YRHO - BACSU - GREMLIN Contacts

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YRHO - Uncharacterized protein YrhO

UniProt:	O05405	Sequences: MKENMLDILKNLNFTEYESKAYLALLQESPLTGYAVAKKSGVPRSKIYEVLESLVIRGDVFVSHGNTPQYVPVPAKELIKNRRLKAEEHFDQAEKYFEKFEQTANDRENIWNITGRSEILEKVKACILSAKKRILLEIWKEDFKEIEAELKQAAEQGVIVTIIAYGDIVSDFANVYLHDMSSEITEEYDGRWLVYSGDDSEVVAGIVSLGNDSRAAWTMHVGLVMPITEVIIHDLYLMEILKKHRELLEESFGKNLIQLRRKFSIHSDFKKHYLE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	275 (234)
Sequences:	2320 (1863)
Seq/√Len:	121.8

BACSU - YRHO
HALSA - Q9HNY8 TRMBR
SULSO - Q7LYK2 Q97ZZ5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
153_A	156_Q	3.721	1.00
18_E	53_S	3.306	1.00
25_L	60_V	3.072	1.00
130_A	197_G	3.053	1.00
18_E	57_R	3.041	1.00
133_R	199_D	2.878	1.00
17_Y	43_P	2.865	1.00
22_Y	26_L	2.807	1.00
46_K	49_E	2.745	1.00
135_L	199_D	2.695	1.00
130_A	134_I	2.510	1.00
161_T	232_I	2.484	1.00
137_E	234_D	2.381	1.00
59_D	78_L	2.374	1.00
17_Y	46_K	2.326	1.00
51_L	60_V	2.208	1.00
15_T	53_S	2.174	1.00
115_G	118_E	2.158	1.00
28_E	31_L	2.137	1.00
128_L	152_Q	2.129	1.00
32_T	35_A	2.072	1.00
125_A	129_S	2.056	1.00
87_E	94_E	1.988	1.00
51_L	70_Y	1.957	1.00
15_T	18_E	1.953	1.00
199_D	228_T	1.931	1.00
119_I	215_A	1.918	1.00
159_I	183_E	1.911	1.00
126_C	203_V	1.851	1.00
126_C	201_E	1.823	1.00
161_T	235_L	1.754	1.00
137_E	163_I	1.751	1.00
231_I	235_L	1.731	1.00
21_A	47_I	1.730	1.00
17_Y	40_S	1.712	1.00
187_E	238_M	1.698	1.00
24_A	39_K	1.693	1.00
43_P	46_K	1.688	1.00
17_Y	42_V	1.681	1.00
21_A	50_V	1.646	1.00
151_K	155_E	1.640	1.00
146_I	150_L	1.605	1.00
16_E	20_K	1.604	1.00
196_S	228_T	1.594	1.00
61_F	71_V	1.589	1.00
22_Y	75_A	1.581	1.00
34_Y	38_K	1.577	1.00
136_L	195_Y	1.565	1.00
163_I	234_D	1.550	1.00
19_S	23_L	1.503	1.00
134_I	197_G	1.500	1.00
21_A	42_V	1.488	1.00
81_N	85_K	1.473	1.00
122_K	217_W	1.472	1.00
21_A	36_V	1.466	1.00
153_A	158_V	1.456	1.00
111_W	122_K	1.455	1.00
185_T	235_L	1.439	1.00
221_V	225_M	1.438	1.00
127_I	134_I	1.434	1.00
135_L	228_T	1.420	1.00
14_F	59_D	1.373	1.00
30_P	69_Q	1.373	1.00
127_I	197_G	1.372	1.00
130_A	153_A	1.340	1.00
44_R	48_Y	1.336	1.00
124_K	152_Q	1.328	1.00
27_Q	39_K	1.327	1.00
122_K	125_A	1.323	1.00
134_I	153_A	1.320	1.00
17_Y	49_E	1.316	1.00
24_A	40_S	1.313	1.00
