	0.914	1.00
77_K	80_T	0.910	1.00
126_W	237_A	0.905	1.00
74_T	158_M	0.896	1.00
240_G	246_T	0.895	1.00
235_D	251_Y	0.892	1.00
136_L	159_F	0.886	1.00
40_S	44_V	0.881	1.00
78_F	158_M	0.880	1.00
104_S	182_Q	0.880	1.00
82_V	162_V	0.876	1.00
94_A	98_E	0.874	1.00
58_N	264_A	0.872	1.00
72_F	249_L	0.871	1.00
80_T	84_V	0.861	1.00
230_T	234_I	0.856	1.00
39_Y	267_A	0.852	1.00
126_W	164_A	0.850	1.00
59_F	271_V	0.847	1.00
86_G	90_S	0.846	1.00
26_V	30_I	0.845	1.00
105_R	108_Q	0.843	1.00
42_Q	46_P	0.842	1.00
112_L	175_L	0.837	1.00
45_D	48_G	0.837	1.00
277_V	281_T	0.833	1.00
197_A	205_K	0.832	1.00
202_R	207_A	0.829	1.00
180_A	211_I	0.829	1.00
212_A	215_S	0.823	1.00
62_L	272_V	0.823	1.00
90_S	174_F	0.822	1.00
165_S	226_A	0.821	1.00
177_F	211_I	0.819	1.00
72_F	76_I	0.819	1.00
50_S	53_F	0.817	1.00
78_F	165_S	0.817	1.00
279_V	283_V	0.816	1.00
164_A	233_V	0.815	1.00
41_L	54_V	0.813	1.00
173_N	177_F	0.809	1.00
119_P	168_K	0.805	1.00
211_I	214_V	0.805	1.00
39_Y	43_S	0.804	1.00
102_R	105_R	0.804	1.00
65_D	69_L	0.803	1.00
256_E	265_S	0.803	1.00
97_V	108_Q	0.802	1.00
204_F	208_L	0.801	1.00
68_Y	269_Q	0.799	1.00
94_A	174_F	0.797	1.00
199_P	203_F	0.796	1.00
256_E	269_Q	0.795	1.00
73_W	76_I	0.794	1.00
203_F	208_L	0.792	1.00
96_L	101_V	0.791	1.00
159_F	162_V	0.785	1.00
283_V	286_R	0.779	1.00
127_I	131_N	0.777	1.00
222_N	226_A	0.776	1.00
85_S	88_L	0.773	1.00
66_S	70_D	0.772	1.00
212_A	287_Y	0.766	1.00
284_Q	287_Y	0.762	1.00
254_Y	258_F	0.741	1.00
81_F	166_V	0.737	1.00
58_N	61_T	0.734	1.00
273_L	277_V	0.729	1.00
71_S	74_T	0.728	1.00
86_G	169_Q	0.726	1.00
90_S	177_F	0.722	1.00
86_G	173_N	0.721	1.00
86_G	226_A	0.720	1.00
54_V	57_D	0.720	1.00
123_A	232_P	0.718	1.00
188_L	206_I	0.715	1.00
44_V	48_G	0.715	1.00
94_A	181_L	0.713	1.00
191_A	195_D	0.711	1.00
156_Q	160_L	0.710	1.00
17_L	20_P	0.705	1.00
267_A	270_S	0.705	1.00
157_A	160_L	0.702	1.00
249_L	273_L	0.700	1.00
87_L	177_F	0.698	1.00
60_V	63_F	0.695	1.00
83_T	223_L	0.692	1.00
55_G	59_F	0.692	1.00
43_S	53_F	0.689	1.00
230_T	248_T	0.688	1.00
123_A	236_A	0.688	1.00
97_V	178_Y	0.687	1.00
36_A	267_A	0.687	1.00
169_Q	222_N	0.686	1.00
42_Q	51_S	0.686	1.00
282_V	285_F	0.682	1.00
112_L	115_Y	0.682	1.00
184_I	211_I	0.680	1.00
25_T	29_F	0.676	1.00
119_P	232_P	0.675	1.00
69_L	72_F	0.674	1.00
26_V	29_F	0.674	1.00
191_A	194_I	0.673	1.00
215_S	218_L	0.671	1.00
203_F	207_A	0.671	1.00
56_L	59_F	0.670	1.00
36_A	270_S	0.670	1.00
169_Q	225_Y	0.669	1.00
161_V	238_T	0.667	1.00
122_A	167_W	0.667	1.00
265_S	269_Q	0.667	1.00
71_S	249_L	0.661	1.00
97_V	107_Y	0.661	1.00
61_T	262_D	0.660	1.00
79_S	83_T	0.659	1.00
41_L	55_G	0.652	1.00
251_Y	255_R	0.652	1.00
186_R	193_A	0.651	1.00
238_T	247_T	0.647	1.00
46_P	52_Q	0.646	1.00
15_Y	18_V	0.646	1.00
28_F	32_P	0.646	1.00
20_P	23_I	0.645	1.00
93_F	170_I	0.644	1.00
278_I	282_V	0.643	1.00
128_F	131_N	0.639	1.00
