MlaE - PFAM28P - GREMLIN Contacts

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MlaE - Permease MlaE

PFAM:	PF02405	Sequences: IVRQMYFIGVGSLPIVALTGFFIGMVLALQGAYQLRRFGAESYVGDLVALSLVRELGPVLTALIVAGRVGSAIAAELGTMRVTEQIDALETMGIDPVRYLVVPRVLALVIMLPLLTIIADLVGILGGYLVAVLLLGISPGAYLSGLQDALDLSDVLVGLIKAVVFGFIIALIGCYQGLRTKGGAEGVGRATTRAVVTSSVLILVADYLLTAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	212 (210)
Sequences:	35125 (16716)
Seq/√Len:	1153.5
META:	0.903

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
168_I	205_A	4.616	1.00
108_L	170_A	3.380	1.00
5_M	111_M	3.202	1.00
176_Q	197_T	3.180	1.00
128_Y	139_P	3.168	1.00
6_Y	11_G	2.954	1.00
52_L	123_G	2.816	1.00
176_Q	193_R	2.814	1.00
20_G	119_A	2.662	1.00
7_F	11_G	2.567	1.00
17_A	118_I	2.479	1.00
17_A	122_V	2.294	1.00
36_R	41_E	2.172	1.00
65_V	112_L	2.134	1.00
55_E	161_K	2.105	1.00
109_V	167_F	2.002	1.00
116_T	120_D	1.952	1.00
180_T	190_A	1.932	1.00
49_A	146_L	1.919	1.00
116_T	162_A	1.903	1.00
144_S	148_D	1.901	1.00
164_V	209_L	1.898	1.00
81_R	90_E	1.883	1.00
185_E	189_R	1.829	1.00
81_R	86_I	1.817	1.00
172_I	201_L	1.815	1.00
46_D	145_G	1.815	1.00
132_V	139_P	1.785	1.00
4_Q	104_R	1.774	1.00
175_Y	179_R	1.769	1.00
105_V	167_F	1.765	1.00
176_Q	179_R	1.754	1.00
21_F	126_G	1.725	1.00
189_R	193_R	1.706	1.00
8_I	73_I	1.701	1.00
48_V	127_G	1.673	1.00
152_L	156_L	1.666	1.00
145_G	148_D	1.652	1.00
12_S	69_V	1.631	1.00
13_L	118_I	1.613	1.00
101_V	174_C	1.576	1.00
109_V	163_V	1.548	1.00
46_D	149_A	1.523	1.00
94_I	99_Y	1.523	1.00
168_I	201_L	1.520	1.00
128_Y	143_L	1.518	1.00
156_L	160_I	1.489	1.00
63_L	199_S	1.482	1.00
31_G	47_L	1.453	1.00
128_Y	132_V	1.399	1.00
55_E	206_D	1.392	1.00
90_E	96_P	1.362	1.00
8_I	108_L	1.331	1.00
57_G	120_D	1.326	1.00
173_G	194_A	1.316	1.00
138_S	141_A	1.316	1.00
77_L	100_L	1.311	1.00
3_R	7_F	1.302	1.00
105_V	170_A	1.287	1.00
181_K	186_G	1.280	1.00
180_T	186_G	1.275	1.00
120_D	158_G	1.272	1.00
70_G	173_G	1.265	1.00
129_L	133_L	1.240	1.00
173_G	198_S	1.235	1.00
86_I	100_L	1.218	1.00
165_F	206_D	1.216	1.00
4_Q	7_F	1.216	1.00
140_G	144_S	1.198	1.00
53_V	150_L	1.185	1.00
49_A	150_L	1.181	1.00
143_L	147_Q	1.179	1.00
144_S	147_Q	1.176	1.00
207_Y	211_A	1.167	1.00
61_T	119_A	1.145	1.00
84_E	87_D	1.142	1.00
82_V	187_V	1.141	1.00
52_L	57_G	1.139	1.00
50_L	54_R	1.127	1.00
6_Y	10_V	1.113	1.00
97_V	101_V	1.112	1.00
54_R	154_D	1.109	1.00
117_I	159_L	1.103	1.00
14_P	17_A	1.101	1.00
151_D	154_D	1.099	1.00
101_V	178_L	1.096	1.00
127_G	142_Y	1.089	1.00
131_A	135_L	1.081	1.00
81_R	179_R	1.074	1.00
116_T	158_G	1.072	1.00
34_Q	37_R	1.066	1.00
8_I	111_M	1.060	1.00
201_L	205_A	1.059	1.00
40_A	43_Y	1.059	1.00
76_E	104_R	1.045	1.00
193_R	197_T	1.042	1.00
