YDBA - BACSU - GREMLIN Contacts

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YDBA - Uncharacterized protein YdbA

UniProt:	P96596	Sequences: MPTERKEDLHQQLKEIEKWEKDQQKVWFWEKLSRLPFQLLDKLTPEFIQKKIGKLLDEVGSFVQTGGQYLTSEKQIIRMFQKKLPEEIFESLEDIRKAPLPVMDEIAEGMGKNRTNAATVQGATTGVGGVFTLAADIPAVLGLSLKTLQDIAVAYGYDPKEKKERVFIVKCLQLTSADVVGKRSILQELKHYDQDRTYKNVASQIQGWREVVLGYRDTFGWKKLFQIVPVAGMVFGAAANRSTLNDITETGMMLYKKRRILERLKETEREME	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	272 (231)
Sequences:	653 (533)
Seq/√Len:	35.0

BACSU - YDBA ECSC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
157_Y	262_E	6.760	1.00
147_T	248_T	5.023	1.00
148_L	251_G	4.654	1.00
223_K	226_Q	3.714	1.00
253_M	256_K	3.535	1.00
123_A	237_A	3.507	1.00
108_E	252_M	3.454	1.00
164_E	258_R	3.251	1.00
111_G	248_T	2.888	1.00
164_E	255_Y	2.823	1.00
191_H	194_Q	2.607	1.00
228_V	231_A	2.528	1.00
232_G	236_G	2.496	1.00
107_A	151_I	2.469	1.00
147_T	151_I	2.458	1.00
127_V	233_M	2.442	1.00
115_T	245_N	2.430	1.00
124_T	225_F	2.361	0.99
157_Y	259_R	2.339	0.99
151_I	251_G	2.327	0.99
148_L	168_I	2.300	0.99
89_F	94_D	2.257	0.99
139_A	142_G	2.206	0.99
112_K	116_N	2.204	0.99
100_L	104_D	2.141	0.99
104_D	155_Y	2.130	0.99
128_G	132_T	2.048	0.99
226_Q	232_G	1.866	0.97
126_G	129_G	1.860	0.97
238_A	242_S	1.858	0.97
158_D	161_E	1.827	0.97
144_S	247_I	1.783	0.96
107_A	155_Y	1.632	0.94
171_C	251_G	1.596	0.93
155_Y	256_K	1.595	0.93
59_V	238_A	1.555	0.92
155_Y	164_E	1.554	0.92
36_P	190_K	1.545	0.92
60_G	64_Q	1.541	0.92
146_K	150_D	1.532	0.92
82_K	86_E	1.511	0.91
119_T	241_R	1.506	0.91
111_G	115_T	1.488	0.91
110_M	154_A	1.469	0.90
168_I	255_Y	1.453	0.89
120_V	127_V	1.441	0.89
121_Q	143_L	1.407	0.88
199_K	204_Q	1.357	0.86
36_P	39_L	1.352	0.86
115_T	240_N	1.333	0.85
100_L	167_F	1.307	0.84
107_A	154_A	1.294	0.83
130_V	133_L	1.290	0.83
171_C	180_V	1.259	0.81
129_G	226_Q	1.259	0.81
231_A	234_V	1.257	0.81
101_P	105_E	1.257	0.81
78_R	81_Q	1.247	0.81
77_I	124_T	1.243	0.81
94_D	97_K	1.236	0.80
172_L	233_M	1.231	0.80
35_L	39_L	1.209	0.79
120_V	124_T	1.208	0.79
129_G	138_P	1.204	0.78
160_K	191_H	1.199	0.78
147_T	244_L	1.184	0.77
28_F	31_K	1.162	0.76
171_C	254_L	1.158	0.76
175_T	250_T	1.155	0.75
122_G	126_G	1.153	0.75
122_G	236_G	1.146	0.75
