LEP4 - BACSU - GREMLIN Contacts

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LEP4 - Type 4 prepilin-like proteins leader peptide-processing enzyme

UniProt:	P15378	Sequences: MLSILFIFGLILGSFYYTAGCRIPLHLSIIAPRSSCPFCRRTLTPAELIPILSFLFQKGKCKSCGHRISFMYPAAELVTACLFAAAGIRFGISLELFPAVVFISLLIIVAVTDIHFMLIPNRILIFFLPFLAAARLISPLDSWYAGLLGAAAGFLFLAVIAAITHGGVGGGDIKLFAVIGFVLGVKMLAAAFFFSVLIGALYGAAAVLTGRLAKRQPLPFAPAIAAGSILAYLYGDSIISFYIKMALG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	248 (234)
Sequences:	2635 (2093)
Seq/√Len:	136.8

ECOLI - PPPA LEP4
BACSU - LEP4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
47_E	62_K	5.050	1.00
71_M	115_H	4.555	1.00
33_R	42_T	3.643	1.00
127_F	178_V	3.088	1.00
109_V	119_I	2.994	1.00
83_F	104_S	2.742	1.00
20_G	111_V	2.707	1.00
6_F	80_A	2.645	1.00
179_I	191_A	2.624	1.00
47_E	63_S	2.544	1.00
105_L	123_I	2.480	1.00
41_R	47_E	2.418	1.00
41_R	63_S	2.402	1.00
170_G	173_I	2.379	1.00
12_L	16_Y	2.354	1.00
121_N	174_K	2.344	1.00
6_F	84_A	2.278	1.00
5_L	87_G	2.263	1.00
103_I	229_I	2.246	1.00
110_A	225_A	2.136	1.00
10_L	51_I	2.086	1.00
200_A	203_G	2.064	1.00
96_L	100_V	2.019	1.00
54_F	70_F	2.017	1.00
86_A	96_L	1.992	1.00
98_P	134_A	1.983	1.00
47_E	57_Q	1.955	1.00
79_T	107_I	1.885	1.00
143_W	147_L	1.875	1.00
79_T	83_F	1.826	1.00
38_F	66_H	1.796	1.00
52_L	56_F	1.752	1.00
86_A	103_I	1.752	1.00
27_L	35_S	1.743	1.00
28_S	32_P	1.738	1.00
179_I	228_S	1.731	1.00
5_L	84_A	1.693	1.00
29_I	32_P	1.675	1.00
202_Y	223_A	1.674	1.00
44_T	47_E	1.663	1.00
10_L	80_A	1.640	1.00
43_L	63_S	1.618	1.00
43_L	48_L	1.610	1.00
131_L	182_V	1.608	1.00
106_L	225_A	1.606	1.00
82_L	103_I	1.602	1.00
191_A	227_G	1.599	1.00
70_F	74_A	1.597	1.00
198_I	230_L	1.593	1.00
83_F	100_V	1.585	1.00
16_Y	108_I	1.572	1.00
87_G	96_L	1.536	1.00
44_T	62_K	1.534	1.00
19_A	23_I	1.533	1.00
227_G	231_A	1.522	1.00
119_I	221_A	1.516	1.00
119_I	124_L	1.501	1.00
99_A	232_Y	1.495	1.00
58_K	65_G	1.480	1.00
150_A	181_F	1.463	1.00
78_V	111_V	1.449	1.00
101_V	130_F	1.448	1.00
41_R	44_T	1.432	1.00
6_F	10_L	1.429	1.00
51_I	77_L	1.416	1.00
212_L	216_Q	1.395	1.00
161_A	166_G	1.356	1.00
9_G	80_A	1.356	1.00
161_A	170_G	1.355	1.00
195_S	224_I	1.312	1.00
120_P	174_K	1.306	1.00
79_T	104_S	1.274	1.00
187_M	191_A	1.266	1.00
213_A	216_Q	1.263	1.00
