YTFT - ECOLI - GREMLIN Contacts

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YTFT - Inner membrane ABC transporter permease protein YtfT

UniProt:	P39328	Sequences: MMPQSLPDTTTPKRRFRWPTGMPQLVALLLVLLVDSLVAPHFWQVVLQDGRLFGSPIDILNRAAPVALLAIGMTLVIATGGIDLSVGAVMAIAGATTAAMTVAGFSLPIVLLSALGTGILAGLWNGILVAILKIQPFVATLILMVAGRGVAQLITAGQIVTFNSPDLSWFGSGSLLFLPTPVIIAVLTLILFWLLTRKTALGMFIEAVGINIRAAKNAGVNTRIIVMLTYVLSGLCAAIAGIIVAADIRGADANNAGLWLELDAILAVVIGGGSLMGGRFNLLLSVVGALIIQGMNTGILLSGFPPEMNQVVKAVVVLCVLIVQSQRFISLIKGVRSRDKT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12520
Length:	341 (269)
Sequences:	30980 (19371)
Seq/√Len:	1181.1

ECOLI - YTFT LSRC YPHD ARAH LIVM LSRD XYLH YJFF RBSC ALSC MGLC 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
115_L	235_L	3.968	1.00
119_I	231_V	3.660	1.00
119_I	235_L	3.084	1.00
96_T	117_T	2.987	1.00
123_L	231_V	2.892	1.00
212_I	226_V	2.836	1.00
100_M	113_S	2.714	1.00
74_T	285_S	2.624	1.00
67_A	185_A	2.578	1.00
205_I	229_T	2.500	1.00
221_N	224_I	2.499	1.00
131_I	223_R	2.447	1.00
122_G	234_G	2.381	1.00
118_G	238_A	2.351	1.00
195_L	201_L	2.316	1.00
224_I	228_L	2.297	1.00
193_W	197_R	2.225	1.00
194_L	198_K	2.197	1.00
125_N	143_L	2.186	1.00
123_L	227_M	2.184	1.00
263_D	296_N	2.158	1.00
204_F	225_I	2.112	1.00
201_L	228_L	2.100	1.00
127_I	131_I	2.086	1.00
191_L	195_L	2.028	1.00
91_A	151_A	2.012	1.00
106_S	109_I	1.981	1.00
69_L	264_A	1.959	1.00
97_T	114_A	1.945	1.00
115_L	239_I	1.922	1.00
108_P	112_L	1.910	1.00
118_G	234_G	1.892	1.00
63_A	293_Q	1.772	1.00
190_I	194_L	1.770	1.00
97_T	242_I	1.765	1.00
111_L	242_I	1.762	1.00
208_V	225_I	1.742	1.00
70_A	285_S	1.703	1.00
76_V	233_S	1.693	1.00
207_A	215_A	1.683	1.00
145_V	148_R	1.677	1.00
126_G	227_M	1.637	1.00
75_L	192_F	1.624	1.00
200_A	204_F	1.591	1.00
67_A	289_A	1.567	1.00
101_T	110_V	1.564	1.00
172_S	175_L	1.561	1.00
63_A	290_L	1.555	1.00
263_D	313_K	1.549	1.00
121_A	147_G	1.537	1.00
78_A	206_E	1.519	1.00
201_L	205_I	1.504	1.00
92_I	121_A	1.481	1.00
115_L	242_I	1.480	1.00
213_R	216_K	1.473	1.00
212_I	216_K	1.455	1.00
99_A	154_I	1.454	1.00
88_A	148_R	1.444	1.00
131_I	227_M	1.431	1.00
100_M	103_A	1.425	1.00
100_M	105_F	1.423	1.00
189_L	286_V	1.419	1.00
69_L	90_M	1.414	1.00
143_L	147_G	1.405	1.00
228_L	231_V	1.393	1.00
90_M	244_V	1.391	1.00
204_F	215_A	1.371	1.00
79_T	229_T	1.368	1.00
204_F	220_V	1.368	1.00
271_G	284_L	1.354	1.00
281_N	284_L	1.339	1.00
169_W	172_S	1.333	1.00
72_G	236_C	1.310	1.00
105_F	109_I	1.306	1.00
109_I	112_L	1.302	1.00
75_L	229_T	1.292	1.00
55_S	297_T	1.292	1.00
271_G	288_G	1.290	1.00
68_L	243_I	1.280	1.00
68_L	240_A	1.280	1.00
168_S	172_S	1.279	1.00
