YKOE - BACSU - GREMLIN Contacts

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YKOE - Putative HMP/thiamine permease protein YkoE

UniProt:	O34738	Sequences: MKSWKVKEIVIMSVISIVFAVVYLLFTHFGNVLAGMFGPIAYEPIYGIWFIVSVIAAYMIRKPGAALVSEIIAALVECLLGNPSGPMVIVIGIVQGLGAEAVFLATRWKAYSLPVLMLAGMGSSVASFIYDLFVSGYAAYSPGYLLIMLVIRLISGALLAGLLGKAVSDSLAYTGVLNGMALGKELKKKRKRASEHASL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	199 (184)
Sequences:	608 (453)
Seq/√Len:	33.4

BACSU - YKOE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
13_S	68_V	6.454	1.00
102_V	122_G	4.663	1.00
74_A	92_G	4.038	1.00
165_K	169_D	3.593	1.00
84_S	88_V	2.882	1.00
106_T	115_V	2.657	1.00
120_G	156_G	2.644	1.00
57_A	66_A	2.606	1.00
121_M	153_L	2.529	1.00
56_A	69_S	2.401	0.99
47_G	155_S	2.328	0.99
58_Y	116_L	2.236	0.99
44_P	151_I	2.220	0.99
150_V	154_I	2.141	0.99
19_F	51_I	2.085	0.98
54_V	164_G	2.035	0.98
169_D	173_Y	1.958	0.98
101_A	105_A	1.891	0.97
48_I	158_L	1.880	0.97
23_Y	52_V	1.793	0.96
16_S	185_E	1.779	0.96
54_V	119_A	1.757	0.95
130_Y	134_V	1.706	0.95
91_I	131_D	1.692	0.94
4_W	65_A	1.685	0.94
75_L	89_I	1.650	0.94
43_E	152_R	1.639	0.93
113_L	165_K	1.632	0.93
159_L	163_L	1.620	0.93
55_I	168_S	1.595	0.92
19_F	55_I	1.582	0.92
101_A	104_L	1.581	0.92
99_A	119_A	1.579	0.92
117_M	157_A	1.567	0.92
127_S	152_R	1.532	0.91
58_Y	168_S	1.526	0.91
142_P	146_L	1.523	0.91
58_Y	169_D	1.504	0.90
20_A	76_V	1.484	0.89
26_F	48_I	1.479	0.89
27_T	77_E	1.473	0.89
180_M	183_G	1.462	0.89
46_Y	131_D	1.447	0.88
71_I	93_I	1.446	0.88
110_A	114_P	1.419	0.87
113_L	162_L	1.412	0.87
55_I	167_V	1.405	0.87
128_F	149_L	1.399	0.86
143_G	147_I	1.394	0.86
43_E	46_Y	1.376	0.85
91_I	130_Y	1.354	0.84
59_M	119_A	1.327	0.83
27_T	82_N	1.312	0.82
70_E	95_Q	1.288	0.81
11_I	180_M	1.269	0.80
33_L	37_F	1.236	0.78
99_A	123_S	1.217	0.77
120_G	157_A	1.215	0.77
12_M	60_I	1.214	0.77
102_V	115_V	1.202	0.76
146_L	154_I	1.201	0.76
44_P	107_R	1.199	0.76
46_Y	152_R	1.193	0.76
168_S	182_L	1.192	0.76
12_M	72_I	1.189	0.76
15_I	111_Y	1.187	0.76
58_Y	165_K	1.175	0.75
79_L	186_L	1.154	0.73
51_I	164_G	1.149	0.73
146_L	150_V	1.146	0.73
120_G	124_S	1.141	0.73
168_S	171_L	1.136	0.72
67_L	93_I	1.129	0.72
54_V	116_L	1.110	0.71
102_V	118_L	1.110	0.71
40_I	144_Y	1.106	0.70
59_M	173_Y	1.104	0.70
41_A	45_I	1.102	0.70
121_M	124_S	1.102	0.70
124_S	156_G	1.091	0.69
32_V	101_A	1.075	0.68
19_F	52_V	1.045	0.66
70_E	77_E	1.040	0.65
