YDFC - BACSU - GREMLIN Contacts

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YDFC - Uncharacterized transporter YdfC

UniProt:	P96680	Sequences: MRKKTVQIMISHSLMIGLWASAFPGIRAGLEGYTPEHLALFRLLIGSMALLLFAVLTQMRLPDLKDIPAIFLLGFLGFAFYHILLNIGEKTVSAGVASLLVTTAPIFSAMLSRLFYKEHFGFTKWLGSMISLLGVLLIAFGAGDFTYSMSGILVILLAAFSESIYFVFQARYIKKYGFIPFVTFTIWGGTIPMLVFLPGLGEEMMNASISATLSIVYLGLLPTVIPYFALAYVTSFVGASEATLSLYVTPALALIISWLWIGEIPTLLSLLGGVVTVGGVCFTYLKVNKMNKIFITHFSAKRVKKL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	306 (277)
Sequences:	39178 (28698)
Seq/√Len:	1724.3

ECOLI - YHBE YICL YEDA YIJE YTFF EAMA RARD YDDG RHTA YIGM
BACSU - YDFC YVBV YDED YBFH YRDR YWFM YCXC YXXF YETK YYAM YDEK YOAV YCBK YOJE
HALSA - Q9HHP6 Q9HQ34 Q9HPI0
SULSO - Q97UX3 Q97X73 Q97UE8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
88_G	155_I	3.329	1.00
11_S	232_Y	2.896	1.00
96_V	152_I	2.769	1.00
232_Y	236_F	2.684	1.00
257_S	263_E	2.563	1.00
47_S	187_W	2.511	1.00
40_L	194_L	2.510	1.00
87_I	154_V	2.473	1.00
84_L	157_L	2.390	1.00
127_G	279_G	2.371	1.00
25_G	217_Y	2.324	1.00
63_D	66_D	2.317	1.00
232_Y	235_S	2.233	1.00
107_F	159_A	2.182	1.00
118_E	170_A	2.143	1.00
111_L	167_V	2.102	1.00
84_L	154_V	2.100	1.00
27_R	263_E	2.083	1.00
98_S	253_A	1.987	1.00
44_L	190_T	1.959	1.00
20_A	252_L	1.956	1.00
12_H	233_V	1.924	1.00
113_R	120_F	1.916	1.00
45_I	219_G	1.901	1.00
26_I	86_N	1.896	1.00
80_F	161_S	1.876	1.00
109_A	128_S	1.866	1.00
153_L	157_L	1.806	1.00
92_V	152_I	1.804	1.00
51_L	183_T	1.795	1.00
66_D	175_K	1.773	1.00
103_T	107_F	1.770	1.00
108_S	243_T	1.761	1.00
52_L	55_V	1.757	1.00
112_S	118_E	1.744	1.00
177_G	180_P	1.743	1.00
191_I	195_V	1.717	1.00
121_G	124_K	1.712	1.00
91_T	150_S	1.664	1.00
219_G	224_V	1.659	1.00
47_S	190_T	1.658	1.00
20_A	256_I	1.634	1.00
281_C	285_L	1.629	1.00
92_V	151_G	1.629	1.00
84_L	161_S	1.622	1.00
238_G	241_E	1.613	1.00
131_S	247_Y	1.558	1.00
195_V	198_P	1.557	1.00
107_F	163_S	1.544	1.00
17_G	252_L	1.542	1.00
21_S	217_Y	1.538	1.00
40_L	190_T	1.527	1.00
266_T	269_S	1.499	1.00
33_Y	211_A	1.478	1.00
127_G	283_T	1.475	1.00
149_M	152_I	1.452	1.00
53_F	57_T	1.440	1.00
267_L	271_L	1.425	1.00
87_I	91_T	1.420	1.00
111_L	115_F	1.414	1.00
107_F	160_F	1.410	1.00
65_K	68_P	1.408	1.00
97_A	155_I	1.403	1.00
65_K	69_A	1.402	1.00
51_L	55_V	1.380	1.00
209_I	213_L	1.376	1.00
15_M	233_V	1.362	1.00
94_A	257_S	1.348	1.00
68_P	72_L	1.337	1.00
134_G	272_G	1.334	1.00
18_L	221_L	1.334	1.00
64_L	67_I	1.332	1.00
137_L	275_V	1.331	1.00
270_L	274_V	1.329	1.00
169_Q	231_A	1.320	1.00
72_L	168_F	1.317	1.00
256_I	260_W	1.310	1.00
112_S	116_Y	1.309	1.00
69_A	168_F	1.305	1.00
64_L	68_P	1.304	1.00
48_M	52_L	1.303	1.00
127_G	282_F	1.296	1.00
