YOJE - BACSU - GREMLIN Contacts

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YOJE - Uncharacterized transporter YojE

UniProt:	O31859	Sequences: MQHAETKKGVIYTAVSFIMWGLFPLYWKLLEQLPALDILAHRIIWSFVFMCIVLFFLRQWKIGWQELRSLKKNGGILSLFLASILISINWFVYIWAVNHGFLLEASLGYYINPLVSVLLGILFLKEKLNRLQLVAVSIAAAGVIISAFQYGSIPYVALLLAFSFGLYGLSKKRTSLPSAIGLTLETFMIMPIALGYLLFSGHVQPAGAESGGTWLLLFLAGVFTALPLLLFAEGAKRLPLYQVGILQYIAPTITLLIGLFVYHEPFSSSKAFTFSCIWAALLLFTFSQVKWKRASKSH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	298 (268)
Sequences:	37290 (27531)
Seq/√Len:	1681.7

ECOLI - RARD YEDA YTFF YICL YHBE YIJE RHTA YDDG EAMA
BACSU - YOJE YVBV YBFH YCXC YDED YRDR YWFM YETK YXXF YDFC YCBK YYAM YOAV YDEK
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
96_A	157_A	3.666	1.00
12_Y	233_E	3.143	1.00
233_E	237_R	2.990	1.00
258_G	264_E	2.905	1.00
95_W	156_V	2.772	1.00
47_F	187_F	2.649	1.00
92_V	159_L	2.499	1.00
40_A	194_L	2.491	1.00
135_A	280_A	2.435	1.00
233_E	236_K	2.411	1.00
106_S	254_T	2.328	1.00
92_V	156_V	2.237	1.00
21_G	253_I	2.227	1.00
115_V	161_A	2.227	1.00
126_E	172_K	2.223	1.00
28_K	264_E	2.195	1.00
27_W	94_I	2.165	1.00
13_T	234_G	2.146	1.00
119_L	169_L	2.132	1.00
121_I	128_L	2.078	1.00
120_G	126_E	1.957	1.00
44_I	190_M	1.954	1.00
21_G	257_I	1.929	1.00
100_G	104_E	1.900	1.00
52_I	55_F	1.886	1.00
88_I	163_S	1.886	1.00
116_S	244_G	1.883	1.00
111_I	115_V	1.881	1.00
129_N	132_Q	1.875	1.00
26_Y	218_F	1.874	1.00
51_C	183_T	1.845	1.00
117_V	136_V	1.817	1.00
139_A	248_Y	1.774	1.00
177_P	180_I	1.758	1.00
191_P	195_G	1.748	1.00
195_G	198_L	1.732	1.00
155_Y	159_L	1.727	1.00
47_F	190_M	1.715	1.00
18_I	253_I	1.713	1.00
239_P	242_Q	1.688	1.00
210_S	214_W	1.680	1.00
282_L	286_F	1.662	1.00
115_V	165_G	1.649	1.00
267_S	270_K	1.641	1.00
95_W	99_H	1.640	1.00
92_V	163_S	1.614	1.00
22_L	218_F	1.612	1.00
51_C	55_F	1.600	1.00
105_A	157_A	1.577	1.00
53_V	57_L	1.547	1.00
135_A	284_F	1.519	1.00
16_S	234_G	1.515	1.00
30_L	38_I	1.507	1.00
115_V	162_F	1.473	1.00
171_K	232_A	1.463	1.00
45_W	220_A	1.462	1.00
12_Y	230_L	1.455	1.00
40_A	190_M	1.449	1.00
268_S	272_F	1.436	1.00
120_G	124_L	1.420	1.00
210_S	213_T	1.419	1.00
101_F	104_E	1.415	1.00
145_I	276_C	1.404	1.00
220_A	225_A	1.400	1.00
74_G	175_S	1.396	1.00
102_L	258_G	1.386	1.00
46_S	186_T	1.383	1.00
165_G	169_L	1.380	1.00
119_L	123_F	1.376	1.00
253_I	257_I	1.374	1.00
130_R	134_V	1.361	1.00
95_W	98_N	1.358	1.00
52_I	56_F	1.351	1.00
72_K	75_G	1.348	1.00
135_A	283_L	1.345	1.00
139_A	280_A	1.337	1.00
103_L	255_L	1.331	1.00
34_P	37_D	1.327	1.00
257_I	261_V	1.318	1.00
10_V	246_L	1.315	1.00
131_L	283_L	1.314	1.00
