PPPA - ECOLI - GREMLIN Contacts

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PPPA - Leader peptidase PppA

UniProt:	Q46836	Sequences: MLFDVFQQYPTAMPVLATVGGLIIGSFLNVVIWRYPIMLRQQMAEFHGEMSSAQSKISLALPRSHCPHCQQTIRIRDNIPLFSWLMLKGRCRDCQAKISKRYPLVELLTALAFLLASLVWPESGWGLAVMILSAWLIAASVIDLDHQWLPDVFTQGVLWTGLIAAWAQQSPLTLQDAVTGVLVGFITFYSLRWIAGIVLRKEALGMGDVLLFAALGGWVGALSLPNVALIASCCGLIYAVITKRGSTTLPFGPCLSLGGIATLYLQALF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12992
Length:	269 (236)
Sequences:	2617 (2025)
Seq/√Len:	131.8

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
77_D	92_R	4.949	1.00
101_R	145_D	4.417	1.00
63_R	72_T	3.604	1.00
157_V	214_A	2.975	1.00
139_A	149_L	2.897	1.00
113_F	134_A	2.706	1.00
32_I	141_V	2.600	1.00
215_L	227_V	2.537	1.00
14_P	114_L	2.520	1.00
18_T	110_A	2.509	1.00
77_D	93_D	2.447	1.00
135_W	153_F	2.380	1.00
71_Q	93_D	2.367	1.00
24_I	28_L	2.361	1.00
151_D	210_L	2.321	1.00
71_Q	77_D	2.256	1.00
206_M	209_V	2.253	1.00
17_A	117_S	2.219	1.00
57_I	65_H	2.217	1.00
133_S	260_I	2.179	1.00
18_T	114_L	2.138	1.00
22_L	81_L	2.115	1.00
37_I	57_I	2.059	1.00
140_S	256_S	2.059	1.00
128_A	164_A	2.029	1.00
195_A	199_L	2.006	1.00
59_L	62_P	2.003	1.00
84_W	100_K	2.003	1.00
236_L	239_A	1.997	1.00
77_D	87_L	1.935	1.00
116_A	126_G	1.918	1.00
58_S	62_P	1.867	1.00
126_G	130_M	1.816	1.00
109_T	137_I	1.811	1.00
109_T	113_F	1.808	1.00
68_H	96_A	1.760	1.00
195_A	203_A	1.757	1.00
74_R	77_D	1.672	1.00
215_L	259_G	1.661	1.00
82_F	86_M	1.640	1.00
174_L	178_V	1.637	1.00
116_A	133_S	1.621	1.00
100_K	104_L	1.616	1.00
184_G	224_L	1.614	1.00
28_L	138_A	1.609	1.00
22_L	110_A	1.604	1.00
112_A	133_S	1.596	1.00
136_L	256_S	1.593	1.00
73_I	78_N	1.592	1.00
234_C	261_A	1.560	1.00
113_F	130_M	1.544	1.00
73_I	93_D	1.539	1.00
17_A	114_L	1.532	1.00
227_V	258_G	1.532	1.00
238_Y	254_C	1.531	1.00
129_V	263_L	1.522	1.00
31_V	35_Y	1.508	1.00
108_L	141_V	1.497	1.00
18_T	22_L	1.485	1.00
161_G	218_W	1.442	1.00
71_Q	74_R	1.442	1.00
88_K	95_Q	1.428	1.00
149_L	154_T	1.423	1.00
81_L	107_L	1.421	1.00
74_R	92_R	1.417	1.00
149_L	252_G	1.412	1.00
258_G	262_T	1.397	1.00
21_G	110_A	1.390	1.00
232_S	236_L	1.349	1.00
223_S	227_V	1.343	1.00
192_R	202_E	1.342	1.00
192_R	206_M	1.333	1.00
150_P	210_L	1.310	1.00
131_I	160_T	1.308	1.00
244_R	247_T	1.296	1.00
