YPHD - ECOLI - GREMLIN Contacts

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YPHD - Probable ABC transporter permease protein YphD

UniProt:	P77315	Sequences: MSASSLPLPQGKSVSLKQFVSRHINEIGLLVVIAILYLVFSLNAPGFISLNNQMNVLRDAATIGIAAWAMTLIIISGEIDVSVGPMVAFVSVCLAFLLQFEVPLAVACLLVLLLGALMGTLAGVLRGVFNVPSFVATLGLWSALRGMGLFMTNALPVPIDENEVLDWLGGQFLGVPVSALIMIVLFALFVFISRKTAFGRSVFAVGGNATAAQLCGINVRRVRILIFTLSGLLAAVTGILLAARLGSGNAGAANGLEFDVIAAVVVGGTALSGGRGSLFGTLLGVLVITLIGNGLVLLGINSFFQQVVRGVIIVVAVLANILLTQRSSKAKR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13465
Length:	332 (268)
Sequences:	31181 (19643)
Seq/√Len:	1199.9

ECOLI - YPHD ARAH XYLH YTFT ALSC LSRD RBSC LSRC MGLC YJFF LIVM LIVH
BACSU - RBSC YUFP YUFQ
HALSA - Q9HR22 Q9HR23
SULSO - Q97UZ8 Q97UZ9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
112_L	232_L	3.936	1.00
116_A	228_T	3.600	1.00
116_A	232_L	3.048	1.00
93_C	114_L	2.928	1.00
120_T	228_T	2.860	1.00
209_A	223_R	2.786	1.00
97_L	110_L	2.605	1.00
71_T	281_T	2.555	1.00
64_G	182_M	2.533	1.00
202_V	226_I	2.471	1.00
218_N	221_R	2.443	1.00
128_V	220_R	2.425	1.00
115_G	235_A	2.367	1.00
119_G	231_G	2.327	1.00
192_I	198_F	2.221	1.00
221_R	225_L	2.220	1.00
122_A	140_L	2.215	1.00
190_V	194_R	2.208	1.00
191_F	195_K	2.174	1.00
120_T	224_I	2.163	1.00
259_D	292_G	2.150	1.00
201_S	222_V	2.078	1.00
198_F	225_L	2.062	1.00
188_L	192_I	2.036	1.00
124_V	128_V	2.021	1.00
103_P	106_V	1.959	1.00
112_L	236_V	1.952	1.00
66_A	260_V	1.930	1.00
88_A	148_G	1.927	1.00
94_L	111_V	1.913	1.00
105_A	109_L	1.911	1.00
115_G	231_G	1.881	1.00
187_A	191_F	1.870	1.00
60_A	289_T	1.809	1.00
205_V	222_V	1.776	1.00
108_C	239_I	1.736	1.00
94_L	239_I	1.735	1.00
67_A	281_T	1.711	1.00
73_I	230_S	1.708	1.00
142_S	145_R	1.691	1.00
204_A	212_A	1.687	1.00
123_G	224_I	1.659	1.00
72_L	189_F	1.655	1.00
60_A	286_L	1.609	1.00
170_G	173_L	1.603	1.00
197_A	201_S	1.595	1.00
166_D	169_G	1.560	1.00
118_M	144_L	1.537	1.00
75_I	203_F	1.528	1.00
64_G	285_V	1.508	1.00
259_D	309_R	1.503	1.00
89_F	118_M	1.473	1.00
198_F	202_V	1.470	1.00
96_F	151_M	1.466	1.00
112_L	239_I	1.460	1.00
267_G	280_G	1.459	1.00
210_T	213_Q	1.447	1.00
186_F	282_L	1.423	1.00
85_P	145_R	1.421	1.00
140_L	144_L	1.419	1.00
209_A	213_Q	1.416	1.00
66_A	87_V	1.409	1.00
128_V	224_I	1.405	1.00
87_V	241_L	1.394	1.00
277_S	280_G	1.373	1.00
201_S	217_I	1.353	1.00
225_L	228_T	1.352	1.00
96_F	99_Q	1.349	1.00
201_S	212_A	1.349	1.00
102_V	106_V	1.345	1.00
72_L	226_I	1.340	1.00
76_S	226_I	1.337	1.00
69_A	233_L	1.321	1.00
106_V	109_L	1.316	1.00
163_E	166_D	1.314	1.00
65_I	237_T	1.290	1.00
65_I	240_L	1.285	1.00
97_L	102_V	1.280	1.00
224_I	228_T	1.276	1.00
