YHBE - ECOLI - GREMLIN Contacts

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YHBE - Uncharacterized inner membrane transporter YhbE

UniProt:	P0AA73	Sequences: MKQQAGIGILLALTTAICWGALPIAMKQVLEVMEPPTIVFYRFLMASIGLGAILAVKKRLPPLRVFRKPRWLILLAVATAGLFGNFILFSSSLQYLSPTASQVIGQLSPVGMMVASVFILKEKMRSTQVVGALMLLSGLVMFFNTSLVEIFTKLTDYTWGVIFGVGAATVWVSYGVAQKVLLRRLASPQILFLLYTLCTIALFPLAKPGVIAQLSHWQLACLIFCGLNTLVGYGALAEAMARWQAAQVSAIITLTPLFTLFFSDLLSLAWPDFFARPMLNLLGYLGAFVVVAGAMYSAIGHRIWGGLRKHTTVVSQPRAGE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11499
Length:	321 (275)
Sequences:	38194 (28006)
Seq/√Len:	1688.8

ECOLI - YHBE YICL YTFF YEDA YIJE RARD YDDG EAMA RHTA
BACSU - YDFC YDED YXXF YRDR YCXC YVBV YBFH YETK YWFM YCBK YYAM YDEK YOAV YOJE
HALSA - Q9HHP6 Q9HQ34 Q9HPI0
SULSO - Q97X73 Q97UX3 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
92_S	164_G	3.303	1.00
11_L	238_E	2.896	1.00
100_A	161_V	2.866	1.00
238_E	242_R	2.712	1.00
263_S	277_P	2.564	1.00
91_S	163_F	2.499	1.00
25_A	224_F	2.402	1.00
40_F	203_F	2.392	1.00
47_S	196_T	2.389	1.00
88_L	166_G	2.329	1.00
238_E	241_A	2.307	1.00
131_G	293_G	2.300	1.00
111_G	168_A	2.219	1.00
122_E	179_K	2.162	1.00
102_Q	259_T	2.143	1.00
88_L	163_F	2.093	1.00
115_A	176_V	2.069	1.00
27_K	277_P	2.061	1.00
67_R	70_R	2.035	1.00
216_H	220_A	2.015	1.00
12_A	239_A	1.996	1.00
26_M	90_S	1.992	1.00
45_M	226_G	1.975	1.00
20_G	258_F	1.974	1.00
117_V	124_M	1.915	1.00
113_M	132_A	1.832	1.00
44_L	199_T	1.812	1.00
96_L	161_V	1.792	1.00
84_G	170_V	1.790	1.00
51_G	192_F	1.783	1.00
200_I	204_P	1.758	1.00
112_M	249_S	1.755	1.00
107_L	111_G	1.754	1.00
125_R	128_Q	1.753	1.00
116_S	122_E	1.739	1.00
95_Y	159_W	1.718	1.00
96_L	160_G	1.717	1.00
52_A	55_A	1.712	1.00
20_G	262_F	1.706	1.00
162_I	166_G	1.689	1.00
186_A	189_Q	1.686	1.00
295_M	299_I	1.678	1.00
204_P	207_K	1.676	1.00
215_S	218_Q	1.651	1.00
226_G	230_L	1.603	1.00
111_G	172_V	1.599	1.00
21_A	224_F	1.588	1.00
244_Q	247_Q	1.580	1.00
32_V	218_Q	1.579	1.00
17_I	258_F	1.572	1.00
88_L	170_V	1.569	1.00
70_R	184_R	1.561	1.00
131_G	297_S	1.550	1.00
135_L	253_T	1.544	1.00
47_S	199_T	1.536	1.00
280_N	283_G	1.530	1.00
91_S	95_Y	1.498	1.00
33_M	218_Q	1.476	1.00
53_I	57_K	1.473	1.00
101_S	164_G	1.447	1.00
51_G	55_A	1.434	1.00
111_G	169_T	1.425	1.00
158_T	161_V	1.410	1.00
178_Q	237_A	1.396	1.00
40_F	199_T	1.390	1.00
52_A	56_V	1.362	1.00
29_V	38_I	1.357	1.00
28_Q	221_C	1.356	1.00
91_S	94_Q	1.351	1.00
15_T	239_A	1.345	1.00
115_A	119_I	1.339	1.00
99_T	260_L	1.323	1.00
19_W	232_G	1.317	1.00
98_P	263_S	1.316	1.00
69_P	73_I	1.309	1.00
48_I	52_A	1.284	1.00
116_S	120_L	1.284	1.00
95_Y	163_F	1.281	1.00
131_G	296_Y	1.280	1.00
69_P	72_L	1.278	1.00
