YJBE - BACSU - GREMLIN Contacts

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YJBE - Uncharacterized membrane protein YjbE

UniProt:	O31603	Sequences: MEHDYLISLLVIVGIDLILGGDNAVVIAMASRHLPDKQRQQAIILGTFIAVAMRIGLTSAAVYLLNIPFLQCAGGIFLLYLGYQLLIEKKDTKHIKSSTSLWRAIRTIVLADLFMSLDNVIAVAGASHGEFSLVVIGLCVSVPVIIWGSKLIHIALEKIPLLIYAGSGLLAYTGGEMIVRDKKLSLFMAQHGTVETLLPILTVAFVILASIYYQQVEK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	218 (204)
Sequences:	4371 (2455)
Seq/√Len:	171.9

ECOLI - YGDQ ALX YOAE YEGH
BACSU - YJBE YCEF YKOY

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
203_V	207_I	3.486	1.00
36_D	39_R	3.396	1.00
75_G	178_I	3.342	1.00
55_I	135_V	3.137	1.00
53_M	113_L	2.981	1.00
49_I	109_V	2.952	1.00
82_G	171_A	2.378	1.00
96_K	99_T	2.291	1.00
12_I	123_V	2.286	1.00
95_I	98_S	2.237	1.00
9_L	140_V	2.200	1.00
9_L	136_I	2.125	1.00
42_A	108_I	2.071	1.00
55_I	59_S	2.065	1.00
15_I	126_A	2.060	1.00
199_P	206_V	2.046	1.00
40_Q	150_K	2.030	1.00
132_S	136_I	1.997	1.00
95_I	99_T	1.989	1.00
202_T	206_V	1.952	1.00
192_G	196_T	1.948	1.00
37_K	41_Q	1.933	1.00
83_Y	87_I	1.918	1.00
45_L	49_I	1.871	1.00
192_G	195_E	1.840	1.00
4_D	8_S	1.827	1.00
192_G	207_I	1.788	1.00
34_L	104_A	1.767	1.00
13_V	140_V	1.754	1.00
38_Q	41_Q	1.717	1.00
150_K	154_I	1.701	1.00
7_I	11_V	1.680	1.00
203_V	206_V	1.653	1.00
49_I	53_M	1.638	1.00
94_H	98_S	1.636	1.00
40_Q	44_I	1.635	1.00
204_A	207_I	1.605	1.00
204_A	208_L	1.603	1.00
195_E	199_P	1.592	1.00
35_P	38_Q	1.569	1.00
84_Q	87_I	1.569	1.00
84_Q	88_E	1.558	1.00
71_Q	180_R	1.547	1.00
94_H	99_T	1.536	1.00
51_V	139_C	1.508	1.00
80_Y	84_Q	1.504	1.00
59_S	131_F	1.491	1.00
195_E	207_I	1.474	1.00
192_G	203_V	1.471	1.00
72_C	181_D	1.466	1.00
79_L	174_G	1.456	1.00
10_L	14_G	1.412	1.00
189_A	193_T	1.397	1.00
199_P	203_V	1.394	1.00
193_T	207_I	1.377	1.00
34_L	42_A	1.373	1.00
52_A	56_G	1.368	1.00
86_L	164_Y	1.357	1.00
198_L	205_F	1.347	1.00
16_D	20_G	1.337	1.00
195_E	198_L	1.321	1.00
64_L	70_L	1.319	1.00
5_Y	133_L	1.315	1.00
193_T	199_P	1.314	1.00
136_I	140_V	1.306	1.00
48_F	52_A	1.298	1.00
88_E	91_D	1.298	1.00
192_G	206_V	1.296	1.00
200_I	204_A	1.272	1.00
201_L	205_F	1.245	1.00
193_T	196_T	1.239	1.00
193_T	203_V	1.233	1.00
199_P	202_T	1.210	1.00
41_Q	45_L	1.208	1.00
194_V	198_L	1.201	1.00
193_T	198_L	1.198	1.00
195_E	206_V	1.190	1.00
199_P	207_I	1.188	1.00
127_S	133_L	1.186	1.00
45_L	105_I	1.179	1.00
41_Q	101_L	1.172	1.00
58_T	138_L	1.151	1.00
182_K	185_S	1.143	1.00
193_T	197_L	1.125	1.00
154_I	158_K	1.124	1.00
175_G	179_V	1.120	1.00
185_S	188_M	1.114	1.00
75_G	174_G	1.109	1.00
56_G	60_A	1.103	1.00
5_Y	130_E	1.078	1.00
191_H	195_E	1.075	1.00
87_I	91_D	1.069	1.00
196_T	206_V	1.066	1.00
