YRDR - BACSU - GREMLIN Contacts

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YRDR - Uncharacterized transporter YrdR

UniProt:	O07086	Sequences: MKKGQLFIGALTCLVASMSWGAMFPVADHALEFVDPFYFSFIRYGVVTIMLVILLLVREGKKSFHLEGKAKWIILFGVMAFTIYNVLIFLGQRLMGKSGIMTASIAEALMPMLSIVILWGYKHVKPKKYTMISILIAFLGASMVITKGNISFFFSLGDHLFSILFIFIGVLGWVVYTMGGQIFREWSTLRYSTLTCLFGTAITGIMTAILTAQGYVSVPSIKVIAAIKYDFLFMITLPGIIALLSWNYGIKILSSINGILFINFVPITTLLIMVIKGYNITAFDIVGTLFVIIGLILNNIYQRKEDYKQVLQKEKTNLTIT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	321 (277)
Sequences:	38744 (28301)
Seq/√Len:	1700.4

ECOLI - YEDA YHBE YICL YTFF RARD YIJE EAMA RHTA YDDG YIGM
BACSU - YRDR YVBV YDED YCXC YBFH YDFC YXXF YYAM YETK YCBK YWFM YOJE YDEK YOAV
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
91_G	166_I	3.416	1.00
12_T	248_Y	2.947	1.00
102_T	163_I	2.889	1.00
248_Y	252_I	2.775	1.00
273_M	278_Y	2.681	1.00
90_L	165_F	2.539	1.00
48_T	197_L	2.469	1.00
26_V	233_F	2.457	1.00
133_S	294_G	2.400	1.00
87_L	168_I	2.382	1.00
41_F	204_G	2.367	1.00
248_Y	251_K	2.272	1.00
124_V	181_Q	2.217	1.00
113_L	170_V	2.188	1.00
28_D	278_Y	2.162	1.00
87_L	165_F	2.114	1.00
104_S	269_T	2.092	1.00
117_I	178_M	2.084	1.00
225_A	229_Y	2.080	1.00
21_G	268_T	2.050	1.00
46_V	235_I	2.048	1.00
13_C	249_G	1.984	1.00
66_L	69_K	1.959	1.00
95_M	99_G	1.932	1.00
27_A	89_F	1.921	1.00
118_L	124_V	1.901	1.00
119_W	126_P	1.867	1.00
45_G	200_T	1.866	1.00
83_I	172_G	1.847	1.00
52_V	193_T	1.824	1.00
115_I	134_I	1.810	1.00
95_M	162_S	1.798	1.00
95_M	163_I	1.785	1.00
235_I	240_I	1.768	1.00
109_L	113_L	1.766	1.00
164_L	168_I	1.764	1.00
114_S	259_I	1.760	1.00
21_G	272_I	1.756	1.00
127_K	130_T	1.734	1.00
94_L	161_F	1.706	1.00
22_A	233_F	1.646	1.00
296_I	300_I	1.642	1.00
87_L	172_G	1.628	1.00
201_A	205_I	1.627	1.00
205_I	208_A	1.623	1.00
187_S	190_R	1.603	1.00
69_K	185_E	1.600	1.00
48_T	200_T	1.600	1.00
18_M	268_T	1.571	1.00
113_L	174_V	1.569	1.00
224_I	227_I	1.556	1.00
34_V	227_I	1.550	1.00
137_A	263_N	1.540	1.00
254_S	257_N	1.530	1.00
281_T	284_D	1.511	1.00
133_S	298_N	1.494	1.00
53_I	56_L	1.492	1.00
90_L	94_L	1.472	1.00
103_A	166_I	1.454	1.00
16_A	249_G	1.407	1.00
180_G	247_N	1.401	1.00
67_E	71_K	1.391	1.00
41_F	200_T	1.390	1.00
113_L	171_L	1.383	1.00
68_G	71_K	1.382	1.00
54_L	58_R	1.378	1.00
282_A	286_V	1.370	1.00
100_I	273_M	1.360	1.00
19_S	237_L	1.345	1.00
133_S	297_L	1.329	1.00
160_L	163_I	1.329	1.00
118_L	122_K	1.325	1.00
12_T	245_S	1.317	1.00
52_V	56_L	1.315	1.00
101_M	270_L	1.314	1.00
47_V	196_C	1.301	1.00
30_A	39_F	1.297	1.00
20_W	242_A	1.294	1.00
33_F	227_I	1.293	1.00
90_L	93_R	1.290	1.00
268_T	272_I	1.288	1.00
50_M	240_I	1.283	1.00
285_I	289_L	1.280	1.00
143_M	290_F	1.272	1.00
