YHBD - BACSU - GREMLIN Contacts

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YHBD - Uncharacterized protein YhbD

UniProt:	P97032	Sequences: MLCFVFGLNNVTVLCYNVPIKGAGLMEEQLISKKELLERTSISYGQLYRWKRKNLIPEEWFIRKSTFTGQETFFPREEILKRISMIQKMKENLSLDEMREMLSPKMKDVSMTADELLHKGLVSRPALEAYSEDGGSPVFSSSDLLSLFVLEGLLQSGNVSLAEAKMAAEVLKKHDTEEIEKQTELIVLRKLGVTTCFIAAAADSILFESSVKVVERVDLLKASEELKTTFMQEGHQWM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	238 (205)
Sequences:	142 (124)
Seq/√Len:	8.7

BACSU - YHBD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
150_L	164_A	4.175	0.98
76_R	220_L	3.291	0.93
63_R	66_T	3.276	0.93
167_A	196_C	3.102	0.91
178_E	183_T	3.002	0.90
53_K	96_D	2.998	0.90
102_L	222_A	2.762	0.85
84_S	87_Q	2.720	0.84
169_E	173_K	2.645	0.82
191_L	196_C	2.498	0.79
144_L	147_L	2.428	0.76
103_S	227_K	2.371	0.75
163_E	189_R	2.156	0.67
27_E	199_A	2.128	0.66
84_S	100_E	2.078	0.64
116_L	144_L	2.026	0.62
152_G	225_E	1.978	0.60
115_E	209_S	1.976	0.60
175_D	216_R	1.954	0.59
126_A	159_V	1.921	0.58
149_V	219_L	1.888	0.56
183_T	206_L	1.875	0.56
39_R	76_R	1.817	0.53
41_S	141_S	1.813	0.53
154_L	157_G	1.811	0.53
66_T	73_F	1.798	0.53
159_V	164_A	1.781	0.52
199_A	211_V	1.775	0.52
161_L	208_E	1.772	0.51
80_L	154_L	1.743	0.50
160_S	195_T	1.735	0.50
63_R	93_L	1.704	0.49
53_K	157_G	1.704	0.49
35_E	112_T	1.669	0.47
117_L	127_L	1.635	0.46
89_M	144_L	1.625	0.45
59_E	118_H	1.584	0.43
111_M	206_L	1.564	0.43
101_M	193_V	1.561	0.43
187_V	191_L	1.558	0.42
181_K	203_D	1.546	0.42
28_E	174_H	1.537	0.42
63_R	185_L	1.533	0.41
43_S	58_E	1.524	0.41
140_S	160_S	1.520	0.41
123_S	194_T	1.518	0.41
87_Q	195_T	1.515	0.41
38_E	230_F	1.509	0.40
66_T	185_L	1.484	0.39
108_D	129_A	1.482	0.39
100_E	150_L	1.452	0.38
93_L	154_L	1.428	0.37
59_E	209_S	1.391	0.36
151_E	206_L	1.382	0.35
78_E	109_V	1.381	0.35
112_T	158_N	1.375	0.35
79_I	130_Y	1.366	0.35
108_D	115_E	1.362	0.34
108_D	172_K	1.361	0.34
67_F	83_I	1.325	0.33
208_E	228_T	1.315	0.33
156_S	186_I	1.311	0.33
96_D	157_G	1.306	0.32
55_L	63_R	1.304	0.32
46_Q	71_E	1.272	0.31
68_T	71_E	1.272	0.31
46_Q	68_T	1.272	0.31
189_R	192_G	1.269	0.31
85_M	164_A	1.268	0.31
59_E	185_L	1.256	0.31
157_G	163_E	1.255	0.30
102_L	137_P	1.236	0.30
115_E	177_E	1.213	0.29
77_E	132_E	1.209	0.29
171_L	214_V	1.205	0.29
106_M	208_E	1.203	0.29
154_L	189_R	1.199	0.28
87_Q	126_A	1.185	0.28
47_L	74_F	1.164	0.27
97_E	214_V	1.158	0.27
187_V	207_F	1.152	0.27
172_K	193_V	1.139	0.26
36_L	47_L	1.132	0.26
59_E	101_M	1.131	0.26
144_L	169_E	1.104	0.25
152_G	222_A	1.101	0.25
184_E	216_R	1.094	0.25
140_S	213_V	1.091	0.25
187_V	215_E	1.075	0.24
83_I	117_L	1.072	0.24
81_K	175_D	1.063	0.24
64_K	78_E	1.062	0.24
162_A	178_E	1.052	0.24
155_Q	214_V	1.049	0.24