97_V	102_V	1.041	1.00
9_G	111_M	1.041	1.00
153_S	156_L	1.032	1.00
54_R	157_V	1.019	1.00
32_A	135_L	1.010	1.00
27_L	51_S	1.008	1.00
118_I	122_V	1.007	1.00
7_F	76_E	1.007	1.00
142_Y	146_L	1.004	1.00
124_I	146_L	1.003	1.00
46_D	50_L	0.985	1.00
10_V	14_P	0.983	1.00
163_V	167_F	0.978	1.00
141_A	145_G	0.977	1.00
117_I	120_D	0.976	1.00
81_R	178_L	0.968	1.00
89_L	99_Y	0.965	1.00
73_I	108_L	0.963	1.00
161_K	206_D	0.960	1.00
172_I	176_Q	0.957	1.00
105_V	171_L	0.944	1.00
111_M	114_L	0.943	1.00
139_P	143_L	0.943	1.00
141_A	144_S	0.937	1.00
117_I	121_L	0.935	1.00
183_G	186_G	0.931	1.00
16_V	119_A	0.928	1.00
53_V	155_V	0.928	1.00
164_V	205_A	0.927	1.00
78_G	180_T	0.926	1.00
53_V	120_D	0.921	1.00
61_T	116_T	0.920	1.00
112_L	166_G	0.918	1.00
167_F	171_L	0.917	1.00
32_A	36_R	0.916	1.00
197_T	201_L	0.912	1.00
33_Y	37_R	0.907	1.00
121_L	125_L	0.906	1.00
96_P	178_L	0.905	1.00
66_A	202_I	0.904	1.00
81_R	87_D	0.902	1.00
131_A	137_I	0.896	1.00
153_S	157_V	0.890	1.00
109_V	166_G	0.887	1.00
95_D	98_R	0.883	1.00
172_I	197_T	0.880	1.00
164_V	168_I	0.880	1.00
74_A	194_A	0.879	1.00
112_L	169_I	0.879	1.00
125_L	129_L	0.873	1.00
168_I	172_I	0.872	1.00
153_S	160_I	0.868	1.00
81_R	181_K	0.866	1.00
125_L	128_Y	0.861	1.00
157_V	209_L	0.860	1.00
108_L	166_G	0.860	1.00
157_V	160_I	0.855	1.00
4_Q	73_I	0.851	1.00
8_I	69_V	0.846	1.00
87_D	90_E	0.846	1.00
66_A	198_S	0.846	1.00
85_Q	199_S	0.845	1.00
53_V	158_G	0.845	1.00
64_I	199_S	0.845	1.00
13_L	17_A	0.837	1.00
53_V	124_I	0.812	1.00
35_L	47_L	0.812	1.00
25_M	130_V	0.810	1.00
17_A	20_G	0.806	1.00
169_I	198_S	0.805	1.00
57_G	119_A	0.801	1.00
79_T	184_A	0.797	1.00
41_E	44_V	0.794	1.00
81_R	182_G	0.789	1.00
50_L	154_D	0.780	1.00
11_G	14_P	0.778	1.00
155_V	159_L	0.775	1.00
160_I	164_V	0.773	1.00
171_L	175_Y	0.773	1.00
79_T	82_V	0.771	1.00
114_L	117_I	0.771	1.00
21_F	129_L	0.770	1.00
25_M	29_L	0.769	1.00
49_A	124_I	0.766	1.00
176_Q	190_A	0.760	1.00
33_Y	36_R	0.748	1.00
198_S	202_I	0.748	1.00
32_A	44_V	0.747	1.00
22_F	25_M	0.745	1.00
194_A	198_S	0.741	1.00
5_M	110_I	0.734	1.00
19_T	64_I	0.734	1.00
102_V	106_L	0.733	1.00
62_A	202_I	0.728	1.00
107_A	111_M	0.727	1.00
205_A	209_L	0.725	1.00
159_L	163_V	0.725	1.00
21_F	122_V	0.724	1.00
45_G	146_L	0.723	1.00
35_L	40_A	0.717	1.00
67_G	195_V	0.708	1.00
62_A	112_L	0.702	1.00
28_A	131_A	0.701	1.00
45_G	137_I	0.698	1.00
30_Q	51_S	0.692	1.00
186_G	189_R	0.692	1.00
204_V	208_L	0.691	1.00
108_L	112_L	0.691	1.00
18_L	200_V	0.690	1.00
148_D	151_D	0.688	1.00
5_M	9_G	0.688	1.00
42_S	46_D	0.686	1.00
66_A	169_I	0.682	1.00
127_G	131_A	0.680	1.00
3_R	185_E	0.680	1.00
48_V	51_S	0.679	1.00
62_A	165_F	0.679	1.00
79_T	187_V	0.677	1.00
132_V	136_G	0.670	1.00
10_V	13_L	0.668	1.00
