YKOF - BACSU - GREMLIN Contacts

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YKOF - Putative HMP/thiamine-binding protein YkoF

UniProt:	O34911	Sequences: MEHICGTSRIAGFRFSLYPMTDDFISVIKSALKKTDTSKVWTKTDHISTVLRGSIDHVFDAAKAIYLHAANSEQHIVMNGTFSIGCPGDTQGDTYLSKGDKRVNEDAVRGLKAEAPCQFALYPMNEPDYMGLIMEAVDIAKAQGTFVQGVHYASELDGDAHDVFSTLEAVFRMAEQQTNHITMTVNLSANSPSRKNRKQG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	200 (185)
Sequences:	102 (84)
Seq/√Len:	6.1

BACSU - YKOF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
21_T	27_V	4.786	0.98
14_R	140_A	4.071	0.95
18_Y	77_V	3.541	0.89
138_D	141_K	3.110	0.81
17_L	78_M	2.824	0.74
145_T	166_T	2.806	0.74
31_A	73_E	2.541	0.66
30_S	142_A	2.533	0.65
35_T	64_A	2.453	0.63
89_D	152_Y	2.364	0.60
62_A	82_F	2.340	0.59
27_V	74_Q	2.293	0.57
146_F	154_S	2.225	0.55
93_D	152_Y	2.167	0.53
69_A	145_T	2.156	0.52
115_A	163_V	2.110	0.51
60_D	104_N	2.030	0.48
18_Y	186_N	1.978	0.46
14_R	48_S	1.941	0.45
154_S	163_V	1.842	0.41
40_V	52_R	1.804	0.40
146_F	163_V	1.771	0.39
188_S	191_S	1.755	0.38
124_M	182_T	1.748	0.38
110_G	182_T	1.747	0.38
23_D	26_S	1.662	0.35
30_S	134_M	1.647	0.35
11_A	55_I	1.647	0.35
17_L	116_P	1.631	0.34
58_V	93_D	1.590	0.33
16_S	116_P	1.575	0.32
29_K	154_S	1.571	0.32
76_I	155_E	1.553	0.32
166_T	181_I	1.543	0.31
76_I	193_S	1.514	0.31
166_T	170_V	1.444	0.28
93_D	129_Y	1.432	0.28
70_A	189_A	1.430	0.28
10_I	89_D	1.395	0.27
46_H	155_E	1.393	0.27
81_T	184_T	1.378	0.27
87_P	180_H	1.354	0.26
25_I	125_N	1.349	0.26
34_K	100_D	1.348	0.26
66_Y	189_A	1.346	0.26
69_A	76_I	1.341	0.26
15_F	182_T	1.340	0.25
17_L	115_A	1.333	0.25
140_A	166_T	1.333	0.25
18_Y	66_Y	1.314	0.25
119_F	189_A	1.308	0.25
67_L	114_E	1.284	0.24
52_R	60_D	1.279	0.24
63_K	149_G	1.274	0.24
131_G	134_M	1.269	0.24
120_A	127_P	1.258	0.23
15_F	65_I	1.255	0.23
22_D	103_V	1.253	0.23
16_S	77_V	1.247	0.23
59_F	119_F	1.246	0.23
41_W	89_D	1.242	0.23
104_N	152_Y	1.226	0.22
27_V	120_A	1.220	0.22
88_G	130_M	1.194	0.22
86_C	130_M	1.194	0.22
16_S	174_A	1.186	0.22
167_L	171_F	1.183	0.21
101_K	183_M	1.182	0.21
15_F	27_V	1.180	0.21
10_I	152_Y	1.171	0.21
35_T	140_A	1.166	0.21
91_Q	115_A	1.161	0.21
21_T	194_R	1.156	0.21
134_M	141_K	1.153	0.21
110_G	124_M	1.144	0.21
24_F	164_F	1.139	0.20
75_H	180_H	1.135	0.20
26_S	115_A	1.126	0.20
50_V	152_Y	1.119	0.20
19_P	40_V	1.119	0.20
59_F	171_F	1.118	0.20
67_L	128_D	1.107	0.20
23_D	169_A	1.102	0.20
32_L	119_F	1.097	0.19