281_L	285_L	1.274	1.00
126_S	130_V	1.273	1.00
258_F	262_F	1.271	1.00
11_L	235_A	1.266	1.00
46_A	195_Y	1.266	1.00
24_I	262_F	1.263	1.00
172_V	176_V	1.261	1.00
97_S	100_A	1.257	1.00
96_L	100_A	1.254	1.00
262_F	266_L	1.252	1.00
141_M	289_V	1.252	1.00
9_I	251_I	1.246	1.00
68_K	72_L	1.245	1.00
68_K	71_W	1.241	1.00
135_L	293_G	1.238	1.00
72_L	76_A	1.221	1.00
217_W	220_A	1.219	1.00
38_I	225_C	1.218	1.00
34_E	37_T	1.214	1.00
284_Y	288_F	1.208	1.00
138_G	286_G	1.197	1.00
288_F	292_A	1.196	1.00
217_W	221_C	1.183	1.00
27_K	31_E	1.183	1.00
49_G	230_L	1.180	1.00
75_L	78_A	1.179	1.00
93_L	101_S	1.177	1.00
129_V	133_L	1.164	1.00
254_L	258_F	1.163	1.00
103_V	287_A	1.162	1.00
70_R	73_I	1.153	1.00
279_L	284_Y	1.141	1.00
83_F	201_A	1.140	1.00
36_P	205_L	1.137	1.00
127_T	296_Y	1.128	1.00
158_T	162_I	1.128	1.00
201_A	204_P	1.124	1.00
73_I	77_V	1.121	1.00
216_H	219_L	1.120	1.00
55_A	59_R	1.120	1.00
220_A	224_F	1.116	1.00
141_M	282_L	1.112	1.00
159_W	163_F	1.107	1.00
115_A	173_S	1.107	1.00
14_T	235_A	1.102	1.00
112_M	245_A	1.095	1.00
179_K	244_Q	1.092	1.00
133_L	137_S	1.086	1.00
98_P	275_A	1.085	1.00
138_G	290_V	1.082	1.00
240_M	248_V	1.072	1.00
96_L	164_G	1.071	1.00
95_Y	160_G	1.071	1.00
25_A	221_C	1.071	1.00
73_I	177_A	1.071	1.00
126_S	129_V	1.065	1.00
44_L	203_F	1.059	1.00
95_Y	157_Y	1.058	1.00
180_V	183_R	1.056	1.00
19_W	236_L	1.055	1.00
179_K	245_A	1.054	1.00
40_F	44_L	1.047	1.00
21_A	262_F	1.046	1.00
15_T	235_A	1.041	1.00
120_L	176_V	1.039	1.00
117_V	123_K	1.038	1.00
72_L	75_L	1.036	1.00
10_L	14_T	1.033	1.00
81_G	173_S	1.032	1.00
127_T	300_G	1.032	1.00
18_C	235_A	1.029	1.00
81_G	174_Y	1.026	1.00
74_L	78_A	1.023	1.00
179_K	183_R	1.021	1.00
59_R	186_A	1.017	1.00
124_M	129_V	1.013	1.00
15_T	19_W	1.013	1.00
32_V	215_S	1.009	1.00
42_R	229_T	1.008	1.00
40_F	206_A	1.007	1.00
115_A	172_V	1.006	1.00
112_M	175_G	1.006	1.00
26_M	93_L	1.003	1.00
159_W	162_I	1.003	1.00
122_E	128_Q	0.999	1.00
8_G	239_A	0.996	1.00
83_F	202_L	0.996	1.00
213_Q	216_H	0.995	1.00
104_I	168_A	0.988	1.00
47_S	192_F	0.987	1.00
89_F	93_L	0.985	1.00
104_I	161_V	0.982	1.00
39_V	90_S	0.981	1.00
142_F	286_G	0.974	1.00
113_M	124_M	0.974	1.00
144_N	280_N	0.970	1.00
29_V	218_Q	0.967	1.00
79_T	201_A	0.964	1.00
222_L	226_G	0.963	1.00
75_L	197_L	0.961	1.00
55_A	58_K	0.951	1.00
35_P	39_V	0.951	1.00
140_V	144_N	0.950	1.00
29_V	221_C	0.948	1.00
220_A	223_I	0.945	1.00
8_G	242_R	0.941	1.00
127_T	299_I	0.939	1.00
107_L	139_L	0.931	1.00
281_L	284_Y	0.923	1.00
160_G	164_G	0.921	1.00
240_M	244_Q	0.920	1.00
115_A	169_T	0.918	1.00
223_I	226_G	0.917	1.00
75_L	79_T	0.916	1.00
104_I	164_G	0.915	1.00
204_P	208_P	0.915	1.00
76_A	177_A	0.913	1.00
244_Q	248_V	0.911	1.00
168_A	172_V	0.909	1.00