101_R	141_V	1.296	1.00
33_W	57_I	1.295	1.00
114_L	118_L	1.291	1.00
32_I	105_V	1.260	1.00
79_I	83_S	1.251	1.00
147_Q	248_T	1.242	1.00
231_A	255_L	1.236	1.00
109_T	134_A	1.230	1.00
69_C	94_C	1.207	1.00
74_R	93_D	1.199	0.99
179_T	183_V	1.184	0.99
65_H	70_Q	1.173	0.99
173_T	176_D	1.171	0.99
112_A	137_I	1.168	0.99
105_V	141_V	1.160	0.99
223_S	262_T	1.156	0.99
26_S	64_S	1.152	0.99
234_C	254_C	1.146	0.99
149_L	211_L	1.134	0.99
190_S	194_I	1.120	0.99
67_P	98_I	1.116	0.99
133_S	264_Y	1.110	0.99
141_V	145_D	1.108	0.99
180_G	184_G	1.106	0.99
67_P	102_Y	1.105	0.99
99_S	102_Y	1.105	0.99
199_L	203_A	1.102	0.99
117_S	126_G	1.097	0.99
150_P	153_F	1.093	0.99
212_F	255_L	1.092	0.99
192_R	209_V	1.079	0.99
21_G	113_F	1.075	0.99
66_C	94_C	1.073	0.99
31_V	138_A	1.061	0.99
14_P	118_L	1.059	0.99
78_N	87_L	1.059	0.99
132_L	259_G	1.056	0.99
212_F	227_V	1.055	0.99
120_W	123_S	1.031	0.98
181_V	217_G	1.020	0.98
29_N	32_I	1.014	0.98
188_F	192_R	1.014	0.98
236_L	240_V	1.009	0.98
66_C	69_C	1.004	0.98
116_A	129_V	0.998	0.98
166_W	179_T	0.997	0.98
65_H	73_I	0.994	0.98
63_R	74_R	0.979	0.98
16_L	20_G	0.976	0.98
81_L	103_P	0.976	0.98
28_L	134_A	0.975	0.98
184_G	216_G	0.968	0.98
104_L	108_L	0.963	0.98
185_F	209_V	0.958	0.97
185_F	189_Y	0.957	0.97
139_A	153_F	0.947	0.97
58_S	61_L	0.947	0.97
76_R	86_M	0.944	0.97
132_L	215_L	0.931	0.97
19_V	23_I	0.925	0.97
32_I	142_I	0.921	0.97
110_A	114_L	0.906	0.96
195_A	201_K	0.906	0.96
13_M	117_S	0.904	0.96
211_L	252_G	0.893	0.96
138_A	153_F	0.892	0.96
235_G	239_A	0.891	0.96
120_W	126_G	0.891	0.96
260_I	264_Y	0.886	0.96
230_I	258_G	0.883	0.96
190_S	193_W	0.881	0.96
36_P	142_I	0.875	0.96
147_Q	250_P	0.875	0.96
112_A	260_I	0.874	0.96
22_L	103_P	0.874	0.96
69_C	91_C	0.873	0.96
228_A	232_S	0.872	0.96
91_C	94_C	0.867	0.95
206_M	210_L	0.865	0.95
75_I	78_N	0.864	0.95
66_C	91_C	0.863	0.95
25_G	109_T	0.862	0.95
33_W	37_I	0.858	0.95
12_A	16_L	0.846	0.95
229_L	232_S	0.843	0.95
135_W	157_V	0.840	0.95
261_A	265_L	0.827	0.94
139_A	154_T	0.827	0.94
231_A	251_F	0.824	0.94
76_R	92_R	0.822	0.94
123_S	126_G	0.817	0.94
99_S	103_P	0.816	0.94
234_C	257_L	0.809	0.93
77_D	83_S	0.805	0.93
227_V	231_A	0.801	0.93
165_A	177_A	0.801	0.93
30_V	36_P	0.797	0.93
151_D	154_T	0.797	0.93
120_W	129_V	0.795	0.93
180_G	216_G	0.784	0.92
73_I	77_D	0.783	0.92