196_T	207_I	1.061	1.00
53_M	109_V	1.060	1.00
202_T	205_F	1.045	0.99
59_S	63_Y	1.045	0.99
32_R	157_E	1.044	0.99
192_G	198_L	1.038	0.99
24_A	27_I	1.035	0.99
194_V	203_V	1.033	0.99
172_Y	176_E	1.026	0.99
179_V	184_L	1.020	0.99
195_E	203_V	1.015	0.99
196_T	199_P	1.006	0.99
198_L	203_V	1.006	0.99
200_I	203_V	1.003	0.99
164_Y	168_G	0.993	0.99
190_Q	198_L	0.980	0.99
191_H	205_F	0.977	0.99
192_G	200_I	0.970	0.99
205_F	208_L	0.968	0.99
60_A	64_L	0.957	0.99
6_L	10_L	0.956	0.99
192_G	197_L	0.956	0.99
106_R	110_L	0.956	0.99
102_W	106_R	0.953	0.99
188_M	191_H	0.948	0.99
8_S	133_L	0.941	0.99
189_A	192_G	0.939	0.99
83_Y	171_A	0.939	0.99
87_I	161_L	0.939	0.99
61_A	113_L	0.936	0.99
124_A	127_S	0.936	0.99
191_H	197_L	0.935	0.99
44_I	48_F	0.933	0.99
206_V	209_A	0.929	0.99
197_L	201_L	0.920	0.99
12_I	133_L	0.917	0.99
39_R	154_I	0.904	0.98
105_I	108_I	0.902	0.98
11_V	126_A	0.901	0.98
13_V	17_L	0.890	0.98
190_Q	193_T	0.883	0.98
77_F	117_L	0.872	0.98
127_S	130_E	0.872	0.98
53_M	56_G	0.871	0.98
62_V	124_A	0.867	0.98
193_T	200_I	0.865	0.98
194_V	197_L	0.863	0.98
127_S	132_S	0.857	0.98
5_Y	8_S	0.852	0.98
16_D	58_T	0.849	0.98
191_H	194_V	0.846	0.98
187_F	191_H	0.844	0.98
55_I	138_L	0.844	0.98
24_A	177_M	0.840	0.98
176_E	180_R	0.838	0.97
28_A	105_I	0.826	0.97
191_H	199_P	0.823	0.97
93_K	99_T	0.810	0.97
28_A	153_H	0.810	0.97
164_Y	205_F	0.810	0.97
197_L	200_I	0.807	0.97
4_D	7_I	0.800	0.97
191_H	196_T	0.791	0.96
93_K	98_S	0.782	0.96
130_E	133_L	0.782	0.96
189_A	195_E	0.781	0.96
5_Y	132_S	0.777	0.96
165_A	203_V	0.775	0.96
192_G	199_P	0.774	0.96
79_L	83_Y	0.771	0.96
68_P	72_C	0.769	0.96
197_L	204_A	0.768	0.96
202_T	207_I	0.767	0.96
199_P	209_A	0.764	0.96
71_Q	173_T	0.762	0.96
198_L	207_I	0.760	0.96
85_L	167_S	0.759	0.96
28_A	152_I	0.758	0.95
193_T	208_L	0.757	0.95
189_A	204_A	0.753	0.95
31_S	153_H	0.751	0.95
9_L	13_V	0.749	0.95
60_A	63_Y	0.746	0.95
190_Q	194_V	0.745	0.95
154_I	157_E	0.745	0.95
28_A	156_L	0.745	0.95
196_T	203_V	0.744	0.95
198_L	201_L	0.736	0.95
12_I	127_S	0.734	0.95
191_H	198_L	0.732	0.95
191_H	204_A	0.729	0.94
104_A	111_A	0.728	0.94
201_L	204_A	0.725	0.94
128_H	131_F	0.721	0.94
17_L	143_P	0.721	0.94
82_G	174_G	0.716	0.94
94_H	97_S	0.710	0.94
100_S	103_R	0.703	0.93
51_V	146_I	0.702	0.93
198_L	206_V	0.701	0.93
156_L	177_M	0.700	0.93
51_V	142_V	0.700	0.93
93_K	96_K	0.699	0.93
196_T	200_I	0.699	0.93
29_M	163_I	0.697	0.93
193_T	206_V	0.697	0.93
21_G	24_A	0.694	0.93
192_G	208_L	0.694	0.93
190_Q	203_V	0.693	0.93
65_L	120_V	0.693	0.93
190_Q	196_T	0.685	0.92
189_A	199_P	0.681	0.92
193_T	204_A	0.678	0.92
123_V	126_A	0.676	0.92
86_L	90_K	0.675	0.92
24_A	152_I	0.675	0.92
195_E	202_T	0.675	0.92
138_L	141_S	0.674	0.92