75_Q	98_A	1.139	0.74
31_K	35_L	1.131	0.74
125_T	137_I	1.129	0.74
187_Q	191_H	1.128	0.74
59_V	62_F	1.123	0.73
219_F	224_L	1.122	0.73
98_A	102_V	1.117	0.73
138_P	145_L	1.109	0.72
145_L	149_Q	1.107	0.72
114_R	143_L	1.107	0.72
220_G	232_G	1.104	0.72
85_P	163_K	1.099	0.72
100_L	185_I	1.096	0.71
164_E	167_F	1.091	0.71
31_K	38_Q	1.087	0.71
129_G	236_G	1.084	0.71
30_E	34_R	1.082	0.70
120_V	210_E	1.079	0.70
136_D	223_K	1.073	0.70
104_D	107_A	1.068	0.69
104_D	256_K	1.067	0.69
157_Y	255_Y	1.062	0.69
143_L	152_A	1.045	0.68
78_R	157_Y	1.045	0.68
140_V	175_T	1.044	0.68
127_V	230_V	1.034	0.67
46_E	148_L	1.027	0.66
208_W	216_R	1.006	0.65
122_G	240_N	1.006	0.65
89_F	96_R	1.005	0.65
96_R	263_R	1.004	0.65
111_G	241_R	1.002	0.64
106_I	143_L	0.996	0.64
51_K	54_K	0.994	0.64
152_A	204_Q	0.991	0.64
199_K	202_A	0.984	0.63
111_G	151_I	0.981	0.63
59_V	63_V	0.979	0.63
74_K	228_V	0.974	0.62
90_E	93_E	0.972	0.62
81_Q	85_P	0.968	0.62
124_T	147_T	0.960	0.61
30_E	37_F	0.956	0.61
212_V	216_R	0.947	0.60
49_Q	120_V	0.946	0.60
130_V	227_I	0.943	0.60
175_T	247_I	0.941	0.59
191_H	195_D	0.938	0.59
61_S	75_Q	0.933	0.59
39_L	42_K	0.919	0.58
117_A	143_L	0.919	0.58
103_M	175_T	0.917	0.57
67_G	70_L	0.913	0.57
163_K	194_Q	0.905	0.56
98_A	120_V	0.904	0.56
63_V	67_G	0.893	0.55
73_E	231_A	0.893	0.55
215_Y	227_I	0.891	0.55
171_C	232_G	0.883	0.55
111_G	252_M	0.882	0.55
81_Q	94_D	0.879	0.54
129_G	145_L	0.876	0.54
145_L	230_V	0.876	0.54
230_V	234_V	0.875	0.54
128_G	240_N	0.873	0.54
138_P	223_K	0.872	0.54
76_I	140_V	0.871	0.54
65_T	69_Y	0.868	0.53
186_L	190_K	0.865	0.53
153_V	159_P	0.856	0.52
28_F	104_D	0.856	0.52
165_R	238_A	0.855	0.52
205_I	210_E	0.849	0.52
223_K	240_N	0.848	0.52
170_K	188_E	0.840	0.51
55_L	194_Q	0.840	0.51
48_I	54_K	0.837	0.51
148_L	263_R	0.832	0.50
112_K	228_V	0.830	0.50
29_W	32_L	0.828	0.50
36_P	186_L	0.825	0.50
59_V	111_G	0.824	0.50
89_F	95_I	0.824	0.50
54_K	94_D	0.823	0.49
38_Q	48_I	0.818	0.49
34_R	39_L	0.818	0.49
186_L	189_L	0.817	0.49
97_K	106_I	0.815	0.49
63_V	145_L	0.814	0.49
212_V	215_Y	0.813	0.49
89_F	113_N	0.812	0.49
89_F	110_M	0.810	0.48
138_P	175_T	0.810	0.48
212_V	220_G	0.804	0.48
91_S	94_D	0.802	0.48
211_V	218_T	0.800	0.48
33_S	36_P	0.794	0.47
109_G	112_K	0.793	0.47
50_K	61_S	0.792	0.47
101_P	104_D	0.787	0.46
