YKOX - BACSU - GREMLIN Contacts

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YKOX - Uncharacterized membrane protein YkoX

UniProt:	O34908	Sequences: MIHKHETRELVAIEELVMSWIEAFKSLSYFGIFLALSIEFIPAEVVLPLAGYWVSKGDMTLAGVVLAGSLGGVAGPLTLYWIGRYGGRPFLERFGKYLFIKPEALDKSDNFFKKHGGFVAFSGRFLPGIRTLISIPCGIAKMNVWVFSLYTFIAMLPITFVYVYLGVKLGENWKAVGSILDQYMLPIGIAILALFLLYLLMKKRKKRTHSEQLSVFLKNKR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	221 (189)
Sequences:	6593 (4677)
Seq/√Len:	340.2

ECOLI - YABI DEDA YGHB YQJA YOHD YDJX YDJZ
BACSU - YKOX YNGC YBFM YHJE
SULSO - Q97V45

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
77_L	144_V	3.452	1.00
60_T	63_G	3.119	1.00
199_L	203_K	2.918	1.00
69_S	156_L	2.917	1.00
197_L	201_M	2.653	1.00
200_L	204_R	2.536	1.00
115_H	118_F	2.509	1.00
54_V	167_V	2.439	1.00
73_V	152_F	2.432	1.00
65_V	160_F	2.404	1.00
121_F	153_I	2.381	1.00
117_G	146_V	2.348	1.00
37_S	78_T	2.278	1.00
77_L	148_S	2.268	1.00
143_N	146_V	2.216	1.00
101_K	104_A	2.151	1.00
185_L	189_I	2.078	1.00
67_A	71_G	2.048	1.00
109_D	113_K	1.966	1.00
68_G	159_T	1.924	1.00
61_L	164_Y	1.899	1.00
24_F	28_S	1.865	1.00
65_V	163_V	1.839	1.00
29_Y	60_T	1.814	1.00
84_R	141_K	1.772	1.00
117_G	150_Y	1.760	1.00
164_Y	168_K	1.754	1.00
88_R	109_D	1.670	1.00
61_L	65_V	1.665	1.00
47_L	163_V	1.652	1.00
36_L	71_G	1.638	1.00
61_L	163_V	1.631	1.00
37_S	74_A	1.597	1.00
33_F	67_A	1.581	1.00
50_A	64_V	1.580	1.00
39_E	43_A	1.563	1.00
144_V	148_S	1.556	1.00
32_I	68_G	1.546	1.00
33_F	71_G	1.541	1.00
81_W	85_Y	1.529	1.00
102_P	106_D	1.527	1.00
106_D	110_N	1.524	1.00
198_Y	202_K	1.505	1.00
29_Y	63_G	1.500	1.00
203_K	206_K	1.443	1.00
64_V	163_V	1.436	1.00
118_F	122_S	1.433	1.00
33_F	70_L	1.429	1.00
182_Q	186_P	1.400	1.00
92_E	102_P	1.400	1.00
186_P	190_A	1.376	1.00
177_G	181_D	1.358	1.00
123_G	133_I	1.350	1.00
103_E	107_K	1.347	1.00
27_L	31_G	1.342	1.00
125_F	157_P	1.335	1.00
81_W	144_V	1.307	1.00
73_V	155_M	1.300	1.00
179_I	182_Q	1.286	1.00
198_Y	201_M	1.272	1.00
63_G	67_A	1.269	1.00
29_Y	67_A	1.263	1.00
76_P	124_R	1.252	1.00
54_V	61_L	1.249	1.00
145_W	149_L	1.246	1.00
203_K	207_R	1.219	1.00
18_M	22_E	1.178	1.00
22_E	25_K	1.175	1.00
83_G	139_I	1.174	1.00
62_A	164_Y	1.165	1.00
120_A	142_M	1.161	1.00
196_L	200_L	1.160	1.00
194_L	198_Y	1.158	1.00
200_L	203_K	1.156	1.00
85_Y	89_P	1.152	1.00
66_L	70_L	1.151	1.00
79_L	135_I	1.142	1.00
47_L	68_G	1.120	1.00
62_A	66_L	1.113	1.00
59_M	64_V	1.112	1.00
184_M	188_G	1.108	1.00
55_S	167_V	1.093	1.00
109_D	140_A	1.089	1.00
112_F	137_C	1.084	1.00