243_W	248_V	0.895	1.00
134_M	293_G	0.893	1.00
125_R	129_V	0.891	1.00
24_I	266_L	0.890	1.00
115_A	118_F	0.890	1.00
112_M	172_V	0.889	1.00
82_L	174_Y	0.884	1.00
118_F	121_K	0.884	1.00
49_G	52_A	0.874	1.00
73_I	181_L	0.871	1.00
36_P	87_I	0.869	1.00
16_A	20_G	0.868	1.00
74_L	77_V	0.864	1.00
98_P	277_P	0.854	1.00
43_F	198_C	0.853	1.00
87_I	91_S	0.850	1.00
205_L	208_P	0.850	1.00
51_G	196_T	0.842	1.00
49_G	227_L	0.841	1.00
54_L	58_K	0.840	1.00
103_V	140_V	0.838	1.00
219_L	223_I	0.834	1.00
71_W	75_L	0.830	1.00
71_W	197_L	0.829	1.00
243_W	247_Q	0.823	1.00
16_A	258_F	0.820	1.00
214_L	219_L	0.820	1.00
266_L	275_A	0.813	1.00
239_A	248_V	0.811	1.00
37_T	206_A	0.807	1.00
78_A	197_L	0.805	1.00
56_V	59_R	0.804	1.00
257_L	287_A	0.804	1.00
123_K	127_T	0.802	1.00
137_S	289_V	0.799	1.00
157_Y	161_V	0.798	1.00
24_I	263_S	0.796	1.00
41_Y	45_M	0.795	1.00
139_L	143_F	0.790	1.00
221_C	224_F	0.790	1.00
70_R	185_L	0.789	1.00
196_T	200_I	0.786	1.00
12_A	251_I	0.783	1.00
164_G	168_A	0.777	1.00
123_K	126_S	0.773	1.00
141_M	285_L	0.769	1.00
47_S	51_G	0.766	1.00
264_D	279_L	0.761	1.00
199_T	203_F	0.758	1.00
173_S	177_A	0.758	1.00
137_S	141_M	0.755	1.00
260_L	279_L	0.754	1.00
76_A	79_T	0.746	1.00
197_L	200_I	0.742	1.00
55_A	60_L	0.742	1.00
37_T	41_Y	0.739	1.00
282_L	285_L	0.738	1.00
16_A	254_L	0.736	1.00
13_L	258_F	0.732	1.00
73_I	180_V	0.730	1.00
114_V	118_F	0.727	1.00
287_A	291_V	0.726	1.00
56_V	60_L	0.726	1.00
23_P	89_F	0.724	1.00
83_F	87_I	0.723	1.00
110_V	135_L	0.723	1.00
81_G	170_V	0.721	1.00
201_A	205_L	0.721	1.00
260_L	287_A	0.718	1.00
24_I	98_P	0.715	1.00
9_I	247_Q	0.715	1.00
130_V	134_M	0.711	1.00
85_N	170_V	0.707	1.00
231_V	235_A	0.707	1.00
117_V	121_K	0.707	1.00
54_L	192_F	0.706	1.00
26_M	30_L	0.705	1.00
155_T	158_T	0.703	1.00
44_L	48_I	0.701	1.00
84_G	88_L	0.700	1.00
171_W	175_G	0.698	1.00
112_M	176_V	0.697	1.00
193_L	197_L	0.694	1.00
96_L	101_S	0.691	1.00
185_L	190_I	0.689	1.00
74_L	185_L	0.688	1.00
196_T	199_T	0.686	1.00
33_M	38_I	0.684	1.00
50_L	230_L	0.682	1.00
215_S	219_L	0.681	1.00
263_S	275_A	0.681	1.00
254_L	257_L	0.681	1.00
39_V	202_L	0.680	1.00
104_I	165_V	0.678	1.00
285_L	289_V	0.676	1.00
113_M	128_Q	0.676	1.00
191_L	237_A	0.672	1.00
85_N	174_Y	0.671	1.00
200_I	203_F	0.671	1.00
293_G	297_S	0.668	1.00
234_G	238_E	0.667	1.00
33_M	37_T	0.666	1.00
57_K	60_L	0.663	1.00
49_G	226_G	0.662	1.00
279_L	283_G	0.659	1.00
278_M	282_L	0.658	1.00
144_N	147_L	0.656	1.00
264_D	278_M	0.655	1.00
53_I	188_P	0.654	1.00
81_G	177_A	0.654	1.00
124_M	128_Q	0.654	1.00
192_F	196_T	0.653	1.00
107_L	110_V	0.653	1.00
198_C	202_L	0.651	1.00
82_L	233_Y	0.646	1.00
18_C	228_N	0.643	1.00
53_I	56_V	0.643	1.00
111_G	165_V	0.642	1.00
