YVRC - BACSU - GREMLIN Contacts

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YVRC - Uncharacterized ABC transporter substrate-binding lipoprotein YvrC

UniProt:	O34805	Sequences: MKKRAGIWAALLLAAVMLAGCGNPADQKDSKAKQKTEVFPVTIDDASNQDVTIKKEPKKIVSLMPSNTEITYALGLGDKVVGVTTNDTYPKEVKKVEKVGDMNVNVEKVISLKPDLVLAHESSMSASADAIKQLKDAGITVLTVNDAQSFSEVYKSIEMIGEAGGAEKKADQLVKSMKSDLKDIQEKAKTISKDEEKSVFIEVSPDPDIYTTGKDTFMNEMLNVIHAKNAAADQTGWVQMTDEAIVKLNPDAIVTTDGVKAKAVEKRDGWSEINAVKHHRVYDVDPDLVTRSGPRLIEGVEELAESIYPDTFKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	314 (269)
Sequences:	14394 (11246)
Seq/√Len:	685.7

ECOLI - FECB FEPB FHUD BTUF
BACSU - YVRC YFIY YXEB YFMC YCLQ YHFQ FHUD FEUA BTR
HALSA - BTUFA Q9HMF9 Q9HPB0 Q9HMG8 Q9HSB2
SULSO - Q97ZU2 Q980Z0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
158_E	171_D	3.862	1.00
161_G	170_A	3.861	1.00
154_Y	178_K	3.808	1.00
249_N	274_N	3.799	1.00
166_A	169_K	3.382	1.00
180_D	301_E	3.135	1.00
44_D	50_D	2.987	1.00
274_N	278_H	2.966	1.00
162_E	167_E	2.959	1.00
62_S	68_T	2.805	1.00
158_E	174_V	2.802	1.00
222_L	227_A	2.541	1.00
169_K	172_Q	2.528	1.00
182_K	186_E	2.483	1.00
42_T	50_D	2.414	1.00
175_K	179_S	2.407	1.00
108_K	111_S	2.406	1.00
171_D	175_K	2.386	1.00
244_A	247_K	2.309	1.00
61_V	109_V	2.122	1.00
45_D	51_V	2.106	1.00
198_S	228_K	2.086	1.00
178_K	182_K	2.004	1.00
60_I	164_G	2.003	1.00
59_K	81_V	2.002	1.00
219_N	223_N	1.989	1.00
71_T	164_G	1.979	1.00
265_E	279_H	1.946	1.00
76_L	166_A	1.938	1.00
76_L	164_G	1.909	1.00
179_S	183_D	1.898	1.00
262_K	266_K	1.848	1.00
183_D	187_K	1.824	1.00
70_I	157_I	1.824	1.00
133_Q	136_D	1.822	1.00
77_G	80_V	1.798	1.00
251_D	274_N	1.762	1.00
252_A	282_Y	1.721	1.00
118_L	160_I	1.720	1.00
273_I	276_V	1.704	1.00
152_E	155_K	1.702	1.00
40_P	52_T	1.697	1.00
252_A	280_R	1.692	1.00
131_I	135_K	1.685	1.00
172_Q	176_S	1.667	1.00
42_T	52_T	1.656	1.00
274_N	277_K	1.606	1.00
182_K	185_Q	1.603	1.00
180_D	298_E	1.592	1.00
82_G	112_L	1.574	1.00
176_S	180_D	1.573	1.00
168_K	172_Q	1.562	1.00
169_K	173_L	1.522	1.00
155_K	159_M	1.508	1.00
155_K	158_E	1.486	1.00
262_K	265_E	1.483	1.00
272_E	277_K	1.474	1.00
41_V	162_E	1.464	1.00
87_D	90_P	1.459	1.00
76_L	80_V	1.453	1.00
105_N	108_K	1.449	1.00
97_E	108_K	1.445	1.00
132_K	136_D	1.432	1.00
154_Y	174_V	1.424	1.00
61_V	112_L	1.422	1.00
104_V	109_V	1.402	1.00
282_Y	306_S	1.393	1.00
91_K	94_K	1.392	1.00
110_I	137_A	1.364	1.00
128_A	132_K	1.361	1.00
132_K	135_K	1.349	1.00
72_Y	93_V	1.348	1.00
81_V	112_L	1.346	1.00
62_S	71_T	1.326	1.00
142_L	159_M	1.314	1.00
167_E	171_D	1.310	1.00
196_E	228_K	1.306	1.00
199_V	227_A	1.299	1.00
186_E	189_K	1.295	1.00
242_D	267_R	1.285	1.00