20_W	227_P	1.305	1.00
275_S	279_A	1.302	1.00
74_G	77_L	1.300	1.00
25_L	257_I	1.298	1.00
192_I	195_G	1.286	1.00
142_G	273_T	1.280	1.00
249_I	253_I	1.275	1.00
271_A	275_S	1.273	1.00
99_H	156_V	1.272	1.00
48_V	52_I	1.252	1.00
49_F	225_A	1.250	1.00
133_L	137_S	1.245	1.00
73_N	77_L	1.244	1.00
107_L	274_F	1.242	1.00
145_I	269_S	1.238	1.00
11_I	15_V	1.227	1.00
137_S	141_A	1.226	1.00
55_F	59_Q	1.217	1.00
97_V	105_A	1.205	1.00
22_L	257_I	1.192	1.00
40_A	44_I	1.182	1.00
266_F	271_A	1.179	1.00
211_G	215_L	1.172	1.00
42_R	224_T	1.171	1.00
100_G	157_A	1.171	1.00
146_S	273_T	1.171	1.00
47_F	183_T	1.171	1.00
38_I	219_L	1.170	1.00
19_M	222_V	1.153	1.00
128_L	133_L	1.147	1.00
78_S	82_A	1.144	1.00
85_L	166_L	1.142	1.00
122_L	125_K	1.138	1.00
93_Y	97_V	1.135	1.00
40_A	197_L	1.125	1.00
72_K	76_I	1.121	1.00
126_E	132_Q	1.119	1.00
130_R	133_L	1.118	1.00
108_G	161_A	1.116	1.00
73_N	76_I	1.097	1.00
116_S	240_L	1.090	1.00
131_L	286_F	1.090	1.00
87_S	192_I	1.087	1.00
16_S	20_W	1.087	1.00
119_L	165_G	1.087	1.00
211_G	214_W	1.085	1.00
124_L	169_L	1.083	1.00
36_L	196_Y	1.082	1.00
119_L	166_L	1.078	1.00
172_K	239_P	1.076	1.00
87_S	193_A	1.075	1.00
16_S	230_L	1.073	1.00
39_L	94_I	1.071	1.00
102_L	262_Y	1.062	1.00
121_I	127_K	1.061	1.00
131_L	287_S	1.061	1.00
15_V	230_L	1.044	1.00
55_F	58_R	1.040	1.00
9_G	234_G	1.039	1.00
49_F	221_G	1.039	1.00
142_G	277_I	1.039	1.00
19_M	230_L	1.033	1.00
82_A	85_L	1.030	1.00
44_I	194_L	1.022	1.00
83_S	192_I	1.021	1.00
35_A	39_L	1.021	1.00
116_S	168_G	1.020	1.00
235_A	239_P	1.017	1.00
235_A	243_V	1.015	1.00
33_L	212_G	1.015	1.00
27_W	97_V	1.012	1.00
108_G	157_A	1.003	1.00
9_G	237_R	1.002	1.00
172_K	240_L	0.999	1.00
196_Y	200_S	0.996	1.00
213_T	217_L	0.994	1.00
111_I	143_V	0.986	1.00
32_Q	209_E	0.985	1.00
209_E	213_T	0.984	1.00
77_L	81_L	0.976	1.00
20_W	231_F	0.972	1.00
116_S	165_G	0.965	1.00
268_S	271_A	0.960	1.00
239_P	243_V	0.954	1.00
208_A	213_T	0.946	1.00
212_G	215_L	0.946	1.00
119_L	122_L	0.938	1.00
17_F	21_G	0.937	1.00
195_G	199_F	0.937	1.00
129_N	133_L	0.935	1.00
117_V	128_L	0.934	1.00
214_W	218_F	0.933	1.00
119_L	162_F	0.932	1.00
43_I	189_I	0.922	1.00
102_L	264_E	0.921	1.00
36_L	91_F	0.920	1.00
59_Q	177_P	0.919	1.00
151_G	154_P	0.915	1.00
37_D	197_L	0.912	1.00
51_C	187_F	0.911	1.00
49_F	52_I	0.901	1.00
86_I	167_Y	0.898	1.00
56_F	59_Q	0.897	1.00
138_I	280_A	0.892	1.00
238_L	243_V	0.892	1.00
25_L	261_V	0.885	1.00
13_T	246_L	0.884	1.00
76_I	80_F	0.883	1.00
59_Q	62_I	0.883	1.00
161_A	165_G	0.883	1.00
252_T	274_F	0.881	1.00
107_L	144_I	0.878	1.00
77_L	80_F	0.878	1.00
41_H	45_W	0.878	1.00
217_L	221_G	0.871	1.00