79_T	83_T	0.667	1.00
17_A	21_F	0.666	1.00
28_A	48_V	0.663	1.00
34_Q	47_L	0.662	1.00
181_K	189_R	0.662	1.00
2_V	6_Y	0.661	1.00
190_A	193_R	0.661	1.00
23_I	60_L	0.660	1.00
73_I	174_C	0.660	1.00
114_L	118_I	0.653	1.00
143_L	146_L	0.652	1.00
58_P	116_T	0.652	1.00
52_L	120_D	0.652	1.00
128_Y	142_Y	0.652	1.00
20_G	57_G	0.641	1.00
4_Q	8_I	0.641	1.00
77_L	101_V	0.641	1.00
192_T	196_V	0.640	1.00
160_I	163_V	0.638	1.00
66_A	70_G	0.635	1.00
3_R	6_Y	0.634	1.00
12_S	68_R	0.632	1.00
203_L	207_Y	0.631	1.00
57_G	116_T	0.631	1.00
8_I	107_A	0.630	1.00
78_G	190_A	0.628	1.00
105_V	109_V	0.626	1.00
166_G	170_A	0.626	1.00
179_R	190_A	0.626	1.00
73_I	104_R	0.623	1.00
43_Y	46_D	0.623	1.00
192_T	195_V	0.619	1.00
5_M	107_A	0.616	1.00
74_A	191_T	0.614	1.00
86_I	178_L	0.614	1.00
148_D	152_L	0.614	1.00
62_A	66_A	0.612	1.00
82_V	180_T	0.608	1.00
130_V	134_L	0.606	1.00
25_M	207_Y	0.606	1.00
2_V	5_M	0.602	1.00
150_L	155_V	0.590	1.00
169_I	173_G	0.589	1.00
204_V	207_Y	0.588	1.00
47_L	51_S	0.588	1.00
104_R	174_C	0.586	1.00
163_V	166_G	0.586	1.00
16_V	61_T	0.584	1.00
16_V	115_L	0.581	1.00
130_V	133_L	0.579	1.00
45_G	145_G	0.575	1.00
151_D	156_L	0.574	1.00
57_G	61_T	0.573	1.00
7_F	72_A	0.571	1.00
45_G	131_A	0.569	1.00
42_S	145_G	0.568	1.00
14_P	18_L	0.567	1.00
98_R	102_V	0.567	1.00
175_Y	178_L	0.566	1.00
85_Q	94_I	0.562	1.00
77_L	174_C	0.562	1.00
149_A	152_L	0.558	1.00
20_G	61_T	0.555	1.00
20_G	24_G	0.555	1.00
116_T	159_L	0.554	1.00
97_V	178_L	0.553	1.00
106_L	109_V	0.552	1.00
19_T	85_Q	0.552	1.00
28_A	127_G	0.549	1.00
31_G	35_L	0.549	1.00
47_L	50_L	0.547	1.00
27_L	31_G	0.547	1.00
65_V	69_V	0.545	1.00
37_R	46_D	0.540	1.00
90_E	93_G	0.539	1.00
65_V	169_I	0.538	1.00
86_I	96_P	0.537	1.00
110_I	113_P	0.537	1.00
175_Y	197_T	0.537	1.00
37_R	40_A	0.535	1.00
5_M	8_I	0.533	1.00
89_L	94_I	0.531	1.00
145_G	149_A	0.530	1.00
136_G	139_P	0.529	1.00
73_I	173_G	0.526	1.00
206_D	209_L	0.520	1.00
4_Q	107_A	0.520	1.00
112_L	116_T	0.515	1.00
48_V	52_L	0.514	1.00
30_Q	210_T	0.511	1.00
7_F	189_R	0.510	1.00
109_V	170_A	0.508	1.00
20_G	23_I	0.507	1.00
176_Q	194_A	0.507	1.00
182_G	188_G	0.507	1.00
207_Y	210_T	0.506	1.00
40_A	44_V	0.506	1.00
71_S	195_V	0.505	1.00
4_Q	76_E	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
2zy9A	2	0.4811	3.3	0.954	Contact Map
3d31C	2	0.7972	2.7	0.956	Contact Map
3rlfF	1	0.7972	2.5	0.957	Contact Map
4ymuD	2	0.8302	2.4	0.958	Contact Map
2mgyA	1	0.4575	2.2	0.958	Contact Map
2a65A	2	0.8868	2	0.959	Contact Map
2onkC	2	0.4858	1.8	0.961	Contact Map
4tquM	1	0.8443	1.5	0.962	Contact Map
4lz6A	1	0.5472	1.5	0.962	Contact Map
4humA	1	0.5377	1.2	0.965	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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