142_L	163_A	1.278	1.00
175_K	178_K	1.275	1.00
244_A	248_L	1.274	1.00
270_W	276_V	1.268	1.00
173_L	176_S	1.265	1.00
208_D	239_Q	1.263	1.00
253_I	275_A	1.257	1.00
181_L	300_V	1.251	1.00
127_S	130_A	1.247	1.00
180_D	183_D	1.238	1.00
61_V	82_G	1.229	1.00
158_E	178_K	1.226	1.00
71_T	76_L	1.225	1.00
74_L	166_A	1.215	1.00
58_K	115_D	1.208	1.00
179_S	182_K	1.191	1.00
106_V	133_Q	1.184	1.00
184_I	300_V	1.181	1.00
168_K	171_D	1.180	1.00
107_E	243_E	1.170	1.00
198_S	251_D	1.167	1.00
233_D	248_L	1.163	1.00
174_V	178_K	1.153	1.00
86_N	90_P	1.151	1.00
230_A	248_L	1.150	1.00
159_M	162_E	1.148	1.00
183_D	186_E	1.148	1.00
185_Q	224_V	1.148	1.00
230_A	233_D	1.147	1.00
14_A	17_M	1.146	1.00
57_P	115_D	1.141	1.00
119_A	143_T	1.139	1.00
59_K	113_K	1.135	1.00
157_I	170_A	1.133	1.00
231_A	248_L	1.133	1.00
116_L	142_L	1.125	1.00
197_K	252_A	1.118	1.00
53_I	56_E	1.109	1.00
72_Y	77_G	1.109	1.00
200_F	211_T	1.097	1.00
197_K	280_R	1.090	1.00
73_A	173_L	1.065	1.00
90_P	93_V	1.059	1.00
45_D	131_I	1.050	1.00
263_A	266_K	1.036	1.00
60_I	116_L	1.033	1.00
176_S	179_S	1.028	1.00
188_A	191_I	1.028	1.00
202_E	267_R	1.022	1.00
130_A	133_Q	1.022	1.00
214_K	223_N	1.019	1.00
148_Q	151_S	1.017	1.00
228_K	232_A	1.011	1.00
40_P	55_K	1.005	1.00
40_P	56_E	1.001	1.00
181_L	185_Q	0.995	1.00
201_I	222_L	0.991	1.00
185_Q	189_K	0.985	1.00
71_T	80_V	0.970	1.00
80_V	96_V	0.969	1.00
255_T	283_D	0.967	1.00
268_D	271_S	0.962	1.00
180_D	184_I	0.960	1.00
71_T	118_L	0.953	1.00
254_V	303_L	0.949	1.00
231_A	234_Q	0.945	1.00
184_I	304_A	0.935	1.00
188_A	304_A	0.934	1.00
270_W	273_I	0.932	1.00
85_T	98_K	0.931	1.00
72_Y	80_V	0.928	1.00
87_D	91_K	0.924	1.00
220_E	223_N	0.920	1.00
160_I	164_G	0.919	1.00
161_G	174_V	0.914	1.00
53_I	140_T	0.913	1.00
220_E	224_V	0.911	1.00
69_E	295_R	0.911	1.00
301_E	305_E	0.910	1.00
183_D	301_E	0.908	1.00
302_E	305_E	0.899	1.00
158_E	162_E	0.897	1.00
40_P	54_K	0.894	1.00
83_V	98_K	0.892	1.00
199_V	222_L	0.890	1.00
74_L	173_L	0.889	1.00
274_N	280_R	0.888	1.00
117_V	138_G	0.882	1.00
83_V	96_V	0.881	1.00
144_V	159_M	0.875	1.00
231_A	244_A	0.872	1.00
70_I	160_I	0.860	1.00
121_E	145_N	0.859	1.00
56_E	166_A	0.859	1.00
84_T	87_D	0.858	1.00
265_E	281_V	0.855	1.00
14_A	18_L	0.850	1.00
170_A	174_V	0.845	1.00
39_F	55_K	0.844	1.00
72_Y	92_E	0.844	1.00
159_M	163_A	0.841	1.00
156_S	159_M	0.841	1.00
177_M	181_L	0.838	1.00
55_K	58_K	0.834	1.00
45_D	50_D	0.834	1.00
171_D	174_V	0.831	1.00
47_S	135_K	0.825	1.00
229_N	233_D	0.823	1.00
63_L	117_V	0.822	1.00
271_S	276_V	0.822	1.00
204_S	207_P	0.820	1.00
201_I	256_T	0.819	1.00
53_I	57_P	0.818	1.00
47_S	143_T	0.818	1.00
64_M	120_H	0.814	1.00
135_K	141_V	0.814	1.00
