PROX - ECOLI - GREMLIN Contacts

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PROX - Glycine betaine-binding periplasmic protein

UniProt:	P0AFM2	Sequences: MRHSVLFATAFATLISTQTFAADLPGKGITVNPVQSTITEETFQTLLVSRALEKLGYTVNKPSEVDYNVGYTSLASGDATFTAVNWTPLHDNMYEAAGGDKKFYREGVFVNGAAQGYLIDKKTADQYKITNIAQLKDPKIAKLFDTNGDGKADLTGCNPGWGCEGAINHQLAAYELTNTVTHNQGNYAAMMADTISRYKEGKPVFYYTWTPYWVSNELKPGKDVVWLQVPFSALPGDKNADTKLPNGANYGFPVSTMHIVANKAWAEKNPAAAKLFAIMQLPVADINAQNAIMHDGKASEGDIQGHVDGWIKAHQQQFDGWVNEALAAQK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10773
Length:	330 (274)
Sequences:	5199 (3720)
Seq/√Len:	224.8

ECOLI - PROX OSMF
BACSU - OPUCC OPUBC
HALSA - Q9HP83

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
121_K	223_D	4.814	1.00
292_I	301_G	3.954	1.00
121_K	225_V	3.805	1.00
121_K	125_D	3.703	1.00
282_P	285_D	3.358	1.00
133_A	230_P	3.167	1.00
104_Y	263_K	3.000	1.00
308_D	312_K	2.810	1.00
34_V	79_A	2.796	1.00
130_T	225_V	2.738	1.00
19_T	22_A	2.700	1.00
50_R	308_D	2.597	1.00
123_T	127_Y	2.546	1.00
292_I	309_G	2.504	1.00
118_L	208_T	2.441	1.00
105_R	258_H	2.420	1.00
30_T	58_T	2.386	1.00
119_I	129_I	2.344	1.00
309_G	313_A	2.255	1.00
32_N	60_N	2.148	1.00
131_N	228_Q	2.105	1.00
30_T	60_N	2.095	1.00
130_T	134_Q	2.050	1.00
117_Y	205_F	2.032	1.00
17_T	20_F	1.982	1.00
292_I	296_G	1.959	1.00
285_D	289_Q	1.897	1.00
124_A	225_V	1.894	1.00
43_F	293_M	1.878	1.00
33_P	81_F	1.873	1.00
49_S	53_E	1.866	1.00
50_R	53_E	1.848	1.00
263_K	267_E	1.842	1.00
48_V	83_A	1.809	1.00
92_N	96_A	1.807	1.00
46_L	50_R	1.784	1.00
120_D	123_T	1.779	1.00
13_T	16_S	1.761	1.00
301_G	309_G	1.748	1.00
55_L	275_L	1.709	1.00
72_T	75_A	1.679	1.00
216_N	288_A	1.661	1.00
131_N	230_P	1.652	1.00
49_S	62_P	1.631	1.00
140_I	143_L	1.629	1.00
122_K	201_G	1.615	1.00
195_I	218_L	1.613	1.00
95_E	99_G	1.601	1.00
173_A	233_A	1.599	1.00
91_D	95_E	1.584	1.00
130_T	228_Q	1.533	1.00
16_S	19_T	1.517	1.00
53_E	59_V	1.515	1.00
302_D	305_G	1.509	1.00
157_C	163_C	1.508	1.00
51_A	275_L	1.497	1.00
12_A	15_I	1.496	1.00
91_D	94_Y	1.489	1.00
104_Y	266_A	1.480	1.00
301_G	305_G	1.480	1.00
102_K	263_K	1.471	1.00
103_F	260_V	1.459	1.00
18_Q	21_A	1.453	1.00
135_L	205_F	1.452	1.00
266_A	273_A	1.445	1.00
291_A	295_D	1.439	1.00
195_I	199_K	1.402	1.00
50_R	304_Q	1.395	1.00
265_W	269_N	1.392	1.00
49_S	59_V	1.389	1.00
203_P	206_Y	1.347	1.00
296_G	301_G	1.346	1.00
143_L	203_P	1.345	1.00
291_A	296_G	1.335	1.00
116_G	226_W	1.318	1.00
35_Q	45_T	1.298	1.00
120_D	201_G	1.289	1.00
293_M	306_H	1.289	1.00
107_G	277_A	1.288	1.00
46_L	49_S	1.284	1.00
93_M	97_A	1.273	1.00
90_H	93_M	1.262	1.00
104_Y	273_A	1.256	1.00
173_A	231_F	1.246	1.00
