YHBJ - BACSU - GREMLIN Contacts

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YHBJ - Putative efflux system component YhbJ

UniProt:	O31593	Sequences: MIEDETKGENKMNRGRLILTNIIGLIVVLAIIAGGAYYYYQSTNYVKTDEAKVAGDMAAITAPAAGKVSDWDLDEGKTVKKGDTVAKIKGEQTVDVKSIMDGTIVKNEVKNGQTVQAGTTIAQTIDMDNLYITANIKETDIADIEVGNSVDVVVDGDPDTTFDGTVEEIGYATNSTFDMLPSTNSSGNYTKVTQKVPVKISIKNPSDKVLPGMNASVKISE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	221 (183)
Sequences:	25261 (20225)
Seq/√Len:	1495.1

ECOLI - YBHG EMRA EMRK YHII YDHJ YIBH AAEA MDTN YIAV CUSB ACRA MACA ACRE MDTE MDTA
BACSU - YHBJ YVRP YKNX

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
167_E	201_S	3.105	1.00
84_T	95_D	3.082	1.00
70_D	87_K	2.984	1.00
149_S	163_D	2.561	1.00
131_Y	199_K	2.493	1.00
80_K	101_D	2.476	1.00
72_D	87_K	2.403	1.00
87_K	95_D	2.269	1.00
84_T	97_K	2.250	1.00
164_G	200_I	2.243	1.00
151_D	163_D	2.226	1.00
63_P	93_T	2.167	1.00
80_K	83_D	2.166	1.00
151_D	161_T	2.113	1.00
78_T	103_T	2.069	1.00
72_D	84_T	2.046	1.00
105_V	125_I	2.045	1.00
133_T	197_P	2.021	1.00
36_A	39_Y	2.010	1.00
54_A	133_T	2.004	1.00
134_A	217_V	1.972	1.00
160_T	208_K	1.970	1.00
134_A	200_I	1.869	1.00
150_V	200_I	1.849	1.00
129_N	201_S	1.824	1.00
132_I	215_A	1.791	1.00
173_T	196_V	1.763	1.00
149_S	165_T	1.745	1.00
165_T	203_K	1.697	1.00
81_K	101_D	1.686	1.00
154_V	215_A	1.683	1.00
34_G	38_Y	1.647	1.00
168_E	199_K	1.626	1.00
126_D	129_N	1.614	1.00
84_T	87_K	1.592	1.00
107_N	110_K	1.588	1.00
165_T	201_S	1.564	1.00
68_V	109_V	1.524	1.00
133_T	199_K	1.497	1.00
74_D	77_K	1.496	1.00
116_Q	119_T	1.485	1.00
68_V	86_A	1.451	1.00
135_N	197_P	1.425	1.00
33_A	37_Y	1.420	1.00
152_V	202_I	1.414	1.00
35_G	39_Y	1.409	1.00
90_G	94_V	1.402	1.00
36_A	40_Y	1.398	1.00
59_A	120_T	1.384	1.00
104_I	122_A	1.384	1.00
69_S	89_K	1.383	1.00
177_F	194_Q	1.366	1.00
73_L	83_D	1.365	1.00
170_G	197_P	1.355	1.00
98_S	124_T	1.330	1.00
153_V	161_T	1.316	1.00
151_D	218_K	1.308	1.00
53_V	132_I	1.301	1.00
137_K	140_D	1.299	1.00
33_A	36_A	1.298	1.00
56_D	126_D	1.290	1.00
70_D	111_N	1.282	1.00
153_V	218_K	1.281	1.00
86_A	96_V	1.270	1.00
59_A	123_Q	1.267	1.00
85_V	122_A	1.260	1.00
141_I	196_V	1.258	1.00
32_I	36_A	1.257	1.00
157_D	162_F	1.222	1.00
65_A	117_A	1.215	1.00
63_P	67_K	1.209	1.00
34_G	37_Y	1.201	1.00
106_K	123_Q	1.196	1.00
132_I	152_V	1.195	1.00
132_I	217_V	1.173	1.00
47_K	51_A	1.170	1.00
46_V	218_K	1.166	1.00
57_M	123_Q	1.159	1.00
102_G	124_T	1.141	1.00