83_T	87_L	0.638	1.00
93_F	111_M	0.630	1.00
267_A	271_V	0.629	1.00
101_V	107_Y	0.629	1.00
89_V	166_V	0.624	1.00
214_V	218_L	0.623	1.00
31_W	34_G	0.622	1.00
207_A	210_L	0.620	1.00
126_W	129_L	0.618	1.00
120_A	236_A	0.618	1.00
53_F	57_D	0.617	1.00
264_A	267_A	0.617	1.00
160_L	164_A	0.616	1.00
78_F	162_V	0.614	1.00
253_I	269_Q	0.612	1.00
177_F	181_L	0.611	1.00
17_L	21_Q	0.610	1.00
111_M	171_S	0.609	1.00
22_L	26_V	0.607	1.00
43_S	52_Q	0.605	1.00
281_T	285_F	0.605	1.00
66_S	69_L	0.605	1.00
78_F	161_V	0.603	1.00
75_T	250_I	0.600	1.00
102_R	106_F	0.598	1.00
103_G	107_Y	0.594	1.00
234_I	251_Y	0.594	1.00
263_L	266_S	0.594	1.00
51_S	54_V	0.594	1.00
215_S	219_L	0.593	1.00
202_R	206_I	0.592	1.00
108_Q	175_L	0.590	1.00
250_I	273_L	0.590	1.00
263_L	267_A	0.589	1.00
279_V	282_V	0.585	1.00
62_L	269_Q	0.584	1.00
21_Q	25_T	0.578	1.00
53_F	56_L	0.577	1.00
39_Y	44_V	0.575	1.00
204_F	207_A	0.575	1.00
216_F	219_L	0.570	1.00
67_Y	252_K	0.568	1.00
32_P	36_A	0.566	1.00
224_V	229_D	0.565	1.00
100_I	105_R	0.563	1.00
219_L	222_N	0.563	1.00
240_G	244_Q	0.563	1.00
109_T	113_L	0.561	1.00
276_L	279_V	0.560	1.00
176_F	214_V	0.560	1.00
67_Y	247_T	0.559	1.00
101_V	105_R	0.557	1.00
95_A	207_A	0.557	1.00
87_L	91_L	0.553	1.00
165_S	230_T	0.553	1.00
110_L	114_P	0.551	1.00
86_G	166_V	0.550	1.00
115_Y	172_Y	0.550	1.00
105_R	109_T	0.549	1.00
75_T	228_F	0.549	1.00
42_Q	52_Q	0.548	1.00
62_L	265_S	0.547	1.00
74_T	246_T	0.546	1.00
89_V	170_I	0.545	1.00
30_I	34_G	0.542	1.00
135_G	138_T	0.541	1.00
232_P	235_D	0.540	1.00
79_S	226_A	0.539	1.00
78_F	82_V	0.539	1.00
42_Q	53_F	0.538	1.00
79_S	228_F	0.538	1.00
94_A	178_Y	0.534	1.00
225_Y	229_D	0.531	1.00
251_Y	254_Y	0.531	1.00
138_T	240_G	0.531	1.00
104_S	108_Q	0.527	1.00
19_A	22_L	0.526	1.00
161_V	165_S	0.526	1.00
226_A	230_T	0.525	1.00
12_W	15_Y	0.523	1.00
280_L	284_Q	0.523	1.00
93_F	96_L	0.522	1.00
67_Y	71_S	0.522	1.00
114_P	171_S	0.521	1.00
82_V	166_V	0.521	1.00
40_S	271_V	0.521	1.00
27_I	31_W	0.520	1.00
70_D	77_K	0.517	1.00
265_S	268_A	0.516	1.00
123_A	127_I	0.515	1.00
244_Q	255_R	0.515	1.00
160_L	237_A	0.511	1.00
130_F	137_I	0.510	1.00
184_I	189_I	0.508	1.00
108_Q	182_Q	0.506	1.00
43_S	47_F	0.506	1.00
232_P	236_A	0.506	1.00
36_A	39_Y	0.505	1.00
115_Y	171_S	0.504	1.00
95_A	99_Y	0.504	1.00
190_E	193_A	0.502	1.00
90_S	170_I	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
4tquM	1	0.939	100	0.292	Contact Map
2onkC	2	0.8475	100	0.318	Contact Map
3d31C	2	0.8373	100	0.319	Contact Map
4tquN	1	0.8881	100	0.35	Contact Map
3rlfF	1	0.9356	100	0.355	Contact Map
3rlfG	1	0.8983	100	0.366	Contact Map
4ymuD	2	0.7254	99.9	0.516	Contact Map
3tuiA	2	0.7051	99.9	0.543	Contact Map
2kogA	1	0.1356	17.2	0.945	Contact Map
2m8rA	1	0.1254	14.6	0.947	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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