204_R	207_R	1.083	1.00
191_I	194_L	1.078	1.00
73_V	148_S	1.077	1.00
183_Y	186_P	1.067	1.00
51_G	166_G	1.066	1.00
65_V	164_Y	1.062	1.00
27_L	30_F	1.043	1.00
181_D	185_L	1.034	1.00
174_K	178_S	1.031	1.00
188_G	192_L	1.026	1.00
47_L	51_G	1.025	1.00
201_M	205_K	1.024	1.00
91_L	105_L	1.019	1.00
44_E	130_R	1.001	1.00
29_Y	59_M	0.999	1.00
69_S	159_T	0.999	1.00
69_S	73_V	0.996	1.00
88_R	92_E	0.995	1.00
180_L	183_Y	0.994	1.00
32_I	64_V	0.993	1.00
22_E	26_S	0.983	1.00
106_D	109_D	0.967	1.00
195_F	198_Y	0.953	1.00
95_G	98_L	0.952	1.00
89_P	93_R	0.950	1.00
151_T	155_M	0.947	1.00
121_F	157_P	0.945	1.00
110_N	114_K	0.933	1.00
70_L	74_A	0.931	1.00
72_G	155_M	0.927	1.00
77_L	81_W	0.926	1.00
145_W	148_S	0.918	1.00
28_S	31_G	0.917	1.00
65_V	69_S	0.912	1.00
134_S	151_T	0.910	1.00
202_K	205_K	0.908	1.00
157_P	160_F	0.905	1.00
95_G	100_I	0.903	1.00
91_L	100_I	0.898	1.00
81_W	84_R	0.896	1.00
68_G	163_V	0.891	1.00
149_L	153_I	0.887	1.00
51_G	163_V	0.886	1.00
94_F	97_Y	0.885	1.00
76_P	151_T	0.885	1.00
62_A	65_V	0.884	1.00
26_S	30_F	0.883	1.00
33_F	74_A	0.882	1.00
175_A	178_S	0.881	1.00
130_R	158_I	0.880	1.00
104_A	107_K	0.877	1.00
90_F	94_F	0.873	1.00
108_S	140_A	0.872	1.00
66_L	69_S	0.863	1.00
55_S	171_E	0.861	1.00
195_F	199_L	0.860	1.00
175_A	179_I	0.857	1.00
63_G	66_L	0.850	1.00
201_M	204_R	0.849	1.00
111_F	119_V	0.847	1.00
160_F	164_Y	0.837	1.00
116_G	142_M	0.832	1.00
36_L	159_T	0.830	1.00
18_M	21_I	0.820	1.00
86_G	89_P	0.818	1.00
52_Y	55_S	0.809	1.00
73_V	151_T	0.806	1.00
119_V	122_S	0.805	1.00
72_G	124_R	0.795	1.00
82_I	86_G	0.794	1.00
148_S	152_F	0.793	1.00
52_Y	173_W	0.786	1.00
193_A	197_L	0.786	1.00
161_V	164_Y	0.779	1.00
174_K	177_G	0.778	1.00
24_F	31_G	0.777	1.00
19_S	22_E	0.777	1.00
51_G	64_V	0.776	1.00
149_L	152_F	0.775	1.00
25_K	28_S	0.774	1.00
40_F	124_R	0.764	1.00
169_L	172_N	0.762	1.00
54_V	64_V	0.755	1.00
165_L	168_K	0.749	1.00
77_L	151_T	0.749	1.00
43_A	127_P	0.743	0.99
49_L	180_L	0.740	0.99
190_A	194_L	0.733	0.99
118_F	150_Y	0.732	0.99
187_I	191_I	0.731	0.99
90_F	93_R	0.730	0.99
169_L	173_W	0.724	0.99
197_L	200_L	0.723	0.99
94_F	102_P	0.719	0.99
76_P	144_V	0.717	0.99
24_F	27_L	0.714	0.99
177_G	180_L	0.713	0.99
176_V	179_I	0.710	0.99
41_I	131_T	0.707	0.99
188_G	191_I	0.705	0.99
43_A	151_T	0.705	0.99
87_G	91_L	0.703	0.99
126_L	129_I	0.702	0.99
23_A	28_S	0.698	0.99
19_S	23_A	0.697	0.99
80_Y	144_V	0.692	0.99
94_F	98_L	0.692	0.99
54_V	163_V	0.691	0.99
32_I	50_A	0.689	0.99
97_Y	100_I	0.689	0.99
172_N	175_A	0.686	0.99
156_L	160_F	0.684	0.99