223_K	256_K	0.782	0.46
100_L	136_D	0.779	0.46
41_D	168_I	0.777	0.46
118_A	208_W	0.775	0.45
212_V	232_G	0.775	0.45
135_A	237_A	0.774	0.45
92_L	100_L	0.773	0.45
147_T	249_E	0.768	0.45
160_K	193_D	0.767	0.45
138_P	189_L	0.767	0.45
233_M	239_A	0.764	0.44
208_W	215_Y	0.763	0.44
118_A	143_L	0.756	0.44
78_R	260_I	0.756	0.44
173_Q	177_A	0.752	0.43
86_E	90_E	0.746	0.43
126_G	138_P	0.745	0.43
175_T	213_L	0.745	0.43
141_L	190_K	0.745	0.43
123_A	158_D	0.745	0.43
145_L	226_Q	0.744	0.43
131_F	231_A	0.743	0.43
113_N	185_I	0.742	0.43
139_A	231_A	0.740	0.42
202_A	205_I	0.736	0.42
196_R	231_A	0.734	0.42
37_F	41_D	0.733	0.42
29_W	151_I	0.733	0.42
216_R	220_G	0.732	0.42
86_E	211_V	0.732	0.42
74_K	171_C	0.731	0.42
165_R	247_I	0.729	0.41
129_G	229_P	0.727	0.41
118_A	217_D	0.724	0.41
51_K	70_L	0.723	0.41
247_I	256_K	0.720	0.41
58_E	66_G	0.715	0.40
157_Y	258_R	0.715	0.40
147_T	225_F	0.714	0.40
104_D	141_L	0.711	0.40
74_K	87_E	0.704	0.39
75_Q	179_V	0.704	0.39
48_I	51_K	0.702	0.39
171_C	236_G	0.699	0.39
77_I	92_L	0.699	0.39
215_Y	220_G	0.698	0.39
108_E	113_N	0.697	0.39
118_A	123_A	0.693	0.39
165_R	217_D	0.691	0.38
217_D	240_N	0.690	0.38
48_I	250_T	0.690	0.38
76_I	166_V	0.682	0.38
93_E	198_Y	0.678	0.37
62_F	231_A	0.677	0.37
129_G	233_M	0.673	0.37
80_F	89_F	0.673	0.37
33_S	171_C	0.672	0.37
167_F	175_T	0.671	0.37
94_D	102_V	0.671	0.37
81_Q	196_R	0.670	0.37
55_L	184_S	0.670	0.37
108_E	198_Y	0.670	0.37
93_E	120_V	0.670	0.37
176_S	240_N	0.668	0.37
50_K	247_I	0.667	0.36
99_P	234_V	0.666	0.36
35_L	38_Q	0.665	0.36
102_V	263_R	0.664	0.36
100_L	244_L	0.662	0.36
80_F	239_A	0.661	0.36
80_F	211_V	0.660	0.36
167_F	258_R	0.658	0.36
89_F	112_K	0.654	0.35
35_L	41_D	0.653	0.35
257_K	261_L	0.651	0.35
137_I	214_G	0.648	0.35
132_T	228_V	0.645	0.35
47_F	52_I	0.643	0.35
115_T	243_T	0.641	0.34
76_I	172_L	0.641	0.34
66_G	69_Y	0.638	0.34
114_R	150_D	0.638	0.34
103_M	259_R	0.637	0.34
81_Q	110_M	0.637	0.34
136_D	156_G	0.636	0.34
69_Y	259_R	0.633	0.34
78_R	160_K	0.633	0.34
123_A	171_C	0.633	0.34
232_G	258_R	0.631	0.34
55_L	150_D	0.631	0.34
222_K	246_D	0.630	0.34
41_D	145_L	0.629	0.33
222_K	226_Q	0.625	0.33
125_T	139_A	0.625	0.33
149_Q	170_K	0.624	0.33
97_K	101_P	0.624	0.33
63_V	118_A	0.622	0.33
169_V	240_N	0.619	0.33
74_K	82_K	0.619	0.33