30_A	108_I	0.671	0.92
105_I	109_V	0.671	0.92
20_G	148_G	0.670	0.92
42_A	101_L	0.667	0.91
110_L	114_F	0.667	0.91
193_T	205_F	0.665	0.91
98_S	103_R	0.662	0.91
34_L	38_Q	0.660	0.91
200_I	207_I	0.659	0.91
159_I	162_L	0.656	0.91
12_I	134_V	0.655	0.91
184_L	188_M	0.655	0.91
113_L	120_V	0.652	0.90
70_L	73_A	0.651	0.90
117_L	120_V	0.649	0.90
194_V	208_L	0.645	0.90
135_V	139_C	0.644	0.90
103_R	106_R	0.643	0.90
192_G	205_F	0.639	0.90
194_V	202_T	0.637	0.89
34_L	105_I	0.636	0.89
80_Y	83_Y	0.633	0.89
72_C	178_I	0.631	0.89
85_L	163_I	0.627	0.89
47_T	146_I	0.622	0.88
123_V	134_V	0.621	0.88
190_Q	205_F	0.620	0.88
198_L	202_T	0.619	0.88
30_A	111_A	0.618	0.88
31_S	42_A	0.617	0.88
77_F	81_L	0.617	0.88
31_S	108_I	0.613	0.88
31_S	150_K	0.613	0.88
161_L	164_Y	0.610	0.87
77_F	80_Y	0.607	0.87
39_R	149_S	0.607	0.87
194_V	206_V	0.602	0.87
189_A	203_V	0.602	0.87
125_G	173_T	0.601	0.86
144_V	152_I	0.600	0.86
141_S	152_I	0.597	0.86
125_G	180_R	0.597	0.86
34_L	101_L	0.596	0.86
102_W	105_I	0.590	0.85
92_T	98_S	0.587	0.85
5_Y	136_I	0.585	0.85
43_I	146_I	0.576	0.84
156_L	169_L	0.575	0.84
141_S	153_H	0.575	0.84
36_D	40_Q	0.572	0.84
5_Y	9_L	0.571	0.84
194_V	207_I	0.569	0.83
74_G	121_I	0.569	0.83
197_L	205_F	0.568	0.83
195_E	208_L	0.568	0.83
11_V	15_I	0.567	0.83
69_F	72_C	0.565	0.83
44_I	109_V	0.562	0.83
82_G	170_L	0.562	0.83
114_F	117_L	0.562	0.83
191_H	207_I	0.561	0.83
24_A	28_A	0.559	0.82
152_I	155_A	0.558	0.82
138_L	142_V	0.557	0.82
75_G	164_Y	0.556	0.82
62_V	66_N	0.554	0.82
93_K	97_S	0.552	0.82
11_V	16_D	0.551	0.81
16_D	134_V	0.551	0.81
58_T	173_T	0.550	0.81
205_F	209_A	0.550	0.81
190_Q	200_I	0.550	0.81
71_Q	177_M	0.548	0.81
16_D	115_M	0.548	0.81
20_G	57_L	0.547	0.81
59_S	135_V	0.545	0.81
39_R	157_E	0.542	0.80
196_T	204_A	0.540	0.80
188_M	192_G	0.534	0.79
204_A	209_A	0.532	0.79
20_G	134_V	0.530	0.79
24_A	166_G	0.527	0.78
85_L	164_Y	0.520	0.78
194_V	209_A	0.520	0.78
18_I	173_T	0.519	0.77
91_D	94_H	0.512	0.76
86_L	167_S	0.511	0.76
190_Q	206_V	0.509	0.76
168_G	199_P	0.509	0.76
49_I	105_I	0.505	0.76
50_A	112_D	0.504	0.75
149_S	153_H	0.504	0.75
182_K	188_M	0.504	0.75
167_S	171_A	0.502	0.75
24_A	137_G	0.500	0.75

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
2gfpA	2	0.9817	39.6	0.941	Contact Map
3o7qA	1	0.9771	39.2	0.941	Contact Map
1pw4A	1	0.9495	35	0.942	Contact Map
4xnjA	1	0.9725	34.1	0.943	Contact Map
3wdoA	1	0.9862	30.5	0.944	Contact Map
2cfqA	1	0.4725	29.4	0.944	Contact Map
4w6vA	1	0.4037	18.7	0.949	Contact Map
4uvmA	1	0.422	15	0.952	Contact Map
3giaA	1	0.9358	13.8	0.952	Contact Map
2m20A	2	0.1651	13.2	0.953	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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