YKOC - BACSU - GREMLIN Contacts

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YKOC - Putative HMP/thiamine permease protein YkoC

UniProt:	O34572	Sequences: MKQPLHLINPTVKAAAVFCCVVMLSFIYNPYTPACFYIIIVAGVLLAAGIPLKKWLLFTIPFLILAFGCVWTAAVFGKVPTTPDNFLFQAGPISINSDNVSVGISLGFRILCFSALSMMFVFTTDPILFMLSLVQQCRLSPKLAYGVIAGFRFLPLLKDEVQLIQQAHKIRGGAAESGIINKISALKRYTIPLLASAIRKAERTALAMESKGFTGSRNRTYYRTLSVNRRDWVFFCLVLLLFAGSFLVSLCFAS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	254 (233)
Sequences:	5294 (4265)
Seq/√Len:	279.4

BACSU - YKOC ECFT
HALSA - Q9HPH6
SULSO - Q97WT3 Q97X61

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
227_V	232_W	6.810	1.00
13_K	124_T	4.317	1.00
160_E	200_K	3.817	1.00
13_K	123_T	3.367	1.00
85_N	98_D	3.334	1.00
16_A	238_V	3.228	1.00
12_V	227_V	3.223	1.00
53_K	57_L	2.958	1.00
10_P	225_L	2.944	1.00
162_Q	166_Q	2.721	1.00
86_F	94_S	2.643	1.00
88_F	95_I	2.543	1.00
85_N	97_S	2.538	1.00
8_I	234_F	2.393	1.00
232_W	236_C	2.315	1.00
86_F	89_Q	2.306	1.00
86_F	96_N	2.282	1.00
165_Q	169_K	2.267	1.00
12_V	235_F	2.256	1.00
164_I	193_L	2.222	1.00
17_V	120_F	2.169	1.00
243_A	247_L	2.145	1.00
228_N	231_D	2.010	1.00
164_I	168_H	1.991	1.00
70_V	107_G	1.936	1.00
89_Q	94_S	1.930	1.00
11_T	132_S	1.880	1.00
157_L	197_A	1.859	1.00
134_V	141_P	1.815	1.00
37_Y	112_C	1.782	1.00
229_R	233_V	1.736	1.00
145_Y	213_F	1.683	1.00
166_Q	169_K	1.670	1.00
57_L	60_I	1.669	1.00
87_L	97_S	1.661	1.00
208_M	213_F	1.594	1.00
31_Y	35_C	1.580	1.00
87_L	100_V	1.568	1.00
160_E	163_L	1.553	1.00
160_E	196_S	1.540	1.00
125_D	128_L	1.528	1.00
151_F	155_P	1.487	1.00
24_L	36_F	1.480	1.00
51_P	54_K	1.475	1.00
128_L	223_R	1.474	1.00
152_R	193_L	1.462	1.00
101_S	105_S	1.442	1.00
145_Y	149_A	1.438	1.00
74_A	95_I	1.419	1.00
33_P	112_C	1.411	1.00
146_G	150_G	1.411	1.00
137_C	140_S	1.409	1.00
8_I	12_V	1.405	1.00
24_L	112_C	1.391	1.00
31_Y	34_A	1.382	1.00
7_L	230_R	1.365	1.00
170_I	210_S	1.355	1.00
181_N	184_S	1.352	1.00
97_S	101_S	1.349	1.00
139_L	143_L	1.324	1.00
161_V	193_L	1.305	1.00
99_N	103_G	1.303	1.00
227_V	235_F	1.294	1.00
134_V	144_A	1.289	1.00
41_V	116_L	1.276	1.00
32_T	35_C	1.262	1.00
180_I	184_S	1.244	1.00
205_A	209_E	1.232	1.00
230_R	233_V	1.231	1.00
23_M	27_I	1.227	1.00
85_N	89_Q	1.223	1.00
27_I	32_T	1.212	1.00