17_F	249_I	0.870	1.00
157_A	161_A	0.870	1.00
55_F	60_W	0.861	1.00
196_Y	199_F	0.861	1.00
141_A	145_I	0.854	1.00
58_R	61_K	0.849	1.00
238_L	242_Q	0.845	1.00
259_L	266_F	0.844	1.00
14_A	253_I	0.844	1.00
17_F	253_I	0.837	1.00
25_L	258_G	0.837	1.00
148_F	151_G	0.832	1.00
234_G	243_V	0.831	1.00
91_F	95_W	0.826	1.00
89_N	163_S	0.826	1.00
209_E	212_G	0.822	1.00
204_Q	207_G	0.818	1.00
255_L	266_F	0.814	1.00
29_L	215_L	0.812	1.00
85_L	167_Y	0.809	1.00
141_A	276_C	0.808	1.00
114_L	139_A	0.807	1.00
187_F	191_P	0.803	1.00
54_L	58_R	0.798	1.00
127_K	131_L	0.794	1.00
145_I	272_F	0.790	1.00
100_G	105_A	0.785	1.00
47_F	51_C	0.783	1.00
272_F	276_C	0.780	1.00
111_I	114_L	0.770	1.00
39_L	193_A	0.768	1.00
50_M	225_A	0.767	1.00
54_L	183_T	0.766	1.00
143_V	147_A	0.766	1.00
180_I	184_L	0.764	1.00
26_Y	215_L	0.762	1.00
10_V	242_Q	0.762	1.00
166_L	170_S	0.760	1.00
218_F	222_V	0.760	1.00
269_S	272_F	0.759	1.00
214_W	217_L	0.756	1.00
188_M	192_I	0.754	1.00
218_F	221_G	0.753	1.00
126_E	241_Y	0.751	1.00
33_L	213_T	0.750	1.00
87_S	91_F	0.750	1.00
49_F	220_A	0.746	1.00
76_I	79_L	0.746	1.00
255_L	274_F	0.744	1.00
249_I	252_T	0.740	1.00
226_L	230_L	0.739	1.00
134_V	138_I	0.733	1.00
164_F	168_G	0.733	1.00
24_P	93_Y	0.733	1.00
127_K	130_R	0.729	1.00
183_T	187_F	0.728	1.00
83_S	87_S	0.725	1.00
118_L	122_L	0.722	1.00
274_F	278_W	0.722	1.00
85_L	170_S	0.715	1.00
57_L	61_K	0.715	1.00
259_L	265_P	0.714	1.00
116_S	169_L	0.712	1.00
37_D	41_H	0.710	1.00
117_V	132_Q	0.709	1.00
88_I	92_V	0.709	1.00
81_L	85_L	0.705	1.00
108_G	158_L	0.702	1.00
128_L	132_Q	0.700	1.00
176_L	181_G	0.695	1.00
258_G	262_Y	0.695	1.00
215_L	219_L	0.694	1.00
33_L	37_D	0.694	1.00
178_S	182_L	0.692	1.00
121_I	125_K	0.689	1.00
79_L	188_M	0.689	1.00
25_L	102_L	0.686	1.00
229_L	233_E	0.684	1.00
32_Q	212_G	0.682	1.00
89_N	167_Y	0.680	1.00
266_F	270_K	0.674	1.00
33_L	38_I	0.674	1.00
222_V	226_L	0.673	1.00
96_A	105_A	0.672	1.00
24_P	106_S	0.671	1.00
74_G	176_L	0.671	1.00
279_A	283_L	0.668	1.00
115_V	158_L	0.665	1.00
53_V	56_F	0.665	1.00
29_L	262_Y	0.665	1.00
138_I	283_L	0.664	1.00
74_G	78_S	0.664	1.00
85_L	163_S	0.661	1.00
56_F	60_W	0.655	1.00
57_L	60_W	0.655	1.00
188_M	191_P	0.654	1.00
198_L	201_G	0.652	1.00
216_L	220_A	0.651	1.00
30_L	215_L	0.649	1.00
86_I	228_L	0.649	1.00
44_I	48_V	0.647	1.00
187_F	190_M	0.646	1.00
75_G	83_S	0.643	1.00
13_T	238_L	0.642	1.00
270_K	274_F	0.641	1.00
217_L	220_A	0.640	1.00
9_G	238_L	0.633	1.00
190_M	194_L	0.629	1.00
164_F	231_F	0.625	1.00
184_L	188_M	0.625	1.00
132_Q	239_P	0.624	1.00
184_L	187_F	0.623	1.00
107_L	147_A	0.623	1.00
142_G	280_A	0.623	1.00