13_F	62_A	1.094	0.19
22_D	44_T	1.093	0.19
15_F	58_V	1.091	0.19
60_D	168_E	1.085	0.19
51_L	111_L	1.085	0.19
41_W	152_Y	1.081	0.19
49_T	133_I	1.079	0.19
174_A	185_V	1.058	0.19
188_S	193_S	1.051	0.18
126_E	137_V	1.031	0.18
99_G	149_G	1.017	0.18
23_D	107_A	1.009	0.18
82_F	183_M	1.001	0.17
130_M	137_V	0.999	0.17
45_D	118_Q	0.987	0.17
93_D	125_N	0.987	0.17
89_D	151_H	0.982	0.17
89_D	93_D	0.982	0.17
58_V	64_A	0.980	0.17
120_A	187_L	0.973	0.17
35_T	62_A	0.972	0.17
118_Q	181_I	0.970	0.17
64_A	129_Y	0.967	0.17
178_T	181_I	0.958	0.16
45_D	48_S	0.956	0.16
79_N	163_V	0.954	0.16
21_T	31_A	0.953	0.16
25_I	29_K	0.952	0.16
63_K	105_E	0.944	0.16
30_S	127_P	0.941	0.16
29_K	114_E	0.941	0.16
15_F	123_P	0.940	0.16
96_L	115_A	0.938	0.16
88_G	180_H	0.935	0.16
86_C	180_H	0.935	0.16
24_F	45_D	0.933	0.16
41_W	52_R	0.922	0.16
79_N	186_N	0.918	0.16
10_I	41_W	0.918	0.16
58_V	110_G	0.908	0.16
75_H	192_P	0.904	0.15
17_L	42_T	0.900	0.15
13_F	82_F	0.900	0.15
41_W	93_D	0.896	0.15
21_T	32_L	0.892	0.15
131_G	137_V	0.890	0.15
44_T	192_P	0.884	0.15
10_I	144_G	0.870	0.15
106_D	169_A	0.864	0.15
59_F	167_L	0.850	0.14
17_L	69_A	0.850	0.14
132_L	169_A	0.847	0.14
72_S	163_V	0.841	0.14
18_Y	65_I	0.841	0.14
10_I	92_G	0.835	0.14
114_E	194_R	0.834	0.14
113_A	145_T	0.832	0.14
11_A	31_A	0.830	0.14
39_K	179_N	0.827	0.14
57_H	60_D	0.826	0.14
134_M	137_V	0.824	0.14
84_I	181_I	0.822	0.14
27_V	160_A	0.819	0.14
47_I	183_M	0.816	0.14
29_K	43_K	0.810	0.14
24_F	59_F	0.809	0.14
149_G	181_I	0.804	0.14
51_L	116_P	0.802	0.14
107_A	112_K	0.800	0.14
118_Q	154_S	0.795	0.14
51_L	166_T	0.784	0.13
83_S	151_H	0.769	0.13
119_F	123_P	0.768	0.13
24_F	28_I	0.766	0.13
32_L	191_S	0.755	0.13
171_F	184_T	0.749	0.13
136_A	189_A	0.748	0.13
118_Q	150_V	0.734	0.13
143_Q	169_A	0.729	0.12
47_I	61_A	0.728	0.12
145_T	163_V	0.728	0.12
21_T	139_I	0.726	0.12
46_H	116_P	0.725	0.12
46_H	121_L	0.721	0.12
90_T	135_E	0.719	0.12
40_V	129_Y	0.718	0.12
170_V	175_E	0.710	0.12
128_D	194_R	0.706	0.12
52_R	58_V	0.702	0.12
119_F	171_F	0.699	0.12
29_K	160_A	0.699	0.12
117_C	163_V	0.697	0.12
47_I	57_H	0.695	0.12
16_S	24_F	0.690	0.12
60_D	111_L	0.689	0.12
36_D	190_N	0.684	0.12
47_I	123_P	0.680	0.12
140_A	170_V	0.676	0.12
163_V	167_L	0.675	0.12
16_S	19_P	0.670	0.12
52_R	89_D	0.668	0.12
147_V	163_V	0.666	0.11
35_T	152_Y	0.659	0.11
11_A	147_V	0.658	0.11
112_K	186_N	0.655	0.11
35_T	104_N	0.651	0.11
140_A	153_A	0.650	0.11
47_I	70_A	0.644	0.11
124_M	172_R	0.641	0.11