84_A	88_I	1.257	1.00
14_S	34_S	1.256	1.00
71_M	111_V	1.249	1.00
82_L	107_I	1.247	1.00
49_I	53_S	1.240	1.00
149_G	180_G	1.228	1.00
39_C	64_C	1.222	1.00
117_M	217_P	1.220	1.00
196_V	200_A	1.214	1.00
44_T	63_S	1.208	1.00
176_F	191_A	1.202	1.00
103_I	233_L	1.189	1.00
20_G	75_A	1.189	1.00
111_V	115_H	1.184	1.00
9_G	83_F	1.176	0.99
187_M	231_A	1.172	0.99
75_A	111_V	1.169	0.99
153_G	188_L	1.165	0.99
176_F	224_I	1.164	0.99
36_C	39_C	1.152	0.99
148_L	152_A	1.151	0.99
120_P	123_I	1.150	0.99
198_I	223_A	1.148	0.99
69_S	72_Y	1.143	0.99
35_S	40_R	1.125	0.99
119_I	175_L	1.123	0.99
102_F	228_S	1.116	0.99
37_P	68_I	1.114	0.99
142_S	145_A	1.093	0.99
149_G	153_G	1.087	0.99
161_A	173_I	1.072	0.99
37_P	72_Y	1.065	0.99
4_I	8_F	1.057	0.99
35_S	43_L	1.054	0.99
17_Y	20_G	1.054	0.99
136_L	148_L	1.047	0.99
48_L	57_Q	1.041	0.99
36_C	64_C	1.030	0.99
158_A	162_A	1.026	0.99
159_V	163_I	1.015	0.98
86_A	99_A	1.011	0.98
159_V	162_A	1.007	0.98
90_F	99_A	1.002	0.98
109_V	123_I	1.000	0.98
74_A	78_V	1.000	0.98
19_A	108_I	0.997	0.98
33_R	44_T	0.995	0.98
154_F	158_A	0.991	0.98
16_Y	104_S	0.983	0.98
200_A	204_A	0.949	0.98
194_F	227_G	0.939	0.97
24_P	112_T	0.936	0.97
7_I	11_I	0.936	0.97
102_F	179_I	0.933	0.97
46_A	56_F	0.933	0.97
175_L	221_A	0.931	0.97
90_F	93_S	0.930	0.97
61_C	64_C	0.918	0.97
20_G	112_T	0.910	0.97
204_A	208_L	0.907	0.97
117_M	219_P	0.906	0.97
229_I	233_L	0.897	0.97
69_S	73_P	0.894	0.97
105_L	127_F	0.892	0.97
36_C	61_C	0.892	0.97
157_L	192_F	0.877	0.96
170_G	174_K	0.876	0.96
90_F	96_L	0.872	0.96
192_F	196_V	0.868	0.96
109_V	124_L	0.865	0.96
200_A	207_V	0.863	0.96
39_C	61_C	0.862	0.96
199_G	203_G	0.862	0.96
135_R	146_G	0.859	0.96
5_L	100_V	0.858	0.96
145_A	186_K	0.854	0.96
13_G	79_T	0.850	0.95
82_L	229_I	0.844	0.95
51_I	73_P	0.839	0.95
47_E	53_S	0.836	0.95
206_A	210_G	0.835	0.95
80_A	84_A	0.833	0.95
131_L	178_V	0.832	0.95
10_L	73_P	0.828	0.95
108_I	123_I	0.828	0.95
124_L	178_V	0.826	0.95
191_A	195_S	0.825	0.95
195_S	220_F	0.824	0.95
193_F	196_V	0.818	0.94
107_I	111_V	0.816	0.94
183_L	187_M	0.814	0.94
157_L	161_A	0.814	0.94
183_L	231_A	0.813	0.94
169_G	172_D	0.812	0.94
198_I	226_A	0.811	0.94
207_V	210_G	0.807	0.94
230_L	234_Y	0.806	0.94
45_P	48_L	0.806	0.94
118_L	174_K	0.803	0.94
150_A	177_A	0.802	0.94
