LysE - PFAM28P - GREMLIN Contacts

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LysE - LysE type translocator

PFAM:	PF01810	Sequences: LVLALTPGPDNLLVLARGLRRGRRAGLAAALGIALGDLVHILLAALGLGALLAASPLAFTVLKLAGAAYLLYLGIKALRSAPRPAAAAAAAPRRSLRRAFLQGFLVNLLNPKAILFFLAFLPQFVDPAAGPPLLQLLLLGAGFVLGSLLWFLLLALLASRLRRRLRRPRALRWLNRVSGLLLIGLGLRLALSG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	193 (190)
Sequences:	87348 (61664)
Seq/√Len:	4473.5
META:	0.782

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
35_L	100_F	5.185	1.00
75_I	79_R	3.370	1.00
173_W	176_R	2.729	1.00
74_G	183_I	2.705	1.00
39_V	104_F	2.573	1.00
72_Y	76_K	2.544	1.00
60_T	63_K	2.447	1.00
97_R	101_L	2.400	1.00
150_W	154_L	2.361	1.00
172_R	176_R	2.206	1.00
13_L	29_A	2.191	1.00
10_D	33_I	2.147	1.00
28_A	96_L	2.113	1.00
17_R	21_R	2.076	1.00
132_P	135_Q	2.011	1.00
57_L	60_T	1.953	1.00
71_L	186_G	1.852	1.00
78_L	176_R	1.843	1.00
25_A	99_A	1.834	1.00
67_A	190_A	1.820	1.00
59_F	63_K	1.805	1.00
76_K	79_R	1.724	1.00
151_F	154_L	1.716	1.00
64_L	68_A	1.666	1.00
11_N	154_L	1.649	1.00
17_R	29_A	1.628	1.00
101_L	105_L	1.628	1.00
60_T	64_L	1.612	1.00
126_D	129_A	1.601	1.00
154_L	158_A	1.595	1.00
176_R	180_L	1.578	1.00
36_G	108_L	1.563	1.00
31_L	100_F	1.506	1.00
21_R	25_A	1.503	1.00
184_G	188_R	1.490	1.00
17_R	102_Q	1.480	1.00
29_A	103_G	1.467	1.00
16_A	20_R	1.431	1.00
57_L	61_V	1.423	1.00
81_A	176_R	1.413	1.00
4_A	146_G	1.409	1.00
24_R	28_A	1.407	1.00
133_L	136_L	1.399	1.00
180_L	184_G	1.396	1.00
162_R	166_R	1.384	1.00
131_P	134_L	1.382	1.00
147_S	151_F	1.365	1.00
173_W	177_V	1.334	1.00
82_P	176_R	1.327	1.00
78_L	179_G	1.316	1.00
153_L	157_L	1.313	1.00
71_L	183_I	1.296	1.00
26_G	30_A	1.293	1.00
18_G	26_G	1.291	1.00
98_R	101_L	1.284	1.00
76_K	80_S	1.280	1.00
38_L	144_V	1.269	1.00
40_H	114_I	1.248	1.00
26_G	155_A	1.247	1.00
160_R	164_R	1.233	1.00
133_L	137_L	1.225	1.00
36_G	104_F	1.194	1.00
100_F	104_F	1.192	1.00
95_S	98_R	1.189	1.00
64_L	67_A	1.173	1.00
23_R	159_S	1.159	1.00
67_A	186_G	1.159	1.00
13_L	17_R	1.155	1.00
98_R	102_Q	1.153	1.00
41_I	140_G	1.151	1.00
164_R	167_R	1.149	1.00
74_G	179_G	1.145	1.00
130_G	133_L	1.142	1.00
117_F	143_F	1.132	1.00
79_R	83_R	1.114	1.00
69_Y	72_Y	1.105	1.00
50_A	53_A	1.094	1.00
79_R	82_P	1.090	1.00
24_R	96_L	1.088	1.00
61_V	65_A	1.088	1.00
160_R	163_R	1.087	1.00
23_R	156_L	1.086	1.00
69_Y	73_L	1.080	1.00
167_R	170_A	1.063	1.00
27_L	152_L	1.059	1.00
142_G	146_G	1.047	1.00
152_L	156_L	1.045	1.00