110_Y	143_V	0.619	1.00
28_K	31_E	0.617	1.00
156_V	159_L	0.617	1.00
19_M	223_F	0.613	1.00
256_L	260_F	0.613	1.00
215_L	218_F	0.613	1.00
87_S	196_Y	0.612	1.00
267_S	271_A	0.607	1.00
57_L	177_P	0.607	1.00
83_S	188_M	0.606	1.00
124_L	172_K	0.605	1.00
255_L	259_L	0.605	1.00
221_G	225_A	0.605	1.00
86_I	185_E	0.601	1.00
75_G	79_L	0.600	1.00
93_Y	105_A	0.598	1.00
15_V	19_M	0.597	1.00
280_A	284_F	0.593	1.00
113_P	248_Y	0.588	1.00
111_I	161_A	0.586	1.00
265_P	269_S	0.586	1.00
118_L	136_V	0.583	1.00
23_F	223_F	0.583	1.00
53_V	179_A	0.582	1.00
19_M	227_P	0.580	1.00
245_I	284_F	0.580	1.00
52_I	57_L	0.578	1.00
182_L	232_A	0.578	1.00
167_Y	171_K	0.577	1.00
93_Y	160_L	0.577	1.00
117_V	121_I	0.573	1.00
129_N	287_S	0.573	1.00
34_P	201_G	0.569	1.00
17_F	250_A	0.569	1.00
77_L	170_S	0.566	1.00
92_V	160_L	0.565	1.00
256_L	259_L	0.565	1.00
265_P	270_K	0.563	1.00
75_G	82_A	0.563	1.00
189_I	193_A	0.562	1.00
78_S	170_S	0.561	1.00
281_L	284_F	0.560	1.00
167_Y	232_A	0.559	1.00
57_L	179_A	0.559	1.00
24_P	28_K	0.558	1.00
257_I	260_F	0.555	1.00
191_P	194_L	0.554	1.00
78_S	83_S	0.554	1.00
162_F	166_L	0.553	1.00
194_L	198_L	0.552	1.00
32_Q	213_T	0.551	1.00
82_A	188_M	0.550	1.00
22_L	223_F	0.549	1.00
45_W	221_G	0.548	1.00
23_F	94_I	0.545	1.00
48_V	51_C	0.545	1.00
144_I	148_F	0.544	1.00
45_W	48_V	0.543	1.00
168_G	231_F	0.541	1.00
30_L	212_G	0.540	1.00
81_L	170_S	0.538	1.00
94_I	98_N	0.536	1.00
114_L	136_V	0.536	1.00
212_G	216_L	0.535	1.00
140_A	248_Y	0.534	1.00
110_Y	161_A	0.533	1.00
111_I	139_A	0.530	1.00
110_Y	113_P	0.528	1.00
54_L	57_L	0.527	1.00
248_Y	281_L	0.525	1.00
25_L	262_Y	0.525	1.00
21_G	254_T	0.524	1.00
247_Q	250_A	0.523	1.00
107_L	146_S	0.520	1.00
39_L	91_F	0.519	1.00
120_G	241_Y	0.518	1.00
46_S	220_A	0.516	1.00
36_L	200_S	0.515	1.00
10_V	14_A	0.513	1.00
25_L	254_T	0.513	1.00
14_A	17_F	0.512	1.00
86_I	189_I	0.512	1.00
45_W	49_F	0.512	1.00
13_T	231_F	0.510	1.00
234_G	238_L	0.510	1.00
100_G	103_L	0.510	1.00
182_L	185_E	0.507	1.00
42_R	90_W	0.501	1.00
149_Q	154_P	0.500	1.00
142_G	276_C	0.500	1.00
124_L	173_R	0.500	1.00
36_L	193_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	0.2584	99	0.75	Contact Map
3b5dA	2	0.3389	98.1	0.807	Contact Map
2cfqA	1	0.8154	41.2	0.927	Contact Map
4he8J	1	0.5134	34.1	0.93	Contact Map
1u7gA	3	0.7819	32	0.931	Contact Map
3wdoA	1	0.9396	29.2	0.932	Contact Map
2kluA	1	0.1477	21.3	0.937	Contact Map
4qtnA	3	0.6544	20.5	0.937	Contact Map
4pypA	1	0.8322	16.1	0.94	Contact Map
2rddB	1	0.1074	13.4	0.942	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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