YUFP - BACSU - GREMLIN Contacts

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YUFP - Uncharacterized ABC transporter permease protein YufP

UniProt:	O05254	Sequences: MVKRLSHLLVPLIAIILGLAAGALIMLVSGYSVASGYSALWNGIFGEIYYVGETIRQITPYILSGLAVAFAFRTGLFNIGVEGQLLVGWTAAVWVGTAFDGPAYIHLPLALITAAAAGGLWGFIPGILKARFYVHEVIVTIMMNYIALHMTNYIISNVLTDHQDKTGKIHESASLRSPFLEQITDYSRLHLGIIVALLAAVIMWFIINKSTKGFELRAVGFNQHASQYAGMSVRKNIMTSMLISGAFAGLAGAMEGLGTFEYAAVKGAFTGVGFDGIAVALLGGNTAVGVVLAACLLGGLKIGALNMPIESGVPSEVVDIVIAIIILFVASSYAIRFVMGKLKKKGAN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	348 (285)
Sequences:	30944 (20014)
Seq/√Len:	1185.5

ECOLI - YPHD LSRD LIVM XYLH YTFT LSRC YJFF MGLC ARAH RBSC ALSC LIVH
BACSU - YUFP YUFQ RBSC
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
115_A	246_A	4.027	1.00
119_G	242_L	3.686	1.00
119_G	246_A	3.227	1.00
123_F	242_L	2.997	1.00
223_Q	237_I	2.950	1.00
91_A	117_A	2.942	1.00
95_V	113_T	2.751	1.00
216_L	240_S	2.609	1.00
62_I	196_A	2.559	1.00
69_A	290_V	2.544	1.00
131_R	234_R	2.517	1.00
232_S	235_K	2.496	1.00
235_K	239_T	2.380	1.00
206_I	212_K	2.353	1.00
204_W	208_N	2.352	1.00
122_G	245_G	2.346	1.00
118_G	249_G	2.328	1.00
215_E	236_N	2.207	1.00
123_F	238_M	2.190	1.00
125_P	143_M	2.187	1.00
205_F	209_K	2.178	1.00
212_K	239_T	2.169	1.00
275_D	301_K	2.156	1.00
127_I	131_R	2.147	1.00
202_I	206_I	2.080	1.00
92_A	114_A	2.048	1.00
115_A	250_L	1.977	1.00
86_L	151_T	1.966	1.00
64_S	276_G	1.955	1.00
219_V	236_N	1.870	1.00
118_G	245_G	1.859	1.00
108_P	112_I	1.852	1.00
58_I	298_G	1.834	1.00
201_V	205_F	1.796	1.00
92_A	253_A	1.786	1.00
111_L	253_A	1.774	1.00
65_G	290_V	1.759	1.00
102_P	109_L	1.753	1.00
71_A	244_S	1.724	1.00
70_F	203_M	1.704	1.00
126_G	238_M	1.696	1.00
218_A	226_S	1.696	1.00
145_Y	148_L	1.692	1.00
180_L	183_I	1.657	1.00
73_R	217_R	1.632	1.00
211_T	215_E	1.619	1.00
94_W	98_A	1.617	1.00
121_W	147_A	1.614	1.00
62_I	294_A	1.586	1.00
212_K	216_L	1.565	1.00
275_D	322_I	1.559	1.00
96_G	110_A	1.529	1.00
58_I	295_C	1.518	1.00
224_H	227_Q	1.514	1.00
115_A	253_A	1.508	1.00
95_V	99_F	1.507	1.00
83_G	148_L	1.492	1.00
87_V	121_W	1.474	1.00
94_W	154_I	1.460	1.00
223_Q	227_Q	1.452	1.00
131_R	238_M	1.452	1.00
178_P	181_E	1.451	1.00
200_A	291_V	1.444	1.00
85_L	255_E	1.426	1.00
143_M	147_A	1.420	1.00
102_P	108_P	1.420	1.00
239_T	242_L	1.412	1.00
64_S	85_L	1.407	1.00
179_F	182_Q	1.405	1.00
169_I	172_S	1.395	1.00
179_F	183_I	1.393	1.00
215_E	231_M	1.392	1.00
283_G	289_G	1.384	1.00
172_S	175_L	1.373	1.00
102_P	107_L	1.366	1.00
109_L	112_I	1.357	1.00
215_E	226_S	1.352	1.00
63_L	251_A	1.336	1.00
70_F	240_S	1.312	1.00
63_L	254_M	1.310	1.00
238_M	242_L	1.285	1.00
226_S	231_M	1.280	1.00
67_A	247_F	1.273	1.00
231_M	236_N	1.272	1.00
81_V	248_A	1.265	1.00
127_I	238_M	1.264	1.00