53_K	64_K	1.039	0.23
185_L	204_S	1.034	0.23
106_M	211_V	1.032	0.23
88_K	202_A	1.029	0.23
152_G	188_L	1.027	0.23
92_N	175_D	1.026	0.23
111_M	222_A	1.021	0.23
108_D	140_S	1.007	0.22
116_L	221_K	1.001	0.22
105_K	118_H	1.000	0.22
163_E	212_K	0.995	0.22
148_F	151_E	0.993	0.22
32_S	65_S	0.976	0.21
154_L	163_E	0.974	0.21
88_K	100_E	0.970	0.21
31_I	205_I	0.965	0.21
128_E	132_E	0.954	0.21
56_I	66_T	0.953	0.21
167_A	187_V	0.953	0.21
29_Q	128_E	0.950	0.21
105_K	230_F	0.946	0.21
93_L	224_E	0.945	0.21
123_S	224_E	0.941	0.20
26_M	230_F	0.931	0.20
223_S	230_F	0.927	0.20
46_Q	95_L	0.924	0.20
71_E	95_L	0.924	0.20
68_T	95_L	0.924	0.20
30_L	62_I	0.923	0.20
119_K	191_L	0.920	0.20
176_T	219_L	0.913	0.20
134_G	225_E	0.911	0.20
35_E	137_P	0.911	0.20
29_Q	84_S	0.907	0.19
129_A	152_G	0.900	0.19
115_E	188_L	0.900	0.19
122_V	164_A	0.897	0.19
40_T	72_T	0.893	0.19
27_E	76_R	0.892	0.19
92_N	230_F	0.892	0.19
185_L	219_L	0.891	0.19
28_E	114_D	0.889	0.19
211_V	230_F	0.887	0.19
66_T	91_E	0.886	0.19
36_L	94_S	0.884	0.19
111_M	152_G	0.882	0.19
96_D	120_G	0.882	0.19
28_E	173_K	0.873	0.19
109_V	173_K	0.868	0.18
27_E	124_R	0.861	0.18
163_E	190_K	0.860	0.18
81_K	179_I	0.857	0.18
138_V	179_I	0.851	0.18
101_M	196_C	0.849	0.18
160_S	187_V	0.844	0.18
28_E	230_F	0.843	0.18
115_E	160_S	0.841	0.18
160_S	182_Q	0.832	0.18
35_E	87_Q	0.827	0.17
30_L	64_K	0.827	0.17
115_E	197_F	0.815	0.17
27_E	138_V	0.812	0.17
100_E	135_G	0.809	0.17
102_L	203_D	0.806	0.17
157_G	224_E	0.806	0.17
168_A	171_L	0.803	0.17
119_K	141_S	0.801	0.17
158_N	210_S	0.800	0.17
137_P	197_F	0.799	0.17
162_A	217_V	0.790	0.17
53_K	121_L	0.787	0.16
134_G	194_T	0.786	0.16
166_M	211_V	0.783	0.16
188_L	197_F	0.781	0.16
109_V	208_E	0.780	0.16
54_N	102_L	0.776	0.16
150_L	226_L	0.775	0.16
62_I	122_V	0.775	0.16
125_P	138_V	0.765	0.16
129_A	185_L	0.755	0.16
190_K	193_V	0.743	0.15
59_E	126_A	0.742	0.15
66_T	195_T	0.742	0.15
121_L	157_G	0.741	0.15
93_L	123_S	0.735	0.15
81_K	191_L	0.732	0.15
139_F	219_L	0.732	0.15
135_G	144_L	0.730	0.15
88_K	206_L	0.728	0.15
103_S	168_A	0.727	0.15
124_R	129_A	0.725	0.15
29_Q	178_E	0.718	0.15
148_F	158_N	0.715	0.15
186_I	223_S	0.714	0.15
129_A	132_E	0.714	0.15
55_L	122_V	0.712	0.15
78_E	230_F	0.710	0.15
88_K	219_L	0.709	0.15
59_E	167_A	0.700	0.15
128_E	152_G	0.695	0.14
188_L	195_T	0.692	0.14
126_A	197_F	0.690	0.14
88_K	214_V	0.689	0.14
150_L	205_I	0.682	0.14
66_T	187_V	0.681	0.14
151_E	202_A	0.680	0.14
129_A	215_E	0.677	0.14
54_N	150_L	0.676	0.14
212_K	221_K	0.673	0.14
101_M	191_L	0.673	0.14
105_K	134_G	0.669	0.14
89_M	207_F	0.667	0.14
104_P	139_F	0.662	0.14
124_R	128_E	0.660	0.14
107_K	170_V	0.659	0.14
150_L	184_E	0.654	0.14
29_Q	147_L	0.651	0.14
28_E	135_G	0.651	0.14
142_S	158_N	0.650	0.13
