LEP4 - ECOLI - GREMLIN Contacts

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

UniProt:	P25960	Sequences: MTMLLPLFILVGFIADYFVNAIAYHLSPLEDKTALTFRQVLVHFRQKKYAWHDTVPLILCVAAAIACALAPFTPIVTGALFLYFCFVLTLSVIDFRTQLLPDKLTLPLLWLGLVFNAQYGLIDLHDAVYGAVAGYGVLWCVYWGVWLVCHKEGLGYGDFKLLAAAGAWCGWQTLPMILLIASLGGIGYAIVSQLLQRRTITTIAFGPWLALGSMINLGYLAWISY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11359
Length:	225 (215)
Sequences:	2703 (2138)
Seq/√Len:	145.8

ECOLI - LEP4 PPPA
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
30_E	45_R	4.966	1.00
54_T	96_R	4.548	1.00
16_D	25_H	3.728	1.00
90_L	100_L	3.172	1.00
108_L	164_A	3.063	1.00
66_A	85_C	2.741	1.00
102_D	160_K	2.615	1.00
165_A	177_I	2.600	1.00
30_E	46_Q	2.561	1.00
86_F	104_L	2.477	1.00
84_F	214_M	2.450	1.00
156_Y	159_F	2.393	1.00
24_Y	46_Q	2.379	1.00
24_Y	30_E	2.370	1.00
11_V	15_A	2.255	1.00
12_G	15_A	2.217	1.00
91_S	210_A	2.190	1.00
79_A	115_F	2.149	1.00
62_A	88_L	2.120	1.00
37_F	53_D	2.072	1.00
145_V	149_C	2.070	1.00
30_E	40_V	2.015	1.00
186_I	189_A	1.989	1.00
62_A	66_A	1.977	1.00
10_L	18_F	1.894	1.00
188_Y	208_W	1.844	1.00
21_A	49_Y	1.823	1.00
35_L	39_Q	1.802	1.00
124_L	128_V	1.790	1.00
77_T	81_F	1.787	1.00
27_S	30_E	1.747	1.00
145_V	153_G	1.724	1.00
87_V	210_A	1.710	1.00
165_A	213_S	1.710	1.00
69_L	77_T	1.683	1.00
26_L	31_D	1.656	1.00
53_D	57_L	1.641	1.00
26_L	46_Q	1.640	1.00
177_I	212_G	1.627	1.00
184_G	215_I	1.617	1.00
69_L	84_F	1.588	1.00
6_P	10_L	1.588	1.00
66_A	81_F	1.566	1.00
212_G	216_N	1.537	1.00
27_S	45_R	1.535	1.00
24_Y	27_S	1.529	1.00
100_L	105_T	1.515	1.00
80_L	217_L	1.498	1.00
34_A	60_C	1.485	1.00
41_L	48_K	1.480	1.00
32_K	36_T	1.436	1.00
61_V	92_V	1.432	1.00
100_L	206_G	1.423	1.00
65_I	84_F	1.421	1.00
134_G	174_L	1.412	1.00
62_A	85_C	1.407	1.00
82_L	111_L	1.377	1.00
98_Q	202_T	1.369	1.00
70_A	77_T	1.351	1.00
58_I	92_V	1.340	1.00
54_T	92_V	1.327	1.00
11_V	14_I	1.320	1.00
101_P	160_K	1.318	1.00
162_L	209_L	1.305	1.00
149_C	153_G	1.297	1.00
181_A	209_L	1.296	1.00
182_S	186_I	1.289	1.00
142_Y	156_Y	1.289	1.00
27_S	46_Q	1.287	1.00
142_Y	152_E	1.284	1.00
198_R	201_T	1.282	1.00
20_N	55_V	1.275	1.00
18_F	23_A	1.253	1.00
92_V	96_R	1.247	1.00
52_H	55_V	1.244	1.00
173_T	177_I	1.240	1.00
186_I	193_Q	1.231	1.00
123_D	126_D	1.227	1.00
20_N	51_W	1.226	1.00
184_G	208_W	1.212	1.00
140_C	144_G	1.209	1.00
65_I	88_L	1.200	1.00
135_Y	159_F	1.198	1.00
100_L	161_L	1.196	1.00
112_G	168_W	1.175	1.00
31_D	40_V	1.163	1.00
57_L	61_V	1.160	1.00
129_Y	133_A	1.147	1.00
173_T	216_N	1.117	0.99
192_S	196_Q	1.117	0.99
130_G	134_G	1.105	0.99
18_F	26_L	1.104	0.99
162_L	177_I	1.103	0.99
89_T	104_L	1.100	0.99
83_Y	213_S	1.098	0.99
135_Y	139_W	1.092	0.99
16_D	27_S	1.087	0.99
180_I	212_G	1.078	0.99
84_F	218_G	1.072	0.99
143_W	146_W	1.062	0.99
