GLTK - ECOLI - GREMLIN Contacts

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GLTK - Glutamate/aspartate transport system permease protein GltK

UniProt:	P0AER5	Sequences: MYEFDWSSIVPSLPYLLDGLVITLKITVTAVVIGILWGTMLAVMRLSSFAPVAWFAKAYVNVFRSIPLVMVLLWFYLIVPGFLQNVLGLSPKNDIRLISAMVAFSMFEAAYYSEIIRAGIQSISRGQSSAALALGMTHWQSMKLIILPQAFRAMVPLLLTQGIVLFQDTSLVYVLSLADFFRTASTIGERDGTQVEMILFAGFVYFVISLSASLLVSYLKRRTA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12662
Length:	224 (205)
Sequences:	17817 (10791)
Seq/√Len:	753.7

ECOLI - GLTK GLTJ ARTQ HISM HISQ ARTM YHDY YHDX GLNP YECS
BACSU - TCYM GLNM YCKA GLNP ARTQ YXEN TCYL TCYB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
159_L	216_V	3.195	1.00
193_T	196_E	3.169	1.00
33_I	105_S	3.111	1.00
100_A	172_V	3.046	1.00
184_A	201_A	2.846	1.00
131_A	141_S	2.770	1.00
137_T	140_Q	2.736	1.00
21_V	25_K	2.573	1.00
44_M	56_A	2.473	1.00
127_Q	149_Q	2.470	1.00
66_I	71_V	2.336	1.00
41_L	113_S	2.325	1.00
128_S	141_S	2.222	1.00
41_L	109_A	2.106	1.00
51_P	55_F	2.055	1.00
139_W	143_K	2.048	1.00
214_L	218_Y	1.976	1.00
132_L	141_S	1.946	1.00
51_P	54_W	1.941	1.00
45_R	57_K	1.848	1.00
42_A	116_I	1.829	1.00
182_R	186_T	1.807	1.00
119_G	154_M	1.792	1.00
128_S	132_L	1.774	1.00
60_V	113_S	1.771	1.00
122_S	153_A	1.770	1.00
95_I	98_I	1.757	1.00
37_W	109_A	1.750	1.00
27_T	166_F	1.730	1.00
188_G	194_Q	1.725	1.00
206_F	210_L	1.700	1.00
20_L	208_I	1.697	1.00
22_I	25_K	1.689	1.00
29_T	101_M	1.671	1.00
50_A	54_W	1.667	1.00
17_L	21_V	1.662	1.00
26_I	172_V	1.657	1.00
184_A	197_M	1.644	1.00
210_L	214_L	1.640	1.00
25_K	97_L	1.619	1.00
137_T	141_S	1.607	1.00
75_F	103_A	1.607	1.00
46_L	121_Q	1.578	1.00
112_Y	158_L	1.540	1.00
34_G	108_E	1.521	1.00
114_E	117_R	1.520	1.00
214_L	217_S	1.481	1.00
18_D	21_V	1.454	1.00
31_V	162_G	1.454	1.00
218_Y	221_R	1.450	1.00
138_H	142_M	1.435	1.00
41_L	56_A	1.433	1.00
215_L	218_Y	1.412	1.00
22_I	177_L	1.411	1.00
27_T	169_T	1.399	1.00
39_T	116_I	1.379	1.00
140_Q	143_K	1.364	1.00
50_A	53_A	1.361	1.00
71_V	107_F	1.351	1.00
97_L	101_M	1.345	1.00
49_F	54_W	1.337	1.00
15_Y	18_D	1.318	1.00
140_Q	144_L	1.318	1.00
63_F	106_M	1.311	1.00
40_M	44_M	1.293	1.00
116_I	154_M	1.284	1.00
132_L	138_H	1.268	1.00
66_I	107_F	1.245	1.00
112_Y	161_Q	1.222	1.00
136_M	140_Q	1.210	1.00
128_S	146_I	1.198	1.00
29_T	105_S	1.196	1.00
45_R	114_E	1.186	1.00
96_R	176_S	1.178	1.00
44_M	47_S	1.176	1.00
46_L	120_I	1.176	1.00
54_W	58_A	1.164	1.00
188_G	198_I	1.158	1.00
72_L	103_A	1.156	1.00
13_L	17_L	1.133	1.00
183_T	186_T	1.129	1.00
131_A	145_I	1.129	1.00
36_L	40_M	1.127	1.00
172_V	179_D	1.119	1.00
182_R	185_S	1.107	1.00
115_I	161_Q	1.092	1.00
53_A	57_K	1.086	1.00
178_A	182_R	1.084	1.00
55_F	59_Y	1.077	1.00
49_F	52_V	1.073	1.00