267_G	284_G	1.273	1.00
212_A	217_I	1.267	1.00
217_I	222_V	1.267	1.00
111_V	115_G	1.261	1.00
164_V	168_L	1.253	1.00
68_W	189_F	1.251	1.00
124_V	224_I	1.251	1.00
52_N	293_N	1.244	1.00
78_E	133_S	1.244	1.00
205_V	219_V	1.243	1.00
70_M	260_V	1.233	1.00
102_V	110_L	1.229	1.00
64_G	282_L	1.221	1.00
127_G	220_R	1.220	1.00
83_V	234_A	1.211	1.00
205_V	212_A	1.198	1.00
97_L	100_F	1.193	1.00
70_M	264_V	1.191	1.00
228_T	232_L	1.183	1.00
56_V	289_T	1.183	1.00
78_E	227_F	1.175	1.00
293_N	296_V	1.173	1.00
93_C	97_L	1.167	1.00
109_L	113_L	1.160	1.00
67_A	263_A	1.143	1.00
78_E	223_R	1.142	1.00
113_L	116_A	1.138	1.00
56_V	290_L	1.131	1.00
107_A	111_V	1.122	1.00
194_R	203_F	1.118	1.00
171_Q	174_G	1.106	1.00
180_L	184_V	1.106	1.00
69_A	83_V	1.105	1.00
225_L	229_L	1.102	1.00
94_L	243_A	1.098	1.00
75_I	276_G	1.098	1.00
86_M	118_M	1.089	1.00
173_L	180_L	1.087	1.00
164_V	167_W	1.086	1.00
67_A	264_V	1.085	1.00
85_P	144_L	1.085	1.00
185_L	233_L	1.080	1.00
60_A	285_V	1.078	1.00
213_Q	220_R	1.076	1.00
190_V	195_K	1.066	1.00
127_G	137_T	1.057	1.00
96_F	152_T	1.057	1.00
231_G	235_A	1.055	1.00
125_L	136_A	1.044	1.00
304_F	307_V	1.041	1.00
187_A	190_V	1.038	1.00
117_L	120_T	1.032	1.00
116_A	235_A	1.020	1.00
92_V	148_G	1.018	1.00
263_A	284_G	1.015	1.00
165_L	168_L	1.014	1.00
122_A	136_A	1.012	1.00
189_F	229_L	1.008	1.00
256_L	259_D	1.002	1.00
92_V	250_A	1.002	1.00
229_L	233_L	0.995	1.00
111_V	239_I	0.994	1.00
202_V	222_V	0.992	1.00
213_Q	219_V	0.991	1.00
177_V	180_L	0.989	1.00
222_V	225_L	0.988	1.00
71_T	264_V	0.985	1.00
145_R	149_L	0.981	1.00
186_F	233_L	0.977	1.00
164_V	169_G	0.977	1.00
66_A	237_T	0.975	1.00
238_G	242_A	0.970	1.00
279_F	283_L	0.970	1.00
198_F	222_V	0.969	1.00
124_V	129_F	0.966	1.00
184_V	188_L	0.962	1.00
84_G	257_E	0.961	1.00
80_D	83_V	0.954	1.00
292_G	309_R	0.954	1.00
109_L	112_L	0.953	1.00
71_T	276_G	0.943	1.00
221_R	224_I	0.939	1.00
294_G	298_L	0.935	1.00
141_W	145_R	0.934	1.00
61_A	179_A	0.930	1.00
54_M	58_R	0.930	1.00
74_I	264_V	0.919	1.00
263_A	285_V	0.917	1.00
62_T	237_T	0.914	1.00
97_L	107_A	0.910	1.00
76_S	202_V	0.906	1.00
89_F	93_C	0.906	1.00
306_Q	309_R	0.905	1.00
230_S	234_A	0.904	1.00
85_P	141_W	0.903	1.00
92_V	152_T	0.902	1.00
91_S	242_A	0.901	1.00
166_D	170_G	0.899	1.00
182_M	186_F	0.896	1.00
67_A	285_V	0.894	1.00
70_M	83_V	0.894	1.00
211_A	215_C	0.892	1.00
169_G	172_F	0.887	1.00
113_L	117_L	0.884	1.00
126_R	136_A	0.883	1.00
64_G	186_F	0.882	1.00
288_I	309_R	0.878	1.00
84_G	255_G	0.877	1.00
87_V	253_A	0.875	1.00
125_L	129_F	0.874	1.00
178_S	240_L	0.873	1.00
130_N	209_A	0.871	1.00
75_I	194_R	0.866	1.00
73_I	80_D	0.860	1.00
112_L	235_A	0.857	1.00