157_L	160_R	1.043	1.00
58_A	61_V	1.042	1.00
131_P	135_Q	1.038	1.00
132_P	136_L	1.035	1.00
32_G	104_F	1.022	1.00
27_L	30_A	1.021	1.00
28_A	99_A	1.021	1.00
21_R	99_A	1.020	1.00
177_V	180_L	1.018	1.00
35_L	104_F	1.017	1.00
37_D	113_A	1.004	1.00
150_W	153_L	1.001	1.00
68_A	72_Y	1.001	1.00
71_L	75_I	0.994	1.00
82_P	85_A	0.993	1.00
55_S	58_A	0.973	1.00
156_L	160_R	0.971	1.00
72_Y	75_I	0.967	1.00
130_G	135_Q	0.966	1.00
169_R	173_W	0.963	1.00
158_A	161_L	0.963	1.00
50_A	54_A	0.962	1.00
18_G	155_A	0.962	1.00
151_F	155_A	0.956	1.00
80_S	175_N	0.953	1.00
143_F	147_S	0.952	1.00
10_D	37_D	0.950	1.00
11_N	15_L	0.948	1.00
6_T	11_N	0.935	1.00
34_A	148_L	0.933	1.00
174_L	177_V	0.927	1.00
134_L	137_L	0.927	1.00
161_L	164_R	0.926	1.00
15_L	158_A	0.924	1.00
77_A	179_G	0.919	1.00
148_L	152_L	0.913	1.00
168_P	171_L	0.911	1.00
126_D	130_G	0.907	1.00
2_V	5_L	0.907	1.00
138_L	142_G	0.901	1.00
141_A	144_V	0.900	1.00
10_D	107_N	0.888	1.00
17_R	20_R	0.886	1.00
137_L	140_G	0.885	1.00
37_D	107_N	0.883	1.00
170_A	173_W	0.876	1.00
137_L	141_A	0.876	1.00
46_L	50_A	0.862	1.00
187_L	191_L	0.862	1.00
140_G	144_V	0.860	1.00
177_V	181_L	0.859	1.00
130_G	134_L	0.858	1.00
143_F	146_G	0.858	1.00
38_L	42_L	0.857	1.00
32_G	100_F	0.854	1.00
119_A	123_Q	0.849	1.00
40_H	108_L	0.849	1.00
47_G	52_L	0.845	1.00
164_R	168_P	0.845	1.00
102_Q	106_V	0.844	1.00
149_L	152_L	0.841	1.00
31_L	34_A	0.835	1.00
23_R	155_A	0.834	1.00
183_I	187_L	0.833	1.00
5_L	150_W	0.833	1.00
40_H	44_A	0.833	1.00
13_L	106_V	0.828	1.00
99_A	102_Q	0.821	1.00
42_L	46_L	0.820	1.00
61_V	64_L	0.815	1.00
25_A	28_A	0.812	1.00
52_L	55_S	0.811	1.00
188_R	191_L	0.807	1.00
37_D	117_F	0.804	1.00
30_A	34_A	0.797	1.00
14_V	33_I	0.795	1.00
149_L	153_L	0.794	1.00
30_A	155_A	0.794	1.00
154_L	157_L	0.793	1.00
49_G	53_A	0.790	1.00
39_V	42_L	0.781	1.00
169_R	172_R	0.781	1.00
174_L	178_S	0.780	1.00
23_R	27_L	0.779	1.00
10_D	106_V	0.779	1.00
34_A	37_D	0.777	1.00
33_I	107_N	0.776	1.00
141_A	145_L	0.776	1.00
27_L	156_L	0.775	1.00
140_G	143_F	0.771	1.00
2_V	6_T	0.770	1.00
14_V	151_F	0.769	1.00
67_A	71_L	0.766	1.00
56_P	60_T	0.765	1.00
33_I	37_D	0.763	1.00
153_L	156_L	0.761	1.00
171_L	175_N	0.753	1.00
81_A	84_P	0.745	1.00
145_L	149_L	0.742	1.00
89_A	92_P	0.741	1.00
144_V	148_L	0.738	1.00
54_A	57_L	0.738	1.00
34_A	144_V	0.736	1.00
14_V	18_G	0.735	1.00
55_S	59_F	0.734	1.00
75_I	183_I	0.733	1.00
135_Q	139_L	0.730	1.00
116_F	121_L	0.727	1.00
36_G	107_N	0.725	1.00
32_G	36_G	0.721	1.00
146_G	149_L	0.720	1.00