55_F	58_A	1.069	1.00
33_I	101_M	1.065	1.00
120_I	146_I	1.063	1.00
61_N	210_L	1.060	1.00
72_L	172_V	1.059	1.00
25_K	29_T	1.058	1.00
142_M	147_L	1.056	1.00
101_M	105_S	1.054	1.00
15_Y	183_T	1.054	1.00
166_F	208_I	1.051	1.00
115_I	157_L	1.042	1.00
117_R	121_Q	1.037	1.00
97_L	177_L	1.028	1.00
18_D	22_I	1.016	1.00
56_A	113_S	1.008	1.00
38_G	112_Y	1.006	1.00
75_F	99_S	1.005	1.00
215_L	219_L	0.993	1.00
98_I	101_M	0.990	1.00
58_A	61_N	0.985	1.00
30_A	105_S	0.983	1.00
123_I	153_A	0.979	1.00
217_S	220_K	0.979	1.00
123_I	150_A	0.976	1.00
61_N	206_F	0.976	1.00
170_S	205_Y	0.976	1.00
218_Y	222_R	0.970	1.00
187_I	197_M	0.967	1.00
71_V	75_F	0.965	1.00
164_V	168_D	0.960	1.00
217_S	221_R	0.957	1.00
23_T	166_F	0.956	1.00
196_E	199_L	0.935	1.00
72_L	171_L	0.931	1.00
27_T	162_G	0.922	1.00
166_F	212_A	0.915	1.00
126_G	130_A	0.915	1.00
185_S	188_G	0.914	1.00
63_F	110_A	0.913	1.00
186_T	190_R	0.913	1.00
136_M	144_L	0.909	1.00
31_V	165_L	0.908	1.00
20_L	204_V	0.892	1.00
44_M	52_V	0.888	1.00
42_A	46_L	0.887	1.00
138_H	141_S	0.880	1.00
78_I	82_F	0.872	1.00
211_S	215_L	0.872	1.00
14_P	18_D	0.865	1.00
32_V	36_L	0.862	1.00
98_I	102_V	0.861	1.00
74_W	78_I	0.861	1.00
47_S	138_H	0.858	1.00
153_A	157_L	0.856	1.00
142_M	146_I	0.856	1.00
73_L	77_L	0.852	1.00
45_R	60_V	0.851	1.00
166_F	209_S	0.851	1.00
104_F	169_T	0.843	1.00
29_T	33_I	0.840	1.00
19_G	183_T	0.840	1.00
191_D	194_Q	0.837	1.00
108_E	161_Q	0.835	1.00
28_V	32_V	0.833	1.00
35_I	158_L	0.832	1.00
68_L	107_F	0.830	1.00
24_L	28_V	0.827	1.00
96_R	177_L	0.819	1.00
59_Y	63_F	0.812	1.00
48_S	53_A	0.795	1.00
100_A	175_L	0.794	1.00
59_Y	110_A	0.790	1.00
125_R	129_S	0.790	1.00
54_W	57_K	0.783	1.00
184_A	188_G	0.780	1.00
126_G	129_S	0.780	1.00
207_V	211_S	0.775	1.00
49_F	55_F	0.773	1.00
59_Y	109_A	0.773	1.00
68_L	168_D	0.773	1.00
20_L	180_F	0.771	1.00
23_T	205_Y	0.770	1.00
108_E	168_D	0.769	1.00
47_S	56_A	0.766	1.00
128_S	138_H	0.756	1.00
174_V	178_A	0.751	1.00
76_Y	99_S	0.749	1.00
49_F	53_A	0.747	1.00
181_F	205_Y	0.744	1.00
43_V	142_M	0.742	1.00
181_F	198_I	0.733	1.00
23_T	27_T	0.730	1.00
76_Y	175_L	0.727	1.00
188_G	197_M	0.726	1.00
112_Y	116_I	0.726	1.00
29_T	97_L	0.724	1.00
71_V	103_A	0.723	1.00
120_I	150_A	0.722	1.00
180_F	204_V	0.720	1.00
172_V	177_L	0.719	1.00
57_K	61_N	0.716	1.00
119_G	153_A	0.716	1.00
203_F	207_V	0.712	1.00
198_I	201_A	0.712	1.00
72_L	175_L	0.709	1.00
42_A	120_I	0.708	1.00
22_I	179_D	0.707	1.00
96_R	175_L	0.705	1.00
26_I	169_T	0.702	1.00
170_S	181_F	0.701	1.00
206_F	209_S	0.697	1.00
200_F	204_V	0.694	1.00
74_W	199_L	0.694	1.00
39_T	147_L	0.692	1.00
199_L	203_F	0.691	1.00
104_F	165_L	0.691	1.00
45_R	53_A	0.690	1.00
37_W	41_L	0.690	1.00
213_S	217_S	0.689	1.00
173_Y	182_R	0.689	1.00
123_I	146_I	0.685	1.00