127_I	160_V	1.311	1.00
152_Q	155_E	1.307	1.00
43_P	50_V	1.303	1.00
31_L	39_K	1.300	1.00
137_E	191_R	1.283	1.00
169_V	186_E	1.270	1.00
228_T	232_I	1.262	1.00
96_Y	99_K	1.256	1.00
224_V	228_T	1.254	0.99
113_I	217_W	1.250	0.99
59_D	82_R	1.241	0.99
28_E	39_K	1.240	0.99
97_F	101_E	1.233	0.99
17_Y	50_V	1.228	0.99
127_I	153_A	1.220	0.99
176_Y	179_D	1.212	0.99
88_E	92_Q	1.208	0.99
40_S	47_I	1.208	0.99
147_E	151_K	1.201	0.99
136_L	162_I	1.193	0.99
110_I	223_L	1.189	0.99
76_K	94_E	1.178	0.99
111_W	219_M	1.170	0.99
36_V	47_I	1.167	0.99
10_K	16_E	1.162	0.99
86_A	89_H	1.146	0.99
134_I	160_V	1.139	0.99
42_V	47_I	1.136	0.99
52_E	56_I	1.115	0.99
43_P	47_I	1.099	0.99
63_S	71_V	1.095	0.99
87_E	91_D	1.093	0.99
89_H	93_A	1.092	0.99
55_V	62_V	1.090	0.99
122_K	126_C	1.078	0.98
166_G	186_E	1.075	0.98
26_L	75_A	1.069	0.98
24_A	36_V	1.063	0.98
131_K	200_S	1.060	0.98
235_L	238_M	1.058	0.98
83_R	93_A	1.056	0.98
178_H	182_S	1.052	0.98
25_L	51_L	1.041	0.98
147_E	150_L	1.023	0.98
35_A	38_K	1.012	0.98
78_L	83_R	1.012	0.98
200_S	219_M	1.004	0.98
17_Y	21_A	1.000	0.97
45_S	49_E	1.000	0.97
137_E	190_G	0.996	0.97
79_I	82_R	0.995	0.97
119_I	214_R	0.993	0.97
92_Q	96_Y	0.989	0.97
216_A	223_L	0.988	0.97
140_K	165_Y	0.987	0.97
141_E	193_L	0.985	0.97
91_D	94_E	0.982	0.97
34_Y	45_S	0.979	0.97
137_E	220_H	0.976	0.97
137_E	194_V	0.965	0.97
196_S	224_V	0.962	0.97
164_A	184_I	0.956	0.97
18_E	50_V	0.946	0.96
86_A	90_F	0.944	0.96
9_L	13_N	0.941	0.96
88_E	91_D	0.941	0.96
196_S	202_V	0.938	0.96
53_S	56_I	0.930	0.96
127_I	150_L	0.926	0.96
120_L	145_E	0.926	0.96
123_V	195_Y	0.922	0.96
124_K	149_E	0.920	0.96
10_K	19_S	0.905	0.95
47_I	60_V	0.902	0.95
187_E	237_L	0.901	0.95
123_V	193_L	0.897	0.95
153_A	197_G	0.891	0.95
40_S	50_V	0.889	0.95
201_E	217_W	0.883	0.95
88_E	95_K	0.882	0.95
137_E	230_V	0.880	0.95
79_I	86_A	0.876	0.95
123_V	127_I	0.875	0.95
58_G	115_G	0.866	0.94
201_E	219_M	0.865	0.94
9_L	19_S	0.863	0.94
226_P	230_V	0.863	0.94
128_L	149_E	0.855	0.94
84_L	88_E	0.854	0.94
177_L	181_S	0.853	0.94
33_G	44_R	0.850	0.94
196_S	231_I	0.849	0.94
99_K	102_Q	0.831	0.93
157_G	198_D	0.829	0.93
187_E	234_D	0.828	0.93
240_I	243_K	0.827	0.93
33_G	48_Y	0.825	0.93
135_L	196_S	0.818	0.92
86_A	93_A	0.816	0.92
62_V	67_T	0.811	0.92
135_L	161_T	0.811	0.92
220_H	225_M	0.809	0.92