277_S	281_T	0.853	1.00
183_I	187_A	0.852	1.00
150_F	304_F	0.848	1.00
200_R	203_F	0.847	1.00
86_M	234_A	0.845	1.00
51_N	54_M	0.844	1.00
96_F	100_F	0.841	1.00
275_R	279_F	0.840	1.00
87_V	256_L	0.838	1.00
157_V	160_D	0.836	1.00
72_L	229_L	0.835	1.00
162_N	166_D	0.831	1.00
205_V	226_I	0.831	1.00
255_G	259_D	0.830	1.00
68_W	185_L	0.826	1.00
208_N	211_A	0.825	1.00
295_L	308_V	0.825	1.00
59_D	63_I	0.823	1.00
315_V	319_A	0.821	1.00
193_S	202_V	0.818	1.00
234_A	238_G	0.816	1.00
90_V	111_V	0.816	1.00
123_G	127_G	0.813	1.00
106_V	110_L	0.812	1.00
281_T	285_V	0.810	1.00
190_V	279_F	0.810	1.00
219_V	223_R	0.808	1.00
68_W	281_T	0.808	1.00
90_V	115_G	0.803	1.00
121_L	125_L	0.802	1.00
165_L	169_G	0.801	1.00
123_G	128_V	0.796	1.00
120_T	124_V	0.793	1.00
86_M	115_G	0.792	1.00
93_C	96_F	0.790	1.00
91_S	248_G	0.789	1.00
220_R	223_R	0.787	1.00
90_V	238_G	0.785	1.00
65_I	182_M	0.783	1.00
205_V	223_R	0.782	1.00
66_A	83_V	0.781	1.00
251_G	254_N	0.777	1.00
112_L	116_A	0.777	1.00
53_Q	294_G	0.777	1.00
72_L	193_S	0.772	1.00
156_P	159_I	0.770	1.00
177_V	181_I	0.769	1.00
95_A	248_G	0.768	1.00
293_N	297_L	0.767	1.00
91_S	252_A	0.757	1.00
220_R	224_I	0.757	1.00
156_P	160_D	0.754	1.00
117_L	121_L	0.753	1.00
286_L	290_L	0.749	1.00
232_L	235_A	0.748	1.00
155_L	158_P	0.748	1.00
66_A	69_A	0.746	1.00
55_N	59_D	0.745	1.00
146_G	149_L	0.739	1.00
209_A	219_V	0.738	1.00
192_I	195_K	0.731	1.00
232_L	236_V	0.728	1.00
81_V	261_I	0.724	1.00
69_A	234_A	0.721	1.00
87_V	237_T	0.720	1.00
201_S	218_N	0.720	1.00
65_I	185_L	0.719	1.00
170_G	174_G	0.717	1.00
188_L	191_F	0.713	1.00
89_F	115_G	0.710	1.00
74_I	261_I	0.709	1.00
100_F	103_P	0.707	1.00
63_I	259_D	0.707	1.00
179_A	183_I	0.706	1.00
311_V	315_V	0.705	1.00
145_R	257_E	0.704	1.00
60_A	64_G	0.701	1.00
133_S	227_F	0.700	1.00
90_V	114_L	0.694	1.00
94_L	107_A	0.688	1.00
61_A	182_M	0.688	1.00
63_I	263_A	0.683	1.00
57_L	61_A	0.682	1.00
86_M	122_A	0.680	1.00
303_F	306_Q	0.679	1.00
172_F	180_L	0.677	1.00
143_A	147_M	0.675	1.00
127_G	224_I	0.674	1.00
78_E	209_A	0.670	1.00
119_G	228_T	0.670	1.00
71_T	75_I	0.669	1.00
86_M	90_V	0.669	1.00
71_T	278_L	0.667	1.00
292_G	305_Q	0.660	1.00
86_M	231_G	0.660	1.00
285_V	289_T	0.659	1.00
73_I	227_F	0.658	1.00
162_N	167_W	0.657	1.00
235_A	239_I	0.657	1.00
191_F	194_R	0.656	1.00
115_G	119_G	0.645	1.00
86_M	144_L	0.644	1.00
198_F	229_L	0.643	1.00
108_C	112_L	0.642	1.00
89_F	144_L	0.642	1.00
56_V	293_N	0.640	1.00
162_N	165_L	0.639	1.00
192_I	225_L	0.637	1.00
241_L	245_L	0.634	1.00
76_S	205_V	0.632	1.00
186_F	190_V	0.631	1.00
189_F	233_L	0.628	1.00
229_L	232_L	0.628	1.00
126_R	133_S	0.627	1.00
168_L	171_Q	0.625	1.00