17_A	130_M	0.780	0.92
189_Y	193_W	0.780	0.92
226_N	262_T	0.777	0.92
219_V	262_T	0.775	0.92
161_G	214_A	0.773	0.92
29_N	105_V	0.772	0.92
148_W	210_L	0.769	0.92
235_G	254_C	0.767	0.91
227_V	259_G	0.766	0.91
26_S	106_E	0.765	0.91
176_D	222_L	0.759	0.91
227_V	262_T	0.759	0.91
182_L	185_F	0.759	0.91
172_L	176_D	0.759	0.91
101_R	105_V	0.758	0.91
219_V	223_S	0.757	0.91
205_G	208_D	0.756	0.91
137_I	141_V	0.751	0.91
204_L	232_S	0.746	0.90
132_L	218_W	0.742	0.90
32_I	138_A	0.738	0.90
36_P	146_H	0.738	0.90
132_L	161_G	0.738	0.90
185_F	206_M	0.735	0.90
103_P	107_L	0.731	0.89
163_I	182_L	0.723	0.89
188_F	228_A	0.722	0.89
151_D	155_Q	0.721	0.89
179_T	221_A	0.719	0.89
136_L	211_L	0.712	0.88
29_N	102_Y	0.710	0.88
163_I	167_A	0.708	0.88
71_Q	92_R	0.707	0.88
108_L	137_I	0.706	0.88
115_L	264_Y	0.704	0.88
24_I	134_A	0.704	0.88
165_A	171_P	0.697	0.87
165_A	217_G	0.697	0.87
113_F	116_A	0.693	0.87
133_S	263_L	0.684	0.86
231_A	258_G	0.683	0.86
79_I	86_M	0.681	0.86
195_A	202_E	0.677	0.85
64_S	106_E	0.670	0.85
158_L	213_A	0.668	0.85
147_Q	249_L	0.667	0.85
116_A	264_Y	0.665	0.84
73_I	82_F	0.664	0.84
72_T	77_D	0.662	0.84
152_V	156_G	0.661	0.84
111_L	115_L	0.660	0.84
219_V	227_V	0.656	0.84
148_W	151_D	0.653	0.83
155_Q	159_W	0.652	0.83
128_A	218_W	0.652	0.83
119_V	122_E	0.649	0.83
130_M	134_A	0.647	0.83
27_F	64_S	0.647	0.83
28_L	137_I	0.647	0.83
28_L	109_T	0.645	0.83
34_R	62_P	0.644	0.83
112_A	116_A	0.643	0.82
180_G	220_G	0.640	0.82
180_G	183_V	0.640	0.82
236_L	254_C	0.639	0.82
192_R	195_A	0.638	0.82
154_T	214_A	0.637	0.82
227_V	255_L	0.637	0.82
129_V	171_P	0.633	0.81
115_L	265_L	0.632	0.81
187_T	191_L	0.630	0.81
193_W	206_M	0.628	0.81
167_A	171_P	0.628	0.81
189_Y	206_M	0.627	0.81
207_G	252_G	0.626	0.81
83_S	87_L	0.625	0.81
180_G	221_A	0.624	0.81
142_I	146_H	0.622	0.80
143_D	208_D	0.615	0.80
64_S	98_I	0.614	0.79
256_S	259_G	0.613	0.79
80_P	106_E	0.612	0.79
212_F	232_S	0.610	0.79
139_A	252_G	0.610	0.79
216_G	220_G	0.609	0.79
63_R	75_I	0.606	0.79
29_N	33_W	0.606	0.79
191_L	195_A	0.603	0.78
181_V	213_A	0.598	0.78
14_P	117_S	0.597	0.78
64_S	69_C	0.594	0.77
21_G	25_G	0.593	0.77
176_D	221_A	0.592	0.77
132_L	255_L	0.590	0.77
211_L	256_S	0.590	0.77
14_P	17_A	0.588	0.76
180_G	195_A	0.587	0.76
57_I	60_A	0.585	0.76
188_F	209_V	0.585	0.76
149_L	207_G	0.584	0.76
84_W	89_G	0.583	0.76
26_S	30_V	0.582	0.76
105_V	137_I	0.580	0.76
123_S	127_L	0.580	0.76
142_I	253_P	0.579	0.75
22_L	107_L	0.578	0.75
33_W	101_R	0.578	0.75
219_V	263_L	0.578	0.75
116_A	130_M	0.576	0.75
156_G	217_G	0.575	0.75
234_C	258_G	0.574	0.75
136_L	215_L	0.574	0.75
33_W	67_P	0.573	0.75
79_I	82_F	0.570	0.74
187_T	228_A	0.567	0.74
97_K	100_K	0.563	0.73
154_T	217_G	0.562	0.73
204_L	251_F	0.562	0.73
37_I	145_D	0.561	0.73
210_L	253_P	0.560	0.73
26_S	34_R	0.559	0.73
65_H	81_L	0.558	0.73
128_A	132_L	0.557	0.73
26_S	98_I	0.557	0.73
15_V	18_T	0.556	0.72
69_C	106_E	0.555	0.72
191_L	231_A	0.552	0.72
29_N	87_L	0.549	0.72
157_V	161_G	0.548	0.71
18_T	107_L	0.547	0.71
64_S	80_P	0.546	0.71
140_S	146_H	0.546	0.71
180_G	188_F	0.546	0.71
58_S	63_R	0.545	0.71
189_Y	209_V	0.543	0.71
242_T	247_T	0.540	0.70
139_A	150_P	0.539	0.70
178_V	182_L	0.538	0.70
143_D	207_G	0.536	0.70
87_L	92_R	0.536	0.70
26_S	69_C	0.535	0.70
121_P	126_G	0.535	0.70
156_G	160_T	0.535	0.70
175_Q	179_T	0.535	0.70
115_L	260_I	0.534	0.69
100_K	103_P	0.533	0.69
192_R	204_L	0.532	0.69
239_A	254_C	0.529	0.69
56_K	61_L	0.529	0.69
61_L	65_H	0.526	0.68
230_I	234_C	0.523	0.68
27_F	78_N	0.523	0.68
234_C	238_Y	0.522	0.68
208_D	253_P	0.521	0.68
73_I	76_R	0.521	0.68
17_A	113_F	0.519	0.67
142_I	153_F	0.516	0.67
142_I	150_P	0.516	0.67
98_I	106_E	0.515	0.67
165_A	173_T	0.513	0.66
26_S	94_C	0.513	0.66
62_P	65_H	0.512	0.66
30_V	78_N	0.512	0.66
142_I	145_D	0.511	0.66
188_F	203_A	0.510	0.66
131_I	241_I	0.509	0.66
168_Q	172_L	0.508	0.66
159_W	185_F	0.508	0.66
37_I	146_H	0.508	0.66
153_F	214_A	0.507	0.65
188_F	224_L	0.506	0.65
12_A	15_V	0.505	0.65
215_L	219_V	0.505	0.65
245_G	249_L	0.504	0.65
143_D	205_G	0.503	0.65
161_G	217_G	0.502	0.65
230_I	261_A	0.500	0.64
94_C	106_E	0.500	0.64

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	0.5316	99.3	0.787	Contact Map
3py7A	1	0.3494	71.1	0.937	Contact Map
2m3lA	1	0.2491	43.4	0.947	Contact Map
3h0gL	1	0.1487	34.1	0.95	Contact Map
2ct0A	1	0.2677	28.2	0.952	Contact Map
2ep4A	1	0.2305	27.5	0.952	Contact Map
3j20Y	1	0.1859	24.6	0.953	Contact Map
1vq8Z	1	0.2714	21.3	0.954	Contact Map
2kizA	1	0.2119	21	0.955	Contact Map
1iymA	1	0.2045	20.9	0.955	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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