52_L	56_L	1.293	1.00
122_F	126_L	1.287	1.00
204_M	207_A	1.286	1.00
92_V	96_V	1.278	1.00
87_I	90_K	1.278	1.00
28_A	214_S	1.278	1.00
29_G	38_L	1.276	1.00
208_S	211_A	1.276	1.00
11_S	229_A	1.273	1.00
24_P	256_I	1.268	1.00
19_W	226_P	1.264	1.00
131_S	279_G	1.259	1.00
95_G	254_L	1.258	1.00
49_A	224_V	1.254	1.00
125_W	129_M	1.254	1.00
38_L	218_L	1.253	1.00
91_T	154_V	1.247	1.00
71_F	188_G	1.247	1.00
252_L	256_I	1.244	1.00
171_R	175_K	1.243	1.00
93_S	96_V	1.236	1.00
46_G	186_I	1.236	1.00
274_V	278_G	1.233	1.00
32_G	211_A	1.227	1.00
265_P	270_L	1.214	1.00
137_L	268_L	1.214	1.00
163_S	167_V	1.213	1.00
111_L	164_I	1.185	1.00
129_M	133_L	1.185	1.00
75_F	192_P	1.184	1.00
9_M	245_S	1.182	1.00
248_V	252_L	1.171	1.00
99_L	273_G	1.166	1.00
40_L	44_L	1.163	1.00
149_M	153_L	1.161	1.00
170_A	238_G	1.160	1.00
192_P	195_V	1.158	1.00
123_T	282_F	1.154	1.00
213_L	217_Y	1.147	1.00
34_T	37_H	1.145	1.00
79_A	193_M	1.143	1.00
150_S	154_V	1.132	1.00
36_E	196_F	1.132	1.00
74_G	188_G	1.122	1.00
108_S	239_A	1.121	1.00
79_A	192_P	1.119	1.00
10_I	14_L	1.116	1.00
171_R	174_K	1.110	1.00
27_R	31_E	1.105	1.00
8_I	233_V	1.099	1.00
114_L	117_K	1.098	1.00
138_I	272_G	1.097	1.00
55_V	59_M	1.092	1.00
91_T	148_S	1.090	1.00
40_L	197_L	1.089	1.00
170_A	174_K	1.079	1.00
89_E	97_A	1.068	1.00
47_S	183_T	1.067	1.00
116_Y	167_V	1.064	1.00
91_T	151_G	1.064	1.00
234_T	242_A	1.056	1.00
134_G	276_T	1.054	1.00
14_L	229_A	1.052	1.00
111_L	163_S	1.046	1.00
120_F	125_W	1.046	1.00
42_R	223_T	1.045	1.00
25_G	214_S	1.044	1.00
210_S	213_L	1.043	1.00
122_F	125_W	1.043	1.00
109_A	120_F	1.035	1.00
21_S	256_I	1.029	1.00
18_L	229_A	1.026	1.00
113_R	119_H	1.026	1.00
170_A	239_A	1.022	1.00
26_I	89_E	1.020	1.00
213_L	216_V	1.016	1.00
76_L	164_I	1.009	1.00
111_L	160_F	1.009	1.00
69_A	172_Y	1.008	1.00
15_M	229_A	1.006	1.00
94_A	261_I	1.001	1.00
150_S	153_L	0.999	1.00
92_V	155_I	0.997	1.00
19_W	230_L	0.997	1.00
66_D	176_Y	0.995	1.00
123_T	286_K	0.995	1.00
39_A	86_N	0.994	1.00
100_L	159_A	0.991	1.00
118_E	124_K	0.987	1.00
209_I	212_T	0.983	1.00
123_T	285_L	0.981	1.00
15_M	19_W	0.980	1.00
108_S	166_F	0.979	1.00
212_T	216_V	0.975	1.00
85_L	89_E	0.970	1.00
36_E	83_I	0.969	1.00
29_G	211_A	0.958	1.00
35_P	39_A	0.955	1.00
59_M	177_G	0.955	1.00
130_I	279_G	0.954	1.00
68_P	71_F	0.947	1.00
151_G	155_I	0.947	1.00
267_L	270_L	0.944	1.00
103_T	135_V	0.942	1.00
121_G	125_W	0.927	1.00
140_F	266_T	0.924	1.00
76_L	161_S	0.924	1.00
100_L	152_I	0.922	1.00
43_L	189_G	0.918	1.00
119_H	123_T	0.914	1.00
108_S	163_S	0.912	1.00
195_V	199_G	0.911	1.00
234_T	238_G	0.909	1.00
136_L	140_F	0.901	1.00
24_P	260_W	0.900	1.00
100_L	155_I	0.898	1.00
159_A	163_S	0.897	1.00
55_V	58_Q	0.894	1.00
29_G	214_S	0.890	1.00