170_S	173_Y	0.683	1.00
37_W	105_S	0.681	1.00
29_T	32_V	0.681	1.00
212_A	216_V	0.673	1.00
107_F	168_D	0.668	1.00
173_Y	176_S	0.667	1.00
181_F	201_A	0.666	1.00
155_V	219_L	0.666	1.00
105_S	109_A	0.665	1.00
26_I	177_L	0.665	1.00
34_G	112_Y	0.661	1.00
178_A	183_T	0.661	1.00
197_M	201_A	0.660	1.00
26_I	100_A	0.656	1.00
116_I	120_I	0.655	1.00
120_I	142_M	0.651	1.00
108_E	112_Y	0.648	1.00
108_E	165_L	0.646	1.00
69_V	174_V	0.643	1.00
125_R	128_S	0.639	1.00
52_V	55_F	0.631	1.00
33_I	36_L	0.629	1.00
107_F	161_Q	0.626	1.00
48_S	138_H	0.624	1.00
26_I	30_A	0.623	1.00
22_I	97_L	0.623	1.00
161_Q	164_V	0.622	1.00
36_L	105_S	0.620	1.00
14_P	17_L	0.619	1.00
78_I	81_G	0.616	1.00
25_K	98_I	0.613	1.00
12_S	187_I	0.610	1.00
163_I	212_A	0.609	1.00
129_S	144_L	0.609	1.00
33_I	37_W	0.607	1.00
76_Y	96_R	0.607	1.00
125_R	132_L	0.606	1.00
44_M	55_F	0.605	1.00
57_K	60_V	0.604	1.00
39_T	151_F	0.602	1.00
128_S	142_M	0.602	1.00
35_I	116_I	0.601	1.00
21_V	24_L	0.601	1.00
79_V	89_L	0.598	1.00
41_L	44_M	0.598	1.00
137_T	144_L	0.596	1.00
190_R	193_T	0.596	1.00
30_A	165_L	0.596	1.00
75_F	78_I	0.596	1.00
211_S	218_Y	0.590	1.00
65_S	167_Q	0.586	1.00
162_G	212_A	0.585	1.00
91_P	98_I	0.584	1.00
19_G	22_I	0.583	1.00
15_Y	19_G	0.581	1.00
16_L	204_V	0.579	1.00
48_S	51_P	0.578	1.00
104_F	172_V	0.575	1.00
146_I	149_Q	0.571	1.00
131_A	136_M	0.571	1.00
30_A	104_F	0.571	1.00
63_F	71_V	0.566	1.00
58_A	62_V	0.566	1.00
69_V	171_L	0.563	1.00
90_S	95_I	0.558	1.00
198_I	202_G	0.557	1.00
156_P	220_K	0.556	1.00
44_M	49_F	0.553	1.00
52_V	56_A	0.550	1.00
195_V	199_L	0.550	1.00
16_L	184_A	0.549	1.00
211_S	214_L	0.549	1.00
27_T	31_V	0.547	1.00
41_L	59_Y	0.547	1.00
201_A	204_V	0.545	1.00
45_R	113_S	0.543	1.00
17_L	20_L	0.540	1.00
119_G	157_L	0.539	1.00
219_L	223_T	0.535	1.00
118_A	157_L	0.534	1.00
37_W	40_M	0.534	1.00
16_L	187_I	0.533	1.00
136_M	141_S	0.528	1.00
141_S	146_I	0.528	1.00
187_I	191_D	0.526	1.00
56_A	60_V	0.524	1.00
206_F	213_S	0.523	1.00
62_V	66_I	0.521	1.00
36_L	39_T	0.520	1.00
155_V	223_T	0.519	1.00
121_Q	156_P	0.518	1.00
69_V	73_L	0.516	1.00
160_T	167_Q	0.514	1.00
157_L	160_T	0.512	1.00
111_Y	168_D	0.512	1.00
15_Y	186_T	0.508	1.00
30_A	101_M	0.500	1.00

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
4ymuD	2	0.9598	100	0.538	Contact Map
3tuiA	2	0.9286	99.9	0.605	Contact Map
3rlfF	1	0.9554	99.9	0.627	Contact Map
2onkC	2	0.9777	99.9	0.632	Contact Map
3d31C	2	0.9598	99.9	0.64	Contact Map
3rlfG	1	0.9732	99.8	0.657	Contact Map
4tquM	1	0.9911	99.8	0.658	Contact Map
4tquN	1	0.942	99.8	0.684	Contact Map
5a63B	1	0.2812	10.8	0.956	Contact Map
4uisB	1	0.1875	7.1	0.959	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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