49_I	53_I	1.272	1.00
29_H	230_D	1.271	1.00
95_M	102_T	1.267	1.00
117_I	121_Y	1.266	1.00
25_P	272_I	1.265	1.00
174_V	178_M	1.262	1.00
137_A	294_G	1.259	1.00
94_L	165_F	1.257	1.00
67_E	70_A	1.249	1.00
72_W	179_G	1.249	1.00
225_A	228_K	1.248	1.00
140_G	287_G	1.243	1.00
39_F	234_M	1.243	1.00
128_K	132_I	1.236	1.00
68_G	72_W	1.233	1.00
10_A	261_F	1.223	1.00
131_M	135_L	1.215	1.00
202_I	205_I	1.213	1.00
53_I	57_V	1.207	1.00
264_F	268_T	1.202	1.00
117_I	175_V	1.200	1.00
71_K	75_L	1.198	1.00
105_I	288_T	1.197	1.00
289_L	293_I	1.197	1.00
226_A	229_Y	1.193	1.00
129_Y	297_L	1.193	1.00
35_D	38_Y	1.192	1.00
99_G	102_T	1.190	1.00
229_Y	233_F	1.173	1.00
226_A	230_D	1.172	1.00
143_M	283_F	1.162	1.00
135_L	139_L	1.162	1.00
160_L	164_L	1.157	1.00
280_I	285_I	1.151	1.00
75_L	179_G	1.141	1.00
74_I	198_F	1.139	1.00
94_L	162_S	1.129	1.00
272_I	275_I	1.128	1.00
28_D	32_E	1.127	1.00
82_T	202_I	1.126	1.00
41_F	45_G	1.125	1.00
43_R	239_G	1.120	1.00
181_Q	254_S	1.114	1.00
41_F	207_T	1.111	1.00
48_T	193_T	1.110	1.00
26_V	230_D	1.107	1.00
161_F	165_F	1.105	1.00
78_V	202_I	1.105	1.00
144_V	287_G	1.096	1.00
92_Q	103_A	1.090	1.00
16_A	245_S	1.088	1.00
218_V	221_I	1.087	1.00
11_L	15_V	1.084	1.00
37_F	206_M	1.082	1.00
114_S	255_S	1.080	1.00
100_I	276_K	1.079	1.00
117_I	174_V	1.063	1.00
22_A	272_I	1.061	1.00
15_V	245_S	1.060	1.00
219_P	222_K	1.058	1.00
140_G	291_V	1.057	1.00
124_V	130_T	1.056	1.00
106_A	170_V	1.055	1.00
9_G	249_G	1.054	1.00
82_T	203_T	1.054	1.00
20_W	246_W	1.051	1.00
94_L	159_H	1.051	1.00
126_P	131_M	1.042	1.00
16_A	20_W	1.041	1.00
128_K	131_M	1.040	1.00
206_M	210_L	1.030	1.00
250_I	258_G	1.027	1.00
27_A	92_Q	1.021	1.00
40_S	89_F	1.021	1.00
119_W	125_K	1.020	1.00
250_I	254_S	1.017	1.00
88_I	92_Q	1.012	1.00
72_W	76_F	1.009	1.00
115_I	126_P	1.007	1.00
181_Q	255_S	1.005	1.00
114_S	177_T	1.004	1.00
122_K	178_M	1.003	1.00
117_I	171_L	0.987	1.00
232_L	235_I	0.987	1.00
72_W	183_F	0.983	1.00
100_I	278_Y	0.983	1.00
129_Y	301_Y	0.981	1.00
129_Y	300_I	0.976	1.00
106_A	163_I	0.973	1.00
19_S	245_S	0.971	1.00
30_A	227_I	0.969	1.00
36_P	40_S	0.968	1.00
161_F	164_L	0.965	1.00
106_A	166_I	0.958	1.00
146_T	281_T	0.956	1.00
109_L	141_A	0.940	1.00
229_Y	232_L	0.936	1.00
228_K	232_L	0.934	1.00
95_M	166_I	0.934	1.00
30_A	230_D	0.932	1.00
9_G	252_I	0.930	1.00
205_I	209_I	0.930	1.00
37_F	86_V	0.929	1.00
117_I	120_G	0.929	1.00
60_G	187_S	0.929	1.00
38_Y	207_T	0.927	1.00
282_A	285_I	0.927	1.00
254_S	258_G	0.924	1.00
162_S	166_I	0.924	1.00
127_K	131_M	0.922	1.00
69_K	186_W	0.921	1.00
114_S	174_V	0.916	1.00
74_I	77_G	0.907	1.00
136_I	294_G	0.904	1.00
17_S	21_G	0.903	1.00
170_V	174_V	0.898	1.00
253_L	258_G	0.896	1.00
45_G	204_G	0.891	1.00