133_L	137_L	0.883	1.00
205_M	208_S	0.878	1.00
206_N	209_I	0.877	1.00
37_H	197_L	0.876	1.00
111_L	114_L	0.875	1.00
187_W	191_I	0.874	1.00
44_L	194_L	0.869	1.00
66_D	69_A	0.869	1.00
99_L	136_L	0.868	1.00
238_G	242_A	0.866	1.00
63_D	67_I	0.864	1.00
39_A	193_M	0.864	1.00
51_L	187_W	0.863	1.00
49_A	52_L	0.860	1.00
49_A	220_L	0.852	1.00
94_A	263_E	0.851	1.00
119_H	122_F	0.850	1.00
16_I	252_L	0.846	1.00
196_F	199_G	0.846	1.00
148_S	152_I	0.843	1.00
258_W	265_P	0.834	1.00
83_I	87_I	0.831	1.00
67_I	188_G	0.830	1.00
8_I	236_F	0.828	1.00
16_I	20_A	0.827	1.00
69_A	171_R	0.827	1.00
55_V	60_R	0.818	1.00
237_V	242_A	0.817	1.00
78_F	165_Y	0.817	1.00
216_V	219_G	0.817	1.00
237_V	241_E	0.816	1.00
56_L	59_M	0.814	1.00
248_V	251_A	0.795	1.00
251_A	273_G	0.794	1.00
24_P	257_S	0.792	1.00
133_L	275_V	0.790	1.00
79_A	83_I	0.788	1.00
215_I	219_G	0.787	1.00
113_R	117_K	0.783	1.00
221_L	225_I	0.780	1.00
268_L	271_L	0.779	1.00
126_L	130_I	0.776	1.00
32_G	208_S	0.775	1.00
137_L	271_L	0.774	1.00
69_A	73_L	0.773	1.00
135_V	139_A	0.769	1.00
164_I	168_F	0.766	1.00
205_M	209_I	0.765	1.00
70_I	176_Y	0.760	1.00
76_L	168_F	0.759	1.00
190_T	194_L	0.756	1.00
233_V	242_A	0.756	1.00
106_I	131_S	0.754	1.00
254_L	265_P	0.751	1.00
271_L	275_V	0.749	1.00
47_S	51_L	0.742	1.00
67_I	71_F	0.740	1.00
50_L	224_V	0.740	1.00
12_H	245_S	0.739	1.00
210_S	214_S	0.736	1.00
162_E	166_F	0.734	1.00
110_M	114_L	0.734	1.00
74_G	79_A	0.734	1.00
155_I	159_A	0.733	1.00
216_V	220_L	0.732	1.00
183_T	187_W	0.725	1.00
254_L	273_G	0.723	1.00
13_S	252_L	0.723	1.00
41_F	45_I	0.722	1.00
109_A	124_K	0.720	1.00
107_F	156_L	0.712	1.00
72_L	75_F	0.711	1.00
188_G	191_I	0.710	1.00
273_G	277_V	0.708	1.00
188_G	192_P	0.708	1.00
211_A	214_S	0.706	1.00
100_L	156_L	0.706	1.00
53_F	179_I	0.703	1.00
184_F	188_G	0.703	1.00
278_G	282_F	0.703	1.00
57_T	177_G	0.700	1.00
80_F	84_L	0.699	1.00
108_S	167_V	0.698	1.00
225_I	229_A	0.697	1.00
120_F	124_K	0.696	1.00
146_T	149_M	0.696	1.00
81_Y	161_S	0.691	1.00
103_T	106_I	0.689	1.00
67_I	70_I	0.687	1.00
26_I	30_L	0.685	1.00
54_A	58_Q	0.682	1.00
182_V	231_A	0.682	1.00
44_L	48_M	0.676	1.00
258_W	264_I	0.676	1.00
16_I	248_V	0.675	1.00
28_A	261_I	0.673	1.00
140_F	143_G	0.667	1.00
203_E	206_N	0.663	1.00
67_I	184_F	0.663	1.00
279_G	283_T	0.661	1.00
70_I	181_F	0.661	1.00
37_H	41_F	0.660	1.00
33_Y	38_L	0.660	1.00
54_A	183_T	0.659	1.00
214_S	217_Y	0.658	1.00
189_G	193_M	0.657	1.00
134_G	279_G	0.657	1.00
176_Y	181_F	0.656	1.00
49_A	219_G	0.656	1.00
69_A	72_L	0.656	1.00
118_E	240_S	0.655	1.00
24_P	94_A	0.652	1.00
88_G	97_A	0.648	1.00
23_F	85_L	0.648	1.00
63_D	68_P	0.647	1.00
88_G	151_G	0.643	1.00
62_P	66_D	0.640	1.00
92_V	97_A	0.639	1.00
257_S	261_I	0.638	1.00