123_T	203_P	1.239	1.00
187_Y	191_M	1.221	1.00
288_A	292_I	1.211	1.00
46_L	304_Q	1.209	1.00
305_G	309_G	1.203	1.00
14_L	17_T	1.196	1.00
129_I	140_I	1.196	1.00
186_N	190_M	1.188	1.00
153_D	183_N	1.183	1.00
11_F	14_L	1.179	1.00
186_N	189_A	1.175	1.00
71_Y	101_K	1.173	1.00
48_V	275_L	1.167	1.00
274_K	278_I	1.158	1.00
80_T	262_N	1.156	1.00
17_T	21_A	1.147	1.00
274_K	277_A	1.146	1.00
51_A	279_M	1.144	1.00
117_Y	167_I	1.141	1.00
187_Y	190_M	1.133	1.00
196_S	200_E	1.130	1.00
73_S	79_A	1.127	1.00
281_L	289_Q	1.126	1.00
167_I	170_Q	1.126	1.00
216_N	287_N	1.117	1.00
108_V	258_H	1.117	1.00
32_N	63_S	1.116	1.00
112_G	283_V	1.111	1.00
15_I	20_F	1.105	1.00
303_I	307_V	1.097	1.00
106_E	261_A	1.095	1.00
18_Q	22_A	1.091	1.00
160_G	164_E	1.088	1.00
123_T	144_F	1.083	1.00
50_R	311_I	1.066	1.00
133_A	231_F	1.064	1.00
34_V	70_G	1.063	1.00
123_T	129_I	1.058	1.00
186_N	192_A	1.048	1.00
140_I	144_F	1.047	1.00
31_V	57_Y	1.039	1.00
259_I	276_F	1.037	1.00
262_N	268_K	1.036	1.00
174_Y	229_V	1.034	1.00
90_H	97_A	1.031	1.00
119_I	123_T	1.027	1.00
141_A	144_F	1.027	1.00
119_I	124_A	1.025	1.00
170_Q	233_A	1.024	1.00
284_A	287_N	1.022	1.00
93_M	96_A	1.021	1.00
71_Y	75_A	1.020	1.00
15_I	18_Q	1.018	1.00
261_A	266_A	1.018	1.00
10_A	13_T	1.016	1.00
47_L	307_V	1.011	1.00
54_K	278_I	1.009	1.00
85_N	260_V	1.007	1.00
217_E	295_D	0.998	1.00
52_L	272_A	0.996	1.00
283_V	287_N	0.991	1.00
289_Q	306_H	0.984	1.00
52_L	57_Y	0.982	1.00
161_W	164_E	0.973	1.00
114_A	210_T	0.972	1.00
19_T	23_D	0.969	1.00
208_T	214_V	0.965	1.00
309_G	312_K	0.964	1.00
285_D	310_W	0.961	1.00
285_D	314_H	0.956	1.00
272_A	276_F	0.956	1.00
116_G	132_I	0.951	1.00
43_F	289_Q	0.949	1.00
273_A	277_A	0.946	1.00
167_I	171_L	0.940	1.00
40_E	286_I	0.934	1.00
106_E	273_A	0.932	1.00
185_G	189_A	0.932	1.00
123_T	126_Q	0.929	1.00
285_D	288_A	0.929	1.00
264_A	268_K	0.928	1.00
94_Y	97_A	0.925	1.00
47_L	50_R	0.921	1.00
116_G	210_T	0.917	0.99
136_K	175_E	0.917	0.99
40_E	84_V	0.914	0.99
157_C	164_E	0.901	0.99
127_Y	140_I	0.900	0.99
31_V	269_N	0.899	0.99
155_T	160_G	0.895	0.99
32_N	80_T	0.893	0.99
12_A	16_S	0.893	0.99
96_A	99_G	0.886	0.99
265_W	272_A	0.884	0.99
194_T	206_Y	0.883	0.99
45_T	62_P	0.882	0.99
169_H	173_A	0.880	0.99
41_E	84_V	0.876	0.99
168_N	172_A	0.876	0.99
47_L	311_I	0.875	0.99
157_C	160_G	0.875	0.99
47_L	281_L	0.874	0.99
94_Y	98_G	0.869	0.99
189_A	192_A	0.868	0.99
141_A	152_A	0.868	0.99
60_N	63_S	0.861	0.99
47_L	310_W	0.860	0.99
193_D	197_R	0.860	0.99
304_Q	308_D	0.859	0.99
77_G	80_T	0.859	0.99
51_A	311_I	0.856	0.99
92_N	95_E	0.853	0.99
122_K	126_Q	0.849	0.99
39_T	294_H	0.844	0.99
42_T	303_I	0.843	0.99
47_L	51_A	0.838	0.99
96_A	100_D	0.837	0.99