142_S	146_T	0.885	1.00
50_M	236_T	0.884	1.00
125_K	129_Y	0.884	1.00
25_P	275_I	0.884	1.00
105_I	142_S	0.883	1.00
69_K	72_W	0.881	1.00
81_F	176_Y	0.881	1.00
120_G	123_H	0.867	1.00
79_M	175_V	0.863	1.00
77_G	198_F	0.862	1.00
267_I	288_T	0.858	1.00
56_L	59_E	0.857	1.00
86_V	90_L	0.853	1.00
56_L	60_G	0.849	1.00
25_P	273_M	0.848	1.00
17_S	268_T	0.847	1.00
71_K	74_I	0.847	1.00
206_M	209_I	0.844	1.00
33_F	224_I	0.844	1.00
72_W	182_I	0.842	1.00
44_Y	199_G	0.839	1.00
253_L	257_N	0.827	1.00
125_K	128_K	0.825	1.00
14_L	268_T	0.825	1.00
139_L	143_M	0.823	1.00
75_L	78_V	0.823	1.00
197_L	201_A	0.811	1.00
208_A	211_T	0.806	1.00
249_G	258_G	0.802	1.00
139_L	290_F	0.788	1.00
79_M	172_G	0.783	1.00
82_T	86_V	0.782	1.00
283_F	286_V	0.781	1.00
230_D	233_F	0.774	1.00
141_A	145_I	0.771	1.00
264_F	267_I	0.771	1.00
198_F	201_A	0.770	1.00
40_S	203_T	0.766	1.00
270_L	280_I	0.765	1.00
13_C	261_F	0.765	1.00
51_L	240_I	0.764	1.00
52_V	197_L	0.764	1.00
182_I	185_E	0.762	1.00
175_V	179_G	0.762	1.00
159_H	163_I	0.761	1.00
270_L	288_T	0.759	1.00
143_M	286_V	0.758	1.00
274_V	280_I	0.755	1.00
112_M	137_A	0.755	1.00
237_L	241_I	0.753	1.00
132_I	136_I	0.751	1.00
173_W	177_T	0.751	1.00
57_V	60_G	0.742	1.00
56_L	61_K	0.737	1.00
17_S	264_F	0.732	1.00
166_I	170_V	0.731	1.00
286_V	290_F	0.726	1.00
42_I	46_V	0.725	1.00
50_M	53_I	0.724	1.00
288_T	292_I	0.722	1.00
84_Y	172_G	0.721	1.00
114_S	178_M	0.721	1.00
13_C	253_L	0.719	1.00
190_R	194_L	0.718	1.00
109_L	112_M	0.718	1.00
126_P	130_T	0.717	1.00
113_L	167_F	0.712	1.00
232_L	236_T	0.708	1.00
241_I	245_S	0.704	1.00
231_F	235_I	0.701	1.00
24_F	88_I	0.701	1.00
50_M	235_I	0.700	1.00
140_G	294_G	0.700	1.00
274_V	279_N	0.699	1.00
193_T	197_L	0.698	1.00
25_P	100_I	0.696	1.00
72_W	75_L	0.695	1.00
106_A	167_F	0.692	1.00
124_V	256_I	0.690	1.00
48_T	52_V	0.688	1.00
83_I	87_L	0.684	1.00
217_S	220_S	0.683	1.00
293_I	297_L	0.681	1.00
119_W	123_H	0.681	1.00
186_W	191_Y	0.680	1.00
116_V	120_G	0.675	1.00
73_I	186_W	0.674	1.00
38_Y	42_I	0.674	1.00
10_A	257_N	0.672	1.00
115_I	130_T	0.665	1.00
84_Y	176_Y	0.664	1.00
224_I	228_K	0.664	1.00
194_L	198_F	0.663	1.00
200_T	204_G	0.663	1.00
23_M	238_P	0.662	1.00
73_I	77_G	0.661	1.00
74_I	78_V	0.660	1.00
146_T	149_N	0.660	1.00
34_V	39_F	0.660	1.00
198_F	202_I	0.660	1.00
79_M	179_G	0.656	1.00
91_G	103_A	0.655	1.00
70_A	73_I	0.652	1.00
81_F	243_L	0.652	1.00
63_S	66_L	0.650	1.00
173_W	246_W	0.649	1.00
58_R	187_S	0.648	1.00
233_F	237_L	0.646	1.00
108_A	141_A	0.646	1.00
45_G	49_I	0.645	1.00
227_I	230_D	0.642	1.00
70_A	74_I	0.641	1.00
64_F	67_E	0.638	1.00
273_M	276_K	0.635	1.00
77_G	82_T	0.635	1.00
244_L	248_Y	0.631	1.00
280_I	284_D	0.631	1.00
88_I	103_A	0.628	1.00