71_M	75_A	0.798	0.94
93_S	96_L	0.798	0.94
199_G	223_A	0.786	0.93
102_F	182_V	0.782	0.93
18_T	24_P	0.778	0.93
46_A	62_K	0.777	0.93
153_G	180_G	0.777	0.93
157_L	173_I	0.777	0.93
43_L	47_E	0.777	0.93
121_N	124_L	0.777	0.93
190_A	231_A	0.771	0.92
151_A	154_F	0.766	0.92
191_A	228_S	0.759	0.92
85_A	233_L	0.758	0.92
17_Y	75_A	0.754	0.92
168_V	196_V	0.754	0.92
158_A	173_I	0.753	0.91
14_S	76_E	0.752	0.91
135_R	140_L	0.750	0.91
21_C	25_L	0.750	0.91
20_G	108_I	0.744	0.91
106_L	175_L	0.738	0.91
17_Y	72_Y	0.737	0.91
103_I	232_Y	0.735	0.90
121_N	125_I	0.724	0.90
24_P	116_F	0.722	0.90
205_A	208_L	0.721	0.90
191_A	231_A	0.714	0.89
53_S	57_Q	0.713	0.89
195_S	227_G	0.713	0.89
41_R	62_K	0.712	0.89
176_F	196_V	0.711	0.89
157_L	167_G	0.710	0.89
149_G	184_G	0.710	0.89
9_G	13_G	0.708	0.89
34_S	76_E	0.708	0.89
207_V	212_L	0.707	0.89
152_A	155_L	0.706	0.89
42_T	47_E	0.705	0.89
135_R	181_F	0.704	0.89
210_G	213_A	0.703	0.88
34_S	39_C	0.698	0.88
125_I	129_P	0.693	0.88
54_F	59_G	0.691	0.88
64_C	76_E	0.688	0.87
12_L	104_S	0.687	0.87
49_I	56_F	0.684	0.87
98_P	182_V	0.681	0.87
16_Y	107_I	0.680	0.87
15_F	34_S	0.679	0.87
135_R	142_S	0.675	0.86
183_L	191_A	0.674	0.86
73_P	77_L	0.665	0.86
43_L	52_L	0.661	0.85
154_F	173_I	0.659	0.85
156_F	160_I	0.657	0.85
133_A	151_A	0.656	0.85
113_D	171_G	0.656	0.85
82_L	86_A	0.652	0.84
113_D	172_D	0.651	0.84
16_Y	79_T	0.651	0.84
78_V	107_I	0.650	0.84
89_R	92_I	0.648	0.84
211_R	214_K	0.647	0.84
21_C	37_P	0.647	0.84
134_A	138_S	0.644	0.84
83_F	86_A	0.643	0.84
157_L	224_I	0.643	0.84
146_G	181_F	0.640	0.83
145_A	185_V	0.640	0.83
162_A	170_G	0.640	0.83
150_A	154_F	0.639	0.83
50_P	76_E	0.638	0.83
168_V	220_F	0.636	0.83
200_A	206_A	0.634	0.83
112_T	116_F	0.631	0.82
157_L	176_F	0.626	0.82
22_R	32_P	0.624	0.82
17_Y	21_C	0.622	0.82
164_T	167_G	0.622	0.82
34_S	50_P	0.621	0.81
148_L	185_V	0.621	0.81
68_I	76_E	0.620	0.81
109_V	120_P	0.620	0.81
49_I	52_L	0.612	0.81
113_D	169_G	0.608	0.80
122_R	126_F	0.604	0.80
210_G	216_Q	0.599	0.79
25_L	115_H	0.598	0.79
225_A	228_S	0.597	0.79
158_A	170_G	0.595	0.79
118_L	121_N	0.595	0.79
33_R	45_P	0.594	0.79
175_L	225_A	0.594	0.79
109_V	221_A	0.591	0.78
135_R	143_W	0.590	0.78
86_A	233_L	0.589	0.78
127_F	154_F	0.588	0.78
124_L	181_F	0.586	0.78
208_L	211_R	0.584	0.77