220_V	225_I	1.257	1.00
71_I	192_F	1.257	1.00
127_I	227_M	1.245	1.00
215_A	220_V	1.233	1.00
81_G	136_P	1.229	1.00
227_M	231_V	1.226	1.00
110_V	114_A	1.223	1.00
81_G	226_V	1.215	1.00
86_V	237_A	1.215	1.00
130_A	223_R	1.215	1.00
114_A	118_G	1.209	1.00
67_A	286_V	1.209	1.00
59_I	293_Q	1.202	1.00
208_V	222_T	1.201	1.00
252_D	255_N	1.200	1.00
73_M	264_A	1.199	1.00
96_T	100_M	1.193	1.00
73_M	268_V	1.193	1.00
112_L	116_G	1.190	1.00
208_V	215_A	1.189	1.00
165_P	168_S	1.180	1.00
105_F	113_S	1.179	1.00
171_G	174_S	1.168	1.00
99_A	155_T	1.165	1.00
116_G	119_I	1.159	1.00
59_I	294_G	1.150	1.00
81_G	230_Y	1.143	1.00
231_V	235_L	1.133	1.00
193_W	198_K	1.130	1.00
173_G	176_L	1.127	1.00
89_V	121_A	1.122	1.00
197_R	206_E	1.118	1.00
297_T	300_L	1.105	1.00
70_A	268_V	1.100	1.00
188_T	236_C	1.099	1.00
70_A	267_A	1.093	1.00
169_W	174_S	1.092	1.00
97_T	246_A	1.085	1.00
216_K	223_R	1.075	1.00
169_W	173_G	1.067	1.00
234_G	238_A	1.060	1.00
296_N	313_K	1.057	1.00
166_D	169_W	1.056	1.00
63_A	289_A	1.052	1.00
183_I	187_L	1.045	1.00
78_A	280_F	1.043	1.00
168_S	171_G	1.042	1.00
57_I	61_N	1.041	1.00
176_L	183_I	1.041	1.00
120_L	123_L	1.039	1.00
114_A	242_I	1.037	1.00
95_A	151_A	1.035	1.00
228_L	232_L	1.031	1.00
130_A	140_T	1.029	1.00
192_F	232_L	1.028	1.00
95_A	253_A	1.025	1.00
72_G	86_V	1.024	1.00
128_L	139_A	1.014	1.00
88_A	147_G	1.013	1.00
267_A	288_G	1.012	1.00
148_R	152_Q	1.006	1.00
98_A	102_V	1.004	1.00
190_I	193_W	1.003	1.00
225_I	228_L	1.003	1.00
216_K	222_T	1.000	1.00
189_L	236_C	0.988	1.00
308_M	311_V	0.987	1.00
168_S	174_S	0.986	1.00
232_L	236_C	0.984	1.00
187_L	191_L	0.984	1.00
119_I	238_A	0.982	1.00
69_L	240_A	0.981	1.00
125_N	139_A	0.976	1.00
74_T	268_V	0.975	1.00
260_L	263_D	0.969	1.00
205_I	225_I	0.967	1.00
144_M	148_R	0.966	1.00
92_I	96_T	0.961	1.00
83_D	86_V	0.956	1.00
292_I	313_K	0.956	1.00
283_L	287_V	0.951	1.00
241_G	245_A	0.949	1.00
87_G	261_E	0.948	1.00
201_L	225_I	0.942	1.00
267_A	289_A	0.940	1.00
64_A	182_V	0.936	1.00
180_T	183_I	0.935	1.00
74_T	280_F	0.935	1.00
127_I	132_L	0.930	1.00
77_I	268_V	0.916	1.00
94_G	256_A	0.907	1.00
88_A	144_M	0.903	1.00
233_S	237_A	0.902	1.00
319_C	323_V	0.900	1.00
299_I	312_V	0.899	1.00
100_M	110_V	0.897	1.00
193_W	283_L	0.889	1.00
203_M	206_E	0.883	1.00
112_L	115_L	0.883	1.00
214_A	218_A	0.881	1.00
224_I	227_M	0.877	1.00
128_L	132_L	0.875	1.00
65_P	240_A	0.874	1.00
70_A	289_A	0.873	1.00
54_G	57_I	0.871	1.00
67_A	189_L	0.870	1.00
185_A	189_L	0.866	1.00
79_T	205_I	0.866	1.00
89_V	237_A	0.865	1.00
71_I	188_T	0.862	1.00
76_V	83_D	0.860	1.00
95_A	155_T	0.860	1.00
133_K	212_I	0.858	1.00
94_G	245_A	0.857	1.00
56_P	298_G	0.855	1.00