187_W	190_T	0.636	1.00
57_T	60_R	0.635	1.00
81_Y	165_Y	0.634	1.00
78_F	227_Y	0.633	1.00
191_I	194_L	0.633	1.00
244_L	283_T	0.633	1.00
12_H	237_V	0.632	1.00
265_P	269_S	0.629	1.00
56_L	60_R	0.626	1.00
61_L	64_L	0.625	1.00
53_F	56_L	0.625	1.00
162_E	230_L	0.622	1.00
9_M	241_E	0.621	1.00
144_D	147_Y	0.620	1.00
102_T	105_P	0.617	1.00
130_I	282_F	0.617	1.00
22_A	222_P	0.615	1.00
18_L	226_P	0.614	1.00
217_Y	221_L	0.614	1.00
109_A	113_R	0.614	1.00
264_I	268_L	0.612	1.00
45_I	49_A	0.608	1.00
105_P	247_Y	0.607	1.00
116_Y	171_R	0.606	1.00
8_I	237_V	0.606	1.00
46_G	224_V	0.605	1.00
85_L	158_A	0.605	1.00
154_V	157_L	0.604	1.00
254_L	258_W	0.600	1.00
23_F	98_S	0.598	1.00
103_T	159_A	0.594	1.00
124_K	238_G	0.594	1.00
228_F	232_Y	0.593	1.00
78_F	185_T	0.593	1.00
196_F	200_L	0.585	1.00
85_L	97_A	0.584	1.00
269_S	273_G	0.584	1.00
71_F	75_F	0.583	1.00
79_A	196_F	0.581	1.00
180_P	184_F	0.580	1.00
147_Y	150_S	0.576	1.00
266_T	270_L	0.565	1.00
102_T	135_V	0.564	1.00
256_I	259_L	0.563	1.00
121_G	286_K	0.562	1.00
84_L	158_A	0.557	1.00
115_F	164_I	0.557	1.00
99_L	139_A	0.556	1.00
86_N	90_K	0.555	1.00
255_I	259_L	0.554	1.00
176_Y	180_P	0.549	1.00
99_L	138_I	0.546	1.00
70_I	74_G	0.544	1.00
165_Y	231_A	0.542	1.00
139_A	152_I	0.542	1.00
182_V	185_T	0.540	1.00
166_F	230_L	0.539	1.00
48_M	51_L	0.539	1.00
110_M	128_S	0.539	1.00
184_F	187_W	0.538	1.00
9_M	13_S	0.535	1.00
18_L	222_P	0.534	1.00
264_I	269_S	0.534	1.00
14_L	18_L	0.534	1.00
259_L	262_G	0.533	1.00
255_I	258_W	0.532	1.00
52_L	57_T	0.532	1.00
16_I	249_T	0.531	1.00
194_L	198_P	0.531	1.00
78_F	82_H	0.531	1.00
24_P	253_A	0.527	1.00
258_W	270_L	0.523	1.00
102_T	159_A	0.523	1.00
282_F	286_K	0.523	1.00
41_F	215_I	0.522	1.00
33_Y	37_H	0.521	1.00
116_Y	170_A	0.521	1.00
280_V	283_T	0.520	1.00
30_L	89_E	0.518	1.00
78_F	189_G	0.514	1.00
152_I	156_L	0.514	1.00
71_F	192_P	0.514	1.00
81_Y	85_L	0.514	1.00
146_T	150_S	0.514	1.00
137_L	269_S	0.511	1.00
88_G	92_V	0.505	1.00
141_G	268_L	0.505	1.00
277_V	281_C	0.505	1.00
126_L	133_L	0.505	1.00
13_S	16_I	0.504	1.00
103_T	131_S	0.503	1.00
54_A	180_P	0.503	1.00
18_L	225_I	0.502	1.00
66_D	70_I	0.502	1.00
57_T	179_I	0.502	1.00
247_Y	280_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
2i68A	2	0.2516	98.9	0.754	Contact Map
3b5dA	2	0.3301	98.3	0.802	Contact Map
4j05A	3	0.9379	77.7	0.908	Contact Map
2cfqA	1	0.6111	68.5	0.914	Contact Map
4he8J	1	0.5098	63.9	0.916	Contact Map
3wdoA	1	0.9575	63.4	0.917	Contact Map
1pw4A	1	0.8791	60.4	0.918	Contact Map
3l1lA	2	0.8791	59.7	0.919	Contact Map
4bwzA	2	0.9444	54.9	0.921	Contact Map
4czbA	2	0.9346	50.9	0.923	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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