70_A	198_F	0.626	1.00
54_L	189_L	0.625	1.00
260_L	298_N	0.622	1.00
24_F	104_S	0.619	1.00
27_A	31_L	0.617	1.00
136_I	297_L	0.617	1.00
294_G	298_N	0.616	1.00
284_D	288_T	0.615	1.00
111_P	263_N	0.615	1.00
9_G	253_L	0.615	1.00
81_F	195_T	0.613	1.00
197_L	200_T	0.613	1.00
279_N	283_F	0.612	1.00
58_R	61_K	0.612	1.00
66_L	70_A	0.609	1.00
105_I	145_I	0.607	1.00
29_H	276_K	0.607	1.00
46_V	50_M	0.606	1.00
91_G	162_S	0.605	1.00
19_S	242_A	0.605	1.00
55_L	59_E	0.604	1.00
87_L	169_G	0.604	1.00
88_I	169_G	0.601	1.00
72_W	77_G	0.597	1.00
281_T	285_I	0.593	1.00
211_T	219_P	0.592	1.00
176_Y	247_N	0.590	1.00
31_L	92_Q	0.590	1.00
115_I	119_W	0.589	1.00
192_S	247_N	0.589	1.00
55_L	193_T	0.589	1.00
60_G	63_S	0.588	1.00
177_T	246_W	0.583	1.00
263_N	295_L	0.582	1.00
15_V	19_S	0.582	1.00
192_S	195_T	0.581	1.00
158_D	161_F	0.580	1.00
89_F	93_R	0.576	1.00
70_A	194_L	0.573	1.00
145_I	163_I	0.573	1.00
95_M	103_A	0.571	1.00
109_L	170_V	0.568	1.00
108_A	111_P	0.565	1.00
165_F	168_I	0.563	1.00
181_Q	184_R	0.562	1.00
73_I	76_F	0.562	1.00
201_A	204_G	0.562	1.00
194_L	197_L	0.561	1.00
270_L	274_V	0.559	1.00
47_V	240_I	0.559	1.00
222_K	225_A	0.559	1.00
23_M	89_F	0.556	1.00
73_I	191_Y	0.556	1.00
199_G	203_T	0.554	1.00
116_V	134_I	0.553	1.00
177_T	259_I	0.552	1.00
262_I	265_V	0.551	1.00
17_S	265_V	0.549	1.00
19_S	238_P	0.548	1.00
130_T	254_S	0.544	1.00
34_V	38_Y	0.543	1.00
55_L	190_R	0.541	1.00
82_T	206_M	0.540	1.00
122_K	182_I	0.539	1.00
171_L	175_V	0.538	1.00
81_F	199_G	0.536	1.00
13_C	246_W	0.534	1.00
108_A	170_V	0.531	1.00
285_I	288_T	0.529	1.00
121_Y	175_V	0.526	1.00
118_L	256_I	0.526	1.00
274_V	285_I	0.525	1.00
55_L	58_R	0.523	1.00
57_V	61_K	0.523	1.00
295_L	298_N	0.523	1.00
143_M	284_D	0.521	1.00
127_K	301_Y	0.518	1.00
23_M	234_M	0.517	1.00
81_F	85_N	0.516	1.00
24_F	28_D	0.515	1.00
140_G	290_F	0.515	1.00
10_A	14_L	0.514	1.00
204_G	208_A	0.513	1.00
249_G	253_L	0.513	1.00
109_L	137_A	0.512	1.00
42_I	231_F	0.511	1.00
112_M	134_I	0.510	1.00
58_R	189_L	0.508	1.00
122_K	181_Q	0.508	1.00
279_N	284_D	0.508	1.00
105_I	144_V	0.506	1.00
54_L	57_V	0.505	1.00
245_S	248_Y	0.504	1.00
188_T	192_S	0.503	1.00
21_G	269_T	0.500	1.00
104_S	108_A	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	0.2368	98.6	0.789	Contact Map
3b5dA	2	0.3146	98.1	0.816	Contact Map
1pw4A	1	0.9408	81.3	0.907	Contact Map
3wdoA	1	0.9252	77.1	0.91	Contact Map
4pypA	1	0.891	68	0.917	Contact Map
4he8J	1	0.486	58.4	0.921	Contact Map
3zuxA	1	0.8785	58.4	0.921	Contact Map
4j05A	3	0.9097	51.6	0.925	Contact Map
4tphA	2	0.8567	49.3	0.926	Contact Map
4w6vA	1	0.9034	36.3	0.931	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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