142_Y	159_F	1.061	0.99
101_P	104_L	1.057	0.99
185_G	208_W	1.055	0.99
138_L	142_Y	1.045	0.99
34_A	56_P	1.044	0.99
52_H	56_P	1.043	0.99
131_A	167_A	1.040	0.99
90_L	104_L	1.037	0.99
117_A	129_Y	1.030	0.99
29_L	39_Q	1.021	0.99
134_G	166_G	1.003	0.99
109_L	163_A	1.002	0.99
114_V	118_Q	0.983	0.98
54_T	58_I	0.981	0.98
44_F	47_K	0.972	0.98
186_I	190_I	0.957	0.98
63_A	67_C	0.941	0.98
161_L	206_G	0.941	0.98
90_L	105_T	0.934	0.98
86_F	108_L	0.921	0.98
19_V	22_I	0.918	0.98
185_G	189_A	0.913	0.98
190_I	194_L	0.913	0.98
88_L	92_V	0.912	0.97
215_I	219_Y	0.909	0.97
98_Q	204_A	0.899	0.97
102_D	105_T	0.885	0.97
26_L	30_E	0.884	0.97
181_A	205_F	0.884	0.97
83_Y	165_A	0.882	0.97
176_M	216_N	0.881	0.97
169_C	173_T	0.872	0.97
22_I	47_K	0.872	0.97
56_P	60_C	0.865	0.97
178_L	182_S	0.860	0.96
145_V	151_K	0.858	0.96
69_L	80_L	0.848	0.96
169_C	216_N	0.843	0.96
28_P	31_D	0.840	0.96
112_G	164_A	0.839	0.96
156_Y	160_K	0.836	0.96
30_E	36_T	0.824	0.95
105_T	164_A	0.820	0.95
15_A	18_F	0.815	0.95
132_V	135_Y	0.813	0.95
53_D	56_P	0.811	0.95
66_A	69_L	0.808	0.95
130_G	166_G	0.807	0.95
179_L	182_S	0.807	0.95
79_A	168_W	0.800	0.95
103_K	107_P	0.800	0.95
65_I	214_M	0.795	0.94
214_M	218_G	0.792	0.94
84_F	217_L	0.785	0.94
116_N	127_A	0.782	0.94
29_L	45_R	0.777	0.94
155_G	158_D	0.768	0.93
146_W	152_E	0.768	0.93
210_A	213_S	0.766	0.93
154_L	182_S	0.765	0.93
93_I	96_R	0.763	0.93
138_L	178_L	0.760	0.93
139_W	143_W	0.757	0.93
177_I	213_S	0.757	0.93
83_Y	112_G	0.753	0.93
184_G	211_L	0.752	0.93
8_F	93_I	0.749	0.93
99_L	160_K	0.745	0.92
93_I	97_T	0.743	0.92
177_I	181_A	0.742	0.92
32_K	39_Q	0.739	0.92
114_V	132_V	0.738	0.92
74_P	77_T	0.734	0.92
87_V	161_L	0.732	0.92
36_T	40_V	0.732	0.92
106_L	110_W	0.731	0.92
37_F	42_V	0.730	0.92
122_I	126_D	0.725	0.91
8_F	97_T	0.724	0.91
116_N	167_A	0.719	0.91
24_Y	45_R	0.718	0.91
51_W	59_L	0.717	0.91
64_A	68_A	0.716	0.91
186_I	192_S	0.714	0.91
19_V	47_K	0.709	0.90
180_I	184_G	0.706	0.90
142_Y	154_L	0.705	0.90
102_D	106_L	0.704	0.90
25_H	30_E	0.704	0.90
177_I	216_N	0.702	0.90
140_C	143_W	0.702	0.90
68_A	71_P	0.700	0.90
98_Q	203_I	0.700	0.90
80_L	121_L	0.699	0.90
162_L	182_S	0.687	0.89
193_Q	196_Q	0.686	0.89
99_L	102_D	0.683	0.89
126_D	171_W	0.682	0.89
58_I	88_L	0.682	0.89
72_F	80_L	0.678	0.88
81_F	85_C	0.676	0.88
61_V	88_L	0.676	0.88
7_L	10_L	0.672	0.88
47_K	59_L	0.670	0.88
184_G	212_G	0.667	0.87
94_D	158_D	0.666	0.87
149_C	152_E	0.665	0.87
126_D	172_Q	0.663	0.87
90_L	206_G	0.661	0.87
32_K	35_L	0.654	0.86
14_I	18_F	0.652	0.86
26_L	35_L	0.651	0.86
40_V	45_R	0.651	0.86
107_P	167_A	0.649	0.86
105_T	167_A	0.648	0.86
191_V	194_L	0.648	0.86
69_L	81_F	0.646	0.86
130_G	133_A	0.640	0.85
68_A	218_G	0.638	0.85
116_N	123_D	0.637	0.85
137_V	178_L	0.637	0.85
181_A	212_G	0.637	0.85
139_W	156_Y	0.636	0.85