54_T	298_G	1.250	1.00
66_L	203_M	1.249	1.00
110_A	114_A	1.245	1.00
76_L	136_E	1.244	1.00
68_V	276_G	1.241	1.00
62_I	291_V	1.240	1.00
76_L	237_I	1.240	1.00
219_V	233_V	1.238	1.00
114_A	118_G	1.234	1.00
283_G	293_A	1.227	1.00
130_A	234_R	1.219	1.00
68_V	280_A	1.212	1.00
112_I	116_A	1.206	1.00
76_L	241_M	1.203	1.00
95_V	101_G	1.195	1.00
38_S	303_G	1.193	1.00
116_A	119_G	1.190	1.00
50_Y	302_I	1.188	1.00
101_G	109_L	1.182	1.00
219_V	226_S	1.177	1.00
208_N	217_R	1.168	1.00
84_Q	121_W	1.156	1.00
175_L	179_F	1.148	1.00
242_L	246_A	1.142	1.00
199_A	247_F	1.140	1.00
91_A	95_V	1.135	1.00
239_T	243_I	1.131	1.00
39_A	42_N	1.125	1.00
204_W	209_K	1.121	1.00
83_G	147_A	1.120	1.00
38_S	42_N	1.118	1.00
54_T	299_G	1.116	1.00
227_Q	234_R	1.110	1.00
65_G	279_V	1.094	1.00
58_I	294_A	1.091	1.00
302_I	305_L	1.088	1.00
130_A	140_T	1.080	1.00
216_L	236_N	1.076	1.00
286_T	289_G	1.069	1.00
120_L	123_F	1.066	1.00
92_A	257_L	1.063	1.00
67_A	81_V	1.048	1.00
65_G	280_A	1.047	1.00
101_G	113_T	1.045	1.00
194_I	198_L	1.043	1.00
243_I	247_F	1.041	1.00
128_L	139_V	1.040	1.00
114_A	253_A	1.039	1.00
94_W	155_I	1.037	1.00
119_G	249_G	1.036	1.00
236_N	239_T	1.031	1.00
317_V	320_I	1.029	1.00
245_G	249_G	1.027	1.00
90_T	151_T	1.027	1.00
125_P	139_V	1.026	1.00
201_V	204_W	1.025	1.00
37_Y	41_W	1.016	1.00
95_V	98_A	1.014	1.00
301_K	322_I	1.008	1.00
227_Q	233_V	1.005	1.00
95_V	110_A	0.999	1.00
252_G	256_G	0.998	1.00
69_A	280_A	0.998	1.00
59_T	193_I	0.997	1.00
272_V	275_D	0.994	1.00
171_E	174_S	0.994	1.00
203_M	243_I	0.993	1.00
144_N	148_L	0.993	1.00
178_P	183_I	0.991	1.00
112_I	115_A	0.984	1.00
72_F	280_A	0.978	1.00
198_L	202_I	0.972	1.00
52_G	56_R	0.971	1.00
82_E	273_G	0.971	1.00
148_L	152_N	0.970	1.00
200_A	247_F	0.968	1.00
64_S	251_A	0.962	1.00
285_N	290_V	0.961	1.00
279_V	293_A	0.957	1.00
212_K	236_N	0.956	1.00
36_G	40_L	0.948	1.00
170_H	173_A	0.947	1.00
177_S	180_L	0.946	1.00
90_T	155_I	0.945	1.00
319_D	322_I	0.945	1.00
60_P	251_A	0.945	1.00
279_V	294_A	0.945	1.00
93_V	97_T	0.942	1.00
74_T	240_S	0.939	1.00
178_P	182_Q	0.938	1.00
83_G	144_N	0.937	1.00
127_I	132_F	0.934	1.00
66_L	199_A	0.930	1.00
244_S	248_A	0.928	1.00
129_K	139_V	0.924	1.00
187_S	194_I	0.922	1.00
288_V	292_L	0.914	1.00
175_L	178_P	0.906	1.00
303_G	307_M	0.904	1.00
168_K	171_E	0.899	1.00
84_Q	248_A	0.899	1.00
116_A	120_L	0.899	1.00
235_K	238_M	0.896	1.00
214_F	217_R	0.894	1.00
192_G	254_M	0.893	1.00
297_L	322_I	0.891	1.00
42_N	46_G	0.891	1.00
196_A	200_A	0.888	1.00
87_V	91_A	0.880	1.00
191_L	194_I	0.879	1.00
88_G	114_A	0.879	1.00
115_A	249_G	0.877	1.00
78_N	81_V	0.877	1.00
88_G	118_G	0.872	1.00
304_A	321_V	0.871	1.00
92_A	96_G	0.865	1.00
65_G	294_A	0.864	1.00
68_V	81_V	0.862	1.00
271_G	275_D	0.862	1.00
219_V	240_S	0.861	1.00
222_N	225_A	0.856	1.00