153_L	308_M	0.848	1.00
87_G	259_W	0.848	1.00
186_V	190_I	0.844	1.00
99_A	103_A	0.843	1.00
259_W	263_D	0.843	1.00
208_V	229_T	0.839	1.00
93_A	114_A	0.838	1.00
93_A	118_G	0.837	1.00
68_L	185_A	0.837	1.00
287_V	329_I	0.836	1.00
78_A	197_R	0.836	1.00
150_V	154_I	0.833	1.00
129_V	139_A	0.830	1.00
73_M	86_V	0.827	1.00
109_I	113_S	0.827	1.00
97_T	101_T	0.825	1.00
169_W	175_L	0.825	1.00
115_L	238_A	0.823	1.00
116_G	120_L	0.821	1.00
181_P	243_I	0.818	1.00
196_T	205_I	0.817	1.00
75_L	232_L	0.814	1.00
90_M	260_L	0.813	1.00
237_A	241_G	0.810	1.00
62_R	66_V	0.808	1.00
279_R	283_L	0.803	1.00
123_L	127_I	0.803	1.00
222_T	226_V	0.798	1.00
126_G	130_A	0.798	1.00
211_N	214_A	0.797	1.00
167_L	171_G	0.796	1.00
96_T	99_A	0.792	1.00
180_T	184_I	0.790	1.00
93_A	241_G	0.789	1.00
281_N	285_S	0.788	1.00
124_W	128_L	0.788	1.00
168_S	175_L	0.787	1.00
285_S	289_A	0.785	1.00
71_I	285_S	0.779	1.00
120_L	124_W	0.776	1.00
223_R	227_M	0.773	1.00
315_V	319_C	0.772	1.00
159_I	162_F	0.771	1.00
149_G	152_Q	0.770	1.00
75_L	196_T	0.769	1.00
266_L	317_V	0.766	1.00
235_L	238_A	0.764	1.00
90_M	257_G	0.762	1.00
223_R	226_V	0.760	1.00
208_V	226_V	0.759	1.00
182_V	186_V	0.758	1.00
98_A	251_A	0.754	1.00
89_V	118_G	0.749	1.00
126_G	131_I	0.744	1.00
212_I	222_T	0.739	1.00
297_T	301_L	0.739	1.00
195_L	198_K	0.738	1.00
69_L	86_V	0.730	1.00
55_S	301_L	0.730	1.00
290_L	294_G	0.730	1.00
97_T	110_V	0.727	1.00
68_L	188_T	0.724	1.00
66_V	263_D	0.724	1.00
84_L	265_I	0.720	1.00
155_T	160_V	0.720	1.00
63_A	67_A	0.718	1.00
204_F	221_N	0.717	1.00
115_L	119_I	0.717	1.00
72_G	237_A	0.712	1.00
58_D	62_R	0.704	1.00
77_I	265_I	0.701	1.00
90_M	240_A	0.699	1.00
235_L	239_I	0.697	1.00
191_L	194_L	0.690	1.00
69_L	72_G	0.689	1.00
92_I	118_G	0.681	1.00
325_S	328_F	0.680	1.00
122_G	231_V	0.678	1.00
296_N	309_N	0.677	1.00
94_G	251_A	0.675	1.00
146_A	150_V	0.674	1.00
59_I	297_T	0.672	1.00
89_V	125_N	0.672	1.00
307_E	310_Q	0.668	1.00
64_A	185_A	0.667	1.00
136_P	230_Y	0.664	1.00
155_T	161_T	0.664	1.00
310_Q	313_K	0.662	1.00
148_R	261_E	0.662	1.00
93_A	117_T	0.661	1.00
175_L	183_I	0.659	1.00
74_T	282_L	0.655	1.00
168_S	173_G	0.655	1.00
74_T	78_A	0.654	1.00
192_F	196_T	0.654	1.00
92_I	147_G	0.651	1.00
165_P	169_W	0.644	1.00
89_V	93_A	0.642	1.00
129_V	136_P	0.635	1.00
130_A	227_M	0.632	1.00
81_G	212_I	0.632	1.00
111_L	115_L	0.632	1.00
76_V	230_Y	0.628	1.00
189_L	193_W	0.624	1.00
188_T	239_I	0.624	1.00
60_L	64_A	0.622	1.00
119_I	122_G	0.622	1.00
58_D	297_T	0.621	1.00
61_N	247_D	0.619	1.00
66_V	267_A	0.617	1.00
201_L	232_L	0.616	1.00
192_F	236_C	0.615	1.00
155_T	159_I	0.615	1.00
100_M	117_T	0.612	1.00
238_A	242_I	0.610	1.00
289_A	293_Q	0.610	1.00