57_R	85_K	0.801	0.92
28_E	84_L	0.801	0.92
192_W	226_P	0.801	0.92
136_L	160_V	0.793	0.91
98_E	102_Q	0.792	0.91
42_V	48_Y	0.791	0.91
12_L	203_V	0.781	0.91
130_A	198_D	0.780	0.90
55_V	60_V	0.771	0.90
174_N	179_D	0.769	0.90
181_S	203_V	0.764	0.90
179_D	182_S	0.756	0.89
150_L	154_A	0.752	0.89
135_L	232_I	0.749	0.89
111_W	217_W	0.747	0.88
22_Y	73_V	0.745	0.88
165_Y	193_L	0.740	0.88
32_T	70_Y	0.735	0.88
25_L	36_V	0.734	0.88
237_L	241_L	0.732	0.87
135_L	231_I	0.729	0.87
155_E	200_S	0.727	0.87
45_S	105_N	0.725	0.87
122_K	219_M	0.720	0.87
83_R	86_A	0.718	0.86
148_A	152_Q	0.718	0.86
139_W	205_G	0.716	0.86
24_A	31_L	0.711	0.86
133_R	159_I	0.708	0.86
218_T	227_I	0.707	0.86
120_L	146_I	0.703	0.85
126_C	217_W	0.701	0.85
133_R	198_D	0.696	0.85
172_F	176_Y	0.695	0.85
106_D	132_K	0.695	0.85
116_R	120_L	0.695	0.85
37_A	47_I	0.694	0.85
17_Y	33_G	0.691	0.84
115_G	119_I	0.691	0.84
93_A	97_F	0.690	0.84
113_I	118_E	0.687	0.84
37_A	44_R	0.686	0.84
140_K	143_F	0.686	0.84
90_F	94_E	0.684	0.84
82_R	86_A	0.683	0.84
38_K	44_R	0.683	0.84
133_R	228_T	0.682	0.84
37_A	60_V	0.681	0.83
42_V	46_K	0.679	0.83
92_Q	151_K	0.679	0.83
221_V	224_V	0.677	0.83
175_V	196_S	0.676	0.83
75_A	79_I	0.676	0.83
74_P	175_V	0.675	0.83
93_A	96_Y	0.673	0.83
128_L	156_Q	0.673	0.83
174_N	177_L	0.673	0.83
166_G	169_V	0.673	0.83
126_C	197_G	0.672	0.83
109_N	219_M	0.672	0.83
150_L	160_V	0.670	0.82
116_R	212_D	0.670	0.82
52_E	55_V	0.665	0.82
57_R	126_C	0.664	0.82
24_A	27_Q	0.663	0.82
43_P	49_E	0.662	0.82
75_A	101_E	0.661	0.82
171_D	174_N	0.661	0.82
202_V	227_I	0.660	0.82
23_L	26_L	0.660	0.82
194_V	230_V	0.658	0.81
175_V	178_H	0.657	0.81
35_A	39_K	0.657	0.81
87_E	130_A	0.655	0.81
234_D	237_L	0.655	0.81
174_N	178_H	0.653	0.81
49_E	52_E	0.652	0.81
32_T	48_Y	0.650	0.81
81_N	206_I	0.646	0.80
188_Y	243_K	0.645	0.80
19_S	48_Y	0.643	0.80
58_G	218_T	0.635	0.79
98_E	101_E	0.635	0.79
23_L	27_Q	0.633	0.79
150_L	177_L	0.632	0.79
178_H	241_L	0.632	0.79
129_S	201_E	0.630	0.78
123_V	169_V	0.628	0.78
154_A	164_A	0.626	0.78
152_Q	179_D	0.626	0.78
73_V	78_L	0.625	0.78
132_K	159_I	0.621	0.77
136_L	146_I	0.619	0.77
194_V	231_I	0.619	0.77
123_V	139_W	0.619	0.77
113_I	215_A	0.618	0.77
138_I	142_D	0.618	0.77
164_A	193_L	0.617	0.77
85_K	89_H	0.616	0.77
109_N	220_H	0.615	0.77