185_L	188_G	0.682	0.99
79_L	131_T	0.682	0.99
49_L	53_W	0.681	0.99
124_R	130_R	0.675	0.99
202_K	206_K	0.675	0.99
49_L	52_Y	0.666	0.99
192_L	196_L	0.666	0.99
119_V	133_I	0.660	0.99
95_G	102_P	0.651	0.99
21_I	53_W	0.651	0.99
88_R	91_L	0.646	0.99
86_G	90_F	0.645	0.99
109_D	141_K	0.644	0.99
89_P	92_E	0.643	0.99
110_N	113_K	0.643	0.99
94_F	100_I	0.641	0.99
159_T	163_V	0.636	0.98
80_Y	138_G	0.627	0.98
137_C	142_M	0.622	0.98
47_L	159_T	0.620	0.98
167_V	171_E	0.618	0.98
44_E	162_Y	0.607	0.98
36_L	68_G	0.607	0.98
135_I	139_I	0.606	0.98
32_I	67_A	0.606	0.98
107_K	110_N	0.605	0.98
152_F	156_L	0.605	0.98
131_T	162_Y	0.596	0.98
161_V	165_L	0.596	0.98
127_P	131_T	0.596	0.98
105_L	112_F	0.594	0.98
35_A	46_V	0.585	0.97
47_L	72_G	0.583	0.97
178_S	182_Q	0.580	0.97
138_G	141_K	0.579	0.97
112_F	119_V	0.573	0.97
199_L	202_K	0.573	0.97
40_F	76_P	0.569	0.97
80_Y	141_K	0.563	0.97
168_K	172_N	0.563	0.97
147_F	151_T	0.563	0.97
146_V	150_Y	0.563	0.97
48_P	52_Y	0.562	0.97
44_E	154_A	0.557	0.96
23_A	27_L	0.554	0.96
78_T	81_W	0.552	0.96
123_G	137_C	0.552	0.96
198_Y	205_K	0.548	0.96
98_L	105_L	0.547	0.96
118_F	136_P	0.546	0.96
20_W	28_S	0.545	0.96
39_E	124_R	0.544	0.96
193_A	200_L	0.540	0.96
123_G	127_P	0.537	0.96
39_E	131_T	0.534	0.95
35_A	41_I	0.533	0.95
185_L	199_L	0.531	0.95
21_I	28_S	0.531	0.95
36_L	154_A	0.528	0.95
157_P	161_V	0.528	0.95
103_E	106_D	0.525	0.95
111_F	115_H	0.525	0.95
44_E	124_R	0.525	0.95
79_L	127_P	0.522	0.95
182_Q	194_L	0.522	0.95
78_T	82_I	0.521	0.95
179_I	183_Y	0.517	0.95
21_I	25_K	0.516	0.95
130_R	155_M	0.516	0.95
28_S	59_M	0.516	0.95
39_E	151_T	0.516	0.95
23_A	31_G	0.516	0.95
94_F	101_K	0.515	0.95
40_F	131_T	0.515	0.95
72_G	131_T	0.514	0.94
50_A	163_V	0.513	0.94
194_L	197_L	0.513	0.94
119_V	154_A	0.511	0.94
191_I	195_F	0.511	0.94
104_A	108_S	0.509	0.94
120_A	137_C	0.507	0.94
51_G	57_G	0.505	0.94
90_F	97_Y	0.504	0.94
189_I	192_L	0.503	0.94
40_F	134_S	0.503	0.94
74_A	78_T	0.501	0.94
72_G	123_G	0.500	0.94
61_L	160_F	0.500	0.94

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
1pw4A	1	0.9367	37.1	0.933	Contact Map
4dx5A	3	0.8009	36.4	0.933	Contact Map
2m20A	2	0.2081	31.6	0.935	Contact Map
2kluA	1	0.2308	30.7	0.935	Contact Map
2cfqA	1	0.8643	27.9	0.937	Contact Map
4ldsA	2	0.8552	27.3	0.937	Contact Map
2l2tA	2	0.1855	27.2	0.937	Contact Map
2rddB	1	0.1674	25.5	0.938	Contact Map
2ks1B	1	0.1991	23.7	0.939	Contact Map
2jwaA	2	0.1991	22.8	0.939	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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