161_V	165_Q	1.207	1.00
72_T	76_F	1.202	1.00
89_Q	92_P	1.192	1.00
20_C	116_L	1.190	1.00
239_L	242_F	1.185	1.00
23_M	242_F	1.184	1.00
168_H	188_R	1.179	1.00
17_V	116_L	1.174	1.00
172_G	192_P	1.167	1.00
156_L	204_T	1.167	1.00
60_I	64_I	1.160	1.00
78_K	96_N	1.145	1.00
149_A	204_T	1.140	1.00
153_F	204_T	1.131	1.00
152_R	156_L	1.127	1.00
161_V	189_Y	1.123	1.00
18_F	22_V	1.117	1.00
164_I	192_P	1.112	1.00
44_V	119_M	1.111	1.00
29_N	32_T	1.107	1.00
184_S	188_R	1.102	1.00
179_I	183_I	1.091	1.00
87_L	90_A	1.088	1.00
46_L	49_G	1.087	1.00
241_L	245_S	1.085	1.00
15_A	235_F	1.075	1.00
155_P	192_P	1.070	1.00
24_L	116_L	1.063	1.00
79_V	98_D	1.054	1.00
74_A	103_G	1.039	1.00
102_V	106_L	1.032	1.00
168_H	185_A	1.032	1.00
155_P	205_A	1.029	1.00
181_N	185_A	1.022	1.00
41_V	44_V	1.020	1.00
33_P	108_F	1.012	1.00
133_L	147_V	1.011	1.00
227_V	231_D	1.003	1.00
64_I	67_F	1.001	1.00
91_G	94_S	1.001	1.00
150_G	208_M	0.997	1.00
149_A	208_M	0.996	1.00
168_H	192_P	0.992	1.00
101_S	104_I	0.991	1.00
10_P	132_S	0.971	1.00
233_V	237_L	0.971	1.00
237_L	241_L	0.970	1.00
157_L	161_V	0.970	1.00
226_S	229_R	0.963	1.00
176_E	182_K	0.945	1.00
19_C	242_F	0.942	1.00
64_I	68_G	0.941	1.00
159_D	162_Q	0.935	1.00
187_K	191_I	0.929	1.00
33_P	36_F	0.926	1.00
30_P	101_S	0.924	1.00
98_D	101_S	0.921	1.00
13_K	128_L	0.918	1.00
43_G	46_L	0.918	1.00
157_L	173_G	0.917	1.00
30_P	105_S	0.916	1.00
182_K	185_A	0.914	1.00
88_F	94_S	0.910	1.00
226_S	231_D	0.908	1.00
70_V	103_G	0.893	1.00
234_F	238_V	0.889	1.00
86_F	90_A	0.887	1.00
236_C	247_L	0.881	1.00
201_A	204_T	0.880	1.00
98_D	102_V	0.880	1.00
131_L	225_L	0.879	1.00
52_L	56_L	0.879	1.00
108_F	112_C	0.878	1.00
34_A	38_I	0.876	1.00
61_P	64_I	0.875	1.00
206_L	209_E	0.871	1.00
179_I	182_K	0.871	1.00
30_P	34_A	0.868	1.00
205_A	208_M	0.862	1.00
12_V	231_D	0.861	1.00
133_L	144_A	0.860	1.00
71_W	75_V	0.853	1.00
53_K	56_L	0.852	1.00
73_A	99_N	0.848	1.00
199_R	203_R	0.838	1.00
90_A	93_I	0.837	1.00
73_A	106_L	0.836	1.00
14_A	132_S	0.834	1.00
244_G	247_L	0.830	1.00
126_P	151_F	0.829	1.00
87_L	98_D	0.829	1.00
124_T	128_L	0.828	1.00
156_L	160_E	0.826	1.00
36_F	112_C	0.822	1.00
215_G	218_N	0.820	0.99
38_I	43_G	0.820	0.99
238_V	242_F	0.818	0.99
56_L	60_I	0.813	0.99
163_L	203_R	0.808	0.99
130_M	148_I	0.806	0.99