82_S	122_A	0.622	1.00
189_F	193_S	0.621	1.00
192_I	196_T	0.621	1.00
69_A	73_I	0.618	1.00
55_N	293_N	0.616	1.00
93_C	110_L	0.615	1.00
267_G	281_T	0.613	1.00
116_A	119_G	0.609	1.00
72_L	192_I	0.607	1.00
63_I	285_V	0.606	1.00
164_V	171_Q	0.606	1.00
138_L	142_S	0.605	1.00
219_V	222_V	0.604	1.00
50_L	53_Q	0.603	1.00
94_L	238_G	0.603	1.00
184_V	187_A	0.603	1.00
52_N	297_L	0.601	1.00
130_N	220_R	0.601	1.00
76_S	223_R	0.600	1.00
302_S	305_Q	0.599	1.00
262_A	313_I	0.598	1.00
56_V	60_A	0.596	1.00
102_V	105_A	0.596	1.00
145_R	254_N	0.596	1.00
90_V	234_A	0.594	1.00
102_V	107_A	0.593	1.00
62_T	244_R	0.592	1.00
112_L	115_G	0.590	1.00
185_L	236_V	0.587	1.00
212_A	219_V	0.586	1.00
80_D	230_S	0.585	1.00
223_R	226_I	0.580	1.00
104_L	243_A	0.577	1.00
210_T	214_L	0.575	1.00
97_L	114_L	0.574	1.00
86_M	119_G	0.573	1.00
142_S	146_G	0.572	1.00
295_L	300_I	0.570	1.00
158_P	161_E	0.570	1.00
266_V	284_G	0.569	1.00
58_R	179_A	0.569	1.00
168_L	172_F	0.568	1.00
89_F	114_L	0.568	1.00
88_A	253_A	0.567	1.00
263_A	281_T	0.567	1.00
62_T	241_L	0.565	1.00
254_N	257_E	0.564	1.00
263_A	288_I	0.563	1.00
126_R	227_F	0.562	1.00
141_W	257_E	0.561	1.00
53_Q	57_L	0.561	1.00
116_A	231_G	0.561	1.00
58_R	244_R	0.560	1.00
241_L	256_L	0.558	1.00
57_L	60_A	0.557	1.00
190_V	277_S	0.555	1.00
175_V	243_A	0.549	1.00
249_N	252_A	0.549	1.00
93_C	111_V	0.546	1.00
266_V	316_A	0.545	1.00
228_T	231_G	0.544	1.00
280_G	284_G	0.541	1.00
138_L	141_W	0.540	1.00
53_Q	56_V	0.539	1.00
52_N	55_N	0.537	1.00
309_R	313_I	0.529	1.00
231_G	234_A	0.529	1.00
259_D	306_Q	0.528	1.00
97_L	101_E	0.527	1.00
83_V	230_S	0.526	1.00
59_D	293_N	0.526	1.00
98_L	107_A	0.526	1.00
63_I	256_L	0.525	1.00
194_R	197_A	0.524	1.00
203_F	276_G	0.524	1.00
181_I	236_V	0.523	1.00
166_D	171_Q	0.522	1.00
68_W	186_F	0.521	1.00
309_R	317_V	0.519	1.00
156_P	161_E	0.518	1.00
93_C	115_G	0.516	1.00
68_W	190_V	0.513	1.00
148_G	151_M	0.513	1.00
305_Q	309_R	0.513	1.00
137_T	141_W	0.513	1.00
258_F	262_A	0.511	1.00
203_F	206_G	0.510	1.00
264_V	281_T	0.510	1.00
181_I	185_L	0.509	1.00
64_G	68_W	0.509	1.00
155_L	160_D	0.508	1.00
61_A	65_I	0.500	1.00
284_G	287_V	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
4g1uA	2	0.7892	96.8	0.886	Contact Map
2qi9A	2	0.8705	96.6	0.889	Contact Map
2nq2A	2	0.8193	96.4	0.89	Contact Map
3d31C	2	0.6958	79.8	0.928	Contact Map
2onkC	2	0.7078	76.8	0.929	Contact Map
1u7gA	3	0.5633	38	0.945	Contact Map
2gfpA	2	0.5422	33.5	0.947	Contact Map
2rddB	1	0.0934	33.2	0.947	Contact Map
2ks1B	1	0.1325	29.6	0.948	Contact Map
2jwaA	2	0.1325	25.7	0.95	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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