177_F	193_T	1.112	1.00
174_N	177_F	1.101	1.00
74_D	107_N	1.100	1.00
154_V	157_D	1.100	1.00
69_S	87_K	1.091	1.00
107_N	122_A	1.087	1.00
78_T	101_D	1.079	1.00
35_G	38_Y	1.076	1.00
145_E	148_N	1.067	1.00
31_I	34_G	1.064	1.00
98_S	101_D	1.055	1.00
131_Y	201_S	1.050	1.00
78_T	127_M	1.047	1.00
87_K	90_G	1.044	1.00
66_G	88_I	1.032	1.00
65_A	116_Q	1.022	1.00
108_E	123_Q	1.012	1.00
86_A	122_A	1.003	1.00
62_A	96_V	1.002	1.00
136_I	144_I	0.998	1.00
73_L	122_A	0.996	1.00
166_V	198_V	0.991	1.00
34_G	39_Y	0.990	1.00
167_E	199_K	0.985	1.00
71_W	86_A	0.983	1.00
73_L	107_N	0.982	1.00
115_V	121_I	0.981	1.00
86_A	121_I	0.970	1.00
153_V	159_D	0.969	1.00
75_E	106_K	0.968	1.00
108_E	120_T	0.953	1.00
153_V	216_S	0.946	1.00
157_D	160_T	0.938	1.00
163_D	203_K	0.937	1.00
204_N	207_D	0.936	1.00
53_V	209_V	0.932	1.00
136_I	198_V	0.917	1.00
135_N	195_K	0.911	1.00
174_N	197_P	0.894	1.00
152_V	164_G	0.889	1.00
140_D	143_D	0.888	1.00
69_S	72_D	0.888	1.00
100_M	124_T	0.886	1.00
62_A	86_A	0.885	1.00
68_V	115_V	0.885	1.00
48_T	218_K	0.878	1.00
71_W	111_N	0.876	1.00
166_V	200_I	0.876	1.00
131_Y	167_E	0.870	1.00
130_L	211_P	0.864	1.00
49_D	134_A	0.863	1.00
39_Y	42_S	0.863	1.00
90_G	95_D	0.861	1.00
152_V	215_A	0.861	1.00
67_K	114_T	0.858	1.00
79_V	83_D	0.852	1.00
57_M	125_I	0.849	1.00
77_K	83_D	0.838	1.00
154_V	209_V	0.836	1.00
58_A	100_M	0.829	1.00
92_Q	97_K	0.825	1.00
62_A	115_V	0.823	1.00
48_T	216_S	0.822	1.00
78_T	207_D	0.820	1.00
144_I	219_I	0.816	1.00
39_Y	43_T	0.814	1.00
146_V	167_E	0.814	1.00
129_N	203_K	0.807	1.00
136_I	219_I	0.797	1.00
103_T	127_M	0.789	1.00
73_L	104_I	0.784	1.00
125_I	211_P	0.783	1.00
79_V	85_V	0.776	1.00
86_A	107_N	0.775	1.00
62_A	121_I	0.775	1.00
73_L	77_K	0.771	1.00
156_G	213_M	0.767	1.00
146_V	169_I	0.765	1.00
210_L	213_M	0.763	1.00
155_D	216_S	0.761	1.00
171_Y	210_L	0.757	1.00
56_D	110_K	0.751	1.00
37_Y	40_Y	0.750	1.00
194_Q	214_N	0.738	1.00
69_S	90_G	0.730	1.00
53_V	130_L	0.725	1.00
144_I	166_V	0.721	1.00
55_G	131_Y	0.719	1.00
55_G	129_N	0.711	1.00
60_I	99_I	0.706	1.00
152_V	217_V	0.698	1.00
32_I	35_G	0.689	1.00
109_V	121_I	0.685	1.00
40_Y	43_T	0.679	1.00
68_V	71_W	0.678	1.00
96_V	121_I	0.672	1.00
30_A	34_G	0.671	1.00
22_I	25_L	0.669	1.00
114_T	118_G	0.668	1.00
65_A	114_T	0.668	1.00
25_L	29_L	0.666	1.00
92_Q	95_D	0.663	1.00
135_N	174_N	0.663	1.00
55_G	201_S	0.663	1.00
68_V	121_I	0.662	1.00
105_V	171_Y	0.659	1.00
134_A	198_V	0.659	1.00
59_A	113_Q	0.658	1.00
51_A	215_A	0.653	1.00