162_Q	165_Q	0.805	0.99
5_L	48_A	0.804	0.99
12_V	234_F	0.798	0.99
168_H	189_Y	0.796	0.99
9_N	225_L	0.794	0.99
79_V	96_N	0.792	0.99
152_R	160_E	0.791	0.99
16_A	234_F	0.790	0.99
14_A	120_F	0.789	0.99
23_M	32_T	0.788	0.99
12_V	232_W	0.788	0.99
232_W	235_F	0.782	0.99
46_L	52_L	0.772	0.99
136_Q	224_T	0.770	0.99
8_I	230_R	0.769	0.99
45_L	55_W	0.762	0.99
6_H	13_K	0.762	0.99
34_A	37_Y	0.759	0.99
120_F	129_F	0.758	0.99
109_R	161_V	0.755	0.99
9_N	12_V	0.754	0.99
37_Y	108_F	0.750	0.99
200_K	203_R	0.744	0.99
42_A	45_L	0.744	0.99
185_A	189_Y	0.741	0.99
164_I	189_Y	0.740	0.99
146_G	204_T	0.739	0.99
134_V	221_Y	0.739	0.99
124_T	129_F	0.732	0.99
110_I	114_S	0.731	0.99
33_P	105_S	0.728	0.99
126_P	157_L	0.727	0.99
87_L	96_N	0.725	0.99
21_V	113_F	0.724	0.99
5_L	44_V	0.722	0.99
170_I	207_A	0.718	0.99
15_A	239_L	0.713	0.99
65_L	110_I	0.711	0.99
19_C	239_L	0.711	0.99
119_M	123_T	0.709	0.99
201_A	205_A	0.706	0.98
38_I	46_L	0.704	0.98
55_W	59_T	0.702	0.98
229_R	232_W	0.702	0.98
141_P	214_T	0.701	0.98
196_S	202_E	0.699	0.98
16_A	20_C	0.698	0.98
107_G	111_L	0.694	0.98
9_N	132_S	0.693	0.98
232_W	237_L	0.692	0.98
62_F	114_S	0.691	0.98
209_E	212_G	0.690	0.98
169_K	176_E	0.689	0.98
145_Y	168_H	0.688	0.98
11_T	225_L	0.688	0.98
236_C	240_L	0.687	0.98
141_P	215_G	0.686	0.98
240_L	243_A	0.684	0.98
191_I	199_R	0.684	0.98
73_A	77_G	0.682	0.98
138_R	144_A	0.681	0.98
230_R	247_L	0.680	0.98
17_V	107_G	0.679	0.98
174_A	182_K	0.678	0.98
126_P	155_P	0.678	0.98
28_Y	33_P	0.675	0.98
17_V	117_S	0.666	0.98
165_Q	189_Y	0.665	0.98
15_A	224_T	0.664	0.98
221_Y	224_T	0.661	0.98
69_C	73_A	0.660	0.98
23_M	241_L	0.654	0.98
120_F	124_T	0.654	0.98
159_D	163_L	0.650	0.97
228_N	232_W	0.649	0.97
113_F	117_S	0.648	0.97
55_W	115_A	0.645	0.97
156_L	211_K	0.644	0.97
20_C	24_L	0.641	0.97
152_R	204_T	0.640	0.97
58_F	62_F	0.640	0.97
60_I	68_G	0.639	0.97
58_F	69_C	0.632	0.97
74_A	99_N	0.631	0.97
90_A	94_S	0.629	0.97
212_G	215_G	0.628	0.97
154_L	208_M	0.626	0.97
132_S	138_R	0.626	0.97
21_V	117_S	0.626	0.97
229_R	243_A	0.626	0.97
136_Q	139_L	0.624	0.97
120_F	209_E	0.623	0.97
35_C	38_I	0.623	0.97
153_F	205_A	0.621	0.97
87_L	95_I	0.618	0.96
58_F	122_F	0.618	0.96
195_A	198_I	0.616	0.96
144_A	155_P	0.615	0.96
233_V	243_A	0.615	0.96
38_I	42_A	0.614	0.96
228_N	235_F	0.613	0.96