169_D	182_L	1.035	0.65
9_I	22_V	1.022	0.64
158_L	162_L	1.004	0.63
87_M	134_V	1.000	0.62
55_I	119_A	0.994	0.62
15_I	69_S	0.992	0.62
74_A	89_I	0.989	0.61
70_E	73_A	0.984	0.61
106_T	118_L	0.973	0.60
101_A	154_I	0.964	0.59
162_L	166_A	0.964	0.59
74_A	105_A	0.960	0.59
126_A	129_I	0.959	0.59
129_I	173_Y	0.958	0.59
28_H	31_N	0.957	0.59
151_I	154_I	0.953	0.59
49_W	70_E	0.939	0.57
181_A	184_K	0.933	0.57
50_F	127_S	0.927	0.56
60_I	138_A	0.925	0.56
30_G	33_L	0.925	0.56
40_I	151_I	0.923	0.56
173_Y	186_L	0.900	0.54
153_L	157_A	0.894	0.54
21_V	25_L	0.888	0.53
82_N	88_V	0.886	0.53
149_L	180_M	0.885	0.53
62_K	175_G	0.875	0.52
104_L	173_Y	0.869	0.52
30_G	34_A	0.866	0.51
98_G	158_L	0.865	0.51
119_A	122_G	0.862	0.51
69_S	131_D	0.861	0.51
7_K	182_L	0.851	0.50
4_W	12_M	0.846	0.50
15_I	56_A	0.844	0.49
154_I	173_Y	0.843	0.49
59_M	180_M	0.843	0.49
147_I	151_I	0.841	0.49
23_Y	77_E	0.841	0.49
153_L	158_L	0.840	0.49
50_F	54_V	0.839	0.49
172_A	180_M	0.839	0.49
156_G	159_L	0.829	0.48
98_G	122_G	0.827	0.48
53_S	108_W	0.821	0.48
98_G	126_A	0.814	0.47
15_I	59_M	0.813	0.47
86_P	90_V	0.809	0.47
16_S	72_I	0.808	0.46
90_V	97_L	0.808	0.46
36_M	185_E	0.802	0.46
46_Y	50_F	0.802	0.46
25_L	28_H	0.802	0.46
105_A	114_P	0.798	0.46
102_V	119_A	0.798	0.46
78_C	88_V	0.795	0.45
30_G	91_I	0.789	0.45
66_A	106_T	0.788	0.45
51_I	55_I	0.784	0.44
78_C	86_P	0.782	0.44
19_F	111_Y	0.779	0.44
90_V	93_I	0.775	0.44
51_I	159_L	0.773	0.44
132_L	145_L	0.766	0.43
99_A	103_F	0.766	0.43
85_G	94_V	0.763	0.43
75_L	78_C	0.762	0.43
101_A	108_W	0.759	0.42
71_I	89_I	0.757	0.42
170_S	175_G	0.756	0.42
71_I	88_V	0.753	0.42
46_Y	127_S	0.753	0.42
63_P	171_L	0.749	0.42
136_G	140_Y	0.747	0.41
17_I	55_I	0.742	0.41
70_E	96_G	0.736	0.41
26_F	49_W	0.734	0.40
75_L	84_S	0.732	0.40
26_F	50_F	0.726	0.40
15_I	45_I	0.726	0.40
45_I	86_P	0.724	0.40
32_V	35_G	0.722	0.39
57_A	99_A	0.722	0.39
50_F	73_A	0.719	0.39
75_L	82_N	0.718	0.39
91_I	98_G	0.704	0.38
132_L	138_A	0.691	0.37
40_I	147_I	0.689	0.37
17_I	76_V	0.686	0.37
163_L	166_A	0.686	0.37
27_T	78_C	0.685	0.37
29_F	45_I	0.685	0.37
7_K	11_I	0.681	0.36
150_V	170_S	0.674	0.36
29_F	153_L	0.669	0.35
55_I	59_M	0.667	0.35
82_N	89_I	0.666	0.35
25_L	129_I	0.665	0.35
15_I	19_F	0.662	0.35
4_W	24_L	0.659	0.35
78_C	93_I	0.659	0.35
54_V	99_A	0.658	0.34
61_R	175_G	0.657	0.34
101_A	129_I	0.657	0.34
66_A	118_L	0.656	0.34
11_I	33_L	0.655	0.34
5_K	111_Y	0.655	0.34
30_G	42_Y	0.655	0.34