173_T	194_Q	0.652	1.00
81_K	99_I	0.648	1.00
120_T	123_Q	0.645	1.00
152_V	200_I	0.643	1.00
132_I	202_I	0.641	1.00
105_V	170_G	0.639	1.00
157_D	208_K	0.635	1.00
52_K	194_Q	0.634	1.00
62_A	88_I	0.634	1.00
147_G	165_T	0.633	1.00
75_E	107_N	0.631	1.00
67_K	89_K	0.631	1.00
103_T	210_L	0.630	1.00
150_V	164_G	0.629	1.00
53_V	215_A	0.628	1.00
169_I	198_V	0.626	1.00
64_A	93_T	0.623	1.00
125_I	172_A	0.621	1.00
62_A	65_A	0.619	1.00
115_V	119_T	0.616	1.00
64_A	94_V	0.615	1.00
110_K	113_Q	0.612	1.00
40_Y	44_N	0.611	1.00
200_I	217_V	0.610	1.00
33_A	39_Y	0.608	1.00
160_T	206_S	0.606	1.00
130_L	204_N	0.606	1.00
109_V	115_V	0.605	1.00
37_Y	41_Q	0.605	1.00
127_M	207_D	0.602	1.00
55_G	126_D	0.599	1.00
72_D	75_E	0.595	1.00
106_K	168_E	0.595	1.00
41_Q	44_N	0.591	1.00
58_A	124_T	0.589	1.00
162_F	208_K	0.589	1.00
175_S	194_Q	0.589	1.00
196_V	213_M	0.588	1.00
28_V	31_I	0.582	1.00
38_Y	42_S	0.582	1.00
163_D	204_N	0.567	1.00
72_D	83_D	0.566	1.00
159_D	162_F	0.563	1.00
127_M	130_L	0.561	1.00
58_A	62_A	0.559	1.00
54_A	131_Y	0.558	1.00
71_W	107_N	0.558	1.00
173_T	214_N	0.557	1.00
58_A	99_I	0.555	1.00
56_D	100_M	0.554	1.00
138_E	214_N	0.552	1.00
22_I	26_I	0.551	1.00
91_E	94_V	0.551	1.00
35_G	40_Y	0.551	1.00
29_L	32_I	0.551	1.00
54_A	57_M	0.547	1.00
162_F	206_S	0.545	1.00
79_V	124_T	0.542	1.00
106_K	120_T	0.540	1.00
82_G	97_K	0.540	1.00
78_T	83_D	0.539	1.00
27_V	34_G	0.535	1.00
26_I	30_A	0.534	1.00
27_V	30_A	0.534	1.00
38_Y	41_Q	0.532	1.00
63_P	89_K	0.531	1.00
60_I	100_M	0.527	1.00
61_T	120_T	0.527	1.00
113_Q	119_T	0.526	1.00
49_D	52_K	0.526	1.00
25_L	32_I	0.526	1.00
162_F	209_V	0.525	1.00
31_I	35_G	0.522	1.00
136_I	217_V	0.520	1.00
69_S	111_N	0.512	1.00
174_N	195_K	0.511	1.00
100_M	126_D	0.510	1.00
127_M	211_P	0.507	1.00
154_V	158_P	0.506	1.00
125_I	171_Y	0.506	1.00
138_E	156_G	0.505	1.00
174_N	194_Q	0.503	1.00
29_L	33_A	0.502	1.00
128_D	207_D	0.502	1.00
38_Y	43_T	0.502	1.00
49_D	140_D	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
3ne5B	3	0.7376	100	0.328	Contact Map
4tkoB	1	0.724	100	0.345	Contact Map
4kkuA	1	0.7919	100	0.379	Contact Map
3fppA	3	0.7647	100	0.391	Contact Map
2f1mA	2	0.724	100	0.391	Contact Map
4dk0A	5	0.7964	100	0.4	Contact Map
3lnnA	6	0.8688	100	0.404	Contact Map
4l8jA	2	0.8054	100	0.417	Contact Map
1vf7A	5	0.7466	99.9	0.429	Contact Map
2k32A	1	0.3846	99.6	0.631	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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