295_R	298_E	0.813	1.00
177_M	224_V	0.812	1.00
118_L	163_A	0.810	1.00
56_E	165_G	0.809	1.00
57_P	116_L	0.807	1.00
149_S	152_E	0.806	1.00
60_I	71_T	0.805	1.00
16_V	19_A	0.802	1.00
276_V	281_V	0.801	1.00
255_T	281_V	0.801	1.00
62_S	80_V	0.797	1.00
45_D	48_N	0.797	1.00
221_M	300_V	0.797	1.00
74_L	164_G	0.795	1.00
114_P	117_V	0.792	1.00
187_K	304_A	0.790	1.00
285_D	302_E	0.788	1.00
116_L	163_A	0.783	1.00
89_Y	93_V	0.780	1.00
191_I	196_E	0.780	1.00
154_Y	158_E	0.778	1.00
67_N	118_L	0.778	1.00
245_I	273_I	0.777	1.00
86_N	89_Y	0.775	1.00
15_A	18_L	0.772	1.00
172_Q	175_K	0.772	1.00
109_V	134_L	0.771	1.00
151_S	155_K	0.765	1.00
198_S	202_E	0.761	1.00
200_F	245_I	0.761	1.00
240_M	248_L	0.758	1.00
291_R	296_L	0.758	1.00
140_T	143_T	0.758	1.00
97_E	100_G	0.757	1.00
88_T	92_E	0.756	1.00
293_G	297_I	0.754	1.00
181_L	224_V	0.752	1.00
302_E	306_S	0.751	1.00
39_F	165_G	0.750	1.00
173_L	177_M	0.750	1.00
254_V	282_Y	0.748	1.00
41_V	53_I	0.745	1.00
69_E	293_G	0.743	1.00
292_S	297_I	0.743	1.00
74_L	169_K	0.738	1.00
258_G	261_A	0.738	1.00
195_E	198_S	0.738	1.00
39_F	56_E	0.737	1.00
21_C	24_P	0.735	1.00
99_V	112_L	0.733	1.00
212_T	237_W	0.728	1.00
212_T	216_T	0.726	1.00
117_V	137_A	0.717	1.00
129_D	132_K	0.715	1.00
151_S	154_Y	0.710	1.00
299_G	302_E	0.710	1.00
15_A	19_A	0.707	1.00
293_G	298_E	0.706	1.00
246_V	273_I	0.701	1.00
285_D	288_L	0.701	1.00
187_K	190_T	0.701	1.00
191_I	195_E	0.699	1.00
158_E	161_G	0.695	1.00
214_K	234_Q	0.694	1.00
267_R	271_S	0.693	1.00
160_I	163_A	0.692	1.00
241_T	244_A	0.690	1.00
200_F	250_P	0.685	1.00
157_I	173_L	0.683	1.00
246_V	272_E	0.682	1.00
86_N	92_E	0.676	1.00
153_V	177_M	0.675	1.00
246_V	250_P	0.674	1.00
256_T	284_V	0.674	1.00
144_V	160_I	0.673	1.00
67_N	144_V	0.672	1.00
292_S	295_R	0.670	1.00
90_P	94_K	0.669	1.00
75_G	169_K	0.664	1.00
184_I	188_A	0.664	1.00
198_S	230_A	0.663	1.00
77_G	92_E	0.663	1.00
19_A	22_G	0.663	1.00
257_D	283_D	0.662	1.00
196_E	200_F	0.660	1.00
43_I	53_I	0.656	1.00
59_K	115_D	0.652	1.00
211_T	231_A	0.650	1.00
202_E	205_P	0.648	1.00
213_G	219_N	0.647	1.00
17_M	20_G	0.647	1.00
73_A	157_I	0.637	1.00
74_L	161_G	0.635	1.00
74_L	157_I	0.634	1.00
292_S	299_G	0.634	1.00
298_E	302_E	0.631	1.00
87_D	92_E	0.630	1.00
229_N	232_A	0.629	1.00
53_I	116_L	0.628	1.00
61_V	114_P	0.626	1.00
197_K	227_A	0.626	1.00
203_V	207_P	0.626	1.00
154_Y	177_M	0.625	1.00
184_I	297_I	0.622	1.00
82_G	100_G	0.619	1.00
88_T	91_K	0.613	1.00
214_K	232_A	0.613	1.00
74_L	170_A	0.612	1.00
267_R	270_W	0.611	1.00
43_I	142_L	0.608	1.00
164_G	167_E	0.607	1.00
227_A	252_A	0.606	1.00
202_E	253_I	0.605	1.00
180_D	297_I	0.604	1.00
144_V	156_S	0.602	1.00