71_A	78_N	0.855	1.00
255_E	259_T	0.855	1.00
233_V	237_I	0.853	1.00
62_I	200_A	0.850	1.00
128_L	132_F	0.848	1.00
225_A	229_A	0.846	1.00
89_W	256_G	0.846	1.00
328_F	332_S	0.844	1.00
154_I	157_N	0.839	1.00
120_L	124_I	0.839	1.00
57_Q	61_Y	0.839	1.00
89_W	268_A	0.837	1.00
197_L	201_V	0.836	1.00
153_Y	317_V	0.835	1.00
234_R	237_I	0.834	1.00
85_L	272_V	0.833	1.00
88_G	252_G	0.828	1.00
39_A	43_G	0.828	1.00
133_Y	223_Q	0.825	1.00
70_F	207_I	0.820	1.00
91_A	94_W	0.819	1.00
63_L	196_A	0.819	1.00
184_T	187_S	0.818	1.00
150_M	154_I	0.807	1.00
73_R	207_I	0.807	1.00
159_L	162_H	0.807	1.00
35_S	39_A	0.806	1.00
190_H	194_I	0.806	1.00
51_V	303_G	0.804	1.00
248_A	252_G	0.803	1.00
49_Y	52_G	0.803	1.00
40_L	43_G	0.802	1.00
70_F	243_I	0.802	1.00
193_I	197_L	0.801	1.00
124_I	128_L	0.791	1.00
234_R	238_M	0.790	1.00
204_W	288_V	0.790	1.00
69_A	285_N	0.790	1.00
246_A	249_G	0.786	1.00
280_A	285_N	0.781	1.00
109_L	113_T	0.781	1.00
126_G	131_R	0.780	1.00
43_G	47_E	0.775	1.00
85_L	269_F	0.774	1.00
84_Q	118_G	0.773	1.00
286_T	290_V	0.772	1.00
149_H	152_N	0.771	1.00
82_E	271_G	0.769	1.00
53_E	57_Q	0.768	1.00
191_L	195_V	0.768	1.00
207_I	216_L	0.766	1.00
302_I	306_N	0.766	1.00
44_I	47_E	0.765	1.00
223_Q	233_V	0.763	1.00
219_V	237_I	0.762	1.00
123_F	127_I	0.758	1.00
290_V	294_A	0.756	1.00
66_L	290_V	0.756	1.00
64_S	81_V	0.755	1.00
90_T	266_K	0.753	1.00
79_I	277_I	0.751	1.00
126_G	130_A	0.743	1.00
246_A	250_L	0.737	1.00
295_C	299_G	0.733	1.00
156_S	160_T	0.730	1.00
101_G	107_L	0.726	1.00
160_T	164_D	0.726	1.00
115_A	119_G	0.725	1.00
39_A	46_G	0.724	1.00
92_A	110_A	0.717	1.00
67_A	248_A	0.716	1.00
130_A	238_M	0.714	1.00
316_E	319_D	0.712	1.00
38_S	43_G	0.710	1.00
87_V	118_G	0.705	1.00
58_I	62_I	0.704	1.00
111_L	115_A	0.703	1.00
181_E	184_T	0.702	1.00
136_E	241_M	0.700	1.00
88_G	117_A	0.700	1.00
206_I	209_K	0.694	1.00
278_A	326_I	0.691	1.00
146_I	150_M	0.691	1.00
215_E	232_S	0.690	1.00
324_I	328_F	0.690	1.00
61_Y	275_D	0.686	1.00
189_L	258_G	0.686	1.00
202_I	205_F	0.685	1.00
63_L	199_A	0.684	1.00
85_L	251_A	0.676	1.00
148_L	273_G	0.675	1.00
249_G	253_A	0.674	1.00
203_M	247_F	0.673	1.00
40_L	44_I	0.668	1.00
64_S	67_A	0.666	1.00
84_Q	125_P	0.662	1.00
205_F	208_N	0.659	1.00
183_I	186_Y	0.658	1.00
71_A	241_M	0.657	1.00
34_A	38_S	0.656	1.00
55_I	59_T	0.651	1.00
69_A	73_R	0.651	1.00
175_L	180_L	0.648	1.00
35_S	38_S	0.644	1.00
294_A	298_G	0.643	1.00
76_L	223_Q	0.642	1.00
118_G	122_G	0.642	1.00
200_A	204_W	0.639	1.00
157_N	160_T	0.636	1.00
61_Y	279_V	0.636	1.00
119_G	122_G	0.633	1.00
206_I	210_S	0.633	1.00
158_V	162_H	0.631	1.00
53_E	302_I	0.631	1.00
158_V	161_D	0.629	1.00
199_A	250_L	0.629	1.00
72_F	277_I	0.628	1.00
61_Y	272_V	0.626	1.00
122_G	242_L	0.624	1.00
301_K	318_V	0.624	1.00
54_T	302_I	0.623	1.00
203_M	207_I	0.621	1.00