195_L	228_L	0.609	1.00
270_I	320_V	0.608	1.00
96_T	113_S	0.608	1.00
118_G	122_G	0.607	1.00
232_L	235_L	0.607	1.00
105_F	110_V	0.604	1.00
244_V	248_I	0.602	1.00
59_I	63_A	0.601	1.00
89_V	234_G	0.601	1.00
298_G	302_S	0.599	1.00
72_G	76_V	0.597	1.00
320_V	324_Q	0.597	1.00
61_N	182_V	0.595	1.00
156_A	160_V	0.594	1.00
161_T	164_S	0.594	1.00
170_F	174_S	0.594	1.00
66_V	289_A	0.594	1.00
157_G	162_F	0.591	1.00
194_L	197_R	0.590	1.00
255_N	258_L	0.589	1.00
231_V	234_G	0.588	1.00
85_S	125_N	0.588	1.00
299_I	304_F	0.585	1.00
93_A	237_A	0.585	1.00
160_V	163_N	0.584	1.00
222_T	225_I	0.582	1.00
270_I	288_G	0.579	1.00
158_Q	161_T	0.576	1.00
167_L	170_F	0.575	1.00
89_V	147_G	0.573	1.00
101_T	246_A	0.570	1.00
171_G	175_L	0.568	1.00
157_G	160_V	0.567	1.00
263_D	310_Q	0.566	1.00
215_A	222_T	0.566	1.00
105_F	108_P	0.565	1.00
195_L	199_T	0.565	1.00
266_L	313_K	0.564	1.00
107_L	246_A	0.563	1.00
167_L	173_G	0.562	1.00
97_T	241_G	0.560	1.00
79_T	208_V	0.560	1.00
89_V	122_G	0.555	1.00
65_P	244_V	0.555	1.00
187_L	190_I	0.555	1.00
75_L	195_L	0.555	1.00
66_V	260_L	0.554	1.00
267_A	271_G	0.554	1.00
133_K	223_R	0.553	1.00
79_T	226_V	0.551	1.00
71_I	189_L	0.549	1.00
267_A	285_S	0.548	1.00
234_G	237_A	0.547	1.00
166_D	173_G	0.547	1.00
115_L	118_G	0.547	1.00
244_V	260_L	0.546	1.00
226_V	229_T	0.546	1.00
129_V	230_Y	0.542	1.00
56_P	60_L	0.541	1.00
324_Q	328_F	0.539	1.00
175_L	179_P	0.538	1.00
271_G	285_S	0.538	1.00
151_A	155_T	0.537	1.00
141_L	145_V	0.535	1.00
53_F	56_P	0.535	1.00
119_I	234_G	0.535	1.00
267_A	292_I	0.534	1.00
193_W	281_N	0.533	1.00
76_V	81_G	0.533	1.00
91_A	256_A	0.532	1.00
96_T	118_G	0.528	1.00
54_G	58_D	0.528	1.00
144_M	261_E	0.527	1.00
174_S	177_F	0.523	1.00
60_L	63_A	0.522	1.00
155_T	158_Q	0.520	1.00
258_L	261_E	0.518	1.00
188_T	192_F	0.516	1.00
206_E	280_F	0.513	1.00
213_R	217_N	0.511	1.00
145_V	149_G	0.510	1.00
83_D	233_S	0.510	1.00
92_I	117_T	0.509	1.00
156_A	159_I	0.507	1.00
86_V	233_S	0.507	1.00
98_A	160_V	0.506	1.00
62_R	297_T	0.506	1.00
151_A	154_I	0.504	1.00
284_L	288_G	0.504	1.00
99_A	102_V	0.503	1.00
311_V	315_V	0.502	1.00
140_T	144_M	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
2qi9A	2	0.8651	97.3	0.879	Contact Map
2nq2A	2	0.824	96.5	0.892	Contact Map
4g1uA	2	0.7859	96.2	0.895	Contact Map
3d31C	2	0.6921	71.3	0.934	Contact Map
2onkC	2	0.7009	61.6	0.938	Contact Map
1u7gA	3	0.566	50.4	0.942	Contact Map
2cfqA	1	0.563	42.7	0.945	Contact Map
2gfpA	2	0.5513	42.6	0.945	Contact Map
4tphA	2	0.5777	16.8	0.955	Contact Map
4m64A	1	0.5924	14.9	0.956	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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