126_F	130_F	0.583	0.77
103_I	107_I	0.581	0.77
70_F	73_P	0.580	0.77
57_Q	62_K	0.578	0.77
133_A	137_I	0.576	0.76
34_S	68_I	0.574	0.76
117_M	218_L	0.573	0.76
106_L	179_I	0.572	0.76
149_G	185_V	0.571	0.76
205_A	209_T	0.568	0.75
85_A	229_I	0.567	0.75
6_F	77_L	0.566	0.75
81_C	85_A	0.564	0.75
191_A	224_I	0.562	0.75
14_S	18_T	0.562	0.75
67_R	70_F	0.559	0.74
102_F	224_I	0.558	0.74
180_G	184_G	0.555	0.74
98_P	102_F	0.554	0.74
200_A	223_A	0.554	0.74
112_T	115_H	0.554	0.74
85_A	234_Y	0.553	0.73
50_P	64_C	0.553	0.73
99_A	140_L	0.550	0.73
174_K	222_P	0.550	0.73
206_A	212_L	0.549	0.73
183_L	232_Y	0.548	0.73
5_L	83_F	0.547	0.73
91_G	96_L	0.544	0.72
112_T	131_L	0.543	0.72
11_I	53_S	0.542	0.72
112_T	120_P	0.540	0.72
112_T	222_P	0.537	0.71
119_I	171_G	0.536	0.71
194_F	198_I	0.536	0.71
166_G	215_R	0.534	0.71
128_L	177_A	0.534	0.71
141_D	145_A	0.533	0.71
10_L	77_L	0.532	0.71
50_P	53_S	0.531	0.70
14_S	68_I	0.531	0.70
211_R	216_Q	0.530	0.70
101_V	205_A	0.530	0.70
21_C	71_M	0.529	0.70
147_L	151_A	0.528	0.70
207_V	214_K	0.527	0.70
161_A	168_V	0.523	0.69
102_F	131_L	0.521	0.69
105_L	126_F	0.519	0.69
92_I	96_L	0.519	0.69
22_R	34_S	0.517	0.68
14_S	39_C	0.516	0.68
179_I	183_L	0.515	0.68
153_G	157_L	0.515	0.68
171_G	221_A	0.514	0.68
18_T	48_L	0.514	0.68
209_T	212_L	0.514	0.68
17_Y	37_P	0.513	0.68
100_V	104_S	0.512	0.68
14_S	48_L	0.512	0.68
165_H	215_R	0.511	0.68
198_I	227_G	0.509	0.67
123_I	178_V	0.508	0.67
126_F	181_F	0.508	0.67
43_L	46_A	0.508	0.67
202_Y	206_A	0.507	0.67
127_F	131_L	0.507	0.67
98_P	130_F	0.507	0.67
198_I	202_Y	0.507	0.67
207_V	213_A	0.506	0.67
15_F	48_L	0.505	0.67
75_A	107_I	0.505	0.67
203_G	218_L	0.504	0.67
5_L	96_L	0.503	0.66
112_T	123_I	0.503	0.66
102_F	127_F	0.501	0.66
5_L	9_G	0.500	0.66

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
3s0xA	1	0.5968	99.5	0.745	Contact Map
3py7A	1	0.2702	41.9	0.943	Contact Map
4xlgA	1	0.2218	39.5	0.944	Contact Map
2ct0A	1	0.2621	36.9	0.945	Contact Map
1iymA	1	0.1694	27.7	0.948	Contact Map
3u6pA	1	0.1653	23.6	0.95	Contact Map
1ee8A	2	0.2379	21.3	0.951	Contact Map
3j20Y	1	0.2016	20.2	0.952	Contact Map
4pd2A	1	0.2419	18.7	0.952	Contact Map
4v3lC	1	0.2298	18.6	0.952	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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