233_V	240_L	0.612	0.96
168_H	172_G	0.611	0.96
20_C	36_F	0.610	0.96
5_L	8_I	0.605	0.96
63_L	111_L	0.605	0.96
26_F	246_F	0.604	0.96
143_L	150_G	0.603	0.96
226_S	232_W	0.602	0.96
180_I	241_L	0.601	0.96
88_F	91_G	0.599	0.96
33_P	37_Y	0.597	0.96
37_Y	42_A	0.591	0.95
175_A	190_T	0.589	0.95
163_L	166_Q	0.587	0.95
237_L	244_G	0.586	0.95
202_E	206_L	0.583	0.95
146_G	213_F	0.582	0.95
25_S	148_I	0.582	0.95
239_L	243_A	0.581	0.95
88_F	92_P	0.580	0.95
66_A	70_V	0.575	0.95
170_I	211_K	0.575	0.95
11_T	15_A	0.574	0.95
153_F	195_A	0.573	0.95
19_C	246_F	0.572	0.95
67_F	70_V	0.572	0.95
49_G	229_R	0.572	0.95
153_F	156_L	0.571	0.95
6_H	124_T	0.568	0.94
139_L	144_A	0.567	0.94
188_R	192_P	0.566	0.94
146_G	200_K	0.565	0.94
150_G	186_L	0.559	0.94
114_S	127_I	0.557	0.94
62_F	111_L	0.556	0.94
66_A	69_C	0.555	0.94
48_A	123_T	0.554	0.94
202_E	211_K	0.551	0.94
32_T	36_F	0.551	0.94
60_I	63_L	0.550	0.93
100_V	104_I	0.547	0.93
160_E	197_A	0.545	0.93
174_A	185_A	0.541	0.93
59_T	63_L	0.540	0.93
73_A	103_G	0.539	0.93
53_K	60_I	0.539	0.93
104_I	107_G	0.538	0.93
197_A	208_M	0.537	0.93
117_S	154_L	0.536	0.93
218_N	229_R	0.535	0.92
118_M	122_F	0.533	0.92
130_M	144_A	0.533	0.92
59_T	69_C	0.532	0.92
39_I	238_V	0.530	0.92
85_N	88_F	0.529	0.92
97_S	102_V	0.528	0.92
127_I	131_L	0.523	0.92
232_W	240_L	0.522	0.92
230_R	241_L	0.521	0.92
113_F	153_F	0.521	0.92
19_C	238_V	0.520	0.91
70_V	99_N	0.519	0.91
200_K	204_T	0.516	0.91
109_R	171_R	0.515	0.91
227_V	236_C	0.514	0.91
59_T	62_F	0.514	0.91
113_F	201_A	0.512	0.91
144_A	147_V	0.511	0.91
74_A	78_K	0.510	0.91
16_A	24_L	0.507	0.90
8_I	231_D	0.507	0.90
133_L	139_L	0.506	0.90
55_W	145_Y	0.505	0.90
225_L	231_D	0.503	0.90
77_G	102_V	0.502	0.90
228_N	233_V	0.502	0.90
5_L	47_A	0.500	0.90

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
4huqT	1	0.9094	100	0.152	Contact Map
2l0eA	1	0.122	5.1	0.953	Contact Map
4mt1A	3	0.622	4	0.956	Contact Map
2fz1A	8	0.2362	3.7	0.957	Contact Map
4dx5A	3	0.6339	3.3	0.958	Contact Map
2zvkU	1	0.0354	2.8	0.959	Contact Map
2dc0A	2	0.3622	2.6	0.96	Contact Map
4k0jA	3	0.5748	2.2	0.961	Contact Map
3w9iA	3	0.6181	1.9	0.963	Contact Map
2ww9C	1	0.0827	1.5	0.965	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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