19_P	45_D	0.639	0.11
169_A	186_N	0.636	0.11
69_A	109_R	0.635	0.11
15_F	60_D	0.633	0.11
121_L	124_M	0.631	0.11
34_K	50_V	0.630	0.11
15_F	73_E	0.629	0.11
85_G	122_Y	0.628	0.11
101_K	120_A	0.622	0.11
102_R	168_E	0.619	0.11
108_V	111_L	0.617	0.11
54_S	89_D	0.616	0.11
38_S	67_L	0.613	0.11
138_D	142_A	0.612	0.11
47_I	124_M	0.610	0.11
75_H	87_P	0.607	0.11
56_D	102_R	0.605	0.11
52_R	104_N	0.604	0.11
96_L	194_R	0.597	0.11
83_S	88_G	0.593	0.10
26_S	155_E	0.593	0.10
83_S	86_C	0.593	0.10
43_K	160_A	0.592	0.10
149_G	194_R	0.592	0.10
72_S	110_G	0.591	0.10
75_H	85_G	0.590	0.10
71_N	149_G	0.589	0.10
74_Q	190_N	0.586	0.10
108_V	124_M	0.582	0.10
38_S	167_L	0.582	0.10
10_I	104_N	0.581	0.10
25_I	182_T	0.581	0.10
62_A	174_A	0.579	0.10
54_S	94_T	0.574	0.10
17_L	48_S	0.574	0.10
24_F	168_E	0.573	0.10
112_K	161_H	0.573	0.10
80_G	162_D	0.573	0.10
89_D	104_N	0.569	0.10
73_E	121_L	0.567	0.10
42_T	139_I	0.565	0.10
180_H	192_P	0.564	0.10
87_P	130_M	0.564	0.10
35_T	82_F	0.562	0.10
105_E	161_H	0.561	0.10
51_L	61_A	0.558	0.10
68_H	127_P	0.554	0.10
33_K	165_S	0.551	0.10
63_K	161_H	0.549	0.10
68_H	111_L	0.545	0.10
19_P	24_F	0.545	0.10
120_A	150_V	0.544	0.10
59_F	80_G	0.542	0.10
162_D	172_R	0.541	0.10
130_M	180_H	0.541	0.10
120_A	169_A	0.537	0.10
95_Y	153_A	0.536	0.10
16_S	95_Y	0.536	0.10
22_D	74_Q	0.536	0.10
35_T	179_N	0.534	0.10
22_D	30_S	0.534	0.10
61_A	78_M	0.532	0.10
52_R	93_D	0.532	0.10
39_K	104_N	0.531	0.10
67_L	172_R	0.525	0.10
137_V	174_A	0.524	0.10
28_I	188_S	0.524	0.10
14_R	149_G	0.524	0.10
107_A	176_Q	0.520	0.10
63_K	139_I	0.517	0.09
10_I	120_A	0.516	0.09
113_A	137_V	0.515	0.09
34_K	112_K	0.514	0.09
34_K	71_N	0.512	0.09
59_F	168_E	0.509	0.09
62_A	173_M	0.509	0.09
81_T	164_F	0.508	0.09
10_I	94_T	0.506	0.09
84_I	89_D	0.506	0.09
101_K	109_R	0.505	0.09
118_Q	163_V	0.503	0.09
34_K	141_K	0.501	0.09
56_D	106_D	0.501	0.09
48_S	126_E	0.501	0.09
97_S	102_R	0.500	0.09

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
1s99A	2	0.93	100	0.344	Contact Map
2epiA	4	0.455	98.6	0.881	Contact Map
1yqhA	3	0.46	98.5	0.885	Contact Map
2iboA	4	0.425	97.5	0.911	Contact Map
1lxnA	4	0.435	97.3	0.913	Contact Map
1lxjA	4	0.455	97.3	0.913	Contact Map
1vk8A	4	0.445	97	0.918	Contact Map
3iixA	1	0.77	40.4	0.961	Contact Map
3t7vA	1	0.755	33.4	0.963	Contact Map
4rtbA	2	0.835	12.6	0.969	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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