125_A	178_H	0.614	0.77
17_Y	48_Y	0.614	0.77
44_R	214_R	0.606	0.76
229_E	233_H	0.606	0.76
113_I	122_K	0.602	0.75
132_K	199_D	0.602	0.75
78_L	112_N	0.591	0.74
55_V	70_Y	0.590	0.74
203_V	217_W	0.588	0.74
33_G	70_Y	0.587	0.73
122_K	215_A	0.587	0.73
218_T	223_L	0.584	0.73
133_R	232_I	0.583	0.73
206_I	220_H	0.583	0.73
136_L	177_L	0.583	0.73
59_D	73_V	0.582	0.73
84_L	87_E	0.575	0.72
175_V	182_S	0.568	0.71
60_V	70_Y	0.567	0.71
239_E	242_K	0.567	0.71
32_T	44_R	0.566	0.71
144_K	147_E	0.566	0.71
25_L	33_G	0.566	0.71
54_L	89_H	0.563	0.70
206_I	214_R	0.562	0.70
139_W	165_Y	0.560	0.70
167_D	170_S	0.559	0.70
158_V	198_D	0.557	0.70
69_Q	203_V	0.557	0.70
25_L	70_Y	0.554	0.69
97_F	125_A	0.553	0.69
36_V	40_S	0.552	0.69
175_V	195_Y	0.551	0.69
184_I	187_E	0.549	0.68
202_V	205_G	0.549	0.68
146_I	216_A	0.548	0.68
158_V	199_D	0.548	0.68
149_E	222_G	0.544	0.68
194_V	227_I	0.542	0.67
163_I	233_H	0.542	0.67
127_I	147_E	0.541	0.67
156_Q	198_D	0.540	0.67
34_Y	37_A	0.538	0.67
121_E	125_A	0.538	0.67
43_P	110_I	0.536	0.67
140_K	197_G	0.525	0.65
170_S	186_E	0.525	0.65
93_A	101_E	0.524	0.65
66_N	204_A	0.518	0.64
142_D	171_D	0.517	0.64
76_K	98_E	0.517	0.64
138_I	193_L	0.516	0.64
17_Y	20_K	0.516	0.64
206_I	218_T	0.516	0.64
59_D	164_A	0.513	0.63
34_Y	46_K	0.512	0.63
135_L	220_H	0.512	0.63
235_L	240_I	0.512	0.63
149_E	223_L	0.512	0.63
122_K	203_V	0.511	0.63
137_E	226_P	0.510	0.63
31_L	45_S	0.508	0.62
65_G	212_D	0.507	0.62
190_G	193_L	0.507	0.62
47_I	230_V	0.505	0.62
191_R	226_P	0.505	0.62
91_D	129_S	0.505	0.62
88_E	116_R	0.504	0.62
37_A	45_S	0.503	0.62
141_E	144_K	0.503	0.62
123_V	174_N	0.503	0.62
61_F	73_V	0.502	0.62
92_Q	176_Y	0.502	0.62
48_Y	52_E	0.502	0.62
83_R	97_F	0.500	0.61
131_K	171_D	0.500	0.61
139_W	191_R	0.500	0.61

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
3qphA	2	0.9455	100	0.39	Contact Map
2f5tX	2	0.5709	99.4	0.748	Contact Map
1byrA	2	0.4982	99	0.789	Contact Map
4ggjA	2	0.5636	99	0.795	Contact Map
1sfxA	3	0.3673	98.6	0.818	Contact Map
1ku9A	2	0.4982	98.6	0.82	Contact Map
3r0aA	2	0.3818	98.5	0.825	Contact Map
4urjA	1	0.5345	98.5	0.825	Contact Map
1qgpA	1	0.2618	98.5	0.827	Contact Map
4nb5A	4	0.4982	98.4	0.831	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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