69_L	218_G	0.635	0.85
146_W	150_H	0.634	0.85
10_L	13_F	0.633	0.85
70_A	74_P	0.633	0.85
72_F	77_T	0.633	0.85
169_C	177_I	0.630	0.84
194_L	197_R	0.630	0.84
192_S	197_R	0.629	0.84
193_Q	199_T	0.629	0.84
196_Q	201_T	0.628	0.84
191_V	195_L	0.625	0.84
189_A	203_I	0.624	0.84
142_Y	145_V	0.624	0.84
146_W	153_G	0.620	0.83
161_L	210_A	0.620	0.83
93_I	207_P	0.619	0.83
83_Y	168_W	0.617	0.83
129_Y	171_W	0.614	0.83
65_I	69_L	0.613	0.83
189_A	193_Q	0.612	0.83
50_A	53_D	0.610	0.82
100_L	157_G	0.610	0.82
137_V	140_C	0.610	0.82
68_A	214_M	0.607	0.82
115_F	119_Y	0.606	0.82
33_T	59_L	0.602	0.82
90_L	101_P	0.601	0.81
113_L	127_A	0.599	0.81
166_G	170_G	0.599	0.81
91_S	97_T	0.598	0.81
16_D	28_P	0.598	0.81
11_V	18_F	0.597	0.81
22_I	44_F	0.596	0.81
7_L	12_G	0.595	0.81
131_A	163_A	0.591	0.80
124_L	130_G	0.591	0.80
93_I	104_L	0.591	0.80
122_I	125_H	0.589	0.80
72_F	75_I	0.586	0.80
26_L	29_L	0.584	0.80
139_W	159_F	0.582	0.79
18_F	34_A	0.579	0.79
13_F	18_F	0.577	0.79
137_V	141_V	0.577	0.79
17_Y	59_L	0.577	0.79
141_V	145_V	0.575	0.79
94_D	157_G	0.574	0.78
104_L	164_A	0.573	0.78
160_K	207_P	0.572	0.78
83_Y	209_L	0.570	0.78
135_Y	163_A	0.570	0.78
154_L	159_F	0.566	0.78
71_P	74_P	0.564	0.77
199_T	203_I	0.562	0.77
197_R	201_T	0.562	0.77
28_P	32_K	0.560	0.77
93_I	101_P	0.559	0.77
108_L	135_Y	0.558	0.77
188_Y	191_V	0.556	0.76
89_T	93_I	0.555	0.76
135_Y	156_Y	0.554	0.76
169_C	217_L	0.554	0.76
179_L	183_L	0.552	0.76
62_A	81_F	0.549	0.75
87_V	165_A	0.548	0.75
186_I	208_W	0.547	0.75
136_G	140_C	0.546	0.75
116_N	121_L	0.545	0.75
192_S	198_R	0.545	0.75
154_L	205_F	0.543	0.75
108_L	112_G	0.543	0.75
177_I	209_L	0.542	0.74
130_G	170_G	0.539	0.74
185_G	205_F	0.536	0.74
84_F	88_L	0.534	0.73
176_M	180_I	0.531	0.73
138_L	153_G	0.530	0.73
157_G	206_G	0.528	0.73
82_L	191_V	0.527	0.72
142_Y	146_W	0.526	0.72
85_C	89_T	0.526	0.72
143_W	156_Y	0.525	0.72
200_I	203_I	0.525	0.72
184_G	188_Y	0.525	0.72
183_L	187_G	0.525	0.72
193_Q	201_T	0.523	0.72
113_L	124_L	0.521	0.72
138_L	174_L	0.519	0.71
107_P	111_L	0.517	0.71
135_Y	162_L	0.515	0.71
19_V	44_F	0.515	0.71
124_L	127_A	0.512	0.70
174_L	177_I	0.510	0.70
154_L	208_W	0.510	0.70
9_I	97_T	0.507	0.70
43_H	48_K	0.503	0.69
82_L	115_F	0.501	0.69
130_G	138_L	0.501	0.69
57_L	60_C	0.500	0.68

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	0.6578	99.5	0.739	Contact Map
3j20Y	1	0.2089	51.6	0.937	Contact Map
1twfB	2	0.3156	39.2	0.941	Contact Map
1zvfA	2	0.2622	38.4	0.942	Contact Map
4c2mB	1	0.3244	32.1	0.944	Contact Map
3e2iA	3	0.2133	31.5	0.944	Contact Map
4gizC	1	0.2267	27.9	0.946	Contact Map
2fiyA	1	0.5156	24.2	0.947	Contact Map
1twfL	1	0.1822	22.9	0.948	Contact Map
4aybP	1	0.1956	22.7	0.948	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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