62_F	152_A	0.618	0.33
169_V	226_Q	0.618	0.33
131_F	224_L	0.608	0.32
109_G	140_V	0.607	0.32
146_K	237_A	0.605	0.32
176_S	215_Y	0.602	0.31
257_K	260_I	0.598	0.31
57_D	183_R	0.598	0.31
131_F	134_A	0.593	0.31
140_V	243_T	0.592	0.31
56_L	64_Q	0.591	0.31
136_D	140_V	0.591	0.31
119_T	219_F	0.589	0.30
30_E	234_V	0.588	0.30
93_E	230_V	0.588	0.30
152_A	168_I	0.587	0.30
36_P	132_T	0.586	0.30
137_I	196_R	0.582	0.30
80_F	98_A	0.581	0.30
140_V	223_K	0.581	0.30
65_T	209_R	0.580	0.30
203_S	207_G	0.579	0.30
129_G	232_G	0.575	0.29
144_S	243_T	0.574	0.29
254_L	260_I	0.574	0.29
114_R	137_I	0.573	0.29
125_T	175_T	0.572	0.29
88_I	94_D	0.571	0.29
106_I	109_G	0.571	0.29
250_T	254_L	0.570	0.29
73_E	233_M	0.570	0.29
151_I	171_C	0.569	0.29
61_S	230_V	0.569	0.29
144_S	208_W	0.568	0.29
51_K	181_G	0.568	0.29
107_A	255_Y	0.566	0.29
209_R	213_L	0.563	0.29
148_L	165_R	0.562	0.29
121_Q	139_A	0.561	0.28
30_E	51_K	0.559	0.28
155_Y	235_F	0.559	0.28
172_L	241_R	0.554	0.28
50_K	163_K	0.553	0.28
174_L	185_I	0.547	0.28
107_A	221_W	0.547	0.28
127_V	130_V	0.544	0.27
213_L	217_D	0.544	0.27
88_I	104_D	0.543	0.27
115_T	172_L	0.542	0.27
53_G	233_M	0.540	0.27
193_D	197_T	0.539	0.27
61_S	105_E	0.539	0.27
225_F	228_V	0.537	0.27
82_K	109_G	0.532	0.27
139_A	168_I	0.530	0.26
207_G	212_V	0.529	0.26
52_I	133_L	0.525	0.26
56_L	73_E	0.525	0.26
68_Q	79_M	0.523	0.26
76_I	99_P	0.520	0.26
129_G	150_D	0.517	0.26
45_P	195_D	0.513	0.25
74_K	77_I	0.512	0.25
145_L	206_Q	0.511	0.25
73_E	77_I	0.511	0.25
122_G	156_G	0.509	0.25
40_L	230_V	0.508	0.25
160_K	180_V	0.505	0.25
123_A	225_F	0.505	0.25
208_W	226_Q	0.504	0.25
218_T	260_I	0.504	0.25
133_L	149_Q	0.503	0.25
93_E	163_K	0.501	0.24
219_F	247_I	0.501	0.24
76_I	125_T	0.500	0.24
55_L	67_G	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
2qneA	2	0.2463	12.7	0.959	Contact Map
4pt2P	11	0.2904	6.2	0.964	Contact Map
1w53A	2	0.2721	5.8	0.965	Contact Map
4yycA	2	0.2279	5.2	0.966	Contact Map
1rh5B	1	0.2059	4.7	0.966	Contact Map
3sjqC	1	0.1176	4.5	0.967	Contact Map
3dktA	6	0.2941	3.7	0.968	Contact Map
3oq9A	3	0.1985	3.6	0.968	Contact Map
2j6yA	2	0.2831	3.4	0.968	Contact Map
1hgvA	8	0.1691	3.2	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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