292_S	296_L	0.599	1.00
291_R	294_P	0.597	1.00
62_S	67_N	0.597	1.00
106_V	130_A	0.596	1.00
154_Y	181_L	0.594	1.00
264_V	267_R	0.591	1.00
100_G	104_V	0.590	1.00
158_E	167_E	0.589	1.00
39_F	54_K	0.587	1.00
199_V	254_V	0.584	1.00
225_I	300_V	0.584	1.00
71_T	160_I	0.583	1.00
75_G	166_A	0.583	1.00
219_N	232_A	0.583	1.00
197_K	201_I	0.583	1.00
135_K	140_T	0.582	1.00
88_T	93_V	0.580	1.00
157_I	174_V	0.579	1.00
64_M	67_N	0.578	1.00
216_T	219_N	0.578	1.00
87_D	93_V	0.577	1.00
77_G	95_K	0.577	1.00
107_E	110_I	0.577	1.00
20_G	23_N	0.575	1.00
151_S	178_K	0.571	1.00
212_T	218_M	0.571	1.00
108_K	112_L	0.571	1.00
177_M	180_D	0.567	1.00
185_Q	225_I	0.566	1.00
253_I	270_W	0.564	1.00
174_V	177_M	0.564	1.00
199_V	202_E	0.560	1.00
61_V	81_V	0.560	1.00
67_N	160_I	0.557	1.00
89_Y	92_E	0.557	1.00
117_V	134_L	0.556	1.00
106_V	109_V	0.556	1.00
51_V	142_L	0.555	1.00
177_M	297_I	0.555	1.00
215_D	219_N	0.555	1.00
96_V	100_G	0.554	1.00
67_N	70_I	0.554	1.00
231_A	240_M	0.552	1.00
53_I	163_A	0.549	1.00
216_T	236_G	0.547	1.00
61_V	117_V	0.546	1.00
110_I	243_E	0.545	1.00
20_G	24_P	0.545	1.00
215_D	235_T	0.545	1.00
57_P	164_G	0.543	1.00
70_I	73_A	0.542	1.00
221_M	296_L	0.541	1.00
154_Y	224_V	0.539	1.00
184_I	187_K	0.538	1.00
41_V	55_K	0.538	1.00
106_V	137_A	0.536	1.00
288_L	302_E	0.535	1.00
214_K	233_D	0.535	1.00
298_E	301_E	0.535	1.00
196_E	199_V	0.534	1.00
249_N	275_A	0.534	1.00
107_E	241_T	0.533	1.00
130_A	134_L	0.533	1.00
153_V	157_I	0.532	1.00
209_I	212_T	0.529	1.00
222_L	225_I	0.528	1.00
184_I	225_I	0.528	1.00
181_L	184_I	0.525	1.00
37_E	40_P	0.525	1.00
210_Y	239_Q	0.524	1.00
200_F	253_I	0.522	1.00
242_D	270_W	0.522	1.00
291_R	295_R	0.521	1.00
36_T	39_F	0.519	0.99
96_V	99_V	0.515	0.99
128_A	131_I	0.515	0.99
187_K	301_E	0.515	0.99
131_I	143_T	0.514	0.99
137_A	140_T	0.514	0.99
264_V	268_D	0.514	0.99
117_V	141_V	0.511	0.99
185_Q	188_A	0.511	0.99
294_P	298_E	0.509	0.99
86_N	91_K	0.509	0.99
93_V	96_V	0.509	0.99
196_E	226_H	0.508	0.99
62_S	83_V	0.507	0.99
89_Y	295_R	0.506	0.99
178_K	181_L	0.503	0.99
202_E	207_P	0.503	0.99
212_T	219_N	0.502	0.99
134_L	141_V	0.501	0.99
225_I	304_A	0.500	0.99

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
4n01A	1	0.8631	100	0.188	Contact Map
4mlzA	1	0.8662	100	0.216	Contact Map
4hn9A	1	0.8822	100	0.228	Contact Map
4mo9A	1	0.8662	100	0.243	Contact Map
4ovkA	1	0.8535	100	0.249	Contact Map
3pshA	1	0.8567	100	0.252	Contact Map
4ljsA	1	0.9013	100	0.254	Contact Map
4pagA	2	0.8662	100	0.257	Contact Map
4m7oA	1	0.8057	100	0.257	Contact Map
2r79A	5	0.8153	100	0.291	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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