89_F	101_S	0.641	1.00
92_S	101_S	0.638	1.00
180_V	184_R	0.638	1.00
12_A	243_W	0.637	1.00
212_A	215_S	0.635	1.00
292_A	296_Y	0.633	1.00
122_E	246_A	0.632	1.00
197_L	201_A	0.630	1.00
250_A	297_S	0.626	1.00
113_M	117_V	0.624	1.00
120_L	180_V	0.621	1.00
28_Q	275_A	0.621	1.00
218_Q	221_C	0.621	1.00
156_D	159_W	0.620	1.00
46_A	230_L	0.619	1.00
261_F	265_L	0.617	1.00
57_K	186_A	0.615	1.00
106_Q	139_L	0.614	1.00
23_P	102_Q	0.614	1.00
215_S	220_A	0.613	1.00
18_C	232_G	0.612	1.00
73_I	76_A	0.610	1.00
260_L	264_D	0.610	1.00
189_Q	193_L	0.608	1.00
90_S	94_Q	0.607	1.00
174_Y	237_A	0.607	1.00
214_L	218_Q	0.602	1.00
283_G	287_A	0.599	1.00
212_A	216_H	0.598	1.00
138_G	293_G	0.597	1.00
155_T	159_W	0.593	1.00
71_W	74_L	0.592	1.00
109_P	253_T	0.591	1.00
119_I	173_S	0.589	1.00
223_I	227_L	0.587	1.00
9_I	13_L	0.582	1.00
203_F	207_K	0.581	1.00
73_I	78_A	0.578	1.00
57_K	188_P	0.578	1.00
14_T	18_C	0.576	1.00
106_Q	109_P	0.573	1.00
92_S	160_G	0.571	1.00
193_L	196_T	0.570	1.00
143_F	161_V	0.569	1.00
191_L	194_L	0.567	1.00
294_A	297_S	0.566	1.00
21_A	228_N	0.564	1.00
171_W	236_L	0.562	1.00
103_V	142_F	0.560	1.00
8_G	243_W	0.559	1.00
107_L	168_A	0.559	1.00
89_F	167_A	0.559	1.00
134_M	296_Y	0.558	1.00
41_Y	222_L	0.553	1.00
88_L	167_A	0.549	1.00
78_A	83_F	0.549	1.00
102_Q	106_Q	0.549	1.00
187_S	191_L	0.548	1.00
252_I	255_T	0.545	1.00
82_L	194_L	0.542	1.00
16_A	255_T	0.540	1.00
163_F	166_G	0.540	1.00
253_T	294_A	0.539	1.00
30_L	93_L	0.538	1.00
280_N	284_Y	0.537	1.00
128_Q	244_Q	0.537	1.00
34_E	209_G	0.537	1.00
262_F	265_L	0.536	1.00
13_L	16_A	0.536	1.00
145_T	282_L	0.534	1.00
106_Q	168_A	0.529	1.00
48_I	51_G	0.527	1.00
235_A	238_E	0.526	1.00
175_G	249_S	0.525	1.00
22_L	228_N	0.524	1.00
116_S	246_A	0.523	1.00
70_R	74_L	0.522	1.00
239_A	243_W	0.522	1.00
130_V	137_S	0.522	1.00
74_L	190_I	0.520	1.00
67_R	71_W	0.517	1.00
71_W	78_A	0.516	1.00
12_A	236_L	0.515	1.00
24_I	259_T	0.515	1.00
284_Y	287_A	0.514	1.00
103_V	143_F	0.513	1.00
278_M	283_G	0.513	1.00
175_G	236_L	0.512	1.00
85_N	89_F	0.509	1.00
174_Y	178_Q	0.508	1.00
178_Q	190_I	0.508	1.00
261_F	264_D	0.507	1.00
71_W	193_L	0.502	1.00
20_G	255_T	0.500	1.00
138_G	289_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	0.2399	98.9	0.767	Contact Map
3b5dA	2	0.3146	97.9	0.825	Contact Map
4j05A	3	0.9346	92.5	0.888	Contact Map
2cfqA	1	0.5981	85.8	0.902	Contact Map
4pypA	1	0.9097	85.5	0.903	Contact Map
3wdoA	1	0.9315	85.4	0.903	Contact Map
4tphA	2	0.8692	73	0.914	Contact Map
4he8J	1	0.4829	71.4	0.915	Contact Map
1pw4A	1	0.9502	70.8	0.915	Contact Map
4zw9A	1	0.9283	69.3	0.916	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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