165_L	168_P	0.717	1.00
17_R	26_G	0.714	1.00
37_D	40_H	0.714	1.00
39_V	108_L	0.712	1.00
146_G	150_W	0.706	1.00
147_S	150_W	0.705	1.00
163_R	167_R	0.698	1.00
78_L	183_I	0.694	1.00
134_L	138_L	0.692	1.00
105_L	109_L	0.692	1.00
163_R	166_R	0.689	1.00
85_A	88_A	0.686	1.00
3_L	116_F	0.684	1.00
136_L	140_G	0.684	1.00
35_L	39_V	0.680	1.00
25_A	96_L	0.676	1.00
151_F	158_A	0.676	1.00
17_R	99_A	0.673	1.00
162_R	165_L	0.670	1.00
166_R	169_R	0.667	1.00
183_I	186_G	0.664	1.00
22_G	25_A	0.658	1.00
11_N	150_W	0.655	1.00
107_N	113_A	0.655	1.00
95_S	99_A	0.646	1.00
96_L	99_A	0.645	1.00
47_G	54_A	0.643	1.00
144_V	147_S	0.642	1.00
78_L	82_P	0.639	1.00
142_G	147_S	0.639	1.00
129_A	132_P	0.636	1.00
40_H	113_A	0.636	1.00
104_F	108_L	0.634	1.00
6_T	112_K	0.630	1.00
82_P	172_R	0.626	1.00
94_R	102_Q	0.621	1.00
80_S	83_R	0.618	1.00
146_G	151_F	0.617	1.00
65_A	68_A	0.617	1.00
11_N	151_F	0.612	1.00
29_A	106_V	0.610	1.00
135_Q	138_L	0.602	1.00
14_V	29_A	0.602	1.00
14_V	30_A	0.601	1.00
74_G	186_G	0.594	1.00
159_S	162_R	0.592	1.00
97_R	100_F	0.591	1.00
129_A	135_Q	0.588	1.00
87_A	91_A	0.587	1.00
145_L	148_L	0.585	1.00
30_A	152_L	0.584	1.00
178_S	182_L	0.583	1.00
85_A	89_A	0.579	1.00
17_R	25_A	0.575	1.00
13_L	16_A	0.575	1.00
129_A	133_L	0.573	1.00
4_A	11_N	0.566	1.00
33_I	103_G	0.562	1.00
139_L	143_F	0.560	1.00
172_R	175_N	0.560	1.00
126_D	135_Q	0.559	1.00
88_A	91_A	0.555	1.00
123_Q	126_D	0.554	1.00
30_A	151_F	0.552	1.00
86_A	89_A	0.548	1.00
41_I	117_F	0.545	1.00
179_G	183_I	0.544	1.00
158_A	165_L	0.543	1.00
137_L	142_G	0.542	1.00
144_V	151_F	0.540	1.00
11_N	14_V	0.539	1.00
64_L	190_A	0.538	1.00
127_P	130_G	0.537	1.00
12_L	16_A	0.536	1.00
23_R	152_L	0.535	1.00
32_G	103_G	0.531	1.00
96_L	100_F	0.529	1.00
84_P	87_A	0.528	1.00
155_A	159_S	0.525	1.00
161_L	165_L	0.518	1.00
3_L	37_D	0.513	1.00
18_G	158_A	0.510	1.00
27_L	31_L	0.505	1.00
62_L	66_G	0.504	1.00
49_G	52_L	0.500	1.00
4_A	37_D	0.500	1.00
21_R	24_R	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
4bwzA	2	0.4404	9	0.922	Contact Map
3wdoA	1	0.9016	8.4	0.923	Contact Map
3o7qA	1	0.9223	8	0.923	Contact Map
2gfpA	2	0.9223	7.1	0.925	Contact Map
2kncA	1	0.2487	6.6	0.926	Contact Map
1pw4A	1	0.9016	6.1	0.927	Contact Map
2xq2A	2	0.3886	6	0.928	Contact Map
3j1zP	8	0.8705	4.9	0.931	Contact Map
2cfqA	1	0.9119	4.5	0.932	Contact Map
4ldsA	2	0.4145	4.3	0.933	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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