51_I	89_I	0.648	0.34
59_M	171_L	0.647	0.34
52_V	70_E	0.647	0.34
5_K	8_E	0.646	0.34
14_V	102_V	0.644	0.33
9_I	13_S	0.640	0.33
103_F	108_W	0.640	0.33
70_E	74_A	0.639	0.33
25_L	94_V	0.638	0.33
180_M	184_K	0.635	0.33
114_P	117_M	0.631	0.32
172_A	183_G	0.626	0.32
25_L	101_A	0.626	0.32
16_S	78_C	0.624	0.32
136_G	145_L	0.623	0.32
122_G	126_A	0.619	0.32
172_A	182_L	0.616	0.31
54_V	77_E	0.612	0.31
124_S	128_F	0.612	0.31
10_V	61_R	0.611	0.31
172_A	184_K	0.611	0.31
117_M	120_G	0.609	0.31
70_E	98_G	0.609	0.31
8_E	62_K	0.607	0.31
97_L	126_A	0.607	0.31
83_P	176_V	0.605	0.31
145_L	152_R	0.603	0.30
178_N	183_G	0.601	0.30
136_G	139_A	0.601	0.30
27_T	83_P	0.601	0.30
9_I	62_K	0.596	0.30
22_V	88_V	0.594	0.30
16_S	164_G	0.592	0.30
106_T	158_L	0.588	0.29
44_P	106_T	0.583	0.29
23_Y	27_T	0.582	0.29
172_A	177_L	0.579	0.29
8_E	12_M	0.578	0.29
8_E	63_P	0.577	0.29
18_V	24_L	0.576	0.29
66_A	99_A	0.573	0.28
48_I	51_I	0.572	0.28
59_M	177_L	0.567	0.28
11_I	37_F	0.560	0.27
22_V	154_I	0.560	0.27
30_G	37_F	0.560	0.27
78_C	83_P	0.560	0.27
105_A	169_D	0.559	0.27
129_I	133_F	0.552	0.27
54_V	58_Y	0.551	0.27
50_F	123_S	0.549	0.27
118_L	121_M	0.548	0.27
12_M	68_V	0.546	0.27
8_E	61_R	0.545	0.26
90_V	109_K	0.544	0.26
49_W	95_Q	0.544	0.26
178_N	182_L	0.544	0.26
136_G	151_I	0.542	0.26
15_I	124_S	0.540	0.26
68_V	164_G	0.538	0.26
18_V	170_S	0.538	0.26
63_P	67_L	0.537	0.26
57_A	131_D	0.535	0.26
98_G	104_L	0.533	0.26
117_M	162_L	0.533	0.26
105_A	122_G	0.531	0.26
76_V	158_L	0.530	0.25
16_S	92_G	0.528	0.25
9_I	164_G	0.528	0.25
32_V	76_V	0.527	0.25
19_F	56_A	0.521	0.25
11_I	182_L	0.521	0.25
60_I	160_A	0.519	0.25
75_L	160_A	0.512	0.24
33_L	45_I	0.511	0.24
5_K	132_L	0.511	0.24
141_S	173_Y	0.505	0.24
107_R	112_S	0.505	0.24
115_V	121_M	0.505	0.24
77_E	84_S	0.503	0.24
27_T	84_S	0.501	0.24
51_I	170_S	0.501	0.24
65_A	92_G	0.500	0.24
102_V	105_A	0.500	0.24

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
4huqS	1	0.804	94	0.913	Contact Map
4tkrA	2	0.8291	92.9	0.916	Contact Map
3rlbA	1	0.8241	92.7	0.917	Contact Map
4rfsS	1	0.809	91.1	0.92	Contact Map
4z7fA	2	0.804	90.4	0.922	Contact Map
4hzuS	1	0.7889	76.6	0.934	Contact Map
3p5nA	2	0.7739	75.3	0.935	Contact Map
4dveA	3	0.8141	39.9	0.948	Contact Map
2cfqA	1	0.9146	20.5	0.955	Contact Map
2kncB	1	0.3166	15.9	0.957	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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