98_M	145_L	0.647	0.13
93_L	148_F	0.646	0.13
66_T	129_A	0.645	0.13
174_H	191_L	0.645	0.13
199_A	207_F	0.644	0.13
160_S	175_D	0.644	0.13
88_K	92_N	0.641	0.13
66_T	101_M	0.637	0.13
26_M	96_D	0.636	0.13
157_G	189_R	0.636	0.13
76_R	160_S	0.635	0.13
197_F	218_D	0.633	0.13
31_I	164_A	0.633	0.13
76_R	229_T	0.632	0.13
98_M	175_D	0.631	0.13
160_S	216_R	0.627	0.13
114_D	118_H	0.625	0.13
114_D	128_E	0.625	0.13
150_L	170_V	0.622	0.13
96_D	186_I	0.621	0.13
98_M	121_L	0.621	0.13
156_S	179_I	0.621	0.13
92_N	100_E	0.620	0.13
38_E	224_E	0.620	0.13
54_N	209_S	0.618	0.13
63_R	211_V	0.611	0.13
76_R	179_I	0.606	0.13
195_T	227_K	0.603	0.13
121_L	198_I	0.600	0.13
123_S	164_A	0.599	0.13
77_E	124_R	0.597	0.12
189_R	224_E	0.597	0.12
117_L	139_F	0.595	0.12
77_E	97_E	0.593	0.12
185_L	199_A	0.591	0.12
195_T	211_V	0.591	0.12
142_S	151_E	0.590	0.12
145_L	149_V	0.587	0.12
100_E	144_L	0.586	0.12
53_K	62_I	0.585	0.12
78_E	105_K	0.585	0.12
116_L	158_N	0.582	0.12
140_S	155_Q	0.580	0.12
153_L	158_N	0.579	0.12
106_M	172_K	0.578	0.12
186_I	209_S	0.576	0.12
147_L	221_K	0.575	0.12
115_E	140_S	0.572	0.12
47_L	61_F	0.571	0.12
147_L	178_E	0.571	0.12
182_Q	219_L	0.571	0.12
40_T	145_L	0.567	0.12
83_I	134_G	0.565	0.12
58_E	72_T	0.562	0.12
142_S	198_I	0.559	0.12
153_L	215_E	0.558	0.12
161_L	195_T	0.553	0.12
154_L	193_V	0.553	0.12
54_N	171_L	0.552	0.12
59_E	203_D	0.551	0.12
118_H	228_T	0.551	0.12
102_L	175_D	0.549	0.12
135_G	139_F	0.547	0.12
106_M	228_T	0.546	0.12
173_K	209_S	0.544	0.12
121_L	224_E	0.543	0.12
164_A	225_E	0.540	0.11
165_K	176_T	0.536	0.11
95_L	99_R	0.535	0.11
85_M	175_D	0.535	0.11
144_L	182_Q	0.535	0.11
93_L	121_L	0.533	0.11
117_L	219_L	0.531	0.11
126_A	172_K	0.528	0.11
132_E	155_Q	0.525	0.11
59_E	217_V	0.524	0.11
98_M	178_E	0.523	0.11
189_R	193_V	0.523	0.11
144_L	149_V	0.521	0.11
87_Q	180_E	0.521	0.11
198_I	204_S	0.521	0.11
126_A	144_L	0.520	0.11
28_E	193_V	0.518	0.11
122_V	134_G	0.518	0.11
77_E	155_Q	0.515	0.11
124_R	176_T	0.515	0.11
135_G	214_V	0.514	0.11
159_V	196_C	0.512	0.11
66_T	93_L	0.512	0.11
97_E	147_L	0.509	0.11
146_S	171_L	0.508	0.11
177_E	200_A	0.507	0.11
161_L	190_K	0.507	0.11
133_D	159_V	0.505	0.11
59_E	151_E	0.500	0.11

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
4j2nA	4	0.2311	96.5	0.935	Contact Map
3whpA	1	0.5294	96.3	0.937	Contact Map
4r24B	2	0.3487	96.2	0.937	Contact Map
3ucsA	2	0.4076	96.1	0.938	Contact Map
4r4eB	2	0.3487	95.8	0.94	Contact Map
1z4hA	1	0.2773	94.2	0.945	Contact Map
2jmlA	1	0.3277	94	0.945	Contact Map
2vz4A	2	0.416	91.4	0.95	Contact Map
1r8dA	2	0.4538	91.4	0.95	Contact Map
3gpvA	2	0.4874	90.4	0.951	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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