212_K	243_I	0.621	1.00
177_S	181_E	0.618	1.00
133_Y	136_E	0.615	1.00
129_K	241_M	0.614	1.00
56_R	258_G	0.613	1.00
129_K	136_E	0.612	1.00
84_Q	147_A	0.612	1.00
84_Q	88_G	0.611	1.00
96_G	257_L	0.607	1.00
84_Q	245_G	0.607	1.00
35_S	299_G	0.607	1.00
50_Y	306_N	0.607	1.00
87_V	147_A	0.603	1.00
160_T	163_Q	0.603	1.00
133_Y	234_R	0.603	1.00
69_A	287_A	0.600	1.00
59_T	196_A	0.598	1.00
177_S	183_I	0.598	1.00
48_I	51_V	0.597	1.00
66_L	200_A	0.595	1.00
243_I	246_A	0.595	1.00
80_G	125_P	0.594	1.00
204_W	286_T	0.592	1.00
70_F	206_I	0.592	1.00
93_V	160_T	0.591	1.00
41_W	44_I	0.589	1.00
72_F	285_N	0.586	1.00
170_H	174_S	0.586	1.00
145_Y	149_H	0.584	1.00
233_V	236_N	0.579	1.00
282_L	293_A	0.579	1.00
119_G	245_G	0.575	1.00
107_L	257_L	0.574	1.00
255_E	272_V	0.574	1.00
158_V	164_D	0.573	1.00
237_I	240_S	0.573	1.00
101_G	108_P	0.569	1.00
206_I	239_T	0.566	1.00
171_E	175_L	0.565	1.00
88_G	248_A	0.564	1.00
92_A	252_G	0.563	1.00
322_I	326_I	0.562	1.00
91_A	113_T	0.562	1.00
155_I	158_V	0.561	1.00
35_S	42_N	0.559	1.00
91_A	114_A	0.558	1.00
89_W	264_A	0.556	1.00
242_L	245_G	0.556	1.00
57_Q	302_I	0.555	1.00
61_Y	294_A	0.555	1.00
282_L	329_V	0.555	1.00
67_A	71_A	0.552	1.00
132_F	331_S	0.547	1.00
115_A	118_G	0.546	1.00
71_A	76_L	0.543	1.00
226_S	233_V	0.541	1.00
189_L	192_G	0.540	1.00
187_S	191_L	0.540	1.00
279_V	290_V	0.540	1.00
56_R	193_I	0.540	1.00
144_N	273_G	0.539	1.00
48_I	52_G	0.539	1.00
198_L	201_V	0.539	1.00
62_I	66_L	0.538	1.00
87_V	117_A	0.536	1.00
141_I	145_Y	0.536	1.00
158_V	163_Q	0.535	1.00
275_D	319_D	0.534	1.00
95_V	117_A	0.532	1.00
94_W	97_T	0.531	1.00
97_T	164_D	0.528	1.00
38_S	41_W	0.528	1.00
267_G	270_T	0.527	1.00
270_T	273_G	0.525	1.00
195_V	199_A	0.524	1.00
84_Q	122_G	0.524	1.00
245_G	248_A	0.522	1.00
36_G	39_A	0.521	1.00
140_T	144_N	0.521	1.00
208_N	211_T	0.520	1.00
147_A	151_T	0.519	1.00
189_L	194_I	0.519	1.00
55_I	58_I	0.518	1.00
62_I	197_L	0.518	1.00
182_Q	186_Y	0.517	1.00
60_P	258_G	0.517	1.00
304_A	313_V	0.517	1.00
86_L	268_A	0.516	1.00
151_T	155_I	0.515	1.00
159_L	265_V	0.514	1.00
75_G	223_Q	0.514	1.00
224_H	228_Y	0.512	1.00
81_V	244_S	0.508	1.00
78_N	244_S	0.507	1.00
276_G	280_A	0.507	1.00
151_T	154_I	0.504	1.00
54_T	58_I	0.504	1.00
37_Y	43_G	0.500	1.00
60_P	255_E	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
2nq2A	2	0.8075	96.7	0.88	Contact Map
4g1uA	2	0.7874	95.7	0.891	Contact Map
2qi9A	2	0.8247	95.3	0.894	Contact Map
2rddB	1	0.092	29.7	0.945	Contact Map
2m20A	2	0.1063	27.8	0.946	Contact Map
2l2tA	2	0.1207	21.2	0.949	Contact Map
2kluA	1	0.1264	19	0.95	Contact Map
2gfpA	2	0.5345	18.8	0.95	Contact Map
2ksfA	1	0.3075	13.7	0.953	Contact Map
2ks1B	1	0.1264	12.6	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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