73_S	78_D	0.836	0.99
187_Y	192_A	0.836	0.99
81_F	276_F	0.835	0.99
129_I	134_Q	0.833	0.99
153_D	157_C	0.826	0.99
275_L	279_M	0.825	0.99
81_F	261_A	0.819	0.99
90_H	94_Y	0.815	0.99
195_I	217_E	0.814	0.99
301_G	306_H	0.809	0.99
188_A	191_M	0.808	0.99
29_I	269_N	0.803	0.99
123_T	140_I	0.802	0.99
284_A	288_A	0.801	0.99
185_G	188_A	0.797	0.99
81_F	272_A	0.792	0.99
39_T	293_M	0.791	0.99
136_K	141_A	0.789	0.98
171_L	182_H	0.788	0.98
124_A	129_I	0.787	0.98
31_V	272_A	0.787	0.98
118_L	226_W	0.784	0.98
53_E	58_T	0.784	0.98
48_V	276_F	0.784	0.98
91_D	98_G	0.779	0.98
111_N	257_M	0.778	0.98
106_E	277_A	0.776	0.98
43_F	47_L	0.774	0.98
57_Y	271_A	0.772	0.98
305_G	308_D	0.772	0.98
72_T	76_S	0.770	0.98
23_D	26_G	0.765	0.98
70_G	82_T	0.765	0.98
32_N	79_A	0.756	0.98
185_G	190_M	0.756	0.98
281_L	286_I	0.753	0.98
9_T	13_T	0.751	0.98
164_E	184_Q	0.748	0.98
261_A	265_W	0.742	0.98
15_I	19_T	0.738	0.98
33_P	45_T	0.736	0.98
120_D	204_V	0.734	0.98
108_V	256_T	0.731	0.98
16_S	20_F	0.729	0.97
113_A	255_S	0.725	0.97
48_V	259_I	0.724	0.97
90_H	98_G	0.723	0.97
20_F	23_D	0.722	0.97
280_Q	310_W	0.717	0.97
210_T	287_N	0.717	0.97
169_H	172_A	0.716	0.97
160_G	163_C	0.709	0.97
186_N	191_M	0.709	0.97
166_A	169_H	0.708	0.97
48_V	279_M	0.707	0.97
122_K	198_Y	0.705	0.97
14_L	18_Q	0.705	0.97
14_L	19_T	0.701	0.97
95_E	98_G	0.699	0.97
17_T	22_A	0.696	0.97
158_N	187_Y	0.693	0.97
52_L	55_L	0.693	0.97
217_E	291_A	0.692	0.97
154_L	159_P	0.692	0.97
154_L	157_C	0.689	0.96
197_R	202_K	0.688	0.96
47_L	289_Q	0.686	0.96
45_T	83_A	0.686	0.96
132_I	227_L	0.684	0.96
40_E	44_Q	0.681	0.96
106_E	259_I	0.675	0.96
133_A	136_K	0.674	0.96
201_G	204_V	0.673	0.96
47_L	279_M	0.672	0.96
37_T	209_W	0.670	0.96
170_Q	229_V	0.670	0.96
46_L	62_P	0.667	0.96
111_N	286_I	0.664	0.96
213_W	294_H	0.659	0.95
193_D	204_V	0.659	0.95
71_Y	85_N	0.658	0.95
117_Y	132_I	0.656	0.95
262_N	265_W	0.656	0.95
115_Q	163_C	0.655	0.95
172_A	177_T	0.649	0.95
36_S	70_G	0.644	0.95
50_R	307_V	0.642	0.95
163_C	233_A	0.642	0.95
272_A	275_L	0.636	0.94
155_T	161_W	0.635	0.94
36_S	82_T	0.632	0.94
136_K	176_L	0.629	0.94
188_A	192_A	0.626	0.94
37_T	64_E	0.626	0.94
154_L	161_W	0.625	0.94
93_M	98_G	0.625	0.94
13_T	17_T	0.625	0.94
180_V	183_N	0.624	0.94
135_L	227_L	0.623	0.94
159_P	164_E	0.622	0.94
210_T	226_W	0.622	0.94
165_G	169_H	0.620	0.94
271_A	274_K	0.620	0.94
192_A	195_I	0.618	0.94
75_A	102_K	0.616	0.93
14_L	27_K	0.614	0.93
93_M	165_G	0.610	0.93
288_A	291_A	0.609	0.93
33_P	52_L	0.609	0.93
292_I	306_H	0.607	0.93
132_I	176_L	0.606	0.93
215_S	226_W	0.605	0.93
144_F	205_F	0.605	0.93
185_G	191_M	0.604	0.93
129_I	135_L	0.604	0.93
159_P	163_C	0.604	0.93
65_V	70_G	0.603	0.93
125_D	225_V	0.602	0.93
9_T	16_S	0.600	0.93
155_T	193_D	0.597	0.92
22_A	25_P	0.597	0.92
216_N	291_A	0.595	0.92
48_V	109_F	0.590	0.92
25_P	28_G	0.589	0.92
44_Q	286_I	0.588	0.92
292_I	313_A	0.587	0.92
118_L	224_V	0.587	0.92
109_F	281_L	0.586	0.92
44_Q	83_A	0.585	0.92
129_I	144_F	0.584	0.92
35_Q	64_E	0.584	0.92
261_A	273_A	0.582	0.91
24_L	28_G	0.581	0.91
36_S	84_V	0.579	0.91
62_P	65_V	0.579	0.91
210_T	283_V	0.577	0.91
50_R	54_K	0.576	0.91
155_T	185_G	0.576	0.91
104_Y	264_A	0.573	0.91
91_D	97_A	0.571	0.91
104_Y	261_A	0.571	0.91
208_T	215_S	0.569	0.91
134_Q	227_L	0.569	0.91
18_Q	23_D	0.568	0.90
74_L	103_F	0.568	0.90
191_M	194_T	0.568	0.90
119_I	127_Y	0.567	0.90
116_G	215_S	0.566	0.90
175_E	178_N	0.563	0.90
40_E	211_P	0.562	0.90
57_Y	269_N	0.562	0.90
154_L	160_G	0.561	0.90
190_M	193_D	0.559	0.90
35_Q	62_P	0.559	0.90
264_A	267_E	0.558	0.90
196_S	199_K	0.557	0.90
74_L	262_N	0.556	0.89
154_L	167_I	0.554	0.89
51_A	54_K	0.554	0.89
7_F	10_A	0.552	0.89
109_F	259_I	0.552	0.89
11_F	15_I	0.551	0.89
135_L	144_F	0.551	0.89
7_F	11_F	0.550	0.89
35_Q	42_T	0.549	0.89
185_G	193_D	0.546	0.89
31_V	265_W	0.545	0.89
266_A	272_A	0.544	0.88
292_I	305_G	0.544	0.88
29_I	57_Y	0.543	0.88
141_A	179_T	0.541	0.88
11_F	16_S	0.541	0.88
232_S	253_P	0.540	0.88
9_T	12_A	0.540	0.88
265_W	273_A	0.539	0.88
174_Y	231_F	0.535	0.88
191_M	214_V	0.535	0.88
184_Q	189_A	0.534	0.88
257_M	286_I	0.533	0.87
12_A	18_Q	0.533	0.87
39_T	187_Y	0.532	0.87
118_L	215_S	0.531	0.87
71_Y	260_V	0.529	0.87
117_Y	154_L	0.529	0.87
36_S	41_E	0.525	0.87
54_K	312_K	0.524	0.87
124_A	130_T	0.522	0.86
218_L	224_V	0.522	0.86
142_K	145_D	0.522	0.86
134_Q	139_K	0.520	0.86
37_T	66_D	0.520	0.86
111_N	256_T	0.520	0.86
157_C	161_W	0.520	0.86
89_L	105_R	0.520	0.86
10_A	17_T	0.519	0.86
13_T	19_T	0.518	0.86
155_T	164_E	0.517	0.86
154_L	164_E	0.515	0.86
216_N	284_A	0.513	0.85
115_Q	255_S	0.512	0.85
156_G	164_E	0.508	0.85
35_Q	41_E	0.507	0.85
131_N	136_K	0.504	0.84
155_T	159_P	0.503	0.84
125_D	228_Q	0.503	0.84
71_Y	103_F	0.503	0.84
33_P	48_V	0.501	0.84
122_K	313_A	0.501	0.84
55_L	271_A	0.500	0.84
88_P	255_S	0.500	0.84

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
1r9lA	1	0.9364	100	0.324	Contact Map
3o66A	1	0.7545	100	0.427	Contact Map
4ne4A	1	0.7788	100	0.43	Contact Map
2rinA	1	0.8273	100	0.485	Contact Map
3r6uA	1	0.7515	100	0.49	Contact Map
1sw5A	1	0.7485	100	0.516	Contact Map
3tmgA	1	0.803	100	0.535	Contact Map
3l6gA	1	0.7727	100	0.538	Contact Map
2b4lA	1	0.497	100	0.541	Contact Map
